|
| Status |
Public on Feb 26, 2021 |
| Title |
WT MEF + Scr 2 |
| Sample type |
SRA |
| |
|
| Source name |
WT MEF
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 3T3 immortalized mouse embryonic fibroblast
genotype: WT MEF
sirna: Scr
|
| Treatment protocol |
Cells were collected 72 h after transfection with the indicated siRNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel).
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and Rnase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
raw reads were mapped using HISAT version 2.0.4
transcripts were assembled using StringTie version 1.3.3
differential gene expression was analyzed using cufflinks/cuffdiff version 2.2.1
Genome_build: BUILD_GRCm38_RELEASE_91
Supplementary_files_format_and_content: Tab-separated differential gene expression results
|
| |
|
| Submission date |
Nov 18, 2020 |
| Last update date |
Feb 26, 2021 |
| Contact name |
Thomas MacVicar |
| E-mail(s) |
tmacvicar@age.mpg.de
|
| Organization name |
Max Planck Institute for Biology of Ageing
|
| Street address |
Joseph-Stelzmann Str 9B
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE161734 |
Cellular pyrimdine imbalance triggers mitochondrial DNA-dependent innate immunity [Scr_vs_Yme1l-si_RNA-seq] |
| GSE161736 |
Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity |
|
| Relations |
| BioSample |
SAMN16828073 |
| SRA |
SRX9528182 |
