14458 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Data Access Committee for the Medulloblastoma Host Genome Study

  Dac EGAC00001000910

• Southern African Prostate Cancer Study (SAPCS) Data Access Committee

  Dac EGAC00001002768

• AmsterdamUMC Data Access Committee for the EPIC-CD study

  Dac EGAC00001003480

• Analysis of Epigenomes and Genome Topology in Colorectal Cancer

  When diagnosing cancer, pathologists use nuclear morphology as a hallmark of tumor cells, but the topological changes linked to alterations in the shape of the nucleus were poorly understood. To uncover the molecular changes that occur in the 3D structure of cancer genomes, we integrated topological maps for colon tumors and normal colon tissues with epigenetic, transcriptional, and imaging data. We characterized tumor-associated changes in chromatin loops, topologically associated domains (TADs), and large-scale compartments. We found that chromatin loop rewiring contributes to oncogenic gene expression programs. Whereas TAD structures are largely stable, the spatial partitioning of the open and closed genome compartments is compromised in tumors and is accompanied by hypomethylation and histone mark rearrangements. We also identified a compartment that is reorganized in tumors and is at the interface between the canonical A and B compartments. Similar changes were evident in non-malignant cells that had accumulated excessive cellular divisions. Our analyses suggest that these compartment changes repress stemness and invasion programs while inducing immunity genes, and they may therefore restrain malignant progression.

  Study phs002288

• Efficacy and safety of entrectinib in patients with ROS1-positive advanced/metastatic non-small cell lung cancer (NSCLC) from the Blood First Assay Screening Trial (BFAST)

  BFAST is a global, open-label, multicohort trial that evaluates the efficacy and safety of multiple therapies in patients with advanced/metastatic NSCLC and targetable alterations, identified by blood-based molecular testing. We present data from Cohort D (ROS1-positive). Patients ≥18 years old with stage IIIB/IV, ROS1-positive NSCLC detected by blood-based testing, received entrectinib 600 mg daily. At data cut-off (November 2021), 55 patients were enrolled and 54 had measurable disease. Cohort D met its primary endpoint; the confirmed objective response rate (ORR) by investigator was 81.5% which was consistent with the ORR from the integrated analysis of entrectinib (investigator-assessed ORR: 73.4%, data cut-off May 2019, ≥12 months follow-up). The safety profile of entrectinib was consistent with prior reports. These results demonstrate consistency with those from the integrated analysis of entrectinib in patients with ROS1-positive NSCLC identified by tissue-based testing and support the clinical value of blood-based testing to inform clinical decision-making.

  Study EGAS50000000105

• Circulating, Cell-Free DNA Methylation Patterns Indicate Cellular Sources of Allograft Injury after Liver Transplant

  Post-transplant complications reduce allograft and recipient survival. Current approaches for detecting allograft injury non-invasively are limited and do not differentiate between cellular mechanisms. Here, we monitor cellular damages after liver transplants from cell-free DNA (cfDNA) fragments released from dying cells into the circulation. We analyzed longitudinal blood samples collected from patients at different time points after transplant. Sequence-based methylation of cfDNA fragments were mapped to an atlas of cell-type-specific DNA methylation patterns derived from 476 methylomes of purified cells. For liver cell types, DNA methylation patterns and multi-omic data integration show distinct enrichment in open chromatin and regulatory regions functionally important for the respective cell types. We find that multi-tissue cellular damage post-transplant recovers in patients without allograft injury during the first post-operative week. However, sustained elevation of hepatocyte and biliary epithelial cfDNA within the first month indicates early-onset allograft injury. Further, cfDNA composition differentiates amongst causes of allograft injury indicating the potential for non-invasive monitoring and timely intervention.

  Study phs003610

• Relation between transcriptome, karyotype and age in cases of sex chromosome aneuploidies.

