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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 27, 2021 |
| Title |
Female_CAST_PolyA_RNA_Repl2_G164_M17 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: CAST/EiJ (Jackson Labs, cat#:000928)
rna isolation: 1 microgram total liver RNA
Sex: Female
age: 8 weeks
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| Growth protocol |
Male and female C57BL/6J and CAST/EiJ mice, 8-9 weeks of age, were purchased from Jackson Labs.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Snap frozen liver was used as input for RNA purification using TRIzol reagent (Invitrogen, cat#:15596026) following the manufacturer’s directions. Total RNA was quantified using the Qubit RNA BR kit (Invitrogen, cat#:Q10210). 1 microgram of total RNA per sample was used as input for library preparation.
Samples were prepared for sequencing with NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, cat#:E7420) with the PolyA selection with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat#:E7490).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RNA-seq Library
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| Data processing |
READ MAPPING: Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotech, 2010)
QUANTIFICATION: FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq and long noncoding genes (Lodato et al 2017). Transcripts were quantified by counting sequence reads that map to a the gene body of a gene.
DIFFERENTIAL EXPRESSION: Quantification of differential expression was performed using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: EdgeR output for CAST and B6 strains, and FPKM normalized read counts for protein coding and noncoding genes (FPKM_perGene.txt), where BM indicates livers of five individual C57BL/6J males, BF indicates C57BL/6J females, CM indicates livers of five individual CAST/EiJ males, CF indicates CAST/EiJ females.
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| Submission date |
May 08, 2019 |
| Last update date |
Oct 27, 2021 |
| 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 |
GPL24247 |
| Series (2) |
| GSE130913 |
RNA-seq in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ. |
| GSE130914 |
Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model |
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| Relations |
| BioSample |
SAMN11607980 |
| SRA |
SRX5809897 |
| 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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