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| Status |
Public on Jan 30, 2023 |
| Title |
RNA_PA_244 |
| Sample type |
SRA |
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| Source name |
Pancreas
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| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Pancreas
Sex: Female
breed: Beagle
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| Treatment protocol |
Three dogs in healthy condition were euthanized by intravenous administration of alfaxalone and KCl. Eleven common tissues (cerebrum [CR], cerebellum [CL], colon [CO], kidney [KI], liver [LI], lung [LU], mammary gland [MG], ovary [OV], pancreas [PA], spleen [SP] and stomach [ST]) were isolated from the three beagles. All tissues were rinsed with ice-cold PBS before being minced. Immediately after mincing, tissues were divided into 4 tubes based on the types of analysis, and frozen with liquid nitrogen
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| Growth protocol |
One male and two female beagles were kindly donated by Dr. Jong-Gu Kang from the College of Veterinary Medicine at Chungbuk National University.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each tissue using the RNeasy Mini plus kit (Qiagen, USA). Pulverization for sample homogenization was performed with liquid nitrogen prior to RNA isolation, according to the manufacturer's instruction. The RNA quality was assessed by analysis of 18S and 28S rRNA band integrity on a RNA 6000 Nano Kit (part # 5067-1511) using an Agilent Bioanalyzer (Agilent, USA).
Library was prepared using TruSeq Stranded Total RNA sample preparation kit (RS-122-9007) and sequenced using HiSeq 2500 or NovaSeq 6000 (Illumina) by Theragen Inc (Korea).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Data were filtered and trimmed using Trimmomatic
The sequenced reads aligned to the canine reference genome (canFam3.1 assembly) using STAR
TIN values were calculated using RSeQC
Gene expression value were calculated usin RSEM
Assembly: canFam3.1
Supplementary files format and content: bigWig
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| Submission date |
May 16, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Je-Yoel Cho |
| E-mail(s) |
jeycho@snu.ac.kr
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| Organization name |
Seoul National University
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| Department |
Biochemistry
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| Street address |
1, Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL20988 |
| Series (2) |
| GSE203106 |
Integrated mapping of the dog epigenome (RNA-seq) |
| GSE203107 |
Integrated mapping of the dog epigenome |
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| Relations |
| BioSample |
SAMN28450491 |
| SRA |
SRX15289474 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6156912_RNA_PA_244.bw |
78.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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