NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
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 CA
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap