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• Symptom Clusters in Oncology Patients Receiving Chemotherapy

  The parent longitudinal study evaluated the symptom experience of oncology outpatients receiving chemotherapy. Patients completed questionnaires in their homes a total of six times (assessments 1 through 6). The questionnaires were timed to evaluate symptoms associated with the receipt of two cycles of chemotherapy that were administered approximately a month apart. Assessments 1 and 4 evaluated symptoms prior to the receipt of chemotherapy. Assessments 2 and 5 evaluated symptoms in the week following the administration of chemotherapy. Assessments 3 and 6 evaluated symptoms two weeks following the administration of chemotherapy. For this analysis, morning and evening fatigue data from the enrollment assessment (i.e., prior to the second or third cycle of chemotherapy) and the assessment that was done approximately 1 week after administration of chemotherapy were evaluated. Patients completed the Lee Fatigue Scale to obtain information on morning and evening fatigue severity. For the morning fatigue assessment, patients were asked to describe how they “felt over the past week when they woke up in the morning”. For the evening fatigue assessment, they were asked to describe how they felt over the past week “before they went to bed at night”. Medical records were reviewed for disease and treatment information. Epigenome assays (microarray) were completed for 1170 patients. Whole transcriptome sequencing (bulk RNA-Seq) was completed for 651 patients.

  Study phs003863

• EGAD00000000045

  Genomic sequencing and transcriptome shotgun sequencing of a metastatic tumour and its recurrence after drug therapy in a single patient

  Dataset EGAD00000000045

• Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

  Dataset EGAD00001000856

• cqmuGWAS1

  DNA for 1546 individuals from Chongqing was extract from peripheral blood and genotyped by Illumina Omni Zhonghua-8 version 1 gene chips.

  Dataset EGAD00010001527

• oacoch-M-1

  Methylation changes in OA patients with chronic exposure to cobalt and chromium

  Dataset EGAD00010001040

• CIRdb-CEU1

  Single Nucleotide Polymorphisms in autosomes of Canary Islanders

  Dataset EGAD00010002294

• Transcriptome of (peripheral blood), from donor Sample A, replicate 2 FACS processing technical replicates

  FACS processing technical replicates

  Dataset EGAD00001010087

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  Dataset EGAD00001010049

• Targeted capture ctDNA Library CRCQV42Run021-6

  Targeted capture ctDNA Library CRCQV42Run021-6 from patient PBC0001304, saliva sample

  Dataset EGAD00001010447

• Targeted capture ctDNA Library CRCQV42Run051-9

  Targeted capture ctDNA Library CRCQV42Run051-9 from patient PBC0003587, plasma sample

  Dataset EGAD00001010822

• SF10432 Wildtype Primary GBM Female, 50

  Single Cell-RNA Seq of Wildtype Primary GBM for Female, Age 50.

  Dataset EGAD00001006019

• Fecal WMS HV metadata

  Metadata for fecal WMS data from NCT02749630 healthy volunteers.

  Dataset EGAD00001008819

• Reference epigenome ADMSC08 WGBS data generated from KEP study

  ADMSC08 WGBS paired end data

  Dataset EGAD00001007139

• Reference epigenome ADMSC06 WGBS data generated from KEP study

  ADMSC06 WGBS paired end data

  Dataset EGAD00001007137

• Targeted capture ctDNA Library CRCQV42Run022-18

  Targeted capture ctDNA Library CRCQV42Run022-18 from patient PBC0002826, saliva sample

  Dataset EGAD00001010453

• Reference epigenome IPS-NPC02 h3k4me3 ChIP-Seq data generated from KEP study

  IPS-NPC02 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007288

• Targeted capture ctDNA Library CRCQV42Run42-17

  Targeted capture ctDNA Library CRCQV42Run42-17 from patient PBC0001375, saliva sample

  Dataset EGAD00001010828

• RNAseq data for EGAS00001004572

  Bulk RNA-seq data of tumours in EGAS00001004572.

