|
| Status |
Public on Jan 10, 2019 |
| Title |
WT + SFB (IL004) |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Intestinal epithelial cells
age: 14 weeks
genotype: WT
treatment: +SFB
|
| Treatment protocol |
WT and IECΔCDC42 mice were colonized with segmented filamentous bacteria (SFB) and intestinal epithelial cells were isolated to performed RNAseq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For all samples we use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.
For all samples we use ribosomal depletion to remove rRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.
Intestinal epithelial cels were isolated 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
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth, an R package designed to compute transcript and gene-level differential expression from kallisto abundance files.
Genome_build: Mouse GRCm38
Supplementary_files_format_and_content: normalized counts
|
| |
|
| Submission date |
Jan 09, 2019 |
| Last update date |
Jan 10, 2019 |
| Contact name |
Leandro Pires Araujo |
| E-mail(s) |
lpa2111@cumc.columbia.edu
|
| Phone |
6466103421
|
| Organization name |
Columbia University
|
| Department |
Microbiology and Immunology
|
| Lab |
Ivanov Lab
|
| Street address |
701 W 168th St, 9th floor
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE124848 |
Directed endocytosis mediates immune communication between an epithelial commensal microbe and the host |
|
| Relations |
| BioSample |
SAMN10717843 |
| SRA |
SRX5232075 |
