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| Status |
Public on Nov 28, 2024 |
| Title |
IBA Subfornical Organ Replicate 3 |
| Sample type |
SRA |
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| Source name |
Subfornical organ
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| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
tissue: Subfornical organ
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| Growth protocol |
The brain was rapidly dissected and a vibratome (Leica VT1200) was used to cut 300-600 μm coronal slices. The subfornical organ was manually dissected out from the slices using 27G needles and placed immediately into RNA lysis buffer from the Quick-RNA Microprep Kit (Zymo, R1050).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissue using the Quick-RNA Microprep Kit (Zymo, R1050). RNA concentration and integrity number (RIN) were assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). RNA concentrations were in the range of ~8.5 - 25.8 ng/µL and RIN values were in the range of 6.8 – 9.1.
Sequencing libraries were prepared using the Kapa mRNA Hyper Prep kit (KAPA Biosystems, Wilmington, MA).
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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 |
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.39 (Bolger et al., 2014) with default parameters.
Filtered high-quality reads from all samples were aligned to Ictidomys tridecemlineatus reference genome using STAR aligner v2.7.7a with default parameters (Dobin et al., 2013).
Aligned reads were counted by the featureCounts module within the Subread package v2.0.1 with default parameters (Liao et al., 2014).
Processing, normalization, and statistical analysis of read counts was performed using the EdgeR v3.38.4 package in R v4.2.1 (Robinson et al., 2010)
Statistical analysis of differential expression of genes between groups was performed using the GLM approach and the quasi-likelihood F-test, as implemented in the EdgeR package.
Assembly: The SpeTri2.0 [GCA_000236235.1] reference genome and the gene annotation were obtained from the Broad Institute through the National Center for Biotechnology Information (Ictidomys tridecemlineatus; assembly SpeTri2.0; NCBI Ictidomys tridecemlineatus Annotation Release 102; all files accessed on 8/17/2020). Reference genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.fna.gz; Gene annotation: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/235/GCF_000236235.1_SpeTri2.0/GCF_000236235.1_SpeTri2.0_genomic.gff.gz; the gene annotation was filtered to include only protein-coding genes.
Supplementary files format and content: Processed data file in Excel format (.xlsx) contains normalized read counts, normalized mean read counts, P-values, adjusted FDR values, and fold change (log2) for statistical comparison of expression values between 2 groups.
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| Submission date |
Mar 28, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Madeleine Junkins |
| E-mail(s) |
[email protected]
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| Organization name |
Yale University
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| Department |
Cellular & Molecular Physiology; Neuroscience
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| Street address |
333 Cedar Street
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| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platform ID |
GPL30340 |
| Series (1) |
| GSE262723 |
Suppression of neurons in circumventricular organs enables months-long survival without water in thirteen-lined ground squirrels |
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| Relations |
| BioSample |
SAMN40648757 |
| SRA |
SRX24094117 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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