|
| Status |
Public on Aug 07, 2023 |
| Title |
HHV57DSXY_19005482_S54,TT3_A,WT_EFFECTOR |
| Sample type |
SRA |
| |
|
| Source name |
EFFECTOR
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
cell type: EFFECTOR
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Poly-A selected RNA-seq libraries were constructed from 1 mg total RNA using the Illumina TruSeq RNA Sample Prep Kits, version 2. The resulting cDNA was fragmented using a Covaris E210. Library amplification was performed using 11 cycles to minimize the risk of over amplification. Unique barcode adapters were applied to each library. Libraries were quantitated by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) and pooled in an equimolar ratio. The pooled libraries were sequenced on a NovaSeq 6000 with version 1 chemistry. At least 90 million 150-base read pairs were generated for each individual library. Data was processed using RTA 3.4.4.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq data QC with QoRTs (version 1.3.6)
Sequence reads were aligned to mm10 with STAR (version 2.7.6a)
Transcript abundances from RNA-Seq data were quantified by usig RSEM (version 1.3.3)
Expected counts of the transcripts were then analyzed for differential expression with R package DESeq2
Assembly: mm10 (GRCm38.101)
Supplementary files format and content: tab-delimited text files
|
| |
|
| Submission date |
May 03, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Peter McGuire |
| E-mail(s) |
peter.mcguire@nih.gov, payal.banerjee@nih.gov
|
| Organization name |
NHGRI
|
| Street address |
10 Center Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE231553 |
Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro [RNA-Seq] |
| GSE231556 |
Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro |
|
| Relations |
| BioSample |
SAMN34566580 |
| SRA |
SRX20204028 |
