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| Status |
Public on Aug 13, 2023 |
| Title |
SA2 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
colonic epithelial tissue
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| Organism |
Capra hircus |
| Characteristics |
tissue: colonic epithelial tissue
treatment: infusion of sodium propionate
time: Day 13
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for transcriptomic sequencing
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| Data processing |
Briefly, the Fastp software (v0.23.1) was firstly used to perform quality control on the raw data and obtain clean data. Then, the HISAT2 software (v2.1.0) was used to align the obtained clean data referred to the latest reference genome . After that, the Samtools software (v.1.10) was used to sort and convert the SAM files to BAM format, and finally, the Stringtie software (v2.2.1) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: Capra hircus reference genome ARS1.2
Supplementary files format and content: raw counts for each sample
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| Submission date |
May 09, 2023 |
| Last update date |
Aug 13, 2023 |
| Contact name |
Yongkang Zhen |
| E-mail(s) |
dx120220164@stu.yzu.edu.cn
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| Phone |
15062800765
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| Organization name |
Yangzhou University
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| Street address |
Yangzhou University
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| City |
Yangzhou |
| State/province |
— Please Select — |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL32967 |
| Series (2) |
| GSE232035 |
RNA-Seq data of colonic epithelial tissue in goats infusion of three short-chain fatty acids |
| GSE232037 |
RNA-Seq and 16S rRNA seq data of cecal digesta in goats infusion of three short-chain fatty acids |
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| Relations |
| BioSample |
SAMN35007456 |
| SRA |
SRX20263756 |
| 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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