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Sample GSM3557104 Query DataSets for GSM3557104
Status Public on Jan 10, 2019
Title IECΔCDC42 +SFB (IL002)
Sample type SRA
 
Source name Intestinal epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Intestinal epithelial cells
age: 14 weeks
genotype: IEC{delta}CDC42
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 SAMN10717845
SRA SRX5232073

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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