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Sample GSM3959437 Query DataSets for GSM3959437
Status Public on Jun 24, 2020
Title RNA-seq_shCtrl-1
Sample type SRA
 
Source name shCtrl
Organism Mus musculus
Characteristics cell line: AML12 cells
genotype/variation: shCtrl
Treatment protocol The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.
Growth protocol AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
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.
Paired-end reads from RNA-seq were aligned to the mouse mm10 reference assembly by using HISAT2 with parameters "--rna-strandness RF". Not uniquely mapped reads were removed.
For differential gene expression analysis, we counted reads mapped to Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union. Fold-change and p values were calculated by the R package DESeq2.
To quantify the expression level of genes, we acquired the transcripts per million (TPM) using StringTie with options '-e -B -A –rf'.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including TPM values for each replicate.
 
Submission date Jul 22, 2019
Last update date Jun 24, 2020
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Street address 130 Dongan Rd.
City ShangHai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21273
Series (2)
GSE134623 TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [RNA-seq]
GSE134624 TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes
Relations
BioSample SAMN12333876
SRA SRX6481991

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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