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Status |
Public on Sep 15, 2020 |
Title |
545CFA19 |
Sample type |
SRA |
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Source name |
CFA_19d_mouse fecal matter
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 body weight (grams): 18.4 eae clinical score: 0 immunization: CFA day (relative to immunization): 19 molecule subtype: 16S Amplicon
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Treatment protocol |
Each group recieved different treatments: naïve mice recieved no treatment, EAE (MOG+CFA) mice were immunized subcutaneously with 50 μg of myelin oligodendrocyte glycoprotein peptide 35–55 (MOG35–55) (CSBIO #CS0681) emulsified at a 1:1 ratio in Complete Freud’s Adjuvant (Sigma Aldrich #F5881). On days 0 and 2, 250 ng of pertussis toxin (List Biologicals #180) was administered intraperitoneally. CFA imce recieved only the equivalent dose of Complete Freud’s Adjuvant.
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Growth protocol |
Female C57BL/6 mice were maintained on a 12 hours light/dark cycle with lights on at 7am and provided with standard food and water ad libitum. Mice were housed at 2-3 per cage and experimental treatment was assigned randomly to each cage.
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Extracted molecule |
total RNA |
Extraction protocol |
Fecal samples were collected from live mice restrained with a tail scruff. DNA for 16S amplification was extracted with a phenol-chloroform method: Fecal pellets were placed in 2 mL tubes containing 200 μL silica-zirconia beads (0.1 mm). The tubes were filled with 750 μL extraction buffer, 200 μL 20% SDS and 750 μL phenol-chloroform-isoamyl alcohol (25:24:1). After disruption, the aqueous phase was separated by centrifugation and cleaned up with two washes of chloroform-isoamyl alcohol (24:1). The DNA was precipitated and resuspended in 10 mM Tris solution. The V3-V4 region of the 16S rRNA gene was amplified for 25 cycles using specific primers with adapter overhangs as per the Illumina library preparation guide (Forward Primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, Reverse Primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC). Following purification of the PCR products, individual indexes were added to the amplicons by PCR. The amplicons were purified, pooled in equal quantities, and then sequenced on the Illumina MiSeq platform. V3-V4 16S-seq
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Description |
545CFA19_S57_L001
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Data processing |
Demultiplexed FASTQ files were processed with the Dada2 v1.12.1 function "filterAndTrim": truncLen = c(300,250), maxN = 0, maxEE = c(10,10), truncQ = 2, rm.phix = TRUE, compress = TRUE, multithread = TRUE Error learning with Dada2 v1.12.1 "learnErrors" for R1 and R2 reads: multithread = TRUE, Dereplication with "derepFastq": verbose = TRUE Amplicon Sequence Variant Identification with Dada2 v1.12.1 "dada" from learned error rates and dereplicated FASTQ reads: multithread = TRUE Read pair merging with Dada2 v1.12.1 "mergePairs": verbose = TRUE Chimera identification and removal with Dada2 v1.12.1 "removeBimeraDenovo": nethod = "consensus", multithread = TRUE, verbose = TRUE Taxonomy assignment with Dada2 v1.12.1 "assignTaxonomy": multithread = TRUE Genome_build: Taxonomy was assigned manually with input from the following 16S reference databases: Silva v132, Greengenes v13_8_set_97, GTDB bac-arc_ssu_r86, and RefSeq RDB16S v2_May2018 Supplementary_files_format_and_content: comma separated files (.csv) containing: 1. ASV abundances per sample, 2. Taxonomy of each ASV, and 3. Sample parameter data and Identification
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Submission date |
Jun 23, 2020 |
Last update date |
Sep 15, 2020 |
Contact name |
David Michael Johanson |
E-mail(s) |
dmj6ab@virginia.edu
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Phone |
3307327182
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Organization name |
UVa School of Medicine
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Department |
Department of Neuroscience
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Lab |
UVa Neuroscience Bioinformatics
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Street address |
200 Jeanette Lancaster Way
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City |
Charlottesville |
State/province |
VA |
ZIP/Postal code |
22903 |
Country |
USA |
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Platform ID |
GPL16417 |
Series (1) |
GSE153118 |
Experimental Autoimmune Encephalomyelitis is Associated with Changes of the Microbiota Composition in the Gastrointestinal Tract |
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Relations |
BioSample |
SAMN15353865 |
SRA |
SRX8604578 |
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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