|
| Status |
Public on Sep 16, 2022 |
| Title |
Ascl1_MyoD1, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skin
cell type: Mouse Embryonic fibroblasts
genotype: R26-M2rtTA
treatment: Doxycyline
chip antibody: FLAG(Sigma, F1804)
|
| Growth protocol |
DMEM (High Glucose), 10% fetal bovine serum,1x Sodium Pyruvate, 1 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN libraries were prepared using the SimpleChIP® DNA library prep kit for Illumina in combination with SimpleChIP® Multiplex Oligos for Illumina following manufacturer’s instructions and adapting the protocol for CUT&RUN where needed as instructed by the manufacturer. An equal amount of DNA was used for all samples. Input sample DNA was sheared using a 30 seconds on/30 seconds off protocol for a total of 10 cycles on a Bioruptor®Pico sonication device. Libraries were amplified according to manufacturers instructions and libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
The CUT&RUN data was processed using the Nextflow based ChIP-seq workflow from nf-core (version 1.2.2)
For the different samples, a single pseudo antibody was defined and the samples of the same conditions sequenced in multiple experiments were defined as replicates
The computational pipeline was run in 2 independent executions to align against the yest genome (R64-1-1) and against the mouse genome (GRCm38)
The aligned reads from the yeast alignment were used for normalization as per the manufacturer’s instructions.
Assembly: GRCm38
Supplementary files format and content: Raw peak data in .bigWig format
Supplementary files format and content: Normalized peak data in .BroadPeak format (except for Input sample)
Supplementary files format and content: CUT&RUN library size summary from picard deduplication in .tsv format
Supplementary files format and content: Read counts on consensus peaks across all samples in .txt format
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Sep 16, 2022 |
| Contact name |
Bob Hersbach |
| E-mail(s) |
bob.hersbach@helmholtz-muenchen.de
|
| Organization name |
Helmholtz Zentrum Munich
|
| Department |
Institute of Stem Cell Research
|
| Street address |
Großhaderner Str. 9
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE210181 |
Probing cell identity hierarchies by fate titration and collision during direct reprogramming [Cut & Tag] |
| GSE211864 |
Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
|
| Relations |
| BioSample |
SAMN30076700 |
| SRA |
SRX16748387 |
