Bovine milk microbiome sequence data
dataset
posted on 2019-08-02, 06:45 authored by Keith SavinKeith Savin, Jody Zawadzki, Jianghui Wang, Martin J Auldist, Doris Ram, Simone Rochfort, Benjamin G CocksMiSeq sequence data plus additional files of processed data.
Paired end (PE) DNA sequence files from MiSeq sequencing of 16s rRNA gene V4 PCR amplicons from 21 dairy cow milk samples.
The filenames ending in qf.fastq.gz are fastq files that have been quality filtered using Trimmomatic.
Files beginning AEEYU_PCR-Neg contain sequence from PCR and MiSeq sequence steps where water was used in place of microbial DNA from milk (all other ingredients the same as +DNA samples).
Sample identifiers in the fastq filenames refer to these cows:
ID cow
msb001334 c400
msb001335 c604
msb001336 c644
msb001337 c659
msb001338 c666
msb001339 c675
msb001340 c690
msb001342 c774
msb001343 c807
msb001344 c854
msb001345 c1029
msb001347 c5601
msb001348 c5621
msb001349 c6808
msb001350 c8192
msb001351 c7905
msb001353 c8421
msb001354 c9501
msb001355 c9504
msb001356 c9510
msb001357 c9536
Also a file of the unique (dereplicated) 16s v4 sequences closely related to Faecalibacterium, together with the list and membership of swarm clusters of those sequences and a fasta file of the swarm seeds. Also 2 sample x abundance tables (space delimited) for cows vs microbial families and cows vs Greengenes OTU.
