GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2424030

Query DataSets for GSM2424030

Status

Public on Jan 04, 2017

Title

eCLIP from HepG2 (ENCLB482NEH)

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: ENCBS362ASG (SAMN06121857)
dev stage: child
age: 15 year
Sex: male
passage number: 5
lab: Gene Yeo, UCSD
health state: hepatocellular carcinoma
link: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/
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: 1
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: ENCLB482NEH
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

SAMN06121857

SRA

SRX2424489

Named Annotation

GSM2424030_ENCFF248UTB_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2424030_ENCFF399DJZ_peaks_GRCh38.bed.gz

Named Annotation

GSM2424030_ENCFF783TZW_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2424030_ENCFF248UTB_plus_strand_signal_of_unique_reads_GRCh38.bigWig	21.6 Mb	(ftp)(http)	BIGWIG
GSM2424030_ENCFF357WBG_peaks_GRCh38.bigBed	4.1 Mb	(ftp)(http)	BIGBED
GSM2424030_ENCFF364QPG_peaks_hg19.bed.gz	2.1 Mb	(ftp)(http)	BED
GSM2424030_ENCFF380EPE_plus_strand_signal_of_unique_reads_hg19.bigWig	22.3 Mb	(ftp)(http)	BIGWIG
GSM2424030_ENCFF399DJZ_peaks_GRCh38.bed.gz	2.1 Mb	(ftp)(http)	BED
GSM2424030_ENCFF783TZW_minus_strand_signal_of_unique_reads_GRCh38.bigWig	21.0 Mb	(ftp)(http)	BIGWIG
GSM2424030_ENCFF798IHQ_peaks_hg19.bigBed	4.1 Mb	(ftp)(http)	BIGBED
GSM2424030_ENCFF867ZBM_minus_strand_signal_of_unique_reads_hg19.bigWig	21.7 Mb	(ftp)(http)	BIGWIG
GSM2424030_ENCLB482NEH_README.txt.gz	878 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file