Data · dataset · 2014
Panama bacterial phyllosphere sequences
Listed in DataCite
Bacterial 16S rRNA gene sequence data (chloroplast-excluding primers 799f/1115r) and metadata for bacterial communities sampled from plant leaf surfaces on Barro Colorado Island, Panama.
Description
Data collection procedures are described in the paper "Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest" by Kembel et al. (manuscript in press at PNAS). Multiple sets of files are included in this data archive: bacteria_phyllosphere_metadata.txt - a tab-delimited text file with information on barcode sequences and host species identity for each sample.
The columns of the text file include a sample identifier (SampleID), forward and reverse barcode sequences* (ForwardBarcodeSequence and ReverseBarcodeSequence), and the identity of the host plant species from which each sample was collected (HostSpecies).
Read the rest (1 more)
- note that in the raw sequence data, a combinatorial or dual-index barcoding approach was used to uniquely identify samples. The first 6bp of the barcode are on the forward read, and the final 6bp of the barcode are on the reverse read. The barcodes will need to be combined into a single 12bp construct prior to parsing into samples, or parsed with software capable of processing dual-indexed sequences. phyllobacteria.fastq.tgz.part-xx - raw sequence data in FASTQ format, produced by a sequencing run using Illumina HiSeq 150bp paired-end sequencing technology. Due to file size limitations, the original tar/gzip archives have been split into multiple parts. To recombine and uncompress the sequence files, the following command works in a Linux/Unix environment: cat phyllobacteria.fastq.tgz.part-* | tar xz
Links
Where it is published
- Repository landing page figshare.com/articles/dataset/Panama_bacterial_phyllosphere_sequences/928573 ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.928573 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.928573 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.928573 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Biological sciences · Computer and information sciences
- Inferred from text
- Sequencing 75% · Text 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.928573 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:biological-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:computer-and-information-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:text | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |