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| Status |
Public on Oct 29, 2019 |
| Title |
UCD-T2DM 6-month RNA-seq Rep #1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
strain: UCD-T2DM
duration of diabetic phenotype: 6 months
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction protocol not provided.
Libraries were prepared according to the Illumina TruSeq polyA+ Sample Prep Kit protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA
UC Davis type 2 diabetes mellitus rat model
ucdt2dm_normalizedCounts.csv
Sample name:
UCD-4789
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| Data processing |
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9, rn6, and hg19 for mouse, rat, and monkey small RNA-seq, mm10 and rn6 for mouse and rat RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.
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| Submission date |
Oct 31, 2018 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Praveen Sethupathy |
| Organization name |
Cornell University
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| Lab |
Dr. Sethupathy Lab
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| Street address |
Cornell University College of Veterinary Medicine, Box 17
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| City |
Ithica |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE122044 |
MiR-29 Regulates de novo Lipogenesis in the Liver and Circulating Triglyceride Levels in a Sirt1-Dependent Manner |
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| Relations |
| BioSample |
SAMN10356128 |
| SRA |
SRX4963356 |
| 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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