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| Status |
Public on Jan 25, 2018 |
| Title |
PND 21-2 |
| Sample type |
SRA |
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| Source name |
MBH_21 days
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: sprague dawley (SD)
gender: female
age: 21 days
tissue: MBH (Medial Basal hypothalamus)
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| Extracted molecule |
total RNA |
| Extraction protocol |
MBH tissue was removed, flash frozen on dry ice, and RNA was harvested using Qiagen's RNeasy Mini Kit (Valencia, CA). Samples were bioanalyzed on a RNA 6000 Nano chip kit to check for integrity and concentration before sending it to OHSU's Massively Parallel Sequencing Shared Resource for library preparation and sequencing. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA depleted from ribosomal RNA for the construction of sequencing libraries.
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 HiSeq 2500 |
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| Description |
P21_2
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| Data processing |
Intial basecalling using Illumina RTA 1.18.64
Barcode and adapter sequence was removed using Trimmomatic v0.33 ILLUMINACLIP TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:10:34 HEADCROP:13
Alignment using Tophat2 v2.1 /Bowtie2 v2.2.4
Mapping to reads using featureCounts function of Rsubread R package to Ensembl Rn6.08.83 with countMultiMappingReads, allowMultiOverlap, useMetaFeatures TRUE
Differential expression and normalized read counts using edgeR GLM modeling and voom estimation with batch correction
Genome_build: Rattus norvegicus rn6
Supplementary_files_format_and_content: .xlsx file, log2 counts per million per gene
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| Submission date |
Jan 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hollis Wright |
| E-mail(s) |
wrighth@ohsu.edu
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| Organization name |
ONPRC/OHSU
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| Department |
DIvision of Neuroscience
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| Lab |
Ojeda
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| Street address |
505 NW 185th Avenue
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| City |
Beaverton |
| State/province |
OR |
| ZIP/Postal code |
97006-3448 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE94080 |
Genome wide identification of gene sets involved in the regulation of hypothalamic pubertal development |
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| Relations |
| BioSample |
SAMN06272687 |
| SRA |
SRX2518117 |
| 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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