|
| Status |
Public on Feb 23, 2016 |
| Title |
myb-GFP_9h_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
epithelial progenitors (animal cap)
|
| Organism |
Xenopus laevis |
| Characteristics |
ChIP: myb-GFP
harvest time/stage: 9h @ 22 deg after mid-11 (stage 18)
injected mrna: myb-GFP
|
| Treatment protocol |
Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.
|
| Growth protocol |
Epithelial progenitors (animal caps) were dissected from embryos at stage 10 were cultured in 0.5x MMR.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were fixed in 1% paraformaldehyde in PBS for 30 minutes at 22 degrees and fix was quenched with 0.125M glycine. ChIPseq was performed as described (PMID: 24934224) with the following antibodies: GFP (Invitrogen catalog no. A11122, lot no. 1296649), FLAG (Sigma, cat #F1804), H3K4me3 (Active Motif, cat #39159; lot #01609004), H3K27ac (Abcam, cat #ab4729, lot #GR71158-2), or rad21 (Abcam, cat #ab992).
Following sonication and immunoprecipitation of genomic fragments, we polished and adenylated ends (NEB End-It and A-tailing modules) and ligated Truseq v2 adapters (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIPseq reads were aligned to X. laevis genome build v9.1 with bwa mem (PMID: 19451168)
Peaks were called against pooled input background with HOMER (PMID: 20513432). Replicates were pooled to generate peakfiles.
Genome_build: X. laevis build v9.1 (http://www.xenbase.org/)
Supplementary_files_format_and_content: Bed files of called peaks
|
| |
|
| Submission date |
Feb 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ian K Quigley |
| E-mail(s) |
[email protected]
|
| Phone |
858-453-4100
|
| Organization name |
Salk Institute
|
| Department |
Molecular Neurobiology Lab
|
| Lab |
Kintner
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18936 |
| Series (1) |
| GSE78176 |
Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors |
|
| Relations |
| BioSample |
SAMN04507486 |
| SRA |
SRX1596714 |
