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Sample GSM2072466 Query DataSets for GSM2072466
Status Public on Mar 18, 2016
Title total RNA-seq from fibroblast of dermis (ENCLB555AMQ)
Sample type SRA
 
Source name Homo sapiens fibroblast of dermis primary cell female adult (44 years)
Organism Homo sapiens
Characteristics cell_type: fibroblast of dermis
biomaterial_type: primary cell
description: Skin Fibroblasts (NHDF) from the breast dermal layer that were surgically resected from a 44 year old caucasian female.
biosample encode accession: ENCBS476ENC (SAMN04284388)
age: 44 year
donor_id: ENCDO120AAA
dev stage: adult
passage number: 2
Sex: female
health state: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV
lab: Thomas Gingeras, CSHL
link: ENCBS476ENC at ENCODE; https://www.encodeproject.org/ENCBS476ENC/
link: Derived from ENCODE donor ENCDO120AAA; https://www.encodeproject.org/ENCDO120AAA/
link: certificate of analysis; https://www.encodeproject.org/documents/6522df6e-b41d-439d-bd11-87eab3d369d6/@@download/attachment/NHDF7071701.2_Gingeras_protocol.pdf
link: ENCODE dbxrefs NHDF_7071701.2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHDF_7071701.2
link: ENCODE dbxrefs NHDF; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHDF
link: PromoCell sample source; http://www.promocell.com/nc/products/human-primary-cells/fibroblasts/normal-human-dermal-fibroblasts-nhdf/?sword_list%5B%5D=NHDF
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol: https://www.encodeproject.org/documents/342bd00a-96f2-4cc1-bdff-a16af27b524d/@@download/attachment/LID47247.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description https://www.encodeproject.org/experiments/ENCSR000CUH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from skin fibroblasts primary whole cells, NHDF isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUH
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMQ
size range: >200
spikeins used: /references/ENCSR470JZL/
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)
GSE78610 total RNA-seq from fibroblast of dermis (ENCSR000CUH)
Relations
Reanalyzed by GSE111163
SRA SRX1603516
BioSample SAMN04284388
Named Annotation GSM2072466_ENCFF232ZLN_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2072466_ENCFF077KSU_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2072466_ENCFF120SYM_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2072466_ENCFF102NVX_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2072466_ENCFF075CXE_plus_strand_signal_of_unique_reads_hg19.bigWig 321.7 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF077KSU_minus_strand_signal_of_unique_reads_GRCh38.bigWig 328.8 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF081NBY_gene_quantifications_GRCh38.tsv.gz 2.6 Mb (ftp)(http) TSV
GSM2072466_ENCFF102NVX_minus_strand_signal_of_all_reads_GRCh38.bigWig 349.8 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF120SYM_plus_strand_signal_of_all_reads_GRCh38.bigWig 364.6 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF232ZLN_plus_strand_signal_of_unique_reads_GRCh38.bigWig 345.2 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF278HST_plus_strand_signal_of_all_reads_hg19.bigWig 334.9 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF355AYH_plus_strand_signal_of_unique_reads_hg19.bigWig 342.8 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF410HOR_minus_strand_signal_of_all_reads_hg19.bigWig 320.1 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF599RMW_plus_strand_signal_of_all_reads_hg19.bigWig 360.0 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF628WVC_transcript_quantifications_GRCh38.tsv.gz 7.9 Mb (ftp)(http) TSV
GSM2072466_ENCFF748FWL_minus_strand_signal_of_unique_reads_hg19.bigWig 305.9 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF768XLE_transcript_quantifications_hg19.tsv.gz 7.7 Mb (ftp)(http) TSV
GSM2072466_ENCFF786STS_minus_strand_signal_of_all_reads_hg19.bigWig 345.1 Mb (ftp)(http) BIGWIG
GSM2072466_ENCFF870JUS_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2072466_ENCFF883IOU_minus_strand_signal_of_unique_reads_hg19.bigWig 326.1 Mb (ftp)(http) BIGWIG
GSM2072466_ENCLB555AMQ_README.txt.gz 2.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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