GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE37690 Query DataSets for GSE37690
Status Public on Dec 11, 2012
Title Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Agilent]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-level expression estimation with a method to control for variability across replicate samples. Cuffdiff robustly identifies differentially regulated isoforms and genes and reveals differential splicing or promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1 and uncover a critical role for this gene in the maintenance of adult cells. We show that HOXA1 is required for lung fibroblast and HeLa cell cycle progression, and loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle.
Overall design Lung Fibroblasts were transfected with either a HOXA1 directed siRNA pool or a scramble non-targeting siRNA control. RNA was collected 48 hours after transfection and changes in gene expression were assayed for using Agilent microarrays.
Contributor(s) Trapnell C, Hendrickson D, Sauvageau M, Rinn J, Pachter L
Citation(s) 23222703
Submission date May 01, 2012
Last update date Nov 27, 2018
Contact name Cole Trapnell
Organization name Harvard University
Department Stem Cell and Regenerative Biology
Lab John Rinn
Street address 7 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (6)
GSM925635 A1KD_1
GSM925636 A1KD_2
GSM925637 A1KD_3
This SubSeries is part of SuperSeries:
GSE37704 Differential analysis of gene regulation at transcript resolution by RNA-Seq
BioProject PRJNA162925

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37690_RAW.tar 79.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap