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Sample GSM2424031

Query DataSets for GSM2424031

Status

Public on Jan 04, 2017

Title

eCLIP from HepG2 (ENCLB719MGT)

Sample type

SRA

Source name

Homo sapiens HepG2 immortalized cell line

Organism

Homo sapiens

Characteristics

antibody: BUD13
line: HepG2
biomaterial_type: immortalized cell line
biosample encode accession: ENCBS308ZPA (SAMN06121801)
dev stage: child
Sex: male
age: 15 year
health state: hepatocellular carcinoma
passage number: 3
lab: Gene Yeo, UCSD
link: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/
link: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/
link: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027
link: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx

Extracted molecule

total RNA

Extraction protocol

pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Description

https://www.encodeproject.org/experiments/ENCSR830BSQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against BUD13
experiment encode accession: ENCSR830BSQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR777PDA
encode release date: 2015-12-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB719MGT
size range: 175-300

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Dec 11, 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

GPL20301

Series (1)

GSE92091

eCLIP from HepG2 (ENCSR830BSQ)

Relations

BioSample

SAMN06121801

SRA

SRX2424490

Named Annotation

GSM2424031_ENCFF180OLE_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2424031_ENCFF128RBT_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2424031_ENCFF785FUO_peaks_GRCh38.bed.gz

Supplementary file	Size	Download	File type/resource
GSM2424031_ENCFF128RBT_plus_strand_signal_of_unique_reads_GRCh38.bigWig	21.1 Mb	(ftp)(http)	BIGWIG
GSM2424031_ENCFF180OLE_minus_strand_signal_of_unique_reads_GRCh38.bigWig	20.3 Mb	(ftp)(http)	BIGWIG
GSM2424031_ENCFF554MZA_minus_strand_signal_of_unique_reads_hg19.bigWig	20.8 Mb	(ftp)(http)	BIGWIG
GSM2424031_ENCFF785FUO_peaks_GRCh38.bed.gz	2.1 Mb	(ftp)(http)	BED
GSM2424031_ENCFF798KOB_peaks_GRCh38.bigBed	4.2 Mb	(ftp)(http)	BIGBED
GSM2424031_ENCFF893NYT_plus_strand_signal_of_unique_reads_hg19.bigWig	21.6 Mb	(ftp)(http)	BIGWIG
GSM2424031_ENCFF929ITC_peaks_hg19.bed.gz	2.1 Mb	(ftp)(http)	BED
GSM2424031_ENCFF948ZQP_peaks_hg19.bigBed	4.2 Mb	(ftp)(http)	BIGBED
GSM2424031_ENCLB719MGT_README.txt.gz	881 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file