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Sample GSM3062917 Query DataSets for GSM3062917
Status Public on Mar 22, 2019
Title Sample 1_ETS2_ChIPseq_A
Sample type SRA
 
Source name ETS2_ChIPseq
Organism Xenopus laevis
Characteristics tissue: embryo
injected with: tripple-FLAG tagged ETS2 mRNA
time point: mid-gastrulation (stage 11.5)
antibody: FLAG, SIGMA F3165, Lot # SLBN8915V
Treatment protocol Embryos were injected with 750pg tripple-FLAG tagged ETS2 mRNA and collected mid-gastrulation (stage 11.5)
Growth protocol Embryos were cultured in 1/3MR until stage 11.5
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated DNA and ETS2-tripple-FLAG bound DNA complexes were isolated with antibody.
Illumina TruSeq ChIP kit. Libraries were made by the UC Berkeley Functional Genomics Laboratory.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description processed data file:
RHRK_A_S51
ChIPETS_AD_M2_treat_pileup.bw
ChIPETS_AD_M2_peaks.bed
Ets_common_peaks.bed
Data processing ChIP-seq reads were aligned to the Xenopus laevis genome version 9.1 assembly using bowtie 2.2.3.
Peaks were called using MACS2 using defalt settings
File with common peaks between replicate samples was created by R package ChipPeakAnno
bigwig files were created by first removing scaffolds from bedgraph files generated by MACS2, then with command, bedGraphToBigWig
Genome_build: http://www.xenbase.org/common/displayJBrowse.do?data=data/xl9_1
Supplementary_files_format_and_content:
ChIPETS_AD_M2_treat_pileup.bw: Peaks were called using MACS2 using default setings. ChIP sample is Sample 1 and Input Control is Sample 3. Bigwig was made by first removing scaffolds from bedgraph files generated by MACS2, then converted with nedGraphToBigWig command
ChIPETS_CF_M2_treat_pileup.bw: Peaks were called using MACS2 using default setings. ChIP sample is Sample 3 and Input Control is Sample 4. Bigwig was made by first removing scaffolds from bedgraph files generated by MACS2, then converted with nedGraphToBigWig command
ChIPETS_AD_M2_peaks.bed: Peaks were called using MACS2 using default setings. ChIP sample is Sample 1 and Input Control is Sample 3.
ChIPETS_CF_M2_peaks.bed: Peaks were called using MACS2 using default setings. ChIP sample is Sample 3 and Input Control is Sample 4.
Ets_common_peaks.bed: Common peaks were the intersect of peaks from Proccessed samples ChIPETS_AD_M2_peaks.bed and ChIPETS_CF_M2_peaks.bed using the ChIPpeakAnno R package.
 
Submission date Mar 23, 2018
Last update date Mar 22, 2019
Contact name Richard Harland
Organization name University of California, Berkeley
Street address Life Sciences Addition #3200
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL22393
Series (1)
GSE112249 Genome-wide map of ETS2 binding in gastrula stage Xenopus.laevis embryos
Relations
BioSample SAMN08783514
SRA SRX3836834

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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