12403 results for "cancer studies using rna-seq"

in 66.80 milliseconds.

• Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells

  Human Induced Pluripotent Stem Cells (hiPSC) are an established patient-specific model system where opportunities are emerging for cell-based therapies. We compared and contrasted hiPSCs derived from different tissues, skin and blood, in the same individual. We show extensive single-nucleotide mutagenesis in all hiPSC lines, although fibroblast-derived hiPSCs (F-hiPSCs) are particularly heavily mutagenized by ultraviolet (UV)-related damage. We utilized genome sequencing data on 454 F-hiPSCs and 44 blood-derived hiPSCs (B-hiPSCs) to gain further insights. Across 324 whole genome sequenced (WGS) F-hiPSCs derived by the Human Induced Pluripotent Stem Cell Initiative (HipSci), UV-related damage is present in ~72% of cell lines, sometimes causing substantial mutagenesis (range 0.25-15 per Mb). Furthermore, we find remarkable genomic heterogeneity between independent F-hiPSC clones derived from the same reprogramming process in the same donor, due to oligoclonal populations within fibroblasts. Combining WGS and exome-sequencing data of 452 HipSci F-hiPSCs, we identify 272 predicted pathogenic mutations in cancer-related genes, of which 21 genes were hit recurrently three or more times, involving 77 (17%) lines. Notably, 151 of 272 mutations were present in starting fibroblast populations suggesting that more than half of putative driver events in F-hiPSCs were acquired in vivo. In contrast, B-hiPSCs reprogrammed from erythroblasts show lower levels of genome-wide mutations (range 0.28-1.4 per Mb), no UV damage, but a strikingly high prevalence of acquired BCOR mutations in ~57% of lines, indicative of strong selection pressure. All hiPSCs had otherwise stable, diploid genomes on karyotypic pre-screening, highlighting how copy-number-based approaches do not have the required resolution to detect widespread nucleotide mutagenesis. This work strongly suggests that models for cell-based therapies require detailed nucleotide-resolution characterization prior to clinical application.

  Dataset EGAD00001007029

• Privacy Notice for Helpdesk service

  Privacy Notice for EGA Helpdesk service This Privacy Notice explains what personal data is collected by the specific service you are requesting, for what purposes, how it is processed, and how we keep it secure. Note that this service collects personal data directly provided by the user, and also collects personal data from users that is provided by other organisations. 1. Who controls your personal data and how to contact us? European Genome- Phenome Archive - EGA offers a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects, jointly managed by European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI) and Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG). EMBL-EBI and CRG represent joint Data Controllers’ of processing of your personal data. They and their Data protection officers may be contacted for data protection queries and for exercising your rights under Section 8. You may contact EMBL-EBI, represented by dr. Thomas Keane, by: email at: tk2@ebi.ac.uk or post at EMBL-EBI, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridgeshire, UK. EMBL’s Data Protection Officer may be contacted by: telephone at +49 6221 387-8590, email at dpo@embl.org , or post at EMBL Heidelberg, Data protection officer, Meyerhofstraße 1, 69117 Heidelberg, Germany. You may contact CRG, whose EGA team is represented by dr. Jordi Rambla de Argila, by: email at jordi.rambla@crg.eu, or post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), Dr.Aiguader 88, PRBB Building, 08003 Barcelona, Spain. CRG Data protection officer may be contacted by: email at dpo@crg.eu post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain. 2. Which is the lawful basis for processing personal data? We process your personal data on the grounds of important public interest. For monitoring your activities on the website, we process your personal data on the grounds of important public interest. Such legal basis is found in Article 5(1)(a) of EMBL Internal Policy No 68 on General Data Protection (hereinafter IP 68), which is equivalent to Article 6 (1)(e) of the EU General Data Protection Regulation (hereinafter GDPR) and upon which personal data are processed for the achievement of the aims laid down in 1973 agreement establishing EMBL, such as the promotion of the cooperation in the fundamental research, in the development of advanced instrumentation and in advanced teaching in molecular biology and dissemination of information. 3. What personal data is collected from users of the service? How do we use this personal data? We collect the following personal data from users of the service: Name Email address Job title Date and time when the support request was sent We will use your personal data for the following purposes: To provide uninterrupted user access to the service To better understand the needs of the users and guide future improvements of the service To create anonymous usage statistics 4. Who will have access to your personal data? The personal data will be disclosed to: Authorised staff in the data controller’s institutions acting on data controller`s behalf and instructions. 5. Will your personal data be transferred to third countries (i.e. countries not part of EU/EEA) and/or international organisations? There are no personal data transfers to third countries or international organizations. 6. How long do we keep your personal data? Any personal data directly obtained from you will be retained as long as the service is live. Such duration serves the purpose of enabling scientific research and ensures legal compliance and facilitates internal and external audits if they arise. By contrast, the log files for the data categories related to anonymous usage statistics (raw web service logs) are processed only for 30 days and thereafter erased. 7. The joint Data Controllers provide these rights regarding your personal data You have the right to: Not be subject to decisions based solely on an automated processing of data (i.e. without human intervention) without you having your views taken into consideration. Request at reasonable intervals and without excessive delay or expense, information about the personal data processed about you. Under your request we will inform you in writing about, for example, the origin of the personal data or the preservation period. Request information to understand data processing activities when the results of these activities are applied to you. It must be clarified that rights under points 4 and 5 are only available whenever you need support whilst using our website. For other processing based on the grounds of important public interest you cannot exercise your rights to object, rectify or erase your personal data according to the Article 13(2)(a)(b) of IP 68 (equivalent to Article 17(3)(b)(d) and Article 21(6) of the GDPR). 8. Supervisory authority If you wish to complain against the processing of your personal data, you may do so by post at: EMBL Heidelberg, Data Protection Committee, Meyerhofstraße 1, 69117 Heidelberg, Germany, or Autoritat Catalana de Protecció de Dades (Catalan Data Protection Authority), C/Rosselló 214, Esc A, 1r 1a, Barcelona 08008, Spain. Published at: February 6, 2019

