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Sample GSM5974893 Query DataSets for GSM5974893
Status Public on May 23, 2023
Title MBD2aR181C_r1
Sample type SRA
 
Source name Neuronal progenitor
Organism Mus musculus
Characteristics cell type: ES-derived neural progenitor cells
genotype: Mbd3-KO + Mbd2a_R181C
Extracted molecule polyA RNA
Extraction protocol not provided
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing reads were trimmed using trim_galore using standard parameters
reads were aligned to the mouse genome mm9 annotation using STAR with following parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000
counts per gene were obtained in R using quasr::qCount() with the following parameters: reportLevel="gene", orientation="opposite", based on gencode.mouse.v1.annotation.gtf
differential gene expression was calculated using edgeR in R
Assembly: mm9
Supplementary files format and content: gene matrix containing raw counts per gene (rows) for each sample (columns)
 
Submission date Mar 28, 2022
Last update date May 23, 2023
Contact name Tuncay Baubec
Organization name Utrecht University
Department Department of Biology
Lab Genome Biology and Epigenetics
Street address Padualaan 8
City Utrecht
ZIP/Postal code 3584 CH
Country Netherlands
 
Platform ID GPL24247
Series (1)
GSE199541 Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex func-tion during cellular differentiation
Relations
BioSample SAMN27019766
SRA SRX14634344

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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