|
| Status |
Public on Jun 05, 2023 |
| Title |
RNAseq_Dpf2D/D_Tcells_Stimulated_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
sorted CD4+ T helper cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
age: post natal day 28
genotype: Dpf2D/D
treatment: 3 hours with 50ng/ml PMA and 1ug/ml Ionomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was obtained using the RNEasy Plus micro kit (Qiagen, 74034). Ribosomal RNA vas removed using the NEBNext rRNA Depletion kit (New England Biolabs #E6310) following manufacturer’s protocols, and RNA-Seq libraries were prepared using the Illumina’s TruSeq Total-stranded RNA-seq prep kit (NuGEN Technologies). RNA-Seq libraries were sequenced on an Illumina NextSeq 500 High-Output kit platform (paired-end, 75 bp reads) to obtain ~40 M reads/sample.
RNAseq libraries were prepared for sequencing using the Illumina’s TruSeq Total-stranded RNA-seq prep kit (NuGEN Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNAseq
|
| Data processing |
Reads were aligned to the mm10 transcriptome and ERCC spike-in indexes using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations. Differentially expressed genes were determined by DESeq2 (v1.18.1, Wald Test, p-adj < 0.05) after gene counts were corrected based on ERCC variances using RUVseq (v1.12.0).
Genome_build: mm10; hg38
Supplementary_files_format_and_content: For RNAseq samples, the processed data files are in .txt format and contain the expected gene and transcript counts
|
| |
|
| Submission date |
Dec 29, 2021 |
| Last update date |
Jun 05, 2023 |
| Contact name |
Gloria Mas Martin |
| E-mail(s) |
gloriamasmartin@gmail.com
|
| Organization name |
University of Miami
|
| Street address |
1501 NW 10th Avenue
|
| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE192775 |
The SWI/SNF subunit Dpf2 licenses Nrf2-dependent gene expression to enforce multilineage control of inflammation [RNA-seq] |
| GSE192779 |
The SWI/SNF subunit Dpf2 licenses Nrf2-dependent gene expression to enforce multilineage control of inflammation |
|
| Relations |
| BioSample |
SAMN24501261 |
| SRA |
SRX13554572 |
