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| Status |
Public on Apr 24, 2018 |
| Title |
WT_3D_1_1 |
| Sample type |
SRA |
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| Source name |
colon tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: colon
genotype: WT
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| Treatment protocol |
feed 3% DSS ad libitum for 3 days
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| Growth protocol |
6-8week BALB/c mice
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| Extracted molecule |
total RNA |
| Extraction protocol |
The proximal part of the intestine was collected and washed with ice-cold PBS with syringes. The luminal side of the intestine was scraped by a Cell Scraper to remove luminal content and mucus. The colon was cut into 2 mm pieces and further washed with cold PBS with gentle vortexing, total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke, then mapped to reference whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Mapped reads were count using RSEM v1.2.12, and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Apr 23, 2018 |
| Last update date |
Apr 24, 2018 |
| Contact name |
Yuli Lin |
| E-mail(s) |
yulilin@fudan.edu.cn
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| Organization name |
Fudan University
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| Street address |
No.130, Dong'an Road, Xuhui
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE113541 |
mRNA profiles of WT and STAT6-/- mice colon tissue |
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| Relations |
| BioSample |
SAMN08971313 |
| SRA |
SRX3988580 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3108813_WT_3D_1.txt.gz |
183.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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