Data supporting the 1000 plant (1KP) transcriptomes initiative
Dataset type: Transcriptomic
Data released on October 23, 2019
Carpenter EJ; Matasci N; Ayyampalayam S; Wu S; Sun J; Yu J; Jimenez Vieira FR; Bowler C; Dorrell RG; Gitzendanner MA; Li L; Du W; Ullrich K; Wickett NJ; Barkmann TJ; Barker MS; Leebens-Mack JH; Wong GK (2019): Data supporting the 1000 plant (1KP) transcriptomes initiative GigaScience Database. https://doi.org/10.5524/100627
The 1000 Plants (1KP) transcriptomes initiative explored the genetic diversity of green plants (Viridiplantae) by sequencing RNA from 1,342 samples representing 1,173 species. All of the analyses done for the 1KP capstone, and previous studies on subsets of these data, are based on a series of de novo transcriptome assemblies and related outputs that will be described in the accompanying GigaScience publication. We also describe assessments of the data quality and an analysis to remove cross-contamination between the samples. These data will be useful to researchers with interests in specific gene families, either across the green plant tree of life or in more focused lineages.
Additional details
Read the peer-reviewed publication(s):
- Carpenter, E. J., Matasci, N., Ayyampalayam, S., Wu, S., Sun, J., Yu, J., Jimenez Vieira, F. R., Bowler, C., Dorrell, R. G., Gitzendanner, M. A., Li, L., Du, W., K. Ullrich, K., Wickett, N. J., Barkmann, T. J., Barker, M. S., Leebens-Mack, J. H