|
| Status |
Public on Mar 26, 2021 |
| Title |
WT_D4_EB_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryoid bodies
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CJ7 cells
differentiation status: embryoid bodies
condition: wild type
age: 4 days
|
| Treatment protocol |
Cells treated with GSK343 had 4uM of the drug added to the media for three days prior to the start of differentiation trough the end of the experiment. DMSO treated cells had a equivalent volume addeed to the culture media for the same amout of time.
Replated cells were first differentiated as embyoid bodies and then placed into ES media for 5 days prior to collection.
|
| Growth protocol |
All Embryonic Stem cells were cultured in DMEM supplemented with Pen/strep, glutamax, LIF and 20%FBS. The were suported on a feeder layer of PMEF-N from SIgma. Embryoid bodies were differentiated via hanging drops in IMDM supplemented with Pen/strep, glutamx and 20% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted uning the nucleospin kit from Marchery-Nagel. cDNA was made using the Superscript Vilo kit
DNA was extracted as part of the Cut and Run assay orginally published by the Henikoff laboratory
Modified Illumina method detailed in Bowman et al 2013 BMC Genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CJ7 cells
WT_mutant_ESC_D4EB_D8EB_RPKMs.txt
|
| Data processing |
Reads were aligned to the mm10 genome using STAR v2.5.3
Reads in gene exons were counted using featureCounts v1.6.1
Gene annotations were obtained from ncbi refseq
EdgeR was used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3
|
| |
|
| Submission date |
May 29, 2020 |
| Last update date |
Mar 26, 2021 |
| Contact name |
Manashree Damle |
| E-mail(s) |
damle@molbio.mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology
|
| Lab |
Bob Kingston
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE151486 |
H3K27me3 is dispensable for early differentiation but required to maintain differentiated cell identity |
|
| Relations |
| BioSample |
SAMN15060874 |
| SRA |
SRX8428619 |
