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Sample GSM2496425 Query DataSets for GSM2496425
Status Public on Dec 03, 2017
Title shCtrl_RNAseq_rep2
Sample type SRA
 
Source name shCtrl
Organism Mus musculus
Characteristics tissue: AML12 cells
Treatment protocol The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.
Growth protocol AML12 cell were kept in complete growth medium:a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm9 reference assembly by the Tophat2 software.
We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
For differential gene expression analysis, we analyzed raw read counts for GENCODE M1 gene models using HTSeq (Anders et al., 2015), and then calculated statistics of differential expression via DESeq2 version 1.8.2 (Love et al., 2014) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each replicate.
 
Submission date Feb 21, 2017
Last update date May 15, 2019
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21273
Series (2)
GSE95111 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [RNA-Seq]
GSE95116 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture
Relations
BioSample SAMN06350715
SRA SRX2578754

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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