  Dataset EGAD00001006876

• Targeted capture ctDNA Library CRCQV42Run051-8

  Targeted capture ctDNA Library CRCQV42Run051-8 from patient PBC0002294, plasma sample

  Dataset EGAD00001010821

• Targeted capture ctDNA Library CRCQV42Run021-23

  Targeted capture ctDNA Library CRCQV42Run021-23 from patient PBC0001516, saliva sample

  Dataset EGAD00001010444

• Targeted capture ctDNA Library CRCQV42Run020-14

  Targeted capture ctDNA Library CRCQV42Run020-14 from patient PBC0001312, saliva sample

  Dataset EGAD00001010426

• Targeted capture ctDNA Library CRCQV42Run021-24

  Targeted capture ctDNA Library CRCQV42Run021-24 from patient PBC0001653, saliva sample

  Dataset EGAD00001010445

• Targeted capture ctDNA Library CRCQV42Run025-17

  Targeted capture ctDNA Library CRCQV42Run025-17 from patient PBC0003595, saliva sample

  Dataset EGAD00001010481

• Reference epigenome ADMSC05 WGBS data generated from KEP study

  ADMSC05 WGBS paired end data

  Dataset EGAD00001007136

• Reference epigenome ADMSC07 WGBS data generated from KEP study

  ADMSC07 WGBS paired end data

  Dataset EGAD00001007138

• Targeted capture ctDNA Library CRCQV42Run016-17

  Targeted capture ctDNA Library CRCQV42Run016-17 from patient PBC0001467, saliva sample

  Dataset EGAD00001010401

• RCRF release 1

  Transcriptome sequencing from the Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendocrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010198

• Targeted capture ctDNA Library CRCQV34Run011-22

  Targeted capture ctDNA Library CRCQV34Run011-22 from patient PBC0002294, saliva sample

  Dataset EGAD00001010373

• Targeted capture ctDNA Library CRCQV34Run011-23

  Targeted capture ctDNA Library CRCQV34Run011-23 from patient PBC0001328, saliva sample

  Dataset EGAD00001010374

• Targeted capture ctDNA Library CRCQV40Run027-13

  Targeted capture ctDNA Library CRCQV40Run027-13 from patient PBC0005116, saliva sample

  Dataset EGAD00001010389

• Targeted capture ctDNA Library CRCQV42Run016-16

  Targeted capture ctDNA Library CRCQV42Run016-16 from patient PBC0001396, saliva sample

  Dataset EGAD00001010400

• Targeted capture ctDNA Library CRCQV42Run041-5

  Targeted capture ctDNA Library CRCQV42Run041-5 from patient PBC0001375, saliva sample

  Dataset EGAD00001010635

• Targeted capture ctDNA Library CRCQV42Run041-13

  Targeted capture ctDNA Library CRCQV42Run041-13 from patient PBC0001413, saliva sample

  Dataset EGAD00001010627

• Targeted capture ctDNA Library CRCQV42Run051-10

  Targeted capture ctDNA Library CRCQV42Run051-10 from patient PBC0001665, plasma sample

  Dataset EGAD00001010804

• Targeted capture ctDNA Library CRCQV42Run028-23

  Targeted capture ctDNA Library CRCQV42Run028-23 from patient PBC0002533, saliva sample

  Dataset EGAD00001010508

• Small variants in HAE of patients from Canary Islands (ITER)

  Small variants in HAE of several Canary Islanders sequenced with Illumina WES.

  Dataset EGAD00001009318

• Targeted capture ctDNA Library CRCQV42Run026-19

  Targeted capture ctDNA Library CRCQV42Run026-19 from patient PBC0002872, saliva sample

  Dataset EGAD00001010492

• Targeted capture ctDNA Library CRCQV34Run002-22

  Targeted capture ctDNA Library CRCQV34Run002-22 from patient PBC0002459, saliva sample

  Dataset EGAD00001010336

• Targeted capture ctDNA Library CRCQV34Run002-18

  Targeted capture ctDNA Library CRCQV34Run002-18 from patient PBC0002062, saliva sample

  Dataset EGAD00001010333

• Targeted capture ctDNA Library CRCQV34Run002-20

  Targeted capture ctDNA Library CRCQV34Run002-20 from patient PBC0002108, saliva sample

