|
| Status |
Public on Nov 04, 2015 |
| Title |
prdm12_FLAG_noggin_RA_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
neuralized animal cap (neuroectoderm)
|
| Organism |
Xenopus laevis |
| Characteristics |
treatment: prdm12-FLAG + noggin mRNA, RA
chip antibody: Sigma anti-FLAG, cat# F1804
|
| Treatment protocol |
2-cell X. laevis embryos were injected with synthetic mRNAs of indicated constructs. Ectoderm (animal caps) was dissected at roughly stage 10 and cultured in 0.5X MMR prior to harvest for RNAseq or ChIPseq.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
mRNAs were isolated with an RNAspin Mini RNA isolation kit. ChIPseq embryos were first fixed in 1% formaldehyde for 30 minutes and lysed in RIPA buffer prior to sonication. See PMID: 24934224 for a more detailed protocol.
RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits. Following IP, ChIPseq libraries were constructed with end repair mix (NEB), a-tailed (NEB), Truseq v2 adapters ligated (Illumina, NEB) and amplified with Phusion polymerase (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
genomic DNA
|
| Data processing |
RNAseq reads were mapped to a Xenopus transcriptome (X. tropicalis, courtesy of M. Gilcrist and X. laevis Unigene sequences) with bowtie2 (PMID: 22388286, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
RNAseq counts normalized and differential expression tested with edgeR (PMID: 19910308)
ChIPseq reads were mapped to the X. laevis genome v7.1 with bowtie2 (PMID: 22388286, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
ChiPseqd peaks were called with HOMER (PMID: 20513432), using input as a background.
Genome_build: RNAseq: X. tropicalis transcriptome (courtesy M. Gilchrist) and X. laevis Unigene sequences. ChIPseq: X. laevis genome build v7.1 (courtesy of the Xenopus Genome Project Consortium, PMID: 25313157).
Supplementary_files_format_and_content: RNAseq: normalized read counts. ChIPseq: bed files.
|
| |
|
| Submission date |
Dec 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ian K Quigley |
| E-mail(s) |
iquigley@salk.edu
|
| 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) |
| GSE64551 |
Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue |
|
| Relations |
| BioSample |
SAMN03273610 |
| SRA |
SRX825229 |
