|
| Status |
Public on Aug 10, 2017 |
| Title |
CD4-ICOSpos-B447 |
| Sample type |
SRA |
| |
|
| Source name |
tumor infiltrating ICOS+ CD4 T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: tumor infiltrating ICOS+ CD4 T cells
age: post MC38 tumor cell injection day 12
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Activated tumor infiltrating ICOS+ CD4 T cells were sorted directly into RLT buffer (volume) using a FACS AriaFusion cell sorter (BD). Lysates were homogenized using a QiaShredder and RNA extracted using RNeasy Micro kit (Qiagen) according to the manufacturer’s protocol.
Due to low RNA yield from sorted T cell populations from individual mice, libraries were prepared using Ovation single-cell RNAseq system (NuGEN). Indexed libraries were analyzed by 76-nucleotide paired end sequencing on a HiSeq 4000 system (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
anti-PD-1 rep1
|
| Data processing |
RNAseq data was aligned to GRCm38 using TopHat2 with parameter --library-type=fr-firststrand
Gene read counts were generated using htseq-count
Bioconductor R package DESeq2 was used to normalize and analyze the RNA read count matrix
Genome_build: GRCm38
Supplementary_files_format_and_content: comma seperated csv files include read counts matrix for all the samples
|
| |
|
| Submission date |
Jul 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Spencer Wei |
| E-mail(s) |
[email protected]
|
| Phone |
7135633295
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Immunology
|
| Street address |
7455 Fannin St.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE100807 |
Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade [RNA-seq] |
| GSE100809 |
Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade |
|
| Relations |
| BioSample |
SAMN07317088 |
| SRA |
SRX2984185 |
