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| Status |
Public on Apr 24, 2024 |
| Title |
DSS+miR-146a mimics treated, miR-146a-/- 5 |
| Sample type |
SRA |
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| Source name |
Colon
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| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
cell line: C57BL/6
genotype: miR-146a KO
treatment: DSS+miR-146a mimics
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from colon tissues following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
miR-146a KO5_DSS+mimics_FPKM
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| Data processing |
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Nov 09, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Changgeng Peng |
| E-mail(s) |
[email protected]
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| Organization name |
Tongji University
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| Department |
School of Medicine
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| Street address |
Siping Road 1239
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| City |
Yangpu |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE247433 |
MiR-146a alleviates inflammatory bowel disease in mice through systematical regulation of multiple genetic networks |
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| Relations |
| BioSample |
SAMN38194161 |
| SRA |
SRX22478075 |
| 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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