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Sample GSM1434788 Query DataSets for GSM1434788
Status Public on Jul 10, 2014
Title MCIDAS_dnE2F4_9h_RNAseq_rep_3
Sample type SRA
 
Source name animal cap (ectoderm)
Organism Xenopus laevis
Characteristics tissue: animal cap (ectoderm)
harvest time/stage: 9h @ 22 deg after mid-11 (st 18)
injected mrna: MCIDAS-HGR+dnE2F4
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; ~300 animal caps were used per condition for ChIPseq.
Extracted molecule polyA RNA
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 ethanol. For ChIPseq embryos were first fixed in 1% formaldehyde for 30 minutes and lysed in RIPA buffer prior to sonication. See our manuscript (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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Poly-A mrNA
RNAseq (non-stranded)
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)
ChiPseq reads aligned to genome with bowtie2, http://bowtie-bio.sourceforge.ne t/bowtie2/index.shtml, mapping quality scores > 20 retained
ChiPseq aligned reads were pooled and peaks called with HOMER (PMID: 20513432)
Genome_build: Genome: JGI X. laevis v7.1
Genome_build: Transcriptome: Mayball interim models, http://daudin.icmb.utexas.edu/
Supplementary_files_format_and_content: RNAseq files are output from eXpress, ChIPseq peaks are bed files
 
Submission date Jul 10, 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)
GSE59309 Multicilin drives centriole biogenesis via E2f proteins
Relations
BioSample SAMN02908503
SRA SRX649174

Supplementary file Size Download File type/resource
GSM1434788_MCIDAS_dnE2F4_9h_RNAseq_rep_3_express.results.txt.gz 2.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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