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| Status |
Public on Nov 12, 2021 |
| Title |
Control-2-2 |
| Sample type |
SRA |
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| Source name |
brain cells
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague dawley rats
Sex: male
tissue: anterior cingulate cortex
behavioral phenotype: Home cage control
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| Treatment protocol |
Animals underwent successive 90 min sessions of habituation (2 days of chamber familiarization in customized Skinner boxes (60x60x60 cm) and shaping-continuous reinforcement schedule training (variable days to reach 100 lever presses/session for 3+ days) prior to group testing. On the first day of group testing, the lever-pressing behavior rapidly plummeted in all rats (stalemate phase). The length of stalemate days varied between groups before a worker-parasite relationship emerged where one rat performed most of the lever presses, while the other two members consumed most of the food pellets. The criterion for worker-parasite phase was defined as > 200 lever presses by the worker rat, exceeding two parasites’ lever presses by > 150 for 3+ consecutive sessions.
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| Growth protocol |
Young-adult male Sprague-Dawley rats (~8–10 weeks old) were individually housed in a climate-controlled colony room. After one week of free access to food and water and habituation to handling, animals were placed on standard food restriction to gradually reach and maintain 80–85% normal weight. All tests were performed during the dark phase of a 12-h light/dark cycle
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| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were rapidly decapitated 18~19 h after the worker-parasite relationship transpired in group testing. Additional four animals not exposed to the Skinner box were sacrificed as home-cage controls. Brains were removed and coronal slices (2 mm) were fleshly dissected in a cold brain matrix. ACC were then microdissected, using a dissecting microscope and reference coordinates obtained from the Paxinos and Watson rat brain atlas. RNA was isolated with TriZol reagent (Invitrogen) and purified with RNeasy Micro Kits (Qiagen). All RNA samples were determined to have RIN values > 8.5 (BioAnalyzer, Agilent) for RNA-sequencing.
RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, CA). Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Subsequently, the library was sequenced using an Illumina NovaSeq sequencer (Illumina, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Cufflinks_fpkm_table.txt
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| Data processing |
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose qualityscores are less than 20 and reads whose average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Filtered reads were mapped to the mouse reference genome (Ensembl release 77) using the aligner Tophat
Gene expression level was measured with Cufflinks v2.1.1 (Trapnell C. et al, 2012) using the gene annotation database of Ensembl release 77.
Non-coding gene region was removed with -mask option. To improve the accuracy of measurement, multi-read-correction and fragbias-correct options were applied. '-max-bundle-frags' option was set to 10,000,000 to estimate the highly expressed genes.
All other options were set to default values. Differentially expressed genes were identified using Cuffdiff tool with default parameter setting with a significance of p-value < 0.05
Genome_build: version 77 of Rattus norvegicus reference genome Rnor_5.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each sample derived from Cufflinks.
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| Submission date |
Jul 01, 2020 |
| Last update date |
Nov 12, 2021 |
| Contact name |
JA WOOK KOO |
| E-mail(s) |
jawook.koo@gmail.com
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| Organization name |
Korea Brain Research Institute
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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 |
GPL25947 |
| Series (1) |
| GSE153649 |
Next-generation sequencing of anterior cingulate cortex neurons in a social problem setting in rats |
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| Relations |
| BioSample |
SAMN15418640 |
| SRA |
SRX8650251 |
| 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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