  Dataset EGAD00001010334

• Targeted capture ctDNA Library CRCQV34Run002-21

  Targeted capture ctDNA Library CRCQV34Run002-21 from patient PBC0002429, saliva sample

  Dataset EGAD00001010335

• Targeted capture ctDNA Library CRCQV34Run002-23

  Targeted capture ctDNA Library CRCQV34Run002-23 from patient PBC0002595, saliva sample

  Dataset EGAD00001010337

• Targeted capture ctDNA Library CRCQV34Run007-15

  Targeted capture ctDNA Library CRCQV34Run007-15 from patient PBC0001255, saliva sample

  Dataset EGAD00001010356

• Targeted capture ctDNA Library CRCQV34Run007-18

  Targeted capture ctDNA Library CRCQV34Run007-18 from patient PBC0001845, saliva sample

  Dataset EGAD00001010357

• Targeted capture ctDNA Library CRCQV34Run007-20

  Targeted capture ctDNA Library CRCQV34Run007-20 from patient PBC0002680, saliva sample

  Dataset EGAD00001010358

• Targeted capture ctDNA Library CRCQV34Run011-21

  Targeted capture ctDNA Library CRCQV34Run011-21 from patient PBC0002255, saliva sample

  Dataset EGAD00001010372

• Targeted capture ctDNA Library CRCQV34Run011-18

  Targeted capture ctDNA Library CRCQV34Run011-18 from patient PBC0001432, saliva sample

  Dataset EGAD00001010370

• Targeted capture ctDNA Library CRCQV34Run011-20

  Targeted capture ctDNA Library CRCQV34Run011-20 from patient PBC0001673, saliva sample

  Dataset EGAD00001010371

• Targeted capture ctDNA Library CRCQV34Run011-14

  Targeted capture ctDNA Library CRCQV34Run011-14 from patient PBC0001224, saliva sample

  Dataset EGAD00001010368

• Targeted capture ctDNA Library CRCQV40Run027-10

  Targeted capture ctDNA Library CRCQV40Run027-10 from patient PBC0004414, saliva sample

  Dataset EGAD00001010387

• Targeted capture ctDNA Library CRCQV40Run027-11

  Targeted capture ctDNA Library CRCQV40Run027-11 from patient PBC0004565, saliva sample

  Dataset EGAD00001010388

• Targeted capture ctDNA Library CRCQV40Run027-7

  Targeted capture ctDNA Library CRCQV40Run027-7 from patient PBC0003364, saliva sample

  Dataset EGAD00001010396

• Targeted capture ctDNA Library CRCQV40Run027-8

  Targeted capture ctDNA Library CRCQV40Run027-8 from patient PBC0004076, saliva sample

  Dataset EGAD00001010397

• Targeted capture ctDNA Library CRCQV40Run027-9

  Targeted capture ctDNA Library CRCQV40Run027-9 from patient PBC0004350, saliva sample

  Dataset EGAD00001010398

• Targeted capture ctDNA Library CRCQV42Run019-18

  Targeted capture ctDNA Library CRCQV42Run019-18 from patient PBC0001295, saliva sample

  Dataset EGAD00001010421

• Targeted capture ctDNA Library CRCQV42Run020-15

  Targeted capture ctDNA Library CRCQV42Run020-15 from patient PBC0001315, saliva sample

  Dataset EGAD00001010427

• Targeted capture ctDNA Library CRCQV42Run020-23

  Targeted capture ctDNA Library CRCQV42Run020-23 from patient PBC0001310, saliva sample

  Dataset EGAD00001010428

• Sardinia Population SNPs frequencies

  List of SNPs, and their frequencies, extracted from a low pass whole genome sequencing of 3,514 individuals.

