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Sample GSM706496 Query DataSets for GSM706496
Status Public on Apr 14, 2011
Title Exon arrays of Roadmap cell types; Fetal primary tissue, day 115; DS16712-exon
Sample type RNA
 
Source name Fetal primary tissue, day 115; DS16712-exon
Organism Homo sapiens
Characteristics disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Tissue
tissue_type: Fetal Intestine, Small
tissue_depot: UW
collection_method: fetal
donor_id: H-23640
donor_age: day 115
donor_health_status: NA
donor_sex: Male
donor_ethnicity: NA
Treatment protocol None
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
 
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymetrix Gene Chip Scanner 3000
Description sample_term_id: UBERON_0002108
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7205
sample alias: fIntestine_Small.H-23640d115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7051
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
 
Submission date Apr 11, 2011
Last update date Jan 29, 2015
Contact name Northwest REMC
E-mail(s) rharris1@bcm.tmc.edu
Organization name University of Washington
Street address -
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL5188
Series (1)
GSE18927 University of Washington Human Reference Epigenome Mapping Project
Relations
BioSample SAMN00254264

Data table header descriptions
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 105.2109
2315102 73.65744
2315104 161.1662
2315105 41.51339
2315107 298.3969
2315112 176.8303
2315114 78.17262
2315116 109.5623
2315118 1229.252
2315120 350.6801
2315126 36.22843
2315132 6.307425
2315138 119.7247
2315140 53.00678
2315142 27.0879
2315144 18.7866
2315146 132.9493
2315148 144.0814
2315149 284.2796
2315150 112.493

Total number of rows: 1384231

Table truncated, full table size 22666 Kbytes.




Supplementary file Size Download File type/resource
GSM706496_110325_fIntestine_Sm_RS17910_exonlvl_exonanaly_hg19.TXT.gz 23.1 Mb (ftp)(http) TXT
GSM706496_X_Hs_fIntestine_Sm_E_110210_01_RS17910_W.CEL.gz 24.3 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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