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| Status |
Public on Sep 10, 2019 |
| Title |
WT_4_DHIP |
| Sample type |
SRA |
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| Source name |
WT_4_DHIP
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: DHIP
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction and analysis, habenula tissues were homogenized in 500 µl TRIzol Reagent (ThermoFisher Scientific, Carlsbad, CA, USA) according to the manufacturer’s instructions. Samples were sonicated to complete homogenization. 100 µl of chloroform was added and samples were vigorously vortexed for 15 sec. After a 3 min incubation at room temperature, the samples were centrifuged at 12,000 x g at 4°C for 15 min. The aqueous phase of the sample was removed by angling the tube at 45° and pipetting the solution to a fresh tube. 250 µl of 100% isopropanol was added to the aqueous phase and incubated for 10 min at room temperature. Samples were then centrifuged at 12,000 x g for 10 min at 4°C. Supernatant was removed and discarded, leaving behind the RNA pellet. The pellet was washed with 500 μl 75% ethanol twice. The tube was allowed to dry for 5 min at room temperature. The pellet was resuspended in 20 µl nuclease-free water. Residual genomic DNA was removed using the DNA-free Kit (ThermoFisher Scientific, Carlsbad, CA, USA) per the manufacturer’s instructions. The concentration was measured using a NanoDrop machine (ThermoFisher Scientific, Carlsbad, CA, USA). Samples were stored at -80 °C until processing.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
135_16
featureCounts_matrix.csv
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| Data processing |
The paired-end sequencing reads were aligned to the rat genome, using the Spliced Transcripts Alignment to a Reference (STAR).
featureCount was employed to assign aligned reads to genes.
Genome_build: rn6
Supplementary_files_format_and_content: comma-delimited text files include read count values for each sample
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| Submission date |
Sep 09, 2019 |
| Last update date |
Sep 10, 2019 |
| Contact name |
Zichen Wang |
| E-mail(s) |
zichen.wang@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Pharmacological Sciences
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| Lab |
Avi Ma'ayan
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| Street address |
1468 Madison Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE137118 |
Habenular Tcf7l2 links nicotine addiction to diabetes |
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| Relations |
| BioSample |
SAMN12716117 |
| SRA |
SRX6820244 |
| 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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