  Documentation data-protection/privacy-notice/ega-helpdesk

• Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS)

  This pharmacogenomic study focused on the response of patients with MDD to an 8-week course of treatment with citalopram or escitalopram. Briefly, clinical assessments and research assessments were performed at each study visit as summarized in Table 1. Many patients continued on antidepressant medication after the 8 week study. Table 1: Study timeline and patient contacts. Week Consent/Med Hx Write Rx SI Qx SCID HRS-D17 QIDSC16 CGI-I 0 SC RC RC SC SC SC 4 RC RC SC SC RC 8 RC RC SC SC RC HRS-D17=Hamilton Rating Scale for Depression, QIDS-C16=Quick Inventory of Depressive Symptomatology, CGI-I=Clinical Global Impression-Improvement, SCID=Structured Clinical Interview for DSM-IV, SC=Study Coordinator, RC=Research Clinician. Enrollment and baseline assessment. Upon initial intake, the Study Coordinator (SC) obtained informed consent as well as clinical and demographic information, including history of bone marrow or liver transplant or blood transfusion within the previous 6 weeks, and prior history of treatment during the current major depressive episode. The SC completed the Structured Clinical Interview for DSM-IV (SCID), the HRS-D17 (17-item Hamilton Rating Scale for Depression) and the QIDS-C16 (Quick Inventory of Depressive Symptomatology) and reviewed the inclusion/exclusion criteria. After review with the Research Clinician (RC) and when appropriate, after a negative pregnancy test, the SC invited the subject to participate in the study if entry criteria were met. If the subject agreed, he/she received treatment according to the study protocol. Treatment schedule. Participants selected for inclusion in the study were seen at weeks 0, 4, and 8. The appropriate treatment antidepressant (citalopram or escitalopram) was determined following discussion between the patient and RC concerning medical, financial, and insurance considerations. The study medication citalopram was given in tablet or liquid form, depending on the patient's need. A fixed-flexible dose schedule was employed with the possibility of a dose escalation. In particular, the initial dose of citalopram was 20 mg and escitalopram was 10 mg. This dose was increased to 40 mg and 20 mg, respectively, after 4 weeks if the subject had a score of >/= 6 on the QIDS-C16 and the RC concluded that the subject could tolerate the increase. If necessary, dose was reduced at the discretion of the RC. The importance of medication compliance was discussed with the subject, and subjects were asked to bring in the medication at each visit for the purpose of counting remaining pills to assess compliance. Participants may have had an abbreviated course of therapy if they were clearly intolerant of the drug or failed to respond to a 40 mg dose of citalopram or a 20 mg dose of escitalopram. They then received standard treatment from a primary physician or psychiatrist with different medications and/or therapeutic modalities (e.g. psychotherapy). Special attention was given to subjects with suicidal ideation. Those subjects were offered additional appointments as needed to ensure their safety. Participants were also contacted by telephone at week 1 and week 2 by the Clinical Nurse Specialist (CNS) or other study personnel to ensure medication compliance and patient safety. The CNS was supervised by the study psychiatrist and principal investigator and deferred to the physician's judgment as needed. The SC was trained to notify the RC at the time of the