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| Status |
Public on May 26, 2024 |
| Title |
vehicle+IAA rep1 |
| Sample type |
SRA |
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| Source name |
colon
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| Organism |
Mus musculus |
| Characteristics |
tissue: colon
strain: C57BL/6
cell type: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Colon tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
AD_1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Dec 12, 2023 |
| Last update date |
May 26, 2024 |
| Contact name |
Mengfan Li |
| E-mail(s) |
mengfannn@tmu.edu.cn
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| Phone |
18838980065
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| Organization name |
Tianjin Medical University General Hospital
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| Street address |
154 Anshan Road, Heping District, Tianjin
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| City |
Tianjin |
| ZIP/Postal code |
300000 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE249996 |
Gut Microbiota Metabolite Indole-3-Acetic Acid Maintains Intestinal Epithelial Homeostasis Through Mucin Sulfation |
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| Relations |
| BioSample |
SAMN38789922 |
| SRA |
SRX22866931 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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