GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4634552 Query DataSets for GSM4634552
Status Public on Sep 15, 2020
Title H2O Control 1
Sample type SRA
Source name 16S sequencing control with water only
Organism blank sample
Characteristics molecule subtype: 16S Amplicon
sample type: 16S sequencing control with water only
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.
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.
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
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
Description H2O-1_S1_L001
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
Submission date Jun 23, 2020
Last update date Sep 15, 2020
Contact name David Michael Johanson
Phone 3307327182
Organization name UVa School of Medicine
Department Department of Neuroscience
Lab UVa Neuroscience Bioinformatics
Street address 200 Jeanette Lancaster Way
City Charlottesville
State/province VA
ZIP/Postal code 22903
Country USA
Platform ID GPL27039
Series (1)
GSE153118 Experimental Autoimmune Encephalomyelitis is Associated with Changes of the Microbiota Composition in the Gastrointestinal Tract
BioSample SAMN15353793
SRA SRX8604591

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap