|
| Status |
Public on Feb 02, 2011 |
| Title |
Exon arrays of Roadmap cell types; iPS DF 6.9 Cell Line, Induced pluripotent stem cells; DS15164-exon |
| Sample type |
RNA |
| |
|
| Source name |
iPS DF 6.9 Cell Line, Induced pluripotent stem cel, derived from fibroblast. the first set of numbers before the period refer to different clones, the number after the period indicates the sub-clone.; DS15164-exon
|
| Organism |
Homo sapiens |
| Characteristics |
disease: None
biomaterial_provider: James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison
biomaterial_type: Cell Line
line: iPS DF 6.9 Cell Line
lineage: Derived from newborn foreskin fibroblast: Cat# CRL-2097TM, ATCC
differentiation_stage: Induced pluripotent stem cell
differentiation_method: http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1
passage: 32
medium: NA
sex: Unknown
batch: 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: NTR_0001172
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.5448
sample alias: iPS_6_9
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5336
EDACC Genboree Run Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FRUN%2FEDACC.5449
|
| 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 |
Feb 02, 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 |
SAMN00204011 |
