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Sample GSM7256241

Query DataSets for GSM7256241

Status

Public on Apr 30, 2023

Title

TF ChIP-seq from HepG2 (ENCLB091DPE)

Sample type

SRA

Source name

Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CENPBD1

Organism

Homo sapiens

Characteristics

antibody: CENPBD1
line: HepG2
biomaterial_type: cell line
biosample encode accession: ENCBS961QNJ (SAMN34251989)
Sex: male
health state: hepatocellular carcinoma
dev stage: child
age: 15 year
donor_id: ENCDO000AAC
lab: Richard Myers, HAIB
source: Richard Myers
link: ENCBS961QNJ at ENCODE; https://www.encodeproject.org/ENCBS961QNJ/
link: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

Extracted molecule

genomic DNA

Extraction protocol

pipeline protocol: https://www.encodeproject.org/documents/efac5344-6834-4e12-b971-94994d992e86/@@download/attachment/ChIP-seq_Mapping_Pipeline_Overview.pdf
pipeline protocol: https://www.encodeproject.org/documents/d00ffce2-e72c-44d7-a71f-73fd163c2426/@@download/attachment/ChIP-seq_pipeline_overview.pdf
extraction protocol: https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/@@download/attachment/ChIP-seq%20protocol%2C%20ENCODE4%2C%20Myers%20Lab.pdf
pipeline protocol: https://www.encodeproject.org/documents/efac5344-6834-4e12-b971-94994d992e86/@@download/attachment/ChIP-seq_Mapping_Pipeline_Overview.pdf, pipeline protocol: https://www.encodeproject.org/documents/d00ffce2-e72c-44d7-a71f-73fd163c2426/@@download/attachment/ChIP-seq_pipeline_overview.pdf, extraction protocol: https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/@@download/attachment/ChIP-seq%20protocol%2C%20ENCODE4%2C%20Myers%20Lab.pdf

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NovaSeq 6000

Description

https://www.encodeproject.org/experiments/ENCSR539PMH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR539PMH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR555EMB, ENCSR743HNM
encode release date: 2022-07-15
lab: Richard Myers, HAIB
library encode accession: ENCLB091DPE
fragmentation methods: sonication (generic)

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Apr 28, 2023

Last update date

Jul 07, 2023

Contact name

ENCODE DCC

E-mail(s)

encode-help@lists.stanford.edu

Organization name

ENCODE DCC

Street address

300 Pasteur Dr

City

Stanford

State/province

ZIP/Postal code

94305-5120

Country

USA

Platform ID

GPL24676

Series (1)

GSE231277

TF ChIP-seq from HepG2 (ENCSR539PMH)

Relations

BioSample

SAMN34251989

SRA

SRX20151059

Named Annotation

GSM7256241_ENCFF379TOC_signal_p-value_GRCh38.bigWig

Named Annotation

GSM7256241_ENCFF532DNY_fold_change_over_control_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM7256241_ENCFF379TOC_signal_p-value_GRCh38.bigWig	588.8 Mb	(ftp)(http)	BIGWIG
GSM7256241_ENCFF532DNY_fold_change_over_control_GRCh38.bigWig	406.9 Mb	(ftp)(http)	BIGWIG
GSM7256241_ENCFF575WOP_IDR_ranked_peaks_GRCh38.bed.gz	3.8 Mb	(ftp)(http)	BED
GSM7256241_ENCFF644NNL_IDR_thresholded_peaks_GRCh38.bigBed	160.7 Kb	(ftp)(http)	BIGBED
GSM7256241_ENCFF721AJC_IDR_thresholded_peaks_GRCh38.bed.gz	59.1 Kb	(ftp)(http)	BED
GSM7256241_ENCLB091DPE_README.txt.gz	1.3 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record