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Sample GSM6620477 Query DataSets for GSM6620477
Status Public on Oct 14, 2022
Title P10W0
Sample type SRA
 
Source name bacteria
Organism human gut metagenome
Characteristics biology sample: human fecal sample
treatment: without treatment
time: 0 weeks under low-FODMAP diet
Sex: male
cell type: bacteria
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from all fecal samples using the Mobio PowerSoil DNA extraction kit, as described by the manufacturer (MoBio, Carlsbad, CA). DNA concentrations were measured by nanodrop, and 20 ng of DNA was used for 16S library preparation
Library preparation and sequencing were performed by HyLabs Ltd (Israel), as follows: 16S libraries for Illumina sequencing were prepared using a two-step PCR protocol. In the first PCR, primers containing tails were used to amplify the V4 region of the 16S rRNA gene. The Access Array primers for Illumina (Fluidigm) were used in the second PCR to add the adaptor and index sequences to each sample. After the second PCR, the reactions were cleaned using Kapa Pure beads (Roche) to remove unincorporated primers and any primer-dimer produced. The concentration of each library was measured by Qubit (Life Technologies) using the Denovix ds DNA HS assay (Deonvix) and then the samples were combined in equal amounts to a single pool.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Data processing Gut microbiome composition was analyzed by 16S rRNA gene sequencing of IBS patients’ fecal samples collected at 0, 3 and 6 weeks under low-FODMAP diet.
 
Submission date Oct 07, 2022
Last update date Oct 14, 2022
Contact name Nissan Yissachar
E-mail(s) nissany1@gmail.com
Organization name Bar-Ilan University
Street address Bar-Ilan University
City Ramat Gan
ZIP/Postal code 5290002
Country Israel
 
Platform ID GPL29483
Series (2)
GSE215047 Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome (16S)
GSE215050 Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome
Relations
BioSample SAMN31208835
SRA SRX17828369

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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