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| Status |
Public on Aug 21, 2020 |
| Title |
Model_2 [ncRNA] |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Rattus norvegicus |
| Characteristics |
sample type: bleomycin-induced pulmonary fibrosis model
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, USA).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Rattus_norvegicus Ensembl relaese-94
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms
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| Submission date |
Jun 25, 2020 |
| Last update date |
Aug 21, 2020 |
| Contact name |
Xue Liu |
| E-mail(s) |
liuxue0081985@126.com
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| Organization name |
The Affiliated Hospital of Shandong University of TCM
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| Street address |
Wenhua West Road
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| City |
JiNan |
| State/province |
ShangDong |
| ZIP/Postal code |
250014 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE153278 |
Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [ncRNA-seq] |
| GSE153296 |
Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis |
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| Relations |
| BioSample |
SAMN15373833 |
| SRA |
SRX8620580 |
| 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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