 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 22, 2024 |
| Title |
C1_45A |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMCs
age: not applicable
Sex: not applicable
group: not applicable
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue samples obtained by biopsy or autopsy were immediately placed in ice-cold HypoThermosol solution (BioLife Solutions, Bothell, WA) and kept on ice during transfer to the research facility. Tissue was then washed twice with cold phosphate buffered saline. Tissue was then dissociated using the human tumor dissociation kit according to the manufacturer’s instructions (Miltenyi Biotic, Bergisch Gladbach, Germany) with modification such that calcium chloride was added to the enzymatic cocktail to a final concentration of 1.25 mM. Tubes containing tissue fragments in the enzymatic cocktail were placed in a heated shaker at 37° C with shaking at 750 RPM for 25 minutes with the machine placed on its side to prevent tissue fragments from settling. Following incubation, the reaction was quenched through the addition of 100 µl human serum. The mixture was further dissociated through manual trituration followed by filtration through 70 µm mesh. Following centrifugation at 350 x g for 12 minutes, the supernatant was removed and RBC lysis was performed (ACK lysing buffer, Lonza, Basel, Switzerland). Following a wash step, cells were resuspended in phenol-free RPMI with 2% (v/v) human AB serum.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the human reference genome (GRCh38, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: GRCh38
Supplementary files format and content: combined_tissue_data.h5ad includes the counts for all cells that passed QC in .h5 format
Supplementary files format and content: combined_pbmc_data.h5ad includes the counts for all demultiplexed cells that passed QC in .h5 format
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format
Supplementary files format and content: all_contig_annotations_tcr.csv files include the TCR data for the associated samples
Supplementary files format and content: fbc.csv files contains data for featured barcodes for applicable samples (all PBMC samples)
Supplementary files format and content: hashing_info.csv includes information about which samples correspond to which fbc hashtags in the PBMC samples
Supplementary files format and content: cite_info.csv includes information about the antibodies included in the FBC pool
|
| |
|
| Submission date |
Mar 30, 2023 |
| Last update date |
Jun 22, 2024 |
| Contact name |
Neal Patrick Smith |
| E-mail(s) |
nsmith19@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Street address |
149 13th Street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE228597 |
Immunologic drivers of immune checkpoint inhibitor therapy myocarditis, fatality and anti-tumor response in cancer patients |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7133733_C1_45A_all_contig_annotations_tcr.csv.gz |
1.3 Mb |
(ftp)(http) |
CSV |
| GSM7133733_C1_45A_fbc.csv.gz |
28.4 Mb |
(ftp)(http) |
CSV |
| GSM7133733_C1_45A_gex_raw_feature_bc_matrix.h5 |
63.6 Mb |
(ftp)(http) |
H5 |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
|
|
|
|
 |