  Why women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that transposable element (TE) repression declines with age, potentially leading to detrimental effects such as somatic mutations and disrupted gene expression, which may accelerate the aging process. Given that the Y chromosome is rich in repeats, age-related increases in TE expression could be more pronounced in males, likely contributing to their reduced longevity compared to females. In this work, we first studied whether TE expression is associated with the number of sex chromosomes in humans. We analyzed blood transcriptomic data obtained from individuals of different karyotype compositions: 46,XX females (normal female karyotype), 46,XY males (normal male karyotype), as well as males with abnormal karyotypes, such as 47,XXY, and 47,XYY.

  Study EGAS50000001009

• Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

  Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.

  Study EGAS00001002592

• Relation between transcriptome, karyotype and age in cases of sex chromosome aneuploidies.

  Why women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that transposable element (TE) repression declines with age, potentially leading to detrimental effects such as somatic mutations and disrupted gene expression, which may accelerate the aging process. Given that the Y chromosome is rich in repeats, age-related increases in TE expression could be more pronounced in males, likely contributing to their reduced longevity compared to females. In this work, we first studied whether TE expression is associated with the number of sex chromosomes in humans. We analyzed blood transcriptomic data obtained from individuals of different karyotype compositions: 46,XX females (normal female karyotype), 46,XY males (normal male karyotype), as well as males with abnormal karyotypes, such as 47,XXY, and 47,XYY.

