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Sample GSM2363463 Query DataSets for GSM2363463
Status Public on Oct 29, 2016
Title foxn4+mcidas_ChIPseq_rep_1
Sample type SRA
Source name animal cap (dissected ectoderm)
Organism Xenopus laevis
Characteristics tissue: animal cap (dissected ectoderm)
harvest time/stage: 9h @ 22 deg after mid-11 (st 18)
injection: Foxn4-GFP-HGR + Multicilin mRNA
Treatment protocol Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.
Growth protocol Animal caps (ectoderm) dissected from embryos at stage 10 and cultured in 0.5x MMR. 20 animal caps per condition were used for RNAseq.
Extracted molecule genomic DNA
Extraction protocol mRNAs were obtained with proteinase K digestion, phenol chloroform extraction and precipitated with ethanol, treated with DNAse, extracted with phenol chloforom, and precipitated with lithium and again with ethanol. See our manuscript (PMID: 24934224) for a more detailed protocol. RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits.
Chromatin was obtained as in Ma et al. 2014 (PMID: 24934224)
Illumina Truseq v2, poly-a+
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description chromatin/gDNA
Data processing RNAseq reads aligned to transcriptome with RNA-STAR (PMID: 23104886)
RNAseq aligned reads counted with eXpress (PMID: 23160280)
RNAseq counts normalized and differential expression tested with DESeq (PMID: 23975260)
RNAseq and ChIPseq reads aligned to genome with bowtie2 (PMID: 22388286)
Peaks called with HOMER (PMID: 20513432) using input as background (input reads from NCBI GEO: GSE78176, It was pooled reads from GSM2068810 through GSM2068815 (i.e., 6 accessions total)).
BigWigs made with HOMER (PMID: 20513432)
Genome_build: Genome: v7.1,
Genome_build: Transcriptome: Mayball interim models,
Supplementary_files_format_and_content: RNAseq files are output from eXpress
Supplementary_files_format_and_content: ChIPseq files are bed files from HOMER
Submission date Oct 28, 2016
Last update date May 15, 2019
Contact name Ian K Quigley
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)
GSE89271 RNAseq and ChIPseq profiling of Foxn4 and Foxj1 in multiciliated cells
BioSample SAMN05950927
SRA SRX2279692

Supplementary file Size Download File type/resource
GSM2363463_foxn4+mcidas_ChIPseq_v7.1.bed.gz 666.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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