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| Status |
Public on Apr 30, 2024 |
| Title |
Group-LHb-2 |
| Sample type |
SRA |
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| Source name |
brain lateral habenula
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain lateral habenula
strain: C57BL/6 mice
group: group-housed
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were obtained from LHb tissues of group-housed and socially isolated mice using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used for the construction of sequencing libraries, according to the manufacturer’s instructions.
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 NovaSeq 6000 |
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| Data processing |
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the Flexbar software (version 3.5.0), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Apr 03, 2022 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Sehyun Chae |
| E-mail(s) |
shchae@kbri.re.kr
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| Organization name |
Korea Brain Research Institute
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| Department |
Neurovascular Unit Research Group
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| Street address |
61, Cheomdan-ro, Dong-gu
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| City |
Daegu |
| ZIP/Postal code |
41062 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE200082 |
Acute social isolation alters synaptic plasticity in lateral habenula and social decision |
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| Relations |
| BioSample |
SAMN27279485 |
| SRA |
SRX14719305 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6008388_Group-LHb-2.txt.gz |
250.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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