|
| Status |
Public on May 04, 2015 |
| Title |
GROseq siYAP Wnt3a+Activin (+ chain) |
| Sample type |
SRA |
| |
|
| Source name |
H1 human ESCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonic stem cells
passages/media: 40-50/mTeSR
treatment: Wnt3a+Activin A (WA) 6h
sirna: Yap1 (Silencer Select Life Tech)
|
| Treatment protocol |
H1 hESCs were left untreated, or treated with Wnt3a (200ng/ml), Activin (100ng/ml), or both cytokines together for 4h (ChIPseq) or 6h (GRO-seq). For siRNA-GROseq experiments, hESCs were transfected with specific siRNAs (using RNAimax) 48h before adding cytokine treatments.
|
| Growth protocol |
H1 hESCs grown in mTeSR media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For ChIPseq, DNA was extracted Qiaquick PCR extraction kit (cat 28106, Qiagen). For GROseq, nascent RNA purification was done using Trizol LS (Invitrogene).
For ChIPseq, libraries were done with Illumina reagents. For GROseq, libraries were prepared with NEBnext kit (E7300S)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Nascent RNA
Gro-seq
|
| Data processing |
Peak calling was performed using Homer software
Genome_build: hg19
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Jan 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
conchi estaras |
| E-mail(s) |
cestarasibanez@salk.edu
|
| Organization name |
The Salk Institute
|
| Department |
Regulatory Biology
|
| Lab |
Jones lab
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla, San Diego |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE64758 |
Wnt3a-Activin A Synergy Induces eRNAPII Pause-Release and Counteracts a Yap1 Elongation Block during hESC Differentiation |
|
| Relations |
| BioSample |
SAMN03278042 |
| SRA |
SRX833438 |
| Named Annotation |
GSM1579381_siYAP_WA_1.ucsc.bigWig |
