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Status |
Public on May 23, 2023 |
Title |
MBD2aR181C_r1 |
Sample type |
SRA |
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Source name |
Neuronal progenitor
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Organism |
Mus musculus |
Characteristics |
cell type: ES-derived neural progenitor cells genotype: Mbd3-KO + Mbd2a_R181C
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Extracted molecule |
polyA RNA |
Extraction protocol |
not provided
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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)
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Submission date |
Mar 28, 2022 |
Last update date |
May 23, 2023 |
Contact name |
Tuncay Baubec |
Organization name |
Utrecht University
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Department |
Department of Biology
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Lab |
Genome Biology and Epigenetics
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Street address |
Padualaan 8
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City |
Utrecht |
ZIP/Postal code |
3584 CH |
Country |
Netherlands |
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Platform ID |
GPL24247 |
Series (1) |
GSE199541 |
Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex func-tion during cellular differentiation |
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Relations |
BioSample |
SAMN27019766 |
SRA |
SRX14634344 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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