|
| Status |
Public on May 19, 2020 |
| Title |
Control_3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
mouse splenic T cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
treatment: anti-mouse CD3/CD28 only
negatively enriched by magneting beading
cell type: splenic T cells
|
| Treatment protocol |
T cell activation was determined at 72h by flow cytometry. In selected wells, T cells were treated with PD-1 Fc or control IgG Fc (2.5 ug/ml; R&D). In other experiments, T cells were treated with an _PD-L1 mAb (10 ug/ml, 10F.9G2) or Rat IgG2b_ (both Biolegend). FACS-sorting was performed on the SY3200 (Sony, Tokyo, Japan). Cell pellets were re-suspended and cell labeling was performed after blocking Fc_RIII/II with an anti-CD16/CD32 mAb (eBioscience, San Diego, CA) by incubating 1x106 cells with 1ug of fluorescently conjugated mAbs directed against mouse CD45 (30-F11).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNeasy mini kit (Qiagen, Valencia, CA) and cDNA was synthesized using the iScript cDNA Synthesis Kit (BioRad, Hercules, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
RNA-Seq data mapped with STAR and read counting performed using HT-seq
BAM to bedgraph performed using bedtools and bedgraph to bigwig performed using bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files, count table files (txt), genes-barcodes (tsv file) matrices (matrix file)
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
May 19, 2020 |
| Contact name |
Alireza Khodadadi-Jamayran |
| Organization name |
New York University, NYU Langone Medical Center
|
| Department |
Division of Advanced Research Technologies (DART)
|
| Lab |
Applied Bioinformatics Laboratories (ABL)
|
| Street address |
550 1st Ave, MSB 304
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE145905 |
PD-L1 Engagement on T cells Promotes Self-tolerance and Suppression of Neighboring Macrophages and Effector T cells in Cancer |
|
| Relations |
| BioSample |
SAMN14206804 |
| SRA |
SRX7800413 |
