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Sample GSM5258422

Query DataSets for GSM5258422

Status

Public on Apr 22, 2021

Title

DNase-seq from midbrain (ENCLB043OFW)

Sample type

SRA

Source name

Mus musculus strain B6NCrl mixed sex embryo (10.5 days) midbrain tissue

Organism

Mus musculus

Characteristics

tissue_type: midbrain
biomaterial_type: tissue
biosample encode accession: ENCBS559ZQG (SAMN18814528)
Sex: pooled male and female
dev stage: embryonic
age: 10.5 day
donor_id: ENCDO956IXV
lab: John Stamatoyannopoulos, UW
source: Mark Groudine
link: ENCBS559ZQG at ENCODE; https://www.encodeproject.org/ENCBS559ZQG/
link: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/

Extracted molecule

genomic DNA

Extraction protocol

other: https://www.encodeproject.org/documents/926174f5-d14c-4e77-bc52-5517b56daac0/@@download/attachment/Culturedcells_SOP_nuclei_DNase_crosslink_RNA_V1.pdf

Library strategy

DNase-Hypersensitivity

Library source

genomic

Library selection

DNAse

Instrument model

Illumina HiSeq 4000

Description

https://www.encodeproject.org/experiments/ENCSR773SAG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR773SAG
assay title: DNase-seq
assembly: mm10
encode release date: 2017-09-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB043OFW

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Apr 21, 2021

Last update date

May 07, 2021

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

GPL21103

Series (1)

GSE172600

DNase-seq from midbrain (ENCSR773SAG)

Relations

BioSample

SAMN18814528

SRA

SRX10660744

Named Annotation

GSM5258422_ENCFF293YCS_read-depth_normalized_signal_mm10.bigWig

Named Annotation

GSM5258422_ENCFF327SCP_read-depth_normalized_signal_mm10.bigWig

Supplementary file	Size	Download	File type/resource
GSM5258422_ENCFF011SNP_hotspots_mm10.bigBed	2.1 Mb	(ftp)(http)	BIGBED
GSM5258422_ENCFF103XKO_peaks_mm10.bed.gz	1.2 Mb	(ftp)(http)	BED
GSM5258422_ENCFF119URY_peaks_mm10.bed.gz	1.1 Mb	(ftp)(http)	BED
GSM5258422_ENCFF169RMJ_peaks_mm10.bed.gz	740.7 Kb	(ftp)(http)	BED
GSM5258422_ENCFF181QNC_peaks_mm10.bigBed	1.5 Mb	(ftp)(http)	BIGBED
GSM5258422_ENCFF255CPG_FDR_cut_rate_mm10.bigBed	270.7 Mb	(ftp)(http)	BIGBED
GSM5258422_ENCFF293YCS_read-depth_normalized_signal_mm10.bigWig	620.2 Mb	(ftp)(http)	BIGWIG
GSM5258422_ENCFF308KZY_FDR_cut_rate_mm10.bed.gz	277.4 Mb	(ftp)(http)	BED
GSM5258422_ENCFF317OFK_peaks_mm10.bigBed	2.2 Mb	(ftp)(http)	BIGBED
GSM5258422_ENCFF327SCP_read-depth_normalized_signal_mm10.bigWig	649.3 Mb	(ftp)(http)	BIGWIG
GSM5258422_ENCFF422AYC_peaks_mm10.starch	848.6 Kb	(ftp)(http)	STARCH
GSM5258422_ENCFF557LZR_footprints_mm10.bed.gz	2.2 Mb	(ftp)(http)	BED
GSM5258422_ENCFF572NNW_hotspots_mm10.bed.gz	1.4 Mb	(ftp)(http)	BED
GSM5258422_ENCFF855MFI_FDR_cut_rate_mm10.bed.gz	277.8 Mb	(ftp)(http)	BED
GSM5258422_ENCFF935SSE_footprints_mm10.bigBed	3.2 Mb	(ftp)(http)	BIGBED
GSM5258422_ENCFF939QXW_peaks_mm10.bigBed	1.6 Mb	(ftp)(http)	BIGBED
GSM5258422_ENCLB043OFW_README.txt.gz	1.5 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file