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| Status |
Public on Apr 27, 2017 |
| Title |
Mbd3c KO rep2 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
es cell line: E14
genotype: Mbd3c -/-
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| Growth protocol |
Murine ESCs are derived from E14 and cultured on gelatin-coated plates as previously described (Chen et al., 2013). Mbd3ab, Mbd3c, Mbd3abc, and Mbd3cΔN-ab KO ESC lines were generated using the CRISPR/Cas9 system (Cong et al., 2013) to introduce mutations into Mbd3 exon 2 (Mbd3ab KO and Mbd3cΔN−ab KO), intron 2 (Mbd3c KO), or exon 5 (Mbd3abc KO).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 2 biological replicates each of WT, Mbd3ab KO, Mbd3c KO, Mbd3abc KO, and Mbd3cΔN−ab KO ESCs using TRIzol (Life Technologies), and purified with the Zymo RNA Clean and Concentrator kit.
2µg RNA was used for library preparation. RNA was rRNA-depleted (NEB and Clontech) and strand-specific libraries were prepared using the TruSeq Stranded mRNA LT kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
CKO_sig.txt
rRNA-depleted RNA
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| Data processing |
Reads were mapped to the mouse mm10 genome with TopHat2 (Kim et al., 2013), using parameters --library-type fr-firststrand --segment-length 38. Mapped reads were processed in HOMER (Heinz et al., 2010) using the “analyzeRepeats” command to calculate raw counts and normalized reads per kilobase per million mapped reads (rpkm) for each gene. Differential gene expression was calculated with DESeq2 (Love et al., 2014) using the “getDiffExpression” command in HOMER. Genes with an adjusted p value < 0.05 were considered significantly changed.
Genome_build: mm10
Supplementary_files_format_and_content: UCSC bedgraph files were generated using the "makeUCSCfile" command in HOMER. Tab-delimited text files were generated from genes with adj. p < 0.05 from DESeq2 output files.
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| Submission date |
Apr 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Fazzio |
| Organization name |
University of Massachusetts Medical School
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| Street address |
364 Plantation Street
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| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE80708 |
An ES cell–specific NuRD complex functions through interaction with Wdr5 |
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| Relations |
| BioSample |
SAMN04904289 |
| SRA |
SRX1728911 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2133803_CH9.ucsc.bedGraph.gz |
18.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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