|
| Status |
Public on Jan 16, 2024 |
| Title |
COR-3717-D1 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMCs
collection day: D1
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 |
SAMN31038742 |
| SRA |
SRX17724038 |
