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Sample GSM6008739 Query DataSets for GSM6008739
Status Public on Jun 24, 2024
Title WT_Cre_1
Sample type SRA
 
Source name mouse embryonic fibroblasts (immortalised)
Organism Mus musculus
Characteristics treatment: transduced with WT version of human HA-tagged CMTR1
agent: transfected with vector encoding EF1alpha::Cre-GFP
cell type: embryonic fibroblasts
Treatment protocol Cell were transfected with vector encoding EF1α::Cre-GFP and selected with 2µg/mL of puromycin after 24h for 48h. Cell were allowed to recover for 7 days prior to RNA extraction.
Growth protocol Mouse embryonic fibroblasts were grown in Dulbecco's Minimum Essential Medium supplemented with 10% Fetal Bovine Serum, 100U/mL penicillin, 100µg/mL streptomycin and 0.5mg/mL G418. MEFs were cultured at 37 °C with 5 % CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using GeneJET RNA Purification Kit (ThermoFisher Scientific)
Sequencing libraries were prepared by Novogene using ribosomal RNA depletion. The libraries were sequenced by Novogene using NovaSeq 6000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing was performed with a read length of 2×150 bp using a high output kit on Illumina NextSeq 500
The quality of sequencing reads was checked using FastQC and the adaptors were trimmed using Cutadapt (Martin, 2011)
The trimmed reads were aligned to the mouse genome assembly GRCm38/mm10 using STAR
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
Each reads per gene was quantified using htseq (Anders et al., 2015)
Assembly: mm10
Supplementary files format and content: Each reads per gene file contains a tab delimited table of reads per gene counted, the first column indicates the ensembl gene id, the second column shows the read count
 
Submission date Apr 04, 2022
Last update date Jun 24, 2024
Contact name Radoslaw Lukoszek
E-mail(s) rlukoszek@gmail.com
Organization name University of Potsdam
Street address Karl-Liebknecht-Strasse 24-25
City Potsdam
ZIP/Postal code 14476
Country Germany
 
Platform ID GPL24247
Series (1)
GSE200103 CK2 phosphorylation of cap methyltransferase CMTR1 promotes RNAPII interaction
Relations
BioSample SAMN27284916
SRA SRX14721892

Supplementary file Size Download File type/resource
GSM6008739_MEF_WT_Cre_1_ReadsPerGene.tab.gz 217.6 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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