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Title: Transcript abundance in A-T-derived iPSC: Comparing isogenic cells to unrelated individual      
dateReleased:
11-19-2015
description:
Induced pluripotent stem cells (iPSC) were prepared from multiple subjects with Ataxia-telangiectasia (A-T). iPSC were prepared from activated T-cells using commercial Sendai virus to deliver reprogramming factors. ATM protein-expressing and non-expressing cultures would found in multiple sub-lines (sub-lines are generated from distinct founder colonies of cells) from a single subject (Q3). Genetic analysis determined that all sub-lines originated from the same subject and were likely the product of spontaneous reversion by gene correction. To compare gene expression profiles, three iPSC samples were assayed: (1) A reverted ATM+/- subline from subject Q3, (2) An ATM-/- subline from subject Q3, and (3) An iPSC line from an unrelated ATM-/- subject, Q1. Analysis reveals that the majority of significantly-different genes between the unrelated ATM-/- line (Q1SA) and the reverted ATM+/- line (Q3SC) was due to genetic variation between individuals. A more focused set of contrasting genes could be identified between the isogenic Q3-derived lines (Q3SA, ATM-/-, vs. Q3SC, ATM+/-). The 206 transcripts that are significantly different point to a differential regulation of p53-associated pathways. Total cellular RNA was prepared from each iPSC culture. Different passage numbers or sister cultures were used as replicates (n=2).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-71878
refinement:
raw
alternateIdentifiers:
71878
keywords:
functional genomics
dateModified:
11-30-2015
availability:
available
types:
gene expression
name:
Homo sapiens
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-71878/E-GEOD-71878.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-71878/E-GEOD-71878.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71878
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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