NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2343973 Query DataSets for GSM2343973
Status Public on Nov 08, 2016
Title small RNA-seq from gastroesophageal sphincter (ENCLB675VYM)
Sample type SRA
 
Source name Homo sapiens gastroesophageal sphincter tissue male adult (37 years)
Organism Homo sapiens
Characteristics tissue_type: gastroesophageal sphincter
biomaterial_type: tissue
description: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS581RWW (SAMN05897339)
age: 37 year
dev stage: adult
donor_id: ENCDO845WKR
Sex: male
lab: Thomas Gingeras, CSHL
link: ENCBS581RWW at ENCODE; https://www.encodeproject.org/ENCBS581RWW/
link: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol: https://www.encodeproject.org/documents/483dbbe6-2839-45fd-aaea-124733205037/@@download/attachment/LID296540.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description https://www.encodeproject.org/experiments/ENCSR646HQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's esophagogastric junction 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: ENCSR646HQQ
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB675VYM
size range: <200
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 GPL18573
Series (1)
GSE88432 small RNA-seq from gastroesophageal sphincter (ENCSR646HQQ)
Relations
BioSample SAMN05897339
SRA SRX2244378
Named Annotation GSM2343973_ENCFF953UVB_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2343973_ENCFF771LUJ_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2343973_ENCFF055CDW_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2343973_ENCFF359PGI_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2343973_ENCFF055CDW_minus_strand_signal_of_unique_reads_GRCh38.bigWig 760.2 Kb (ftp)(http) BIGWIG
GSM2343973_ENCFF246HFV_gene_quantifications_GRCh38.tsv.gz 281.9 Kb (ftp)(http) TSV
GSM2343973_ENCFF327KWU_gene_quantifications_hg19.tsv.gz 268.1 Kb (ftp)(http) TSV
GSM2343973_ENCFF359PGI_minus_strand_signal_of_all_reads_GRCh38.bigWig 5.8 Mb (ftp)(http) BIGWIG
GSM2343973_ENCFF405BPJ_plus_strand_signal_of_unique_reads_hg19.bigWig 879.8 Kb (ftp)(http) BIGWIG
GSM2343973_ENCFF537CRA_plus_strand_signal_of_all_reads_hg19.bigWig 9.4 Mb (ftp)(http) BIGWIG
GSM2343973_ENCFF771LUJ_plus_strand_signal_of_all_reads_GRCh38.bigWig 9.4 Mb (ftp)(http) BIGWIG
GSM2343973_ENCFF873MCU_minus_strand_signal_of_all_reads_hg19.bigWig 9.4 Mb (ftp)(http) BIGWIG
GSM2343973_ENCFF953UVB_plus_strand_signal_of_unique_reads_GRCh38.bigWig 796.9 Kb (ftp)(http) BIGWIG
GSM2343973_ENCFF988FMU_minus_strand_signal_of_unique_reads_hg19.bigWig 836.5 Kb (ftp)(http) BIGWIG
GSM2343973_ENCLB675VYM_README.txt.gz 1.0 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