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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 23, 2023 |
| Title |
MBD2a-GR_r3 |
| 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_delGR
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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 |
SAMN27019767 |
| SRA |
SRX14634343 |
| 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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