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Series GSE37641 Query DataSets for GSE37641
Status Public on Jan 01, 2013
Title Quantitative polyadenylation map of mouse embryonic epidermal lineages
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We establish an experimental and bioinformatic pipeline using 3SEQ to quantitatively measure mRNA expression and reliably determine 3' end formation by sequencing polyadenylated transcripts. When applied to purified mouse embryonic skin stem cells direct differentiation lineages, we identify 15,651 UTRs representing 10,442 distinct mRNAs that are abundantly expressed in the skin. We determine that ~80% of UTRs are formed by using canonical A[A/U]UAAA polyadenylation signals, whereas ~20% of UTRs utilize alternative signals. We demonstrate that comparing with qPCR, our RNA-Seq approach can precisely measure mRNA fold-change and accurately determine the expression of mRNAs over four orders of magnitude. We also reported 453 out of 10,442 genes (4.3%) show differential 3' end usage between skin stem cells and their direct differentiation lineages. Among them, core components of the miRNA pathway, including Dicer, Dgcr8, Xpo5 and Ago2, show dynamic 3' UTR formation patterns, indicating a self-regulatory mechanism. Together, our quantitative analysis reveals a dynamic picture of mRNA 3' end formation in closely related somatic stem cell lineages.
Overall design Perform 3SEQ in E14 epidermal basal cells and E14 epidermal suprabasal cells.
Contributor(s) Wang L, Dowell DR, Yi R
Citation(s) 23325109
Submission date Apr 27, 2012
Last update date May 15, 2019
Contact name Li Wang
Phone 3037045961
Organization name University of Colorado, Boulder
Street address 347 UCB
City Boulder
State/province CO
ZIP/Postal code 80303
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM923591 E14 basal 3Seq
GSM923592 E14 suprabasal 3Seq
GSM923593 P4 hair follicle 3Seq
BioProject PRJNA162367
SRA SRP012561

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37641_E14_epi+P4_HF.all_peaks.bed.gz 1.3 Mb (ftp)(http) BED
GSE37641_E14_epi+P4_HF.all_peaks.geneSymbol.bed.gz 1.3 Mb (ftp)(http) BED
GSE37641_E14_epi+P4_HF.filtered_peaks.PAS.bed.gz 299.2 Kb (ftp)(http) BED
GSE37641_E14_epi+P4_HF.filtered_peaks.bed.gz 268.5 Kb (ftp)(http) BED
GSE37641_E14_reseq.allpeaks.bed.gz 1.3 Mb (ftp)(http) BED
GSE37641_E14_reseq_filtered.bed.gz 201.4 Kb (ftp)(http) BED
GSE37641_RAW.tar 228.4 Mb (http)(custom) TAR (of BED)
GSE37641_README.txt 5.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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