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| Status |
Public on Mar 06, 2020 |
| Title |
Wheat rhizosphere under decaying root rep2 |
| Sample type |
SRA |
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| Source name |
soil
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| Organism |
soil metagenome |
| Characteristics |
host plant: wheat
growing condition: with decaying root
replicate: 2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The total DNA were extracted using a PowerSoil DNA isolation kit (Mo Bio, Carlsbad, CA, USA) based on the manufacturer’s instructions.
DNA libraries were prepared for sequencing using standard Illumina HiSeq 2000 protocols
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
B2A
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| Data processing |
Library strategy: DNA metagenome
The sequenced reads were removed if they met any one of the following criteria: (1) with ≥ 20% low quality bases, (2) with adapter contamination (15 bases overlapped by reads and adapter with maximal 3 base mismatches allowed), (3) with N base (also removing paired reads), and (4) with low complexity (reads with 10 consecutive reads of the same base).
MEGAHIT was used to assemble all the clean reads with the “meta-large” parameters set up in the software.
Using the assembled contigs with a length of > 300 bp, gene prediction was carried out on MetaGeneMark software with default parameters
Using the CD-HIT software with 95% sequence identity, the redundant predicted metagenomic genes were removed to generate the non-redundant gene catalogue.
The clean reads for each sample were aligned to the non-redundant genes using SoapAligner software with 90% identity to generate the gene abundance table
Genome_build: FASTA file with gene sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include the number of matched reads for each non-redundant gene in each sample
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| Submission date |
Mar 05, 2020 |
| Last update date |
Mar 06, 2020 |
| Contact name |
YI ZHOU |
| E-mail(s) |
yi.zhou@adelaide.edu.au
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| Organization name |
The University of Adelaide
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| Street address |
Waite Campus
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| City |
Urrbrae |
| ZIP/Postal code |
5064 |
| Country |
Australia |
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| Platform ID |
GPL20780 |
| Series (1) |
| GSE146427 |
The preceding root system drives the rhizosphere microbiome |
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| Relations |
| BioSample |
SAMN14306094 |
| SRA |
SRX7855854 |
| 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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