GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2343705 Query DataSets for GSM2343705
Status Public on Nov 08, 2016
Title total RNA-seq from breast epithelium (ENCLB197GXK)
Sample type SRA
Source name Homo sapiens breast epithelium tissue female adult (51 year)
Organism Homo sapiens
Characteristics tissue_type: breast epithelium
biomaterial_type: tissue
description: Mammary breast tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS160KYO (SAMN05896927)
age: 51 year
dev stage: adult
donor_id: ENCDO271OUW
Sex: female
lab: Thomas Gingeras, CSHL
link: ENCBS160KYO at ENCODE;
link: Derived from ENCODE donor ENCDO271OUW;
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol:
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR438YPF
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB197GXK
size range: >200
spikeins used: /references/ENCSR156CIL/
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
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)
GSE88273 total RNA-seq from breast epithelium (ENCSR438YPF)
BioSample SAMN05896927
SRA SRX2244089
Named Annotation GSM2343705_ENCFF874ALU_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2343705_ENCFF180EHY_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2343705_ENCFF756GRG_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2343705_ENCFF428NBV_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2343705_ENCFF082SUT_gene_quantifications_GRCh38.tsv.gz 2.6 Mb (ftp)(http) TSV
GSM2343705_ENCFF099FUF_transcript_quantifications_GRCh38.tsv.gz 7.9 Mb (ftp)(http) TSV
GSM2343705_ENCFF154WCI_plus_strand_signal_of_unique_reads_hg19.bigWig 243.8 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF159SXT_plus_strand_signal_of_all_reads_hg19.bigWig 256.2 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF180EHY_plus_strand_signal_of_all_reads_GRCh38.bigWig 257.8 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF428NBV_plus_strand_signal_of_unique_reads_GRCh38.bigWig 244.1 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF467GZM_minus_strand_signal_of_unique_reads_hg19.bigWig 239.9 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF500GZL_minus_strand_signal_of_all_reads_hg19.bigWig 253.8 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF557XAK_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2343705_ENCFF756GRG_minus_strand_signal_of_unique_reads_GRCh38.bigWig 240.5 Mb (ftp)(http) BIGWIG
GSM2343705_ENCFF777ERL_transcript_quantifications_hg19.tsv.gz 7.8 Mb (ftp)(http) TSV
GSM2343705_ENCFF874ALU_minus_strand_signal_of_all_reads_GRCh38.bigWig 255.2 Mb (ftp)(http) BIGWIG
GSM2343705_ENCLB197GXK_README.txt.gz 1.2 Kb (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