GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3334223

Query DataSets for GSM3334223

Status

Public on Oct 11, 2018

Title

mES_Input_DNA

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: none

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

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