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| Status |
Public on Jun 25, 2021 |
| Title |
CTL2 (RNA-Seq) |
| Sample type |
SRA |
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| Source name |
Colonic epithelia
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: colon
gender: male
treatment: control rats
cell type: Colonic epithelia
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).Paired-end libraries were synthesized by using the TruSeq®RNA Sample Preparation Kit (Illumina, USA) following TruSeq®RNA Sample Preparation Guide.
Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq X10(Illumina, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Tophat v2.0.9 to map the cleaned reads to the rat Rnor_6.0.95 reference genome with two mismatches.
After genome mapping, Cufflinks v2.1.1 wasrun with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) [3,4]. The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: Rnor_6.0.95
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and raw gene counts for each Sample
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| Submission date |
Oct 13, 2020 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Ruiqiang Yan |
| E-mail(s) |
ruiqiang_yan@shbio.com
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| Organization name |
Jinan University
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| Street address |
黄埔大道西601号
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| City |
guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE159438 |
MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats [RNA-Seq] |
| GSE159440 |
MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats |
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| Relations |
| BioSample |
SAMN16427735 |
| SRA |
SRX9285459 |
| 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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