|
| Status |
Public on Sep 29, 2022 |
| Title |
RNA-seq__ESC_G4_wt_mouse_Rep-3 |
| Sample type |
SRA |
| |
|
| Source name |
ESC
|
| Organism |
Mus musculus |
| Characteristics |
Stage: E3.5
strain: G4 (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid)
condition: wt
|
| Growth protocol |
Isolated ESCs were trypsinized, heavily feeder depleted, centrifuged and snap frozen. E11.5 forelimb buds were microdissected from wildtype and mutant embryos in cold PBS and immediately snap-frozen for storage at −80°C. In all cases, mutants were generated using CRISPR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using the RNeasy Mini Kit according to the manufacturer’s instructions.
Samples were poly-A enriched, prepared into libraries using the Kapa HyperPrep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Single-end, 100 bp reads from Illumina sequencing were mapped to the reference genome (mm10) using the STAR mapper (splice junctions based on RefSeq; options: ‐‐alignIntronMin20 ‐‐alignIntronMax500000 ‐‐outFilterMismatchNmax 10).
Differential gene expression was ascertained using the DESeq2 package (Love et al., 2014). The cut-off for significantly altered gene expression was an adjusted P value of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Oct 12, 2021 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Michael I Robson |
| E-mail(s) |
robson@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Street address |
Max Planck Institut für molekulare Genet, Ihnestrasse 63-73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE185766 |
Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [RNA-Seq] |
| GSE185775 |
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes |
|
| Relations |
| BioSample |
SAMN22232224 |
| SRA |
SRX12580818 |
