|
| Status |
Public on Aug 29, 2021 |
| Title |
small intestine, Con1 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine of minipig
|
| Organism |
Sus scrofa domesticus |
| Characteristics |
strain: Gottingen minipigs
genotype: wild type
age: 6 months
tissue: small intestine
treatment: control
|
| Treatment protocol |
Gottingen minipigs were irradiated with 15 Gy applied to the abdomen under a 60Co gamma-ray irradiation unit. IR+Pra group was treated with a twice daily oral dose of 40 mg/day pravastatin for 2 weeks. On day 14, the minipigs were euthanized and small intestine tissue was obtained for RNA sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Con-1
|
| Data processing |
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression_Profile.GCF_000003025.6_Sscrofa11.1.gene.txt (tab-delimited text file includes Read_Counts and FPKM values for each Sample)
|
| |
|
| Submission date |
Aug 26, 2021 |
| Last update date |
Aug 30, 2021 |
| Contact name |
Hyosun Jang |
| E-mail(s) |
hyosun327@gmail.com
|
| Phone |
+8229701302
|
| Organization name |
Korea Institute of Radiological & Medical Science
|
| Street address |
Nowongu Nowonro 75
|
| City |
Seoul |
| ZIP/Postal code |
01812 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL29562 |
| Series (1) |
| GSE182829 |
Analysis of Transcriptome in small intestine after radiation injury with treatment of pravastatin |
|
| Relations |
| BioSample |
SAMN20989788 |
| SRA |
SRX11916333 |
