|
| 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.
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| |
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| 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.
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| |
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| 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 |
| E-mail(s) |
cole@broadinstitute.org
|
| 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)
|
|
| This SubSeries is part of SuperSeries: |
| GSE37704 |
Differential analysis of gene regulation at transcript resolution by RNA-Seq |
|
| Relations |
| BioProject |
PRJNA162905 |
| SRA |
SRP012607 |
| 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 |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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