NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2343500 Query DataSets for GSM2343500
Status Public on Nov 08, 2016
Title small RNA-seq from gastroesophageal sphincter (ENCLB318FPY)
Sample type SRA
 
Source name Homo sapiens gastroesophageal sphincter tissue male adult (54 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: ENCBS812ZNH (SAMN05897593)
age: 54 year
dev stage: adult
donor_id: ENCDO451RUA
Sex: male
lab: Thomas Gingeras, CSHL
link: ENCBS812ZNH at ENCODE; https://www.encodeproject.org/ENCBS812ZNH/
link: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol: https://www.encodeproject.org/documents/d946ce6f-ceec-425d-b40e-eefa33229a73/@@download/attachment/LID296541.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description https://www.encodeproject.org/experiments/ENCSR269YSX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 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: ENCSR269YSX
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB318FPY
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)
GSE88153 small RNA-seq from gastroesophageal sphincter (ENCSR269YSX)
Relations
BioSample SAMN05897593
SRA SRX2243868
Named Annotation GSM2343500_ENCFF303GJG_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2343500_ENCFF529NXY_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2343500_ENCFF950LMM_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2343500_ENCFF382MEB_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2343500_ENCFF025AXP_gene_quantifications_GRCh38.tsv.gz 274.1 Kb (ftp)(http) TSV
GSM2343500_ENCFF075ZHO_minus_strand_signal_of_unique_reads_hg19.bigWig 662.9 Kb (ftp)(http) BIGWIG
GSM2343500_ENCFF124VFZ_plus_strand_signal_of_unique_reads_hg19.bigWig 708.4 Kb (ftp)(http) BIGWIG
GSM2343500_ENCFF144TDE_minus_strand_signal_of_all_reads_hg19.bigWig 4.8 Mb (ftp)(http) BIGWIG
GSM2343500_ENCFF303GJG_minus_strand_signal_of_all_reads_GRCh38.bigWig 4.5 Mb (ftp)(http) BIGWIG
GSM2343500_ENCFF382MEB_minus_strand_signal_of_unique_reads_GRCh38.bigWig 609.2 Kb (ftp)(http) BIGWIG
GSM2343500_ENCFF491FVE_gene_quantifications_hg19.tsv.gz 259.7 Kb (ftp)(http) TSV
GSM2343500_ENCFF529NXY_plus_strand_signal_of_all_reads_GRCh38.bigWig 5.1 Mb (ftp)(http) BIGWIG
GSM2343500_ENCFF950LMM_plus_strand_signal_of_unique_reads_GRCh38.bigWig 650.6 Kb (ftp)(http) BIGWIG
GSM2343500_ENCFF990IHP_plus_strand_signal_of_all_reads_hg19.bigWig 4.8 Mb (ftp)(http) BIGWIG
GSM2343500_ENCLB318FPY_README.txt.gz 1019 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