clinical visits or the phone interviews if the subject endorsed any suicidal ideation or plans. For those subjects who were unable to attend the follow-up visits as scheduled, the patient was contacted by phone to complete the HRS-D17/QIDS-C16. The participant was also asked to return to the clinic to complete a final blood draw for the study. Adjunctive and concurrent medications. Adjunctive treatments were those used to manage transient associated symptoms (e.g., insomnia) or transient or longer-term medication side effects (e.g., sexual dysfunction). Adjunctive treatments that were not used to treat depression were allowed during the study. However, drugs in the exclusion criteria for this study were not used as adjunctive therapies. Subjects were allowed to participate in the study while receiving concurrent medications for general medical conditions as long as there was no contraindication to use while taking citalopram or escitalopram. Drug efficacy phenotype evaluation. The change in QIDS-C16 score and change in HRS-D17 score were used as the major research outcome measures to assess drug response. At each clinical research visit, the RC also completed the Clinician Global Impression of Improvement (CGI-I) scale. For the primary genome-wide association analyses, dichotomous outcome variables, remission and response, were defined based on the QIDS-C16 last visit score. Remission was defined as a QIDS-C16 score of 5 or less, while response was defined as at least a 50% reduction in the QIDS-C16 score from baseline. Specimen collection. Specimen collections were obtained by the General Clinical Research Center (GCRC) at St. Mary's Hospital (SMH). Subjects had blood drawn on an outpatient basis at GCRC-SMH on three separate occasions - baseline (0), week 4 and week 8 visits. Prior to sample collection, date and time of last dose of study medication was gathered at the 4 and 8 week visits. For those patients who were unable to complete the regularly scheduled visits, a dismissal blood draw was requested. GCRC then shipped samples to Mayo Clinic's Biospecimens Accessioning and Processing Lab. Genotyping and biomarker assays. DNA from 529 patients was genotyped by the RIKEN Center for Genomic Medicine (Yokohama, Japan) using Illumina Human610-Quad BeadChips (Illumina, San Diego, CA). The study also included the determination of plasma drug levels at weeks 4 and 8, and metabolite levels at baseline and weeks 4 and 8 for a subset of subjects. The primary genome-wide association study based on these data, which includes a summary of the protocol, subject description, selection of subjects for genetic analyses, and definitions of clinical outcomes, was published in the Pharmacogenomics Journal (Ji et al., 2012).

  Study phs000670

• The Dutch Microbiome Project Batch 1

  The Dutch Microbiome Project (DMP) data includes shotgun metagenomic sequencing of faecal samples 8,208 Dutch individuals. Paired-end sequencing was performed using Illumina HiSeq 2000 platform. Data is archived in two batches to facilitate easier data access and upload to EGA. Batch 1 of DMP includes 4396 samples.

  Dataset EGAD00001007027

• Covid19 WGS variants analysis

  483 samples were collected for WGS and aligned with GRCh38 human genome. The variants were called using GATK (Sentieon v. 201808.03) in GVCF and VCF format.

  Dataset EGAD00001010138

• Irish Covid19 WGS Raw Reads

  Dataset contains 483 Irish origin Individuals with Covid19. paired end sequencing has been performed For WGS and later processed by using sention v 201808.03.

  Dataset EGAD00001010186

• Privacy Notice for Data Access Committee Account

  Privacy Notice for EGA Data Access Committee Account This Privacy Notice explains what personal data is collected by the specific service you are requesting, for what purposes, how it is processed, and how we keep it secure. Note that this service collects personal data directly provided by the user, and also collects personal data from users that is provided by other organisations. 1. Who controls your personal data and how to contact us? European Genome- Phenome Archive - EGA offers a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects, jointly managed by European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI) and Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG). EMBL-EBI and CRG represent joint Data Controllers’ of processing of your personal data. They and their Data protection officers may be contacted for data protection queries and for exercising your rights under Section 8. You may contact EMBL-EBI, represented by dr. Thomas Keane, by: email at: tk2@ebi.ac.uk or post at EMBL-EBI, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridgeshire, UK. EMBL’s Data Protection Officer may be contacted by: telephone at +49 6221 387-8590, email at dpo@embl.org, or post at EMBL Heidelberg, Data protection officer, Meyerhofstraße 1, 69117 Heidelberg, Germany. You may contact CRG, whose EGA team is represented by dr. Jordi Rambla de Argila, by: email at jordi.rambla@crg.eu, or post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), Dr.Aiguader 88, PRBB Building, 08003 Barcelona, Spain. CRG Data protection officer may be contacted by: email at dpo@crg.eu post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain. 2. Which is the lawful basis for processing personal data? We process your personal data on the grounds of important public interest. For monitoring your activities on the website, we process your personal data on the grounds of important public interest. Such legal basis is found in Article 5(1)(a) of EMBL Internal Policy No 68 on General Data Protection (hereinafter IP 68), which is equivalent to Article 6 (1)(e) of the EU General Data Protection Regulation (hereinafter GDPR) and upon which personal data are processed for the achievement of the aims laid down in 1973 agreement establishing EMBL, such as the promotion of the cooperation in the fundamental research, in the development of advanced instrumentation and in advanced teaching in molecular biology and dissemination of information. 3. What personal data is collected from users of the service? How do we use this personal data? We collect the following personal data from you: Name Email address Title/Position Organisation Organisational affiliation Business address Telephone number IP addresses Date and time of a visit to the service website Operating system Amount of data transmitted Browser Username Password The data controller will use your personal data for the following purposes: To provide DAC user account and authenticated access to the service, To publicly publish some information to facilitate scientific research, To better understand the needs of the data subjects and guide future improvements of the service, To create anonymous usage statistics (from number of DACs, datasets per DAC). 4. Who will have access to your personal data? The personal data will be disclosed to: Authorised staff in the data controller’s institutions acting on data controller`s behalf and instructions (for all user account data), The general public via Internet will get access to your name, email address, business address, telephone number and organisation you belong to. 5. Will your personal data be transferred to third countries (i.e. countries not part of EU/EEA) and/or international organisations? Data categories ‘name`, `email address`, `telephone number`, `business address`; `organisation’ of the DAC user are published on the Internet. They thus become accessible to recipients in countries outside the European Economic Area. Insofar as the second joint controller may be subject to GDPR, data transfer to and from the first joint controller (EMBL-EBI), is necessary for important reasons of public interest embedded in the aims of EMBL and justified in the Article 9(4) of IP 68 (equivalent to Article 49(1)(d) of GDPR) read in conjunction with EMBL`s 1973 establishing agreement and Article 179(2) of the Treaty on the Functioning of the European Union 6. How long do we keep your personal data? Any personal data directly obtained from you will be retained as long as the service is live. Such duration serves the purpose of enabling scientific research and ensures legal compliance and facilitates internal and external audits if they arise. By contrast, the log files for the data categories related to anonymous usage statistics (raw web service logs) are processed only for 30 days and thereafter erased. 7. The joint Data Controllers provide these rights regarding your personal data You have the right to: Not be subject to decisions based solely on an automated processing of data (i.e. without human intervention) without you having your views taken into consideration. Request at reasonable intervals and without excessive delay or expense, information about the personal data processed about you. Under your request we will inform you in writing about, for example, the origin of the personal data or the preservation period. Request information to understand data processing activities when the results of these activities are applied to you. It must be clarified that rights under points 4 and 5 are only available whenever you need support whilst using our website. For other processing based on the grounds of important public interest you cannot exercise your rights to object, rectify or erase your personal data according to the Article 13(2)(a)(b) of IP 68 (equivalent to Article 17(3)(b)(d) and Article 21(6) of the GDPR). 8. Supervisory authority If you wish to complain against the processing of your personal data, you may do so by post at: EMBL Heidelberg, Data Protection Committee, Meyerhofstraße 1, 69117 Heidelberg, Germany, or Autoritat Catalana de Protecció de Dades (Catalan Data Protection Authority), C/Rosselló 214, Esc A, 1r 1a, Barcelona 08008, Spain. Published at: February 6, 2019

