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Status |
Public on Oct 14, 2022 |
Title |
P11W0 |
Sample type |
SRA |
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Source name |
bacteria
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Organism |
human gut metagenome |
Characteristics |
biology sample: human fecal sample treatment: without treatment time: 0 weeks under low-FODMAP diet Sex: female cell type: bacteria
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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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.
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Submission date |
Oct 07, 2022 |
Last update date |
Oct 14, 2022 |
Contact name |
Nissan Yissachar |
E-mail(s) |
nissany1@gmail.com
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Organization name |
Bar-Ilan University
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Street address |
Bar-Ilan University
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City |
Ramat Gan |
ZIP/Postal code |
5290002 |
Country |
Israel |
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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 |
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Relations |
BioSample |
SAMN31208832 |
SRA |
SRX17828372 |
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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