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Series GSE48305 Query DataSets for GSE48305
Status Public on Jun 27, 2013
Title Orchestrated intron retention regulates normal granulocyte differentiation [RNA-Seq]
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). There was a significant overlap of IR between human and mouse (P=2.85E-22, hypergeometric test), showing that IR is conserved.Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression.
Overall design Sequencing of polyadenylated RNA from three types of myeloid cells (promyelocytes, myelocytes and granulocytes) using Illumina GAIIx
Contributor(s) Ritchie W, Wong J
Citation(s) 23911323
Submission date Jun 26, 2013
Last update date May 15, 2019
Contact name william ritchie
Organization name centenary institute
Street address Building 93
City Camperdown
State/province NSW
ZIP/Postal code 2050
Country Australia
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (5)
GSM1174469 promyelocytes
GSM1174470 myelocytes
GSM1174471 granulocytes
This SubSeries is part of SuperSeries:
GSE48307 Orchestrated intron retention regulates normal granulocyte differentiation
BioProject PRJNA209629
SRA SRP026331

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Supplementary file Size Download File type/resource
GSE48305_C3.Human.transcripts.gtf.bz2 5.4 Mb (ftp)(http) GTF
GSE48305_RAW.tar 10.8 Mb (http)(custom) TAR (of GTF)
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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