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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 27, 2020 |
| Title |
Stool [34] |
| Sample type |
SRA |
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| Source name |
Stool
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| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
genotype: Wild type
cell type: T cells depleted bone marrow cells only
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| Treatment protocol |
Given WT T cells depleted bone marrow cells only
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| Extracted molecule |
total RNA |
| Extraction protocol |
Microbial DNAs from 1-3 mg of mouse fecal samples were extracted and purified according to the manufacturer’s protocol of EXT3-16S DNA Purification and PCR Amplification Kit of Shoreline Biome (Farmington, CT), and the extended (~2,500 bp) region, which contains 16S rRNA gene, the adjacent Internally Transcribed Spacer (ITS) and part of the 23S gene, was amplified using barcoded primer sets in the same kit.
To construct the SMRTbell libraries, all reagents were provided by PacBio (Menlo Park, CA) SMRTbell Template Prep Kit 1.0. Equal molar quantities of the amplicons were pooled. According to a PacBio standard protocol (Amplicon template preparation and sequencing) the damage of the DNA templates was repaired and their ends were blunted. After ligating adapters, the failed libraries were degraded by treating exonucleases. To load the libraries onto Sequel, the polymerase complexes were produced and the sample plate containing the final loading dilution was loaded on the machine.
Mutiplexing EXT3-16S DNA libraries
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Sequel |
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| Description |
16S rRNA
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| Data processing |
The primary analyses, including real-time signal processing and base calling were processed by a built-in PacBio Blade Center through Sequel ICS, and result stream directly to SMRT Link (v8.0.0.80529).
The CCS reads (> 5 Minimum Number of Passes and 0.99 Minimum Predicted Accuracy) were produced by the Circular Consensus Sequences (CCS) module in SMRT Link (v8.0.0.80529).
The demultiplexing and the taxonomic classification analysis of the CCS reads were carried out using SBanalyzer (v2.4-2) of Shoreline Biome (Farmington, CT) based on Athena V2 database.
Genome_build: Athena V2
Supplementary_files_format_and_content: The Taxonomy.csv file contains the processed data (taxonomic classifications from the CCS raw reads).
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| Submission date |
Oct 05, 2020 |
| Last update date |
Dec 27, 2020 |
| Contact name |
Defu Zeng |
| E-mail(s) |
dzeng@coh.org
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| Phone |
626-218-3587
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| Organization name |
The Beckman Reseach Institute
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| Department |
Immunology & Theragnostics
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| Lab |
Defu Zeng Lab
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| Street address |
1500 East Duarte Road
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| City |
Duarte |
| State/province |
California |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL24198 |
| Series (2) |
| GSE159031 |
IL-22-dependent dysbiosis and mononuclear phagocyte depletion contribute to steroid-resistant gut graft-versus-host disease in mice I |
| GSE159419 |
IL-22-dependent dysbiosis and mononuclear phagocyte depletion contribute to steroid-resistant gut graft-versus-host disease in mice |
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| Relations |
| BioSample |
SAMN16367226 |
| SRA |
SRX9244861 |
| 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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