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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 28, 2020 |
| Title |
Control Female_1 |
| Sample type |
SRA |
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| Source name |
liver tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: Floxed control: Ezh2 f/f
Sex: Female
age: 7 weeks
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| Treatment protocol |
Ezh1-/- mice were generated by the lab of Thomas Jenuwein (Research Institute of Molecular Pathology, Vienna, Austria) and Ezh2-floxed mice (f/f) by the lab of Alexander Tarakhovsky (Rockefeller University, New York, NY, USA). Ezh2fl/fl mice were subsequently bred with Alb-Cre (AC) transgenic mice, and their offspring were bred with Ezh1-/- mice to generate the Ezh1/Ezh2 double knockouts (DKO) used in this study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was polyA-selected and sequencing libraries were prepared using the Illumina TruSeq RNA library preparation kit (Illumina, cat# RS-122-2001), according to the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
M4
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| Data processing |
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing: Male controls to Female controls; Male-DKO to Male controls; Female-DKO to Female controls; and Male-DKO to Female-DKO.
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| Submission date |
Feb 20, 2018 |
| Last update date |
Apr 28, 2020 |
| Contact name |
David J. Waxman |
| E-mail(s) |
djw@bu.edu
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| Organization name |
Boston University
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| Department |
Department of Biology and Bioinformatics Program
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| Street address |
5 Cummington Mall
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE110879 |
RNA-seq gene expression profiling of livers from wild-type male and female mice, and from mice with a Double Knockout (DKO) of Ezh1 and Ezh2. |
| GSE110934 |
Gene expression and histone marks in EZH1/EZH2 double knockout mouse liver |
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| Relations |
| BioSample |
SAMN08568566 |
| SRA |
SRX3727021 |
| 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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