  Study EGAS00001007462

• DAC Portal documentation

  DAC Portal Welcome to the DAC Portal documentation! If you are involved in governance or legal aspects, technical or operational aspects, or serving as a data steward, this page will be helpful for you. By exploring these materials, you can define your own Data Access Committee (DAC) and policies, understand the minimal requirements for a DAC and a policy object, and comprehend how the EGA data access requests are managed. DAC Portal Index Setting up your account DACs and Policies Pending Request table Manage Data Requests History page Audit your DACs, policies, and datasets Deprecation User Preferences DAC API - A programmatic approach Setting up your account Register yourself as an EGA user. The Helpdesk team will validate your account (this could take up to 48 hours). After validation, you will receive an email with a link to verify your email - Make sure you click on the link to verify your account! If you don’t receive the email, please check your spam folder. Once your account is active you can login to the DAC Portal. We recommend you to check out the Take The Tour! DACs and Policies Create a DAC Click on Create a DAC Add the title and description to your DAC. Once ready, click on the ‘Create’ button. You will have to wait until the Helpdesk Team validates the creation of your DAC. Once approved by Helpdesk, your DAC will be assigned with a persistent identifier (EGAC). Edit a DAC Once your DAC is registered and approved, you can edit it and add contacts. Remember, you can add as many contacts as needed. And, you can also remove/add contacts anytime. To add a contact, you must write the username or email of a registered EGA user in the Members field. Once you have typed the whole username or email, a drop-down menu will appear where you can select the contact. Select a contact from the drop-down menu. Make sure you write the full username or email of the contact so it appears as an option. Make sure that you select one main contact. Set up the role you want to grant to the new contact of the DAC. We recommend you to check out the FAQ to learn more about the different roles! After adding all the necessary contacts and assigning roles, click on Update. This will send an email notification to the new DAC member, letting them know about the invitation to managing the DAC. Once they log into the DAC Portal, they will be able to either accept or turn down the invitation. Create a policy First, please note that all information registered in a policy metadata object will be publicly available on the EGA website. For each released dataset, all users will be able to read the policy under the “Data Access” tab. Select Create a Policy from the Policies tab. Select the DAC that you want your policy to depend on. Add the title and terms and conditions for accessing and using your data. If you already have an external website for data access requests, you can add the URL directly here (see example here). You can find a template of a Data Access Agreement (DAA) document in our Policy documentation page. The DAA template is provided for guidance only and should be adapted to suit your own purpose depending on the security policies, terms for publication or embargoes, and restrictions on data use or sharing. You can also add Data Use Ontologies (DUO) to your policy. These DUO codes are used to semantically tag the terms and conditions of using the data linked to the policy (example). For more information, you can refer to the Data Uso Ontology documentation. Once completed, make sure to click the Create button in order to register your policy. A persistent identifier (EGAP) will be assigned automatically. Edit a policy Please, note that you will not be able to edit the policy if it shows in orange. Meaning that you are a member of the DAC linked to that policy. Members don’t have edit rights. Only admins can edit objects. You can check your registered policies on My policies, available at the menu in the top-right corner. Select your policy. It will then display the information of that policy, allowing you to edit the information. Once you are done with the modifications, click Update. Pending Requests Table Table Settings Upon selecting a specific DAC, you will be presented with a customisable table showcasing all pending data access requests. This table allows you to tailor the displayed information according to your preferences by selecting desired columns. Available Columns (Displayed with the Eye Icon): Date: The date when the data access request was submitted. Full Name: Name and surname of the user submitting the request. Email: Email address associated with the user's request. Username: The username linked to the EGA account of the user submitting the request. Organisation: Affiliated organisation of the user submitting the request. Dataset: EGA accession ID for the requested EGA dataset. Dataset Title: Title of the requested dataset. DAC Comment: Space provided for internal comments related to the request. Expiration: Option to specify an expiration date for granted permissions. Check more information on the pending request table here! Table Filters By default, all data access requests are displayed. However, you have the option to apply filters to refine your view. Follow these steps to apply filters: Click on the More button. This action will reveal the different columns available for applying filters. As you select columns, the checked fields will be displayed at the top of the request table. Choose the specific values within the selected columns that you want to filter for. Click the Search button to apply the selected filters. Do you find yourself frequently applying the same filters? You can save multiple combinations of filters for easy access at any time! Here's how: Click the Save button. Provide a descriptive name for the filter combination. Click Save to confirm. To load saved filters, simply select the saved filter from the dropdown menu to apply it automatically. Check more information on filters here! Advanced Search For users requiring more granular control over their data access requests, the DAC Portal offers an Advanced Search feature using JIRA Query Language (JQL). With JQL, you can craft precise and complex queries to filter and retrieve specific data access requests based on various criteria such as date, user details, dataset attributes, and more. Using JQL's flexibility, you can create custom queries to meet your specific needs, allowing for advanced filtering options beyond the standard filters provided. You can find the Advanced Search feature following these steps: Click the … button Select Advanced To view the allowed fields for filtering and explore all available options, simply click on the info icon. Once you have written the filtering values, click the Search button to apply. Check more information on filters here! Manage Data Requests Upon logging into the DAC Portal, you'll notice a sand clock icon next to the DAC ID, indicating the number of pending requests. Click on the DAC to review these requests. Accept requests Click on the right side of the toggle button to grant access to the user. You can manage other requests before proceeding to the next step. After managing the requests, click on the Apply button. A confirmation box will appear summarising the options to be applied. Click on Yes, Confirm to proceed with granting permissions. Deny requests Click on the left side of the toggle button to deny access to the user. Provide a reason for the denial. Note that the user will receive an email with this reason. Click on the Done button. You can manage other requests before proceeding to the next step. After managing the requests, click on the Apply button. A confirmation box will appear summarising the options to be applied. Click on Yes, Confirm to proceed with denying permissions. Tips! Apply a filter to view all requests to be managed at once. Use