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| Status |
Public on Mar 03, 2020 |
| Title |
H4 |
| Sample type |
SRA |
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| Source name |
Left liver lobes
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| Organism |
Mus musculus |
| Characteristics |
treatment type: Non-Irradiated Control
time: 1 month
biological replicate: 3
strain: C57BL16
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA)
rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
STAR alignment program, version 2.5.3a, with the recommended ENCODE options (Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 2013;29(1):15-21 doi: 10.1093/bioinformatics/bts635published Online First: Epub Date]|.) -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: comma-seperated text file which includes raw transcript expression counts (with corresponding ENSEMBL ID) for each sample
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| Submission date |
Aug 21, 2019 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Anna Nia |
| E-mail(s) |
anna.nia@ucla.edu
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| Organization name |
University of Texas Medical Branch
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Mark R. Emmett
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| Street address |
301 University Blvd
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| City |
Galveston |
| State/province |
TX |
| ZIP/Postal code |
77555 |
| Country |
USA |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE136165 |
Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice |
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| Relations |
| BioSample |
SAMN12618054 |
| SRA |
SRX6749769 |
| 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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