Wiki » History » Version 3
Katie Lennard, 06/26/2019 01:03 PM
| 1 | 1 | Katie Lennard | # Wiki |
|---|---|---|---|
| 2 | |||
| 3 | # Sample processing details from Pieter de Waal |
||
| 4 | 'The Illumina® 16S metagenomics workflow will be used to analyze the three differently sourced milk types. Each sample will be analyzed in duplicate, producing a total number of six extracted libraries. A positive control will also be included in the analyses. The hypervariable V3 and V4 regions of the 16S ribosomal RNA gene (16S rRNA) will be amplified, using an Illumina® pre-designed primer pair. Barcoding for multiplexing of the samples will entail the use of the Nextera XT®-Index Kit.' |
||
| 5 | |||
| 6 | # Data expected |
||
| 7 | 'Data collection will take place from 01/03/2019 to 03/03/2019. The samples will be transported to CPGR on Monday, 04/03/2019. Results of the data analysis will be available within two weeks from then.' |
||
| 8 | |||
| 9 | # Bioinformatic analyses to be done |
||
| 10 | * Preprocessing of raw fastq files using the dada2 pipeline |
||
| 11 | * 'Alpha and beta diversity (Shannon diversity (H′) and Bray-Curtis dissimilarity index). Calculation of the relative abundance of each OTU per specimen. Fisher’s exact test for two-way tables. Construction of Log ratio biplots, dendograms and other illustrative (graphical) representation of data analysis.' |
||
| 12 | 2 | Katie Lennard | |
| 13 | 3 | Katie Lennard | # Raw data |
| 14 | Raw (.fastq) copied from CPGR flashdisk to ilifu 26/6/2019 |
||
| 15 | 2 | Katie Lennard | /ceph/cbio/users/katie/Levin/raw/ |