the toggle in the row with column names to grant or deny permissions for multiple requests simultaneously. You can grant and deny permissions in the same action, simplifying the process. The confirmation box will provide a summary of all actions, including grants, denials, DAC comments, and expiration dates. History Page The History page serves as a dedicated space to view information regarding all requests managed by all DAC members. Here, you can review active permissions and revoke them as needed. Go to the History page by clicking on the "HISTORY" button from a DAC page in the DAC Portal. Here are the different row types you may find: Current permissions: row in green with a toggle button to revoke permissions on the right. Approved requests: row in green, with no toggle button. Request denied: row in red with “request denied” on the right. Permission revoked: row in red with “permission revoked” on the right. Distinctions to Note! Between Request Denied and Permission Revoked: Request Denied: Refers to requests that were rejected from the outset, indicating that access to the dataset was never granted. Permission Revoked: Indicates that permissions were previously granted but have since been revoked. Users with permissions revoked have previously accessed the dataset. Between Approved Request and Current Permissions: Approved Request: Represents an entry when a data access request has been approved in the past. Current Permissions: Denotes ongoing permissions where a user has present access to the dataset. An approved request may now appear as Permission Revoked in the present. By observing these different rows, users can gain insight into the complete history of a user's interactions and permissions regarding a dataset over time. To revoke access to a specific user for a dataset, follow these steps: Go to History page Look for the row with the specific permissions. You can use the filters! Click on the toggle button to revoke access. Add a denial reason. Bear in mind that the requester will receive the denial reason! Click on the Apply button. Check more information on the Hisotry page here! Audit your metadata objects In the DAC Portal, you can efficiently manage and audit various metadata objects pertinent to your role as a Data Controller. Upon accessing the DAC Portal, you will encounter three primary tabs on the homepage: DAC: Contains information about Data Access Committees (DACs). Policies: Provides insights into linked policies. Datasets: Displays datasets and relevant details. Within each tab, you'll find a comprehensive list of the objects you manage, these being grouped by type (DAC, Policies, Datasets), as well as by your role (member/admin). Whilst the lists give you a quick look, to check how things are connected, we've added a table at the bottom DACs and policies. DACs Let’s check which policies are linked to a specific DAC: Go to "My DACs." Select a DAC. Click on "EDIT" to see more details. You are now on this page: Scroll down to see the linked policies. Click on “List of linked policies of this DAC” and you will see a list of all policies linked to your selected DAC. Policies Do you want to view a list of datasets connected to a particular policy? Follow the same steps mentioned earlier, but head to the policy tab this time. In the policy tab, you'll find a list of all your policies. Here, you may notice two different icons next to the policy ID (EGAP): DAC Icon (): This represents the DAC. Hover your mouse over the icon to see the DAC ID. Dataset icon (): This indicates datasets falling under that policy. The number next to the icon tells you how many datasets are linked to the policy. For example, if you see "2" next to the icon, it means there are two datasets linked to that policy. If you want to check the linked datasets and their relevant information, simply click on a specific policy. You'll then find the "List of linked datasets of this policy" at the bottom of the page. Datasets Finally, in the dataset tab, by default you will see a list of all the datasets you can manage with all your DACs and policies. Yet, we've included two handy ways to organise them: DAC vs. policy: You can group by datasets, either by DAC or policy. Released vs. unreleased: You can sort out datasets based on their release status. Feel free to experiment with both options! For instance, if you want to see which DACs have unreleased datasets, simply select DAC and unreleased, and you'll get the details you need! Deprecation Do you have a bunch of metadata objects like DACs and policies that you don’t need anymore? This section shows you how to get rid of them! But what does "deprecation" mean for EGA? It's basically changing the status of a metadata object to "deprecated," which means we won't be using it in the future. In simple terms, it's like saying these objects are no longer useful. However, because we believe in making metadata FAIR, once an object has a persistent identifier, we can't just delete it. So, instead of deleting, we deprecate it. Here's a helpful tip! If you want to make a metadata object disappear from the DAC Portal, deprecate it. You won’t see it in the portal anymore! Let’s say you want to deprecate a DAC. Let’s do it! Go to "My DACs." Select a DAC. Click "EDIT" to see more details. You are now in this page: Click on the Deprecate button It will then appear a message. There are two options here: Your DAC is not linked to any policy, hence it’s ready to be deprecated. Click on “Yes. Confirm” to deprecate your DAC object! Your DAC is linked to at least one policy, and you need to either: Deprecate the linked policy first, or Link the policy to a different DAC Now, let’s say you don’t want to get rid of the policy altogether, but you want to change the DAC it’s linked to. Here's how: Go to the policy tab. Find the policy you want to change (for example, EGAP50000000019). Choose a new DAC to link it to. Click on Update. See the Edit Policy section for more details. After ensuring that the DAC we want to deprecate isn’t linked to any policy, return to the "My DACs" section and follow the steps outlined previously. This will lead you to a confirmation message. You can only deprecate DACs and Policies. To deprecate a dataset, please contact our Helpdesk team. Check more information on how deprecation works here! User Preferences We have implemented email notifications in the DAC Portal. Here’s the complete list: DACs: Pending requests Approved by Helpdesk Rejected by Helpdesk DAC Invitation Requesters: Data access request approved Data access request denied Permissions revoked Upcoming expiration date As a DAC member, you will be able to decide whether you want to receive the DAC notifications or not. For that, go to the top-right corner menu, select User Preference. You will be able to decide whether you want to receive notifications for: Approved by Helpdesk Rejected by Helpdesk DAC Invitation For pending requests, you will be able to select how often do you want to receive the notification: Daily Weekly Fortnightly As a DAC member, you are responsible for managing data access requests. Consequently, you will receive notifications for pending requests. If you prefer not to manage these requests, please arrange to be removed as a contact for your DAC. Here's a tip! Do you have a pending request that you don’t want to receive a notification? Add a DAC comment! The EGA understands that a request resolution can take some time, for this reason, if you add a comment (make sure you save it by clicking the APPLY button!) we will filter those requests at the time of sending the notification! DAC API - A programmatic approach In addition to the new DAC Portal, we are excited to announce the release of the DAC API. This enables users to programmatically manage permissions. If you are interested in learning more about the technical specifications, you can click the button below. Check out the DAC API specification!

