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Sample GSM2308566

Query DataSets for GSM2308566

Status

Public on Oct 14, 2016

Title

WGBS from mammary epithelial cell (ENCLB975DHQ)

Sample type

SRA

Source name

Homo sapiens mammary epithelial primary cell female

Organism

Homo sapiens

Characteristics

cell_type: mammary epithelial cell
biomaterial_type: primary cell
biosample encode accession: ENCBS225LHC (SAMN05733840)
age: unknown
dev stage: unknown
donor_id: ENCDO344AAA
Sex: female
health state: unknown
lab: Richard Myers, HAIB
link: ENCBS225LHC at ENCODE; https://www.encodeproject.org/ENCBS225LHC/
link: Derived from ENCODE donor ENCDO344AAA; https://www.encodeproject.org/ENCDO344AAA/
link: growth protocol; https://www.encodeproject.org/documents/d973249b-03ee-45b7-b2c5-c21dca40a8b7/@@download/attachment/HMEC_Bernstein_protocol.pdf
link: Lonza sample source; http://www.lonza.com/products-services/bio-research/primary-and-stem-cells/human-cells-and-media/mammary-epithelial-cells-and-media/hmec-human-mammary-epithelial-cells.aspx

Extracted molecule

genomic DNA

Extraction protocol

growth protocol: https://www.encodeproject.org/documents/6e461240-5af7-462c-843f-3dae804f957a/@@download/attachment/HAIB_Myers_WGBSprotocol_2014-10-30.pdf

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

HiSeq X Ten

Description

https://www.encodeproject.org/experiments/ENCSR656TQD/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HMEC
experiment encode accession: ENCSR656TQD
assay title: WGBS
assembly: GRCh38
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB975DHQ

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Sep 09, 2016

Last update date

May 15, 2019

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

GPL20795

Series (1)

GSE86732

WGBS from mammary epithelial cell (ENCSR656TQD)

Relations

BioSample

SAMN05733840

SRA

SRX2156983

Named Annotation

GSM2308566_ENCFF246TWN_signal_GRCh38.bigWig

Named Annotation

GSM2308566_ENCFF326SHL_methylation_state_at_CHH_GRCh38.bed.gz

Named Annotation

GSM2308566_ENCFF874GGB_methylation_state_at_CpG_GRCh38.bed.gz

Named Annotation

GSM2308566_ENCFF256PKW_methylation_state_at_CHG_GRCh38.bed.gz

Supplementary file	Size	Download	File type/resource
GSM2308566_ENCFF246TWN_signal_GRCh38.bigWig	7.3 Gb	(ftp)(http)	BIGWIG
GSM2308566_ENCFF256PKW_methylation_state_at_CHG_GRCh38.bed.gz	2.5 Gb	(ftp)(http)	BED
GSM2308566_ENCFF326SHL_methylation_state_at_CHH_GRCh38.bed.gz	7.8 Gb	(ftp)(http)	BED
GSM2308566_ENCFF406PKK_methylation_state_at_CpG_GRCh38.bigBed	1.2 Gb	(ftp)(http)	BIGBED
GSM2308566_ENCFF452NGR_methylation_state_at_CHG_GRCh38.bigBed	4.3 Gb	(ftp)(http)	BIGBED
GSM2308566_ENCFF874GGB_methylation_state_at_CpG_GRCh38.bed.gz	632.2 Mb	(ftp)(http)	BED
GSM2308566_ENCFF960SVO_methylation_state_at_CHH_GRCh38.bigBed	10.7 Gb	(ftp)(http)	BIGBED
GSM2308566_ENCLB975DHQ_README.txt.gz	790 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file