|
| Status |
Public on Sep 24, 2015 |
| Title |
RNAseq of SI_GF1 |
| Sample type |
SRA |
| |
|
| Source name |
Small intestinal epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: IQI
colonization: GF
cell type: small intestinal epithelial cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent
RNA library preparation was performed using a NEBNext Ultra RNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
S02345
|
| 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 mm9 whole genome using bowtie v0.12.7 and Tophat v1.4.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Koji Atarashi |
| E-mail(s) |
kojiatarashi@keio.jp
|
| Organization name |
Keio University School of Medicine
|
| Department |
Dept of Microbiology and Immunology
|
| Street address |
35 Shinanomachi
|
| City |
Shinjuku-ku |
| State/province |
TOKYO |
| ZIP/Postal code |
1608582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE71734 |
RNA-seq data of intestinal epithelial cells |
|
| Relations |
| BioSample |
SAMN03956946 |
| SRA |
SRX1133347 |
