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| Status |
Public on Jun 13, 2023 |
| Title |
E10-28 |
| Sample type |
SRA |
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| Source name |
Jejunum
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Jejunum
treatment: Control
diet supplementation: Xylose-free (0percent)
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| Treatment protocol |
Two dietary treatments were evaluated using different concentrations of xylose: a semi-purified xylose-free diet (CTL) and the same diet with 8% D-xylose (DuPont Nutrition & Health, Copenhagen, Denmark)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified from jejunum mucosa, kidney cortex, and liver tissues using the Qiagen RNeasy Plus Mini Kit (Germantown, MD, USA) per the manufacturer’s instructions. For the longissimus dorsi muscle samples, the Qiagen RNeasy Fibrous Tissues Mini Kit (Germantown, MD, USA) was utilized for total RNA isolation and purification per the manufacturer’s instructions.
RNA libraries were constructed using 3’ mRNA-seq QuantSeq technology (Lexicogen, 194 Greenland, NH).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Adapter and low-quality bases were removed using the bbduk.sh program in BBtools software
Reads less than 20 bases and quality score (Phred + 33) ≥ 20 were filtered out
Reads were aligned against the reference genome (Suscrofa11.1) using STAR and the RNA quantification (Counts) using FeatureCounts
Assembly: Pig/Suscrofa11.1
Supplementary files format and content: tab-delimited text files raw counts values for each Sample
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| Submission date |
May 22, 2023 |
| Last update date |
Jun 13, 2023 |
| Contact name |
James Koltes |
| Organization name |
Iowa State University
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| Department |
Department of Animal Science
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| Street address |
1221 Kildee Hall
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| City |
Ames |
| State/province |
Iowa |
| ZIP/Postal code |
50011-3150 |
| Country |
USA |
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| Platform ID |
GPL24486 |
| Series (1) |
| GSE233123 |
Dietary intake of xylose impacts the transcriptome and proteome of tissues involved in xylose metabolism in swine |
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| Relations |
| BioSample |
SAMN35308672 |
| SRA |
SRX20465497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7401734_1-C12-77_S56_L007_R1_001.counts.htseq.txt.gz |
92.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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