|
| Status |
Public on Nov 22, 2024 |
| Title |
RNA-seq in 120-hour mouse gastruloids - control r1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: E14tg2a
cell type: 120h gastruloid
genotype: CTCF-GFP-AID
treatment: 0.002% DMSO
|
| Treatment protocol |
1) ESCs - DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery; reTSA: 4 hours TSA (100 ng/ml) re-treatment following 24 hours of recovery; reREC: 24 hours of recovery following the second round of TSA treatment. 2) Gastruloids - 48h Ctrl: 0.002% DMSO from 44h to 48h; 48h TSA: 20 ng/ul TSA from 44h to 48h; 120h Ctrl: 0.002% DMSO from 44h to 48h followed by washes and 72h recovery; 120h TSA: 20 ng/ul TSA from 44h to 48h followed by washes and 72h recovery
|
| Growth protocol |
ESC were grown in FBS+LIF media with standard conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For mESCs, RNA was extracted usint Rnaeasy mini Qiagen kit with RLT buffer supplemented with 2-mercaptoethanol and on-column DNaseI digestion. For gastruloids, Qiagen columns and buffer were swapped for Zymo RNA Clean & Concentrator reagents.
Total RNA-seq libraries were done by rRNA depletion and constructed by BGI Tech Solutions; polyA RNA-seq libraries were donw by polyA capture by BGI Tech Solutions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Data were mapped and counted using the align andg featureCounts functions of the subread package.
Assembly: mm10
Supplementary files format and content: Processed files represent raw counts for each condition and replicate.
|
| |
|
| Submission date |
Oct 28, 2024 |
| Last update date |
Nov 22, 2024 |
| Contact name |
Marco Di Stefano |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut de Génétique Humaine - CNRS / University of Edinburgh
|
| Lab |
Giacomo Cavalli lab
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE280488 |
A histone hyperacetylation pulse induces cellular memory of gene expression and 3-dimensional genome folding [RNA-seq] |
| GSE281151 |
Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding |
|
| Relations |
| BioSample |
SAMN44369676 |
| SRA |
SRX26447788 |
