NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2072458 Query DataSets for GSM2072458
Status Public on Mar 18, 2016
Title total RNA-seq from hair follicle dermal papilla cell (ENCLB555ASG)
Sample type SRA
 
Source name Homo sapiens hair follicle dermal papilla primary cell female adult (47 years)
Organism Homo sapiens
Characteristics cell_type: hair follicle dermal papilla cell
biomaterial_type: primary cell
description: Follicle Dermal Papilla Cells (HFDPC) from the lateral scalp region of a 47 year old caucasian female with brown hair
biosample encode accession: ENCBS454ENC (SAMN04284368)
age: 47 year
donor_id: ENCDO129AAA
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: ENCBS454ENC at ENCODE; https://www.encodeproject.org/ENCBS454ENC/
link: Derived from ENCODE donor ENCDO129AAA; https://www.encodeproject.org/ENCDO129AAA/
link: certificate of analysis; https://www.encodeproject.org/documents/8ead3de2-da5a-4369-9d24-c4bc8da1cdae/@@download/attachment/HFDPC0100503.2_Gingeras_protocol.pdf
link: ENCODE dbxrefs HFDPC_0100503.2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HFDPC_0100503.2
link: ENCODE dbxrefs HFDPC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HFDPC
link: PromoCell sample source; http://www.promocell.com/nc/products/human-primary-cells/follicle-dermal-papilla-cells/?sword_list%5B%5D=HFDPC
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol: https://www.encodeproject.org/documents/e2498941-45a5-488a-b0e5-9235bb7d2073/@@download/attachment/LID47095.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description https://www.encodeproject.org/experiments/ENCSR000CUB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from hair follicle dermal papilla primary whole cells, HFDPC 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: ENCSR000CUB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASG
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)
GSE78606 total RNA-seq from hair follicle dermal papilla cell (ENCSR000CUB)
Relations
SRA SRX1603500
BioSample SAMN04284368
Named Annotation GSM2072458_ENCFF248NOP_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2072458_ENCFF322RIR_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2072458_ENCFF003RYB_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2072458_ENCFF578NIM_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2072458_ENCFF003RYB_minus_strand_signal_of_unique_reads_GRCh38.bigWig 291.8 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF015QQI_minus_strand_signal_of_unique_reads_hg19.bigWig 273.9 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF192LEW_minus_strand_signal_of_all_reads_hg19.bigWig 287.5 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF210MUL_plus_strand_signal_of_unique_reads_hg19.bigWig 286.4 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF248NOP_plus_strand_signal_of_all_reads_GRCh38.bigWig 321.7 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF249VXI_plus_strand_signal_of_unique_reads_hg19.bigWig 304.5 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF267NCG_plus_strand_signal_of_all_reads_hg19.bigWig 299.0 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF302ULE_transcript_quantifications_hg19.tsv.gz 7.7 Mb (ftp)(http) TSV
GSM2072458_ENCFF322RIR_plus_strand_signal_of_unique_reads_GRCh38.bigWig 304.9 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF343BYT_gene_quantifications_GRCh38.tsv.gz 2.6 Mb (ftp)(http) TSV
GSM2072458_ENCFF502QVK_minus_strand_signal_of_unique_reads_hg19.bigWig 291.4 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF578NIM_minus_strand_signal_of_all_reads_GRCh38.bigWig 310.3 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF646NUD_minus_strand_signal_of_all_reads_hg19.bigWig 309.5 Mb (ftp)(http) BIGWIG
GSM2072458_ENCFF648VTO_transcript_quantifications_GRCh38.tsv.gz 7.9 Mb (ftp)(http) TSV
GSM2072458_ENCFF650BVH_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2072458_ENCFF837BMV_plus_strand_signal_of_all_reads_hg19.bigWig 321.0 Mb (ftp)(http) BIGWIG
GSM2072458_ENCLB555ASG_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
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap