|
| Status |
Public on Apr 27, 2022 |
| Title |
RNA-seq 72 h (kd) rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC with conditional Smarcb1 knockdown
treatment: treated with doxycycline
smarcb1 expression: knockdown
cell line: 81K1 (based on OG2)
|
| Treatment protocol |
Smarcb1 kd cells were treated with 1µg doxycycline per ml medium every day. RNA-seq experiments were performed 48 h, 72 h and 240 h after knockdown induction
|
| Growth protocol |
mESC were cultured on gelatine-coated plates and re-plated every other day. DMEM Glutamax-based medium was supplemented with 10% FBS superior, 1% MEM non-essential amino acids, 1% beta-Mercaptoethanol and 5µg LIF (per 500ml medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, cells were cultured and treated as described above. For RNA isolation, the RNeasy Mini Kit was used according to the manufacturer’s instructions. Quality and quantity of isolated RNA were evaluated using the NanoDrop 2000.
Libraries were prepared and sequenced (~20M single reads per sample) using the Next-Seq 500 sequencing platform (high-output Kit, 75 Cycles v2 Chemie) at the Genomics Core Facility (University Hospital Münster, Münster).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
mRNA-Seq reads were aligned to the mouse reference sequence mm10 (NCBI GRCm38.p6) using STAR version 2.7.0c.
Differential gene expression was calculated using DESeq2 version 1.30.0. Normalised fragments per kilobase per million (FPKM) were calculated using R version 4.0.3.
Differential gene lists were filtered with R to only include genes with an adjusted p-value < 0.05 and an absolute log fold change > 0.58.
Genome_build: mm10
Supplementary_files_format_and_content: bed files include FPKM values per gene for each sample
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Apr 27, 2022 |
| Contact name |
Carolin Walter |
| E-mail(s) |
c_walt03@uni-muenster.de
|
| Organization name |
Westfälische Wilhelms-Universität Münster
|
| Department |
Medical Faculty of the WWU Münster
|
| Lab |
Institute of Medical Informatics
|
| Street address |
Domagkstraße 9
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE186668 |
Smarcb1 is indispensable for the nervous system development and its loss results in a deregulation of esBAF binding [RNA-seq] |
| GSE186669 |
Smarcb1 is indispensable for the nervous system development and its loss results in a deregulation of esBAF binding. |
|
| Relations |
| BioSample |
SAMN22601064 |
| SRA |
SRX12798088 |
