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Sample GSM4339162 Query DataSets for GSM4339162
Status Public on May 19, 2020
Title Ctrl_Fc_1 (RNA-seq)
Sample type SRA
 
Source name mouse splenic T cells
Organism Mus musculus
Characteristics genotype: WT
treatment: anti-mouse CD3/CD28 + control Fc
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 SAMN14206803
SRA SRX7800414

Supplementary file Size Download File type/resource
GSM4339162_Ctrl_Fc_1_S39_ct_genes.txt.gz 154.5 Kb (ftp)(http) TXT
GSM4339162_Ctrl_Fc_1_S39_mm10_RPM.bw 18.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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