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| Status |
Public on Jul 17, 2024 |
| Title |
WSH female arcuate nucleus, HF sedentary, rep 2 |
| Sample type |
SRA |
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| Source name |
Hypothalamic arcuate nucleus
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| Organism |
Rattus rattus |
| Characteristics |
tissue: Hypothalamic arcuate nucleus
Sex: Female
diet: 60% HFD
treatment: HFD, sedentary
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| Extracted molecule |
total RNA |
| Extraction protocol |
Coronal brain sections of the hypothalamus were sliced using a cryostat (-2.3 to -4.5 mm Bregma, using Paxison and Watson coordinates) and the ARC was extracted with a 1 mm disposable Miltex biopsy punch plunger (Bar Noar Ltd). Punches from each hemisphere were immersed in RNA Save (Biological Industries, Kibbutz Beit-Haemek, Israel) for downstream RNA extraction. RNA was isolated using TriReagent (Molecular Research Center, Cincinnati, OH) in DIO/voluntary running experiment. RNA was isolated using RNA/DNA Purification Micro Kit (Cat. 50300) (Norgen BioTek Corporation, Thorold, ON, Canada) in miR-injection experiment.
A bulk adaptation of the MARS-Seq protocol was used
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw fastq data were aligned to the rat (Rnor6) reference genome using STAR (v 2.7.9a)
SAMtools collectionwas used to sort, remove PCR duplicates (rmdup), index BAM files (index), and calculate library statistics (flagstat)
Mapped reads were processed by HTseq (v 0.13.5), with the following parameters: 'htseq-count -s no --mode=union’
Read count matrix was assembled and pair-wise differential gene expression analysis was performed using DESeq2
Assembly: Rnot6
Supplementary files format and content: Read count for each sample
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| Submission date |
May 15, 2023 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Noam Meiri |
| E-mail(s) |
noam.meiri@mail.huji.ac.il
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| Organization name |
Agricultural Research Organization, The Volcani Center
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| Street address |
68 HaMakkabbim Road
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| City |
Rishon LeZiyyon |
| ZIP/Postal code |
7528809 |
| Country |
Israel |
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| Platform ID |
GPL28964 |
| Series (1) |
| GSE232510 |
Exercise rescues aberrantly expressed genes in diet-induced obese rats: a potential role of miR-211 modulation in the hypothalamic arcuate nucleus |
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| Relations |
| BioSample |
SAMN35084054 |
| SRA |
SRX20340649 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7349358_HFS_Rep2_count.txt.gz |
118.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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