|
| Status |
Public on Jun 15, 2022 |
| Title |
KO Th1 #3 (17424X14) |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
genetics: Tet2 KO
background: C57BL/6
cell type: Mouse SMARTA CD4 T Cells
cell subset: Th1
infection: LCMV Armstrong
time point: 7 days post infection
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from FACS sorted cells using Direct-zol RNA MicroPrep kit (Zymo Research).
RNA libraries were constructed using Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold (Human, Mouse, Rat)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
17424X14
|
| Data processing |
The mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 98
Reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using DESeq2 version 1.30.1 with a 5% FDR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts
|
| |
|
| Submission date |
Sep 02, 2021 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Jeffrey Scott Hale |
| E-mail(s) |
scott.hale@path.utah.edu
|
| Phone |
801-587-1885
|
| Organization name |
University of Utah
|
| Department |
Pathology
|
| Lab |
Hale Lab
|
| Street address |
15 North Medical Drive
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE183316 |
Tet2-mediated epigenetic programing of T follicular helper cell differentiation (RNA-Seq) |
| GSE183317 |
Tet2-mediated epigenetic programing of T follicular helper cell differentiation |
|
| Relations |
| BioSample |
SAMN21209351 |
| SRA |
SRX12002301 |
