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Series GSE115789 Query DataSets for GSE115789
Status Public on Sep 01, 2018
Title Ubiquitin-specific protease USP34 controls osteogenic differentiation and bone formation by regulating BMP2 signaling
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The aim is to analyze the transcriptome profiling (RNA-seq) of Mettl3 knockout mesenchymal stem cells (MSCs) and identify m6A modified mRNThe aim is to analyze the transcriptome profiling (RNA-seq) of USP34 knockdown mesenchymal stem cells (MSCs). Total RNAs from human MSCs of siCTRL and siUSP34 were extracted using an RNeasy mini kit (Qiagen). Libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit according to manufacturer’s instruction, and single-end sequenced on an Illumina HiSeq 3000 machine. The reads were aligned to hg19 genome using Tophat. Analysis of RNA-seq data was done using Cufflinks with Refseq mRNAs to guide assembly and the cummeRbund package in R. Transcripts, which were regulated greater than 2-fold were considered significant difference.
Overall design The mRNA profiles of siCTRL and siUSP34 MSCs were generated by deep sequencing, in duplicate, using Illumina HiSeq 3000.
Contributor(s) Yuan Q
Citation(s) 30181118
Submission date Jun 14, 2018
Last update date Dec 23, 2018
Contact name Quan Yuan
Organization name West China Hospital of Stomatology, Sichuan University
Lab State Key laboratory of Oral Diseases
Street address 14 Third section, Renmin Nan Road
City Chengdu
State/province Sichuan
ZIP/Postal code 610041
Country China
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (4)
GSM3189988 siCTRL1
GSM3189989 siCTRL2
GSM3189990 siUSP341
BioProject PRJNA476060
SRA SRP150508

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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
GSE115789_Gene_expression_Cuffdiff.txt.gz 874.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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