GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3263053

Query DataSets for GSM3263053

Status

Public on Jul 09, 2019

Title

day00.Input.Batch1.Rep2

Sample type

SRA

Source name

Embryonic stem cell

Organism

Homo sapiens

Characteristics

tissue: Embryonic stem cell
differentiation time: day00
genotype: H9 MLC2v:H2B
matched input: N/A
chip antibody: none (input)

Extracted molecule

genomic DNA

Extraction protocol

ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441). Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf, Library preparation: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 4000

Data processing

base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq and Hi-C, rnaSTAR for RNA-seq. Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with juicebox.jar provided by Aiden lab).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for ChIP-seq and input, juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) for RNA-seq.

Submission date

Jul 10, 2018

Last update date

Jul 11, 2019

Contact name

Bing Ren

E-mail(s)

biren@ucsd.edu

Organization name

Ludwig Institute for Cancer Research

Street address

9500 Gilman Dr.

City

San Diego

State/province

ZIP/Postal code

92093

Country

USA

Platform ID

GPL20301

Series (2)

GSE116862	Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries.
GSE186958	Chromatin structure dynamics during human cardiomyocyte differention

Relations

BioSample

SAMN09637473

SRA

SRX4377112

Supplementary file	Size	Download	File type/resource
GSM3263053_Input_D0_2_AY2440.filt.nodup.srt.bw	653.6 Mb	(ftp)(http)	BW
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file