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Sample GSM3165063 Query DataSets for GSM3165063
Status Public on Aug 07, 2018
Title 2C-WT-2-LPS
Sample type SRA
 
Source name Ileum
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Ileum
genotype: WT
stress: LPS-challenge
Extracted molecule total RNA
Extraction protocol For transcriptome (RNASeq/RefSeq) analysis , ileum from each WT, Casp8–/–Ripk3–/– and Casp11-negative mouse (5 male mice per group) harvested at 1.5 hpc was placed in RNAlater (Thermo-Fisher) at 4C. 24 h post-harvest, intestines were cleaned with cold RNAlater and mucus was scraped, homogenized and pelleted as described for immunoblot analysis. RNA isolation and further steps for transcriptome analysis were carried out as described (Sandler et al., 2014) in the NHP Genomics Core, Yerkes National Primate Research Center. Briefly, total RNA was isolated from mucus pellet for each sample using RNeasy Micro and RNA integrity was tested using Agilent Bioanalyzer capillary electrophoresis.
cDNA libraries were prepared using Illumina Stranded RNATruSeq kits and barcoded as well as sequenced on an Illumina HiSeq 3000. Five million 150-base pair mapping reads were obtained per sample, with >90% reads having Q-Scores of >30 (>99.9% estimated accuracy for 150 base reads).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the mouse (GRCm38.p3) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCm38.p3 from ENCODE (GRCm38.p3.genome.fa, gencode.vM3.annotation.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
 
Submission date May 30, 2018
Last update date Aug 07, 2018
Contact name Gregory K Tharp
E-mail(s) gktharp@emory.edu
Phone 404-727-7797
Organization name Yerkes National Primate Research Center
Department Developmental and Cognitive Neuroscience
Lab Genomics Core
Street address 954 Gatewood Dr
City Atlanta
State/province GA
ZIP/Postal code 30329-4208
Country USA
 
Platform ID GPL21493
Series (1)
GSE115094 Casp8- and Casp11-dependent gene expression in ileal mucosa of LPS-challenged male mice
Relations
BioSample SAMN09281540
SRA SRX4140993

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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