|
| Status |
Public on Feb 15, 2022 |
| Title |
Myeloid Cells - SCC 10x SCC002 |
| Sample type |
SRA |
| |
|
| Source name |
SCC-derived Myloid Cells
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: CD45+HLADR+
donors: SCC002
tissue: Squamous Cell Carcinoma
|
| Treatment protocol |
T cells were stimulated for 2 hour with PMA/ Ionomycin or IL-12, IL-15, IL-18
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using BD Rhapsody or 10x genomics protocols
RNA was constructed using BD Rhapsody or 10x genomics protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Samples 1-8 (10x) samples were processed using CellRanger pipline version 2.1.1 or 3.0.2
Sample 9 aligned RNA reads using 1342_Fred_Hutch_suppt2_amplicons.fasta
Sample 10 aligned RNA reads using 1342_Fred_Hutch_suppt2_amplicons.fasta and aligned protein reasd using AbSeq_Prlic_NEW_v2.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline hosted by SevenBridges Genomics
FASTQ files were processed with CellRanger software v2.1.1 or v3.0.1 and corresponding sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.
|
| |
|
| Submission date |
Dec 21, 2020 |
| Last update date |
Feb 17, 2022 |
| Contact name |
Martin Prlic |
| E-mail(s) |
mprlic@fredhutch.org
|
| Phone |
2066672216
|
| Organization name |
Fred Hutch
|
| Street address |
1100 Fairview Ave, Mail stop E5-110
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98108 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE163633 |
Identification of human tumor-unique signaling networks between antigen-presenting cells and T cells using multi-omic single cell analysis |
|
| Relations |
| BioSample |
SAMN17129178 |
| SRA |
SRX9711341 |
