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Sample GSM6603114 Query DataSets for GSM6603114
Status Public on Jan 16, 2024
Title COR-3717-D2
Sample type SRA
 
Source name PBMCs
Organism Homo sapiens
Characteristics cell type: PBMCs
collection day: D2
disease state: case
Sex: M
age bin: 3
chromium batch: batch 18
number of sequencer models used: 2
Extracted molecule total RNA
Extraction protocol Whole blood was collected in EDTA tubes before and 24h after a cardiopulmonary exercise test (CPET) for each subject in the study. PBMCs were isolated with SepMate tubes and cryopreserved with 1-10 x10^6 cells per vial. Frozen PBMCs were recovered following the 10x Genomics Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (CG00039) and resuspended in 1x PBS containing 0.04% BSA. For a target of 5,000 cells per final library, 8,000 cells were loaded onto the 10x Chromium chip.
Libraries were constructed using the Chromium Single Cell 3สน v3 kit (10x Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing cellranger mkfastq was used to generate fastq files by the sequencing facility
Because some samples were sequenced on different (or multiple) Illumina sequencers with different read lengths, all reads were trimmed for analysis and for upload to GEO (R1=28bp, R2=55bp). Samples are annotated with the number of different sequencer models used (NextSeq, HiSeq, and NovaSeq) and final fastq files are annotated by the instrument that generated the majority of reads.
cellranger count (v6) was used to generate raw count tables (h5 files), with the following parameters: --expect-cells=5000 --r1-length=28 --r2-length=55 --nosecondary
Assembly: 10x Genomics reference: refdata-gex-GRCh38-2020-A
Supplementary files format and content: h5
 
Submission date Sep 27, 2022
Last update date Jan 16, 2024
Contact name Jennifer K Grenier
Organization name Cornell University
Department Biomedical Sciences
Lab Biotechnology Building rm 333
Street address 526 Campus Rd
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
 
Platform ID GPL24676
Series (2)
GSE214283 Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation
GSE214284 Transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation
Relations
BioSample SAMN31038743
SRA SRX17724037

Supplementary file Size Download File type/resource
GSM6603114_COR-3717-D2_filtered_feature_bc_matrix.h5 10.3 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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