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Series GSE37703 Query DataSets for GSE37703
Status Public on Dec 11, 2012
Title Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Illumina]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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 02, 2012
Last update date May 15, 2019
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 (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (12)
GSM925762 LFB_scramble_hiseq_repA
GSM925763 LFB_scramble_hiseq_repB
GSM925764 LFB_scramble_hiseq_repC
This SubSeries is part of SuperSeries:
GSE37704 Differential analysis of gene regulation at transcript resolution by RNA-Seq
BioProject PRJNA162905
SRA SRP012607

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
GSE37703_hiseq_cuffdiff_cds.diff.gz 478.3 Kb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_cds.fpkm_tracking.gz 1.6 Mb (ftp)(http) FPKM_TRACKING
GSE37703_hiseq_cuffdiff_cds_exp.diff.gz 1.5 Mb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_gene_exp.diff.gz 822.5 Kb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_genes.fpkm_tracking.gz 920.2 Kb (ftp)(http) FPKM_TRACKING
GSE37703_hiseq_cuffdiff_isoform_exp.diff.gz 1.8 Mb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_isoforms.fpkm_tracking.gz 2.3 Mb (ftp)(http) FPKM_TRACKING
GSE37703_hiseq_cuffdiff_promoters.diff.gz 431.0 Kb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_splicing.diff.gz 561.7 Kb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_tss_group_exp.diff.gz 1.1 Mb (ftp)(http) DIFF
GSE37703_hiseq_cuffdiff_tss_groups.fpkm_tracking.gz 1.2 Mb (ftp)(http) FPKM_TRACKING
GSE37703_miseq_cuffdiff_cds.diff.gz 445.0 Kb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_cds.fpkm_tracking.gz 1.5 Mb (ftp)(http) FPKM_TRACKING
GSE37703_miseq_cuffdiff_cds_exp.diff.gz 1.4 Mb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_gene_exp.diff.gz 823.1 Kb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_genes.fpkm_tracking.gz 915.8 Kb (ftp)(http) FPKM_TRACKING
GSE37703_miseq_cuffdiff_isoform_exp.diff.gz 1.7 Mb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_isoforms.fpkm_tracking.gz 2.2 Mb (ftp)(http) FPKM_TRACKING
GSE37703_miseq_cuffdiff_promoters.diff.gz 408.9 Kb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_splicing.diff.gz 528.3 Kb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_tss_group_exp.diff.gz 1.1 Mb (ftp)(http) DIFF
GSE37703_miseq_cuffdiff_tss_groups.fpkm_tracking.gz 1.2 Mb (ftp)(http) FPKM_TRACKING
GSE37703_readme.txt.gz 147 b (ftp)(http) TXT
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Raw data are available in SRA

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