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| Status |
Public on Jul 05, 2019 |
| Title |
RNA sequencing for mouse arcuate nucleus in male miR-17-92 knockout mice and female miR-7-sponge mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To address the molecular basis of miR-7 and miR-17-92 regulation in the POMC neuron and sex-differential expression of genes in the arcuate nucleus.
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| Overall design |
To address the molecular basis of miR-7 and miR-17-92 regulation in the POMC neuron, sequencing was performed. 2 samples (17-92-1, 17-92-2) in the male miR-17-92 knockout group and 2 samples (17-92-C1, 17-92-C2) in its control group (male wild type littermates) were sequenced and compared, and 2 samples in the female miR-7-sponge group (7-sp-1, 7-sp-2) and 2 samples (7-sp-C2, 7-sp-C4) in its control group (female wild type littermates) were sequenced and compared. To explore sex-differential expression of genes in the arcuate nucleus, 2 samples in the male wild type group and 2 samples in the female wild type group were compared. Arcuate nucleus from 2 mice were included in each sample.
ARC tissues in the coronal brain sections were accurately cut with syringe needles under the microscope and homogenized immediately in the TRIZOL reagent (Invitrogen). Total RNA was separated using chloroform and precipitated with isopropanol. Whole RNA sequencing was performed at the go beyond RNA arraystar company in the United States using the Illumina HiSeq 4000. The transcript abundances for each sample were estimated with StringTie (Pertea et al., 2015) and the Fragments per kilobase of transcript per million mapped reads (FPKM) (Mortazavi, Williams, McCue, Schaeffer, & Wold, 2008) value for gene and transcript level were calculated with R package Ballgown (Frazee et al., 2015).
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| Contributor(s) |
Gao Y, Sun T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 05, 2018 |
| Last update date |
Jul 05, 2019 |
| Contact name |
Yanxia Gao |
| E-mail(s) |
gaoyanxia0222@sjtu.edu.cn
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| Organization name |
Shanghai Jiaotong University
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| Street address |
No. 800, Dongchuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA479862 |
| SRA |
SRP152324 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116682_All_Differentially_Expressed_Genes.xlsx |
9.7 Mb |
(ftp)(http) |
XLSX |
| GSE116682_All_Differentially_Expressed_Transcripts.xlsx |
17.1 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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