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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 10, 2020 |
| Title |
sample S04 CS status C. scindens (ATCC(R) 35704) |
| Sample type |
SRA |
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| Source name |
Granulocyte macrophage progenitors
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| Organism |
Mus musculus |
| Characteristics |
agent: C. scindens (ATCC(R) 35704)
strain: CBA/J
Sex: male
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| Treatment protocol |
CBA/J mice were colonized with bile acid 7?-dehydroxylating bacteria C. scindens (ATCC(R) 35704) over three weeks prior to intracecal infection with E. histolytica. Mice were gavaged with 100ul of overnight culture at an optical density of 1.4 at 600nm or media control (BHI, Anerobe Systems, AS-872) once per week.
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| Growth protocol |
Five week old male CBA/J mice (Jackson Laboratories or RAG 1 KO mice (Jackson Laboratories) were housed in a specific pathogen?free facility in micro isolator cages and provided autoclaved food (Lab diet 5010) and water ad libitum. Specific pathogen free status was monitored quarterly. A sentinel mouse was removed from each room and was humanely euthanized for serologic evaluation, examination of pelage for fur mites, and examination of cecal contents for pinworms. The serologic assays, conducted in-house using CRL reagents, are MHV, EDIM, GD-7, MVM, MPV, and MNV, (Sendai, PVM, RPV/ KRV/H-1, M. pulmonis). In the final quarter, a comprehensive serology was performed which included the above agents plus K-virus, MCMV, MTV, LCM, Ectromelia, Polyomavirus, Reovirus-3, and mouse adenoviruses (K87 and FL). All procedures were approved by the Institutional Animal Care and Use Committee of the University of Virginia. All experiments were performed according to provisions of the USA Animal Welfare Act of 1996 (Public Law 89.544).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from approximately 17,000 sorted GMPs utilizing the Qiagen RNeasy Micro Kit.
Ribosomal reduction was performed to concentrate for mRNA. Directional cDNA libraries were generated and samples sequenced in multiplex (50PE reads) using the Illumina HiSeq v4 platform. For library prep, the NEBNext(R) Ultra? Directional RNA Library Prep Kit for Illumina(R) and NEBNext(R) rRNA Depletion Kit (Human/Mouse/Rat) and alternate protocol for low yield RNA and 15 PCR cycles of amplification was utilized. For sequencing, libraries were sequenced with the NGS NextSeq kit - 150 cycle High Output Kit, paired end 75x75 bp read.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
total RNA-seq from sample S04 CS status C. scindens (ATCC(R) 35704) Mus musculus
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| Data processing |
Transcript-level quantitation with Salmon
Gene level summarization with txImport
Normalization with DESeq2
Differential expression with DESeq2
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: normalized gene level counts for GRCm38 genes
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| Submission date |
Oct 18, 2018 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Stephen Turner |
| Organization name |
Signature Science, LLC
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| Street address |
1670 Discovery Drive
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22911 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE121503 |
Gut microbiome communication with the bone marrow regulates intestinal inflammation and susceptibility to amebiasis. |
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| Relations |
| BioSample |
SAMN10258857 |
| SRA |
SRX4905907 |
| 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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