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Sample GSM4817904 Query DataSets for GSM4817904
Status Public on Dec 27, 2020
Title Stool [8]
Sample type SRA
Source name Stool
Organism Mus musculus
Characteristics strain: BALB/c
genotype: Wild type
cell type: IL-22-/- donor T cells
agent: Dexamathosone (5mg/kg) at days 3
Treatment protocol Given IL-22-/- donor T cells and treated Dexamathosone (5mg/kg) at days 3,10, 15 and 20 after bone marrow transplantation
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
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Sequel
Description 16S rRNA
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).
Submission date Oct 05, 2020
Last update date Dec 27, 2020
Contact name Defu Zeng
Phone 626-218-3587
Organization name The Beckman Reseach Institute
Department Immunology & Theragnostics
Lab Defu Zeng Lab
Street address 1500 East Duarte Road
City Duarte
State/province California
ZIP/Postal code 91010
Country USA
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
BioSample SAMN16367249
SRA SRX9244844

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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