  Dataset EGAD00001003141

• Reference epigenome IPS01_N_Fibroblast_WGBS data generated from KEP study

  A IPS01_N_Fibroblast_WGBS paired end data for iPSC(Oct4)

  Dataset EGAD00001003473

• HipSci - Monogenic Diabetes - RNA Sequencing - April 2015

  HipSci - Monogenic Diabetes - RNA Sequencing - April 2015

  Dataset EGAD00001001953

• HipSci - Monogenic Diabetes - RNA Sequencing - January 2016

  HipSci - Monogenic Diabetes - RNA Sequencing - January 2016

  Dataset EGAD00001001955

• Reference epigenome IPS04_X_Fibroblast_WGBS data generated from KEP study

  A IPS04_X_Fibroblast_WGBS paired end data for iPSC(Oct4)

  Dataset EGAD00001003476

• MPB_Bonn

  1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness

  Dataset EGAD00001001456

• mRNA-Seq dataset

  mRNA-Seq, HiSeq 2000 dataset of the Cell-line use case

  Dataset EGAD00001002250

• Targeted capture ctDNA Library CRCQV42Run021-19

  Targeted capture ctDNA Library CRCQV42Run021-19 from patient PBC0001299, saliva sample

  Dataset EGAD00001010441

• Targeted capture ctDNA Library CRCQV42Run021-21

  Targeted capture ctDNA Library CRCQV42Run021-21 from patient PBC0001323, saliva sample

  Dataset EGAD00001010442

• Targeted capture ctDNA Library CRCQV42Run021-22

  Targeted capture ctDNA Library CRCQV42Run021-22 from patient PBC0001470, saliva sample

  Dataset EGAD00001010443

• Targeted capture ctDNA Library CRCQV42Run022-16

  Targeted capture ctDNA Library CRCQV42Run022-16 from patient PBC0002406, saliva sample

  Dataset EGAD00001010451

• Targeted capture ctDNA Library CRCQV42Run022-17

  Targeted capture ctDNA Library CRCQV42Run022-17 from patient PBC0002744, saliva sample

  Dataset EGAD00001010452

• Targeted capture ctDNA Library CRCQV42Run024-20

  Targeted capture ctDNA Library CRCQV42Run024-20 from patient PBC0001589, saliva sample

  Dataset EGAD00001010470

• Targeted capture ctDNA Library CRCQV42Run025-12

  Targeted capture ctDNA Library CRCQV42Run025-12 from patient PBC0003014, saliva sample

  Dataset EGAD00001010478

• Targeted capture ctDNA Library CRCQV42Run025-13

  Targeted capture ctDNA Library CRCQV42Run025-13 from patient PBC0003334, saliva sample

  Dataset EGAD00001010479

• Targeted capture ctDNA Library CRCQV42Run026-22

  Targeted capture ctDNA Library CRCQV42Run026-22 from patient PBC0003364, saliva sample

  Dataset EGAD00001010494

• Targeted capture ctDNA Library CRCQV42Run026-24

  Targeted capture ctDNA Library CRCQV42Run026-24 from patient PBC0005064, saliva sample

  Dataset EGAD00001010495

• Targeted capture ctDNA Library CRCQV42Run026-21

  Targeted capture ctDNA Library CRCQV42Run026-21 from patient PBC0003587, saliva sample

  Dataset EGAD00001010493

• Targeted capture ctDNA Library CRCQV42Run029-17

  Targeted capture ctDNA Library CRCQV42Run029-17 from patient PBC0004173, saliva sample

  Dataset EGAD00001010514

• Targeted capture ctDNA Library CRCQV42Run029-21

  Targeted capture ctDNA Library CRCQV42Run029-21 from patient PBC0001353, saliva sample

  Dataset EGAD00001010515

• Targeted capture ctDNA Library CRCQV42Run051-14

  Targeted capture ctDNA Library CRCQV42Run051-14 from patient PBC0002989, plasma sample

  Dataset EGAD00001010808

• Targeted capture ctDNA Library CRCQV42Run051-11

  Targeted capture ctDNA Library CRCQV42Run051-11 from patient PBC0002989, plasma sample

  Dataset EGAD00001010805

• Targeted capture ctDNA Library CRCQV42Run051-12

  Targeted capture ctDNA Library CRCQV42Run051-12 from patient PBC0001516, plasma sample

