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| Status |
Public on Feb 05, 2023 |
| Title |
Liver CC046 F |
| Sample type |
SRA |
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| Source name |
Liver tissue
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| Organism |
Mus musculus |
| Characteristics |
mouse: CC046 F
strain: CC046/Unc
Sex: female
tissue: liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts, livers, and kidneys were removed, flash frozen, and RNA was harvested using Trizol reagent. KAPA mRNA HyperPrep Kit (Roche) was used with total RNA for the construction of sequencing libraries.
Pooled libraries were sequenced on the NovaSeq 6000 platform (Illumina) using the S1 Reagent Kit v1, yielding 20-40M (target 30M) 1 x 1000bp single-end reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
liver_total_gene_counts.txt
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| Data processing |
Reads were aligned to the pooled transcriptomes (mm10) of the eight founder strains using bowtie v1.0.0 with parameters -q -p 8 -a --best --strata --sam -v 3 -m 100.
Aligned reads were input into the Genotype recontruction by RNA-Seq (GBRS) software which estimated total gene counts using the Expectation-Maximization for Allele Specific Expression (EMASE) software.
Filtered out genes for which > 50% of samples had no expression.
Assembly: mm10
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| Submission date |
Mar 29, 2022 |
| Last update date |
Feb 05, 2023 |
| Contact name |
Carol Bult |
| E-mail(s) |
Carol.Bult@jax.org
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| Phone |
207-288-6000
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| Organization name |
The Jackson Laboratory
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| Lab |
The Bult Lab
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| Street address |
600 Main St
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE199702 |
Transcriptomics analysis of heart, kidney, and liver tissues from 58 Collaborative Cross strains |
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| Relations |
| BioSample |
SAMN27062427 |
| SRA |
SRX14651829 |
| 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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