  Documentation access/data-access-committee/dac-portal

• Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

  Low coverage paired end Illumina WGS from cells amplified with Picoplex, PTA, and droplet MDA. Two brains with Multiple System, Atrophy, one control, and non-brain controls (fibroblasts, NA12878)

  Study EGAS50000000020

• Whole-exome sequences of ovarian clear cell carcinomas and paired normal DNA

  Whole-exome sequencing dataset for the Australian Ovarian Cancer Study (AOCS) and The Jikei University School of Medicine (JIKEI) ovarian clear cell carcinoma (OCCC) clinical outliers project, representing 10 donors. Consists of 20 fastq files: one normal and one tumour from each patient.

  Dataset EGAD00001006004

• Exome Sequencing of Spanish Patients with rare genetic diseases.

  Whole exome sequencing of Spanish patients suffering from a rare genetic disease. The study was carried out in 2013 as a part of a public call from CNAG (Centro Nacional de Análisis Genómico), where data of eight spanish families were sent to analyse. The study concluded with three solved cases: two of aniridia and one syndromic RP.

  Study EGAS00001004028

• Netherlands Cancer Institute (NKI-AVL) general DAC

  Data is available under reasonable request. All data requests will be reviewed by the NKI IRB and must be supported by the Principal Investigator of the study. The researcher will need to sign a data access agreement with the NKI after approval. Go to https://ega.nki.nl to fill out the form to request access.

  Dac EGAC50000000055

• English Longitudinal Study for Ageing (ELSA) Genetic Data Access

  Dac EGAC00001000270

• Ludwig Data Access Committee for the Study of Oesophageal Cancer

  Dac EGAC00001000978

• Hoag Family Cancer Institute Carcinoid Multiomic Study Data Access Committee

  Dac EGAC00001003084

• Two monogenic disorders masquerading as one: Severe congenital neutropenia with monocytosis and non-syndromic sensorineural hearing loss

  Study EGAS00001004176

• Mechanisms of patient response to Dabrafenib in Melanoma

  Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled)*NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing]*CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)]Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence)

  Dataset EGAD00001001375

• Investigation of chromatin accessibility in clear cell renal cell carcinoma using ATAC-seq

  To identify regions of open and accessible chromatin in clear cell renal cell carcinoma (ccRCC), we performed ATAC-seq on the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and processed narrowPeak fomats. Data were processed using the nf-core atacseq pipeline.

  Dataset EGAD50000001885

• LifeChange Data Access Committee

  The LifeChange study aimed at tracking the biological consequences of the societal changes undergone by the Yakut people of Far Eastern Siberia, after the colonization of the region by Russians in the 17th century. This study builds upon more than 15 years of archaeological research conducted in Yakutia, Sakha Republic, an autonomous region of the Russian Federation located in northeastern Siberia. The fieldwork was conducted under the MAFSO program (“Mission Archéologique Française en Sibérie Orientale”, or “French Archaeological Mission in Eastern Siberia”), a collaboration between French researchers and local Yakut experts, including scholars from North-Eastern Federal University in Yakutsk. The program was supported by several inter-university collaborative research agreements, notably between Université Paul Sabatier, Krasnoyarsk State Medical University, and North-Eastern Federal University in Yakutsk. It also received endorsement from the Institute of Ecology and Evolution at CNRS through the International Associated Laboratory “Co-evolution Human-Environment in Eastern Siberia”. The LifeChange Data Access Committee, composed of French and Russian archaeogeneticists, geneticists and archaeologists, reviews any access request to LifeChange data, consisting of genomes of ancient and modern Yakut, Eveni and Evenki individuals sampled in Eastern Siberia for the LifeChange study. The DAC grants access to any academic researcher aiming to study the population history of autochthonous peoples from Siberia. When reviewing data access requests, the DAC members ensure that the applicant will not re-use the data to trace present-day descendants of studied ancient individuals. They also ensure that secondary use of the modern genomic data is conducted in full respect of the conditions stipulated in living participants’ informed consent. Specifically, the applicant is not authorised to (i) use the data for diagnostic purposes, (ii) store the data outside of secure servers, (iii) reidentify research participants, and (iv) share the data with a third party.

  Dac EGAC50000000713

• DAC for Sarcopenia HNSCC

  Data access committee for Sarcopenia HNSCC study

  Dac EGAC50000000420

• WGS of B-cell lymhpoma tumor and control, HiSeq XTen sequencing, one patient, H021

  paired WGS sequencing of nodal B-cell lymphoma, one tumor and one control, one patient (H021). Sequencing on Hiseq XTen with TruSeq Nano library preparation kit.

  Dataset EGAD00001006057

• The CHOP Pediatric Genetic Sequencing (PediSeq) Project : Applying Genomic Sequencing in Pediatrics

  The purpose of this research study is to learn more about newer types of genetic testing called whole exome sequencing and whole genome sequencing. Current genetic testing usually examines one gene or a few genes at a time. Exome and genome sequencing allow us to test most of a person's genes at one time with a single test. This testing might identify the reason for a person's unexplained condition or diagnosis. We hope this study will help us identify the best methods for: Educating patients and families about exome and genome sequencing Analyzing exome and genome sequencing data to identify results relevant to patients Giving results to families in a clear, appropriate, and informative manner The current data only includes WES for 159 samples. The WGS samples for 20 samples will be uploaded in the near future.

  Study phs000935

• Combinatorial Indexed 10x Genomics Single-Cell ATAC-seq on Human Cerebral Cortex

  Single-cell chromatin accessibility profiling (scATAC) using droplet fluidics (10x Genomics) is inherently limited in throughput due to the number of available indexed droplets. This study leverages single-cell combinatorial indexing workflows with modified adapter designs to enable indexed tagmentation and superloading of pre-indexed nuclei into the 10x Genomics scATAC workflow, enabling a substantial increase in the number of cell profiles that can be obtained per channel. This workflow, 10x single-cell combinatorial indexed ATAC-seq (txsciATAC), is demonstrated on human brain tissue (middle frontal gyrus), along with mouse brain tissue to enable doublet and crosstalk assessment. This study includes all human data and includes a single preparation taken through nuclei isolation and indexed tagmentation using 96 indexes then split to produce two datasets, one targeting 20k cells and one targeting 70k, each using a single channel of the 10x Chromium controller.

  Study phs003497