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Sample GSM2072543 Query DataSets for GSM2072543
Status Public on Mar 18, 2016
Title total RNA-seq from skeletal muscle myoblast (ENCLB493TSJ)
Sample type SRA
 
Source name Homo sapiens skeletal muscle myoblast primary cell
Organism Homo sapiens
Characteristics cell_type: skeletal muscle myoblast
biomaterial_type: primary cell
description: skeletal muscle myoblasts
biosample encode accession: ENCBS328AAA (SAMN04284352)
age: unknown
donor_id: ENCDO094AAA
dev stage: unknown
Sex: not collected
lab: John Stamatoyannopoulos, UW
link: ENCBS328AAA at ENCODE; https://www.encodeproject.org/ENCBS328AAA/
link: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/
link: growth protocol; https://www.encodeproject.org/documents/076b9a67-5536-42f7-86fe-d21abb71b642/@@download/attachment/HSMM_Stam_protocol.pdf
link: ENCODE dbxrefs HSMM; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HSMM
link: Lonza sample source; http://www.lonza.com/
Extracted molecule total RNA
Extraction protocol data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/382c7b4d-d3db-41c7-a3bd-09d2aaf4b809/@@download/attachment/291757.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description https://www.encodeproject.org/experiments/ENCSR444WHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myoblasts. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR444WHQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB493TSJ
size range: >200
spikeins used: /references/ENCSR156CIL/
Data processing See GSM*_README.txt supplementary file linked below
 
Submission date Feb 25, 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 GPL11154
Series (1)
GSE78649 total RNA-seq from skeletal muscle myoblast (ENCSR444WHQ)
Relations
Reanalyzed by GSE111163
SRA SRX1603586
BioSample SAMN04284352
Named Annotation GSM2072543_ENCFF662OVY_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2072543_ENCFF330JWP_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2072543_ENCFF475THA_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2072543_ENCFF080PBN_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2072543_ENCFF027LTC_plus_strand_signal_of_all_reads_hg19.bigWig 96.4 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF080PBN_minus_strand_signal_of_all_reads_GRCh38.bigWig 100.1 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF230ZGM_minus_strand_signal_of_all_reads_hg19.bigWig 98.7 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF330JWP_plus_strand_signal_of_all_reads_GRCh38.bigWig 100.1 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF351SUL_transcript_quantifications_GRCh38.tsv.gz 7.7 Mb (ftp)(http) TSV
GSM2072543_ENCFF475THA_minus_strand_signal_of_unique_reads_GRCh38.bigWig 92.3 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF531OTQ_plus_strand_signal_of_all_reads_hg19.bigWig 55.7 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF551YKI_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2072543_ENCFF574KWX_plus_strand_signal_of_unique_reads_hg19.bigWig 53.5 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF602WDZ_minus_strand_signal_of_all_reads_hg19.bigWig 55.1 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF662OVY_plus_strand_signal_of_unique_reads_GRCh38.bigWig 90.4 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF707VPB_minus_strand_signal_of_unique_reads_hg19.bigWig 52.7 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF752XQX_plus_strand_signal_of_unique_reads_hg19.bigWig 91.2 Mb (ftp)(http) BIGWIG
GSM2072543_ENCFF803CZZ_gene_quantifications_GRCh38.tsv.gz 2.6 Mb (ftp)(http) TSV
GSM2072543_ENCFF865SBB_transcript_quantifications_hg19.tsv.gz 7.6 Mb (ftp)(http) TSV
GSM2072543_ENCFF891TPX_minus_strand_signal_of_unique_reads_hg19.bigWig 93.1 Mb (ftp)(http) BIGWIG
GSM2072543_ENCLB493TSJ_README.txt.gz 1.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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