|
Status |
Public on Jun 24, 2020 |
Title |
RNA-seq_shCtrl-2 |
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 |
SAMN12333887 |
SRA |
SRX6481992 |