|
| Status |
Public on Sep 23, 2022 |
| Title |
AGO2-dms-REP_3 |
| Sample type |
SRA |
| |
|
| Source name |
AGO2 -/- treated with DMSO
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic fibroblasts
genotype: AGO2 +/+
treatment: treated with DMSO
|
| Treatment protocol |
induction of ER stress by adding 500 nM thapsigargin
|
| Growth protocol |
We passaged and plated AGO2 -/- and AGO-2 +/+ MEF cells into 150-cm2 flasks for collection of samples. After a 3-d growth (at around 70% confluency), we induced ER stress by adding 500 nM thapsigargin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 ml of Trizol was added to cells and cells were frozen at -80°C for at least 1h. Subsequently cells were thawed at 37°C. RNA release was performed using silica beads and using the Precellys 24- Dual cell homogenizer (Peq-Lab) twice for 20 s at 5000 rpm. Samples were incubated for 15 min at room temperature. Subsequently, 100 µl 1-bromo-3-chloropropane was added to the samples and centrifuged for 15 min at 8000 rcf at 4°C to separate aqueous and organic phase. The aqueous phase was used to isolate total RNA with the RNeasy mini kit (Qiagen) following manufacturer instructions.
RNA libraries were prepared using the RNAeasy mini kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Quality check: FastQC 0.11.7
Alignment: Hisat version 2.1.0
Guided assembly: StringTie 1.3.4d; -p 18 -G ORIGINAL_GTF -f 0.99
Merging assemblies: Cuffmerge 2.2.1; --min-isoform-fraction 1.0
Quantification: Cuffquant 2.2.1
Differential analysis: Cuffdiff 2.2.1; --dispersion-method per-condition
Supplementary_files_format_and_content: tab-separated values or excel table of gene expression
Genome_build: GRCm38_RELEASE_91
|
| |
|
| Submission date |
Nov 09, 2020 |
| Last update date |
Sep 23, 2022 |
| Contact name |
Jorge Boucas |
| Organization name |
Max Planck Institute for Biology of Ageing
|
| Department |
Bioinformatics
|
| Street address |
Joseph-Stelzmann-Str. 9b
|
| City |
Koln |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE161121 |
RNA sequencing of AGO2 -/- Mouse embryonic fibroblast under ER stress conditions |
|
| Relations |
| BioSample |
SAMN16709846 |
| SRA |
SRX9462566 |
