GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2344260

Query DataSets for GSM2344260

Status

Public on Nov 08, 2016

Title

total RNA-seq from hepatocyte (ENCLB816UYB)

Sample type

SRA

Source name

Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

Organism

Homo sapiens

Characteristics

cell_type: hepatocyte
biomaterial_type: in vitro differentiated cells
description: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia
biosample encode accession: ENCBS077RUJ (SAMN04284314)
age: 5 day
donor_id: ENCDO222AAA
dev stage: embryonic
Sex: female
health state: healthy
lab: Richard Myers, HAIB
link: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/
link: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/
link: differentiation protocol; https://www.encodeproject.org/documents/c7707280-f681-4c88-9b16-9271082c8b32/@@download/attachment/SESCC_ENCODE_differentiation_SOPs_May30_2014.pdf

Extracted molecule

total RNA

Extraction protocol

extraction method: Ambion mirVana
extraction protocol: https://www.encodeproject.org/documents/f0cc5a7f-96a5-4970-9f46-317cc8e2d6a4/@@download/attachment/cms_055423.pdf, extraction protocol: https://www.encodeproject.org/documents/428a184d-7fa1-4599-9d8d-749c2eba7edd/@@download/attachment/cms_055740.pdf, extraction protocol: https://www.encodeproject.org/documents/49fd5b3b-9878-4ec8-92bf-ef6dce9116e3/@@download/attachment/SMARTer%20Ultra%20Low%20RNA%20Kit%20for%20Illumina%20Sequencing%20User%20Manual%20%28PT5163-1%29_120213.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR859HWB/
***************
biological replicate number: 2
technical replicate number: 1
description: hepatocyte
experiment encode accession: ENCSR859HWB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB816UYB
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Oct 13, 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

GPL16791

Series (1)

GSE88601

total RNA-seq from hepatocyte (ENCSR859HWB)

Relations

BioSample

SAMN04284314

SRA

SRX2244659

Named Annotation

GSM2344260_ENCFF275VBE_signal_of_all_reads_hg19.bigWig

Named Annotation

GSM2344260_ENCFF656TLG_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344260_ENCFF501GEF_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344260_ENCFF108UQP_signal_of_unique_reads_hg19.bigWig

Supplementary file	Size	Download	File type/resource
GSM2344260_ENCFF108UQP_signal_of_unique_reads_hg19.bigWig	181.7 Mb	(ftp)(http)	BIGWIG
GSM2344260_ENCFF122SAC_transcript_quantifications_GRCh38.tsv.gz	8.2 Mb	(ftp)(http)	TSV
GSM2344260_ENCFF275VBE_signal_of_all_reads_hg19.bigWig	203.7 Mb	(ftp)(http)	BIGWIG
GSM2344260_ENCFF407VLB_gene_quantifications_GRCh38.tsv.gz	2.8 Mb	(ftp)(http)	TSV
GSM2344260_ENCFF407XTM_transcript_quantifications_hg19.tsv.gz	8.1 Mb	(ftp)(http)	TSV
GSM2344260_ENCFF501GEF_signal_of_all_reads_GRCh38.bigWig	204.3 Mb	(ftp)(http)	BIGWIG
GSM2344260_ENCFF624LQL_gene_quantifications_hg19.tsv.gz	2.7 Mb	(ftp)(http)	TSV
GSM2344260_ENCFF656TLG_signal_of_unique_reads_GRCh38.bigWig	182.1 Mb	(ftp)(http)	BIGWIG
GSM2344260_ENCLB816UYB_README.txt.gz	926 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file