  Dataset EGAD00001010806

• Targeted capture ctDNA Library CRCQV42Run051-13

  Targeted capture ctDNA Library CRCQV42Run051-13 from patient PBC0001319, plasma sample

  Dataset EGAD00001010807

• Targeted capture ctDNA Library CRCQV42Run051-5

  Targeted capture ctDNA Library CRCQV42Run051-5 from patient PBC0002533, plasma sample

  Dataset EGAD00001010819

• Targeted capture ctDNA Library CRCQV42Run051-6

  Targeted capture ctDNA Library CRCQV42Run051-6 from patient PBC0002995, plasma sample

  Dataset EGAD00001010820

• Targeted capture ctDNA Library CRCQV42Run051-4

  Targeted capture ctDNA Library CRCQV42Run051-4 from patient PBC0001224, plasma sample

  Dataset EGAD00001010818

• Targeted capture ctDNA Library CRCQV42Run42-10

  Targeted capture ctDNA Library CRCQV42Run42-10 from patient PBC0003643, saliva sample

  Dataset EGAD00001010823

• Spatial mapping of skin fibroblasts

  10x Visium section (lesional skin - atopic dermatitis) used to map location of skin fibroblasts.

  Dataset EGAD00001015704

• Paired-end RNA-seq analysis of GBM, additional patient.

  Dataset contains one paired-end RNA-seq sample.

  Dataset EGAD00001011990

• Targeted capture ctDNA Library CRCQV34Run002-14

  Targeted capture ctDNA Library CRCQV34Run002-14 from patient PBC0001051, saliva sample

  Dataset EGAD00001010331

• Targeted capture ctDNA Library CRCQV34Run002-16

  Targeted capture ctDNA Library CRCQV34Run002-16 from patient PBC0001627, saliva sample

  Dataset EGAD00001010332

• Targeted capture ctDNA Library CRCQV42Run018-20

  Targeted capture ctDNA Library CRCQV42Run018-20 from patient PBC0001859, saliva sample

  Dataset EGAD00001010418

• Targeted capture ctDNA Library CRCQV42Run041-9

  Targeted capture ctDNA Library CRCQV42Run041-9 from patient PBC0001404, saliva sample

  Dataset EGAD00001010639

• HLA sequence data and final calls for VaccGene and 1000Gp3 African populations

  HLA sequence data and final calls for VaccGene and 1000Gp3 African populations

  Dataset EGAD00001011379

• WES data for study of the microenviroment of angioimmunoblastic T-cell lymphoma

  Exome sequencing data for study of the microenviroment of angioimmunoblastic T-cell lymphoma

  Dataset EGAD00001011581

• National Cancer Institute Genome-Wide Association Study of Renal Cell Carcinoma

  The National Cancer Institute (NCI) genome-wide association study (GWAS) of renal cell carcinoma (RCC) was conducted to investigate common genetic variants associated with RCC risk. The GWAS includes 1,453 RCC cases and 3,531 controls of European background from 4 studies (3 cohort, 1 case-control), scanned using the Illumina InfiniumHumanHap 550, 610 and 660W chips. This project was supported by the Intramural Research Program of the National Institutes of Health and NCI. Data from this GWAS were pooled with those from another GWAS of RCC (2,639 cases and 5,392 controls) conducted in Europe by the International Agency for Research on Cancer and the Centre National de Gènotypage. Findings from this collaboration are described in an upcoming report (Purdue et al. Nature Genetics 2011;43(1):60-65; PMID: 21131975). Only data from the NCI scan are included in this dbGaP submission.

  Study phs000351

• Genomic Correlates of Response and Resistance to Immune Checkpoint Blockade in Solid Tumors

  Immune checkpoint inhibitors yield clinical benefit in many cancer types, but molecular predictors of response have not yet been robustly characterized. In this study, we pursued whole exome sequencing (WES) of pre-treatment tumors from patients treated with immune checkpoint therapies - including monoclonal antibodies targeting programmed cell death-1 (PD-1) and cytotoxic T-lymphocyte-associated protein-4 (CTLA-4). Using these data, we aim to apply computational pipelines for mutation-calling, neoantigen prediction, and other analyses to validate pre-existing hypotheses regarding response to immune checkpoint therapies and discover new relationships with greater power. Further, by pursuing genomic characterization of tumors from patients with a variety of cancer types, we hope to describe molecular features of intrinsically sensitive or resistant tumors that are both context-specific and shared across cancer types.

