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Sample GSM1574081 Query DataSets for GSM1574081
Status Public on Nov 04, 2015
Title prdm12_FLAG_ChIPseq
Sample type SRA
 
Source name animal cap (ectoderm)
Organism Xenopus laevis
Characteristics treatment: prdm12-FLAG mRNA
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 SAMN03273614
SRA SRX825228

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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