|
| Status |
Public on Oct 22, 2020 |
| Title |
CASTAT5 spleen CD4+ T cells RNA-seq 1 |
| Sample type |
SRA |
| |
|
| Source name |
FACS_sorted CD4 T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell surface marker: CD4+Thy1.1+
genotype/variation: Stat5a (H229R & S711F) mutant
strain: Balb/c
|
| Treatment protocol |
A20HA Tumor cells were subcutaneously injected to the right flank of mice. When tumor sizes reached the desired sizes, mice were randomly assigned into groups to receive the specified treatments. Cyclophosphamide (CTX) was i.p. injected to mice at 150 mg/kg one day before T cell transfer. For adoptive CD4 T-cell transfer, in vitro cultured T cells were harvested and injected into each recipient via tail vein (10^5 cells/mouse).
|
| Growth protocol |
CD4 T cells were purified from 6.5-TCR Tg mouse splenocytes and stimulated with mouse CD3/CD28 activation Dynabeads in the presence of hrIL2 overnight. Cells were harvested and transduced twice in two consecutive days with retroviral supernatant. Cells were harvested 24 hours after the second transduction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from FACS-sorted donor CD4+ T cells using TRIzol reagent.
100 ng of total RNA was used for RNAseq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide. The RNA-seq libraries were subjected to quantification process, pooled for cBot amplification and subsequently sequenced on a HiSeq3000 (Illumina) sequencer with 50bp single-end cycling.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
CASTAT5_SP_rep1
|
| Data processing |
Demultiplexing with Bcl2fastq2 were employed to generate the fastq file for each sample.
The RNAseq analysis was performed on Galaxy main server (usegalaxy.org). The raw reads were mapped to mouse genome mm10 using HISTAT2 (Galaxy Version 2.1.0) with default settings.
Reads mapped to annotated features were counted using featureCounts (Galaxy v1.6.3).
The DEseq2 v1.18.1 implemented in Galaxy (v2.11.40.2) was used to normalize the raw accounts and identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: DEseq2 output files including differential analysis results and normalized count table as well as raw count files generated by featureCounts
|
| |
|
| Submission date |
Jun 10, 2020 |
| Last update date |
Oct 22, 2020 |
| Contact name |
Huidong Shi |
| E-mail(s) |
hshi@augusta.edu
|
| Phone |
706-721-6000
|
| Organization name |
Augusta University
|
| Department |
Georgia Cancer Center
|
| Lab |
2125 K
|
| Street address |
1120 15th Street, CN2138
|
| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE152237 |
Persistent STAT5 activation reprograms the epigenetic landscape in CD4+ T cells to drive polyfunctionality and antitumor immunity [RNA-Seq] |
| GSE152242 |
Persistent STAT5 activation reprograms the epigenetic landscape in CD4+ T cells to drive polyfunctionality and antitumor immunity |
|
| Relations |
| BioSample |
SAMN15203617 |
| SRA |
SRX8525383 |
