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Sample GSM6783763

Query DataSets for GSM6783763

Status

Public on Dec 04, 2022

Title

DNase-seq from suppressor macrophage (ENCLB698XOA)

Sample type

SRA

Source name

Homo sapiens male adult (21 years) suppressor macrophage primary cell treated with lipopolysaccharide for 1 hour

Organism

Homo sapiens

Characteristics

cell_type: suppressor macrophage
biomaterial_type: primary cell
description: LPS_1h
biosample encode accession: ENCBS324LUD (SAMN18814264)
Sex: male
dev stage: adult
age: 21 year
donor_id: ENCDO733YAB
lab: John Stamatoyannopoulos, UW
source: Shelly Heimfeld
treatments: treatment_term_id: CHEBI:16412; treatment_term_name: lipopolysaccharide; treatment_type: chemical; duration: 1; duration_units: hour;
link: ENCBS324LUD at ENCODE; https://www.encodeproject.org/ENCBS324LUD/
link: Derived from ENCODE donor ENCDO733YAB; https://www.encodeproject.org/ENCDO733YAB/

Extracted molecule

genomic DNA

Extraction protocol

extraction protocol: https://www.encodeproject.org/documents/980de32c-f7ec-4cd7-b736-61faf723c186/@@download/attachment/newnuclei_isolation_from_human_tissue-combined.pdf

Library strategy

DNase-Hypersensitivity

Library source

genomic

Library selection

DNAse

Instrument model

Illumina NextSeq 500

Description

https://www.encodeproject.org/experiments/ENCSR564XXO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR564XXO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB698XOA
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Dec 03, 2022

Last update date

Jan 20, 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

GPL18573

Series (1)

GSE220035

DNase-seq from suppressor macrophage (ENCSR564XXO)

Relations

BioSample

SAMN18814264

SRA

SRX18486499

Named Annotation

GSM6783763_ENCFF309OMY_read-depth_normalized_signal_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM6783763_ENCFF064XZR_peaks_GRCh38.starch	2.6 Mb	(ftp)(http)	STARCH
GSM6783763_ENCFF205IGG_FDR_cut_rate_GRCh38.bigBed	470.2 Mb	(ftp)(http)	BIGBED
GSM6783763_ENCFF270RUA_footprints_GRCh38.bed.gz	4.2 Mb	(ftp)(http)	BED
GSM6783763_ENCFF309OMY_read-depth_normalized_signal_GRCh38.bigWig	707.3 Mb	(ftp)(http)	BIGWIG
GSM6783763_ENCFF595FGB_FDR_cut_rate_GRCh38.bed.gz	456.1 Mb	(ftp)(http)	BED
GSM6783763_ENCFF607DEQ_peaks_GRCh38.bed.gz	2.5 Mb	(ftp)(http)	BED
GSM6783763_ENCFF805NMF_peaks_GRCh38.bed.gz	3.4 Mb	(ftp)(http)	BED
GSM6783763_ENCFF838OSM_footprints_GRCh38.bigBed	5.3 Mb	(ftp)(http)	BIGBED
GSM6783763_ENCFF938YCE_peaks_GRCh38.bigBed	4.4 Mb	(ftp)(http)	BIGBED
GSM6783763_ENCFF996IKB_peaks_GRCh38.bigBed	5.9 Mb	(ftp)(http)	BIGBED
GSM6783763_ENCLB698XOA_README.txt.gz	1.1 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file