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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 07, 2018 |
| Title |
5C-WT-5-LPS |
| Sample type |
SRA |
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| Source name |
Ileum
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Ileum
genotype: WT
stress: LPS-challenge
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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).
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| Submission date |
May 30, 2018 |
| Last update date |
Aug 07, 2018 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
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| Phone |
404-727-7797
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| Organization name |
Yerkes National Primate Research Center
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| Department |
Developmental and Cognitive Neuroscience
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| Lab |
Genomics Core
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| Street address |
954 Gatewood Dr
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE115094 |
Casp8- and Casp11-dependent gene expression in ileal mucosa of LPS-challenged male mice |
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| Relations |
| BioSample |
SAMN09281537 |
| SRA |
SRX4140996 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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