  Study phs001565

• NHLBI TOPMed - NHGRI CCDG: Malmo Preventive Project (MPP)

  The Malmö Preventive Project (MPP) was a community-based disease prevention program including 33,346 inhabitants from the city of Malmö in Southern Sweden. Complete birth cohorts between 1921-1949 were invited, and the participation rate was 71%. Participants underwent screening between 1974 to 1992 for cardiovascular risk factors, alcohol abuse, and breast cancer. Between 2002-2006, surviving participants were invited to a reexamination which included blood sampling from which DNA has been extracted. Subjects with prevalent or incident AF were identified from national registers as previously described, and cases with DNA were then matched in a 1:1 fashion to controls with DNA from the same cohort by sex, age (±1 year), and date of baseline exam (±1 year). Also, controls required a follow-up exceeding that of the corresponding AF case.

  Study phs001544

• Pilot study for Illumina TST170 NGS panel on cutaneous T cell lymphoma samples

  A number of genomic studies using next generation sequencing (NGS) techniques have attempted to understand the underlying genetic basis of cutaneous T-cell lymphoma and found alterations in genes that are involved in T-cell activation, NF-kB and JAK-signal transducer and activator of transcription (STAT) pathways. 8 diagnostic skin biopsy samples (2xplaque, 6xtumour) on FFPE blocks were selected from 8 MF patients (stage IB:n=1, IIB:n=6, IVA2:n=1). An H&E was performed in order to assess percentage of tumor cells, viable cells, necrosis and immune infiltration, to determine the number of slides required for NGS. Freshly cut unstained slides were manually macrodissected prior to DNA and RNA extraction. Targeted deep sequencing was performed using panel of 170 genes associated with common solid tumours (Illumina TruSight Tumour 170 NGS panel). VCF files generated via the Illumina’s Basespace platform.

  Study EGAS00001002567

• Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands

  Identification and quantification of low-frequency mutations remain challenging despite improvements in the baseline error rate of next-generation sequencing technologies. Here, we describe a method, termed SaferSeqS, that addresses this challenge by (1) efficiently introducing identical molecular barcodes in the Watson and Crick strands of template molecules and (2) enriching target sequences with strand-specific PCR. The method achieves high sensitivity and specificity and detects variants at frequencies below 1 in 100,000 DNA template molecules with a background mutation rate of <5 × 10-7 mutants per base pair (bp). We demonstrate that it can evaluate mutations in a single amplicon or simultaneously in multiple amplicons, assess limited quantities of cell-free DNA with high recovery of both strands and reduce the error rate of existing PCR-based molecular barcoding approaches by >100-fold.

  Study EGAS00001005048

• Single cell RNAseq of PBMC from bladder cancer patients

  Frozen PBMC samples containing at least 1 million cells were thawed for 1 minute at 37C and washed twice with RPMI complete media (10% FBS with glutamate and Pen/Strep). All of the samples had >80% viable cells. Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v2 (PN-120237) following manufacturer’s user guide (CG00052, 10x Genomics, Pleasanton, CA). The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following manufacturer’s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively. Libraries were profiled, quantified, and sequenced as 5’ single-cell gene expression libraries.

  Study EGAS00001004008

• Single cell RNAseq of PBMC from RCC patients

  Frozen PBMC samples containing at least 1 million cells were thawed for 1 minute at 37C and washed twice with RPMI complete media (10% FBS with glutamate and Pen/Strep). All of the samples had >80% viable cells. Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v2 (PN-120237) following manufacturer’s user guide (CG00052, 10x Genomics, Pleasanton, CA). The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following manufacturer’s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively. Libraries were profiled, quantified, and sequenced as 5’ single-cell gene expression libraries.

  Study EGAS00001004451