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Sample GSM3334221 Query DataSets for GSM3334221
Status Public on Oct 11, 2018
Title mES_H3K4me3_ChIPSeq
Sample type SRA
 
Source name mouse embryonic stem cells
Organism Mus musculus
Characteristics tissue: mouse embryonic stem cells
cell type: E14
strain: 129/Ola
genotype: wild type
age: Passage 15
chip antibody: anti-H3K4me3 (Abcam, ab8580)
Extracted molecule genomic DNA
Extraction protocol Unfixed cells were lysed and treated with Micrococcal nuclease. Libraries were prepared using ThruPLEX-FD or ThruPLEX DNA-seq kit (Rubicon Genomics)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description MACS_peak_annotation_ES.xlsx
Data processing For ChIP-seq analysis, the replicate was concatenated and mapped using Bowtie2 at default setting.
ChIP-seq peaks were called using MACS14 against the input control data. The parameter set used in MACS14 was as follows: H3K4me3 (Band width 300, Pvalue cutoff 1e-05, the nearby regions to calculate dynamic lambda 1000-10000) and H3K27me3 (Band width 2900, Pvalue cutoff 1e-04 (mES and MM(Cited1)) or 1e-03 (UB), the nearby regions to calculate dynamic lambda 1000-20000).
Peaks were annotated with overlapping genes using AnnotateGenomicRegions ( https://sourceforge.net/projects/annotatelocus/files/webarchive/JSFversion/AnnotateGenomicRegions.war/download)
For RNA-seq analysis, all sequencing reads were mapped using Tophat at default setting.
Aligned RNA-seq reads were further analyzed using Cufflinks, Cuffmerge, and Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: BED files with called peaks on sample records and peak annotation files on series record.
RNA-seq: text file with FPKM
 
Submission date Aug 15, 2018
Last update date Oct 11, 2018
Contact name Masaki Nishikawa
E-mail(s) masakiwestriver@gmail.com
Organization name UCLA / VA
Lab Yanagawa
Street address 16111 Plummer st
City North Hills
State/province CA
ZIP/Postal code 91343
Country USA
 
Platform ID GPL13112
Series (1)
GSE118607 Comprehensive analysis of chromatin signature and transcriptome in nephron progenitor cells
Relations
BioSample SAMN09839552
SRA SRX4557396

Supplementary file Size Download File type/resource
GSM3334221_ES401_402_peaks.bed.gz 977.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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