  Documentation data-protection/privacy-notice/ega-dac

• Cellular indexing of transcriptomes and epitopes sequencing of peritoneal fluid from patients with achalasia

  The data published here contains cellular indexing of transcriptomes and epitopes sequencing (CITEseq) using the oligo-tagged TotalSeq™-B Human Universal Cocktail, V1.0 from BioLegend on peritoneal fluid (PF) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000. Below an overview of the epitopes to oligotags as obtained from BioLegend: DNA_ID Description clone Sequence Ensembl ID B0006 anti-human CD86 IT2.2 GTCTTTGTCAGTGCA ENSG00000114013 B0007 anti-human CD274 (B7-H1, PD-L1) 29E.2A3 GTTGTCCGACAATAC ENSG00000120217 B0020 anti-human CD270 (HVEM, TR2) 122 TGATAGAAACAGACC ENSG00000157873 B0023 anti-human CD155 (PVR) SKII.4 ATCACATCGTTGCCA ENSG00000073008 B0024 anti-human CD112 (Nectin-2) TX31 AACCTTCCGTCTAAG ENSG00000130202 B0026 anti-human CD47 CC2C6 GCATTCTGTCACCTA ENSG00000196776 B0029 anti-human CD48 BJ40 CTACGACGTAGAAGA ENSG00000117091 B0031 anti-human CD40 5C3 CTCAGATGGAGTATG ENSG00000101017 B0032 anti-human CD154 24-31 GCTAGATAGATGCAA ENSG00000102245 B0033 anti-human CD52 HI186 CTTTGTACGAGCAAA ENSG00000169442 B0034 anti-human CD3 UCHT1 CTCATTGTAACTCCT ENSG00000167286 B0046 anti-human CD8 SK1 GCGCAACTTGATGAT ENSG00000153563 B0047 anti-human CD56 (NCAM) 5.1H11 TCCTTTCCTGATAGG ENSG00000149294 B0050 anti-human CD19 HIB19 CTGGGCAATTACTCG ENSG00000177455 B0052 anti-human CD33 P67.6 TAACTCAGGGCCTAT ENSG00000105383 B0053 anti-human CD11c S-HCL-3 TACGCCTATAACTTG ENSG00000140678 B0058 anti-human HLA-A,B,C W6/32 TATGCGAGGCTTATC ENSG00000206503 B0063 anti-human CD45RA HI100 TCAATCCTTCCGCTT ENSG00000081237 B0064 anti-human CD123 6H6 CTTCACTCTGTCAGG ENSG00000185291 B0066 anti-human CD7 CD7-6B7 TGGATTCCCGGACTT ENSG00000173762 B0068 anti-human CD105 43A3 ATCGTCGAGAGCTAG ENSG00000106991 B0070 anti-human/mouse CD49f GoH3 TTCCGAGGATGATCT ENSG00000091409 B0071 anti-human CD194 (CCR4) L291H4 AGCTTACCTGCACGA ENSG00000183813 B0072 anti-human CD4 RPA-T4 TGTTCCCGCTCAACT ENSG00000010610 B0073 anti-mouse/human CD44 IM7 TGGCTTCAGGTCCTA ENSG00000026508 B0081 anti-human CD14 M5E2 TCTCAGACCTCCGTA ENSG00000170458 B0083 anti-human CD16 3G8 AAGTTCACTCTTTGC ENSG00000203747 B0085 anti-human CD25 BC96 TTTGTCCTGTACGCC ENSG00000134460 B0087 anti-human CD45RO UCHL1 CTCCGAATCATGTTG ENSG00000081237 B0088 anti-human CD279 (PD-1) EH12.2H7 ACAGCGCCGTATTTA ENSG00000188389 B0089 anti-human TIGIT (VSTM3) A15153G TTGCTTACCGCCAGA ENSG00000181847 B0090 Mouse IgG1, κ isotype MOPC-21 GCCGGACGACATTAA B0091 Mouse IgG2a, κ isotype MOPC-173 CTCCTACCTAAACTG B0092 Mouse IgG2b, κ isotype MPC-11 ATATGTATCACGCGA B0095 Rat IgG2b, κ isotype RTK4530 GATTCTTGACGACCT B0100 anti-human CD20 2H7 TTCTGGGTCCCTAGA ENSG00000156738 B0101 anti-human CD335 (NKp46) 9E2 ACAATTTGAACAGCG ENSG00000189430 B0124 anti-human CD31 WM59 ACCTTTATGCCACGG ENSG00000261371 B0127 anti-Human Podoplanin NC-08 GGTTACTCGTTGTGT ENSG00000162493 B0134 anti-human CD146 P1H12 CCTTGGATAACATCA ENSG00000076706 B0136 anti-human IgM MHM-88 TAGCGAGCCCGTATA ENSG00000211899 B0138 anti-human CD5 UCHT2 CATTAACGGGATGCC ENSG00000110448 B0141 anti-human CD195 (CCR5) J418F1 CCAAAGTAAGAGCCA ENSG00000160791 B0142 anti-human CD32 FUN-2 GCTTCCGAATTACCG ENSG00000143226 B0143 anti-human CD196 (CCR6) G034E3 GATCCCTTTGTCACT ENSG00000112486 B0144 anti-human CD185 (CXCR5) J252D4 AATTCAACCGTCGCC ENSG00000160683 B0145 anti-human CD103 (Integrin αE) Ber-ACT8 GACCTCATTGTGAAT ENSG00000083457 B0146 anti-human CD69 FN50 GTCTCTTGGCTTAAA ENSG00000110848 B0147 anti-human CD62L DREG-56 GTCCCTGCAACTTGA ENSG00000188404 B0149 anti-human CD161 HP-3G10 GTACGCAGTCCTTCT ENSG00000111796 B0151 anti-human CD152 (CTLA-4) BNI3 ATGGTTCACGTAATC ENSG00000163599 B0152 anti-human CD223 (LAG-3) 11C3C65 CATTTGTCTGCCGGT ENSG00000089692 B0153 anti-human KLRG1 (MAFA) SA231A2 CTTATTTCCTGCCCT ENSG00000139187 B0154 anti-human CD27 O323 GCACTCCTGCATGTA ENSG00000139193 B0155 anti-human CD107a (LAMP-1) H4A3 CAGCCCACTGCAATA ENSG00000185896 B0156 anti-human CD95 (Fas) DX2 CCAGCTCATTAGAGC ENSG00000026103 B0158 anti-human CD134 (OX40) Ber-ACT35 (ACT35) AACCCACCGTTGTTA ENSG00000186827 B0159 anti-human HLA-DR L243 AATAGCGAGCAAGTA ENSG00000204287 B0160 anti-human CD1c L161 GAGCTACTTCACTCG ENSG00000158481 B0161 anti-human CD11b ICRF44 GACAAGTGATCTGCA ENSG00000169896 B0162 anti-human CD64 10.1 AAGTATGCCCTACGA ENSG00000150337 B0163 anti-human CD141 (Thrombomodulin) M80 GGATAACCGCGCTTT ENSG00000178726 B0164 anti-human CD1d 51.1 TCGAGTCGCTTATCA ENSG00000158473 B0165 anti-human CD314 (NKG2D) 1D11 CGTGTTTGTTCCTCA ENSG00000213809 B0167 anti-human CD35 E11 ACTTCCGTCGATCTT ENSG00000203710 B0168 anti-human CD57 Recombinant QA17A04 AACTCCCTATGGAGG ENSG00000109956 B0170 anti-human CD272 (BTLA) MIH26 GTTATTGGACTAAGG ENSG00000186265 B0171 anti-human/mouse/rat CD278 (ICOS) C398.4A CGCGCACCCATTAAA ENSG00000163600 B0174 anti-human CD58 (LFA-3) TS2/9 GTTCCTATGGACGAC ENSG00000116815 B0176 anti-human CD39 A1 TTACCTGGTATCCGT ENSG00000138185 B0179 anti-human CX3CR1 K0124E1 AGTATCGTCTCTGGG ENSG00000168329 B0180 anti-human CD24 ML5 AGATTCCTTCGTGTT ENSG00000272398 B0181 anti-human CD21 Bu32 AACCTAGTAGTTCGG ENSG00000117322 B0185 anti-human CD11a TS2/4 TATATCCTTGTGAGC ENSG00000005844 B0187 anti-human CD79b (Igβ) CB3-1 ATTCTTCAACCGAAG ENSG00000007312 B0189 anti-human CD244 (2B4) C1.7 TCGCTTGGATGGTAG ENSG00000122223 B0206 anti-human CD169 7-239 TACTCAGCGTGTTTG ENSG00000088827 B0214 anti-human/mouse integrin β7 FIB504 TCCTTGGATGTACCG ENSG00000139626 B0215 anti-human CD268 (BAFF-R) 11C1 CGAAGTCGATCCGTA ENSG00000159958 B0216 anti-human CD42b HIP1 TCCTAGTACCGAAGT ENSG00000203618 B0217 anti-human CD54 HA58 CTGATAGACTTGAGT ENSG00000090339 B0218 anti-human CD62P (P-Selectin) AK4 CCTTCCGTATCCCTT ENSG00000174175 B0219 anti-human CD119 (IFN-γ R α chain) GIR-208 TGTGTATTCCCTTGT ENSG00000027697 B0224 anti-human TCR α/β IP26 CGTAACGTAGAGCGA B0236 Rat IgG1, κ isotype RTK2071 ATCAGATGCCCTCAT B0238 Rat IgG2a, κ Isotype RTK2758 AAGTCAGGTTCGTTT B0242 anti-human CD192 (CCR2) K036C2 GAGTTCCCTTACCTG ENSG00000121807 B0246 anti-human CD122 (IL-2Rβ) TU27 TCATTTCCTCCGATT ENSG00000100385 B0352 anti-human FcεRIα AER-37 (CRA-1) CTCGTTTCCGTATCG ENSG00000179639 B0353 anti-human CD41 HIP8 ACGTTGTGGCCTTGT ENSG00000005961 B0355 anti-human CD137 (4-1BB) 4B4-1 CAGTAAGTTCGGGAC ENSG00000049249 B0358 anti-human CD163 GHI/61 GCTTCTCCTTCCTTA ENSG00000177575 B0359 anti-human CD83 HB15e CCACTCATTTCCGGT ENSG00000112149 B0363 anti-human CD124 (IL-4Rα) G077F6 CCGTCCTGATAGATG ENSG00000077238 B0364 anti-human CD13 WM15 TTTCAACGCCCTTTC ENSG00000166825 B0367 anti-human CD2 TS1/8 TACGATTTGTCAGGG ENSG00000116824 B0368 anti-human CD226 (DNAM-1) 11A8 TCTCAGTGTTTGTGG ENSG00000150637 B0369 anti-human CD29 TS2/16 GTATTCCCTCAGTCA ENSG00000150093 B0370 anti-human CD303 (BDCA-2) 201A GAGATGTCCGAATTT ENSG00000198178 B0371 anti-human CD49b P1E6-C5 GCTTTCTTCAGTATG ENSG00000164171 B0373 anti-human CD81 (TAPA-1) 5A6 GTATCCTTCCTTGGC ENSG00000110651 B0384 anti-human IgD IA6-2 CAGTCTCCGTAGAGT ENSG00000211898 B0385 anti-human CD18 TS1/18 TATTGGGACACTTCT ENSG00000160255 B0386 anti-human CD28 CD28.2 TGAGAACGACCCTAA ENSG00000178562 B0389 anti-human CD38 HIT2 TGTACCCGCTTGTGA ENSG00000004468 B0390 anti-human CD127 (IL-7Rα) A019D5 GTGTGTTGTCCTATG ENSG00000168685 B0391 anti-human CD45 HI30 TGCAATTACCCGGAT ENSG00000081237 B0393 anti-human CD22 S-HCL-1 GGGTTGTTGTCTTTG ENSG00000012124 B0394 anti-human CD71 CY1G4 CCGTGTTCCTCATTA ENSG00000072274 B0396 anti-human CD26 BA5b GGTGGCTAGATAATG ENSG00000197635 B0398 anti-human CD115 (CSF-1R) 9-4D2-1E4 AATCACGGTCCTTGT ENSG00000182578 B0404 anti-human CD63 H5C6 GAGATGTCTGCAACT ENSG00000135404 B0406 anti-human CD304 (Neuropilin-1) 12C2 GGACTAAGTTTCGTT ENSG00000099250 B0407 anti-human CD36 5-271 TTCTTTGCCTTGCCA ENSG00000135218 B0408 anti-human CD172a (SIRPα) 15-414 CGTGTTTAACTTGAG ENSG00000198053 B0419 anti-human CD72 3F3 CAGTCGTGGTAGATA ENSG00000137101 B0420 anti-human CD158 (KIR2DL1/S1/S3/S5) HP-MA4 TATCAACCAACGCTT ENSG00000125498 B0446 anti-human CD93 VIMD2 GCGCTACTTCCTTGA ENSG00000125810 B0575 anti-human CD49a TS2/7 ACTGATGGACTCAGA ENSG00000213949 B0576 anti-human CD49d 9F10 CCATTCAACTTCCGG ENSG00000115232 B0577 anti-human CD73 (Ecto-5'-nucleotidase) AD2 CAGTTCCTCAGTTCG ENSG00000135318 B0579 anti-human CD9 HI9a GAGTCACCAATCTGC ENSG00000010278 B0581 anti-human TCR Vα7.2 3C10 TACGAGCAGTATTCA B0582 anti-human TCR Vδ2 B6 TCAGTCAGATGGTAT B0591 anti-human LOX-1 15C4 ACCCTTTACCGAATA ENSG00000173391 B0592 anti-human CD158b (KIR2DL2/L3, NKAT2) DX27 GACCCGTAGTTTGAT ENSG00000243772 B0599 anti-human CD158e1 (KIR3DL1, NKB1) DX9 GGACGCTTTCCTTGA ENSG00000167633 B0822 anti-human CD142 NY2 CACTGCCGTCGATTA ENSG00000117525 B0830 anti-human CD319 (CRACC) 162.1 AGTATGCCATGTCTT ENSG00000026751 B0864 anti-human CD352 (NTB-A) NT-7 AGTTTCCACTCAGGC ENSG00000162739 B0867 anti-human CD94 DX22 CTTTCCGGTCCTACA ENSG00000134539 B0871 anti-human CD162 KPL-1 ATATGTCAGAGCACC ENSG00000110876 B0896 anti-human CD85j (ILT2) GHI/75 CCTTGTGAGGCTATG ENSG00000104972 B0897 anti-human CD23 EBVCS-5 TCTGTATAACCGTCT ENSG00000104921 B0902 anti-human CD328 (Siglec-7) 6-434 CTTAGCATTTCACTG ENSG00000168995 B0918 anti-human HLA-E 3D12 GAGTCGAGAAATCAT ENSG00000204592 B0920 anti-human CD82 ASL-24 TCCCACTTCCGCTTT ENSG00000085117 B0944 anti-human CD101 (BB27) BB27 CTACTTCCCTGTCAA ENSG00000134256 B1046 anti-human CD88 (C5aR) S5/1 GCCGCATGAGAAACA ENSG00000197405 B1052 anti-human CD224 KF29 CTGATGAGATGTCAG ENSG00000100031

  Dataset EGAD50000000252

• LBC1936 fastq files

  1075 members of the LBC1936 were sequenced using the Illumina HiSeq X platform. This dataset contains the paired fastq files.

  Dataset EGAD00001008774

• CD_prognosis_UKB

  Crohn's disease DNA samples genotyped using UK Biobank Axiom array

  Dataset EGAD00010001155