|
| Status |
Public on Nov 24, 2021 |
| Title |
KO Tumor Treg rep1 (I1) |
| Sample type |
SRA |
| |
|
| Source name |
Tumor Treg
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Prdm1fl/flFoxP3YFP-Cre (KO)
tissue: Tumor
tumor stage: less than or equal to 1.5 cm3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a QIAshredder kit (QIAGEN) and an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol.
mRNA was specifically enriched from total RNA by removing rRNA and hydrolyzed into small pieces. The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis. The short cDNA strands were ligated with 3′- and 5′-adapters for amplification and sequencing using the Illumina® platforms (HiSeq 2 x 150 bp, single index, per lane).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: Mus musculus GRCm38 reference genome available on ENSEMBL
Supplementary_files_format_and_content: Matrix table with gene hit counts for every gene and every sample
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Jianmei Wu Leavenworth |
| E-mail(s) |
jleavenworth@uabmc.edu
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Neurosurgery, Microbiology
|
| Lab |
Leavenworth Lab, CHB130
|
| Street address |
1600 6th Ave South
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35233 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE178132 |
Gene expression profile of effector Treg cells isolated from spleens and tumors of tumor-bearing mice |
| GSE178135 |
Treg cells and Treg-specific deletion of Blimp1 |
|
| Relations |
| BioSample |
SAMN19694749 |
| SRA |
SRX11140391 |
