|
| Status |
Public on Feb 06, 2023 |
| Title |
WT rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Follicular helper T cells from LCMV-infected wilid-type mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleens
cell line: primary cell
cell type: Follicular helper T cells
genotype: WT
treatment: wild-type mice
|
| Growth protocol |
Follicular helper T cells (CD3ε+ CD4+ PD-1+ CXCR5+) were flow-sorted from spleens of LCMV-infected wild type and Nr1h2-/- mice on day 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells according to theh manufacturer's instructions (mirVana miRNA Isolation Kit)
mrna sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit).
mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Cleaved RNA Fragments primed with random hexamers were reverse transcribed into first strand cDNA using reverse transcriptase, random primers, dUTP in place of dTTP. (The incorporation of dUTP quenches the second strand during amplification, because the polymerase does not incorporate past this nucleotide.) These cDNA fragments then had the addition of a single ‘A’ base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final strand specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to mouse genome assembly GRCm38 via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with mouse gene annotation GRCm38.86.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample
|
| |
|
| Submission date |
Feb 01, 2023 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Haeseung Lee |
| E-mail(s) |
haeseung@pusan.ac.kr
|
| Organization name |
Pusan National University
|
| Department |
College of Pharmacy
|
| Street address |
63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu
|
| City |
Busan |
| ZIP/Postal code |
46241 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE224303 |
Liver X receptor controls follicular helper T cell differentiation via repression of TCF-1 |
|
| Relations |
| BioSample |
SAMN33010693 |
| SRA |
SRX19253289 |
