|
| Status |
Public on Jun 06, 2012 |
| Title |
Exon arrays of Roadmap cell types; Fetal Intestine, Small primary tissue, day 87; DS16975-exon |
| Sample type |
RNA |
| |
|
| Source name |
Fetal Intestine, Small primary tissue, day 87; DS16975-exon
|
| Organism |
Homo sapiens |
| Characteristics |
molecule: genomic DNA
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-23724
donor_age: day 87
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.12952
sample alias: fIntestine_Small.H-23724d87
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10042
|
| 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 |
Jun 05, 2012 |
| 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 |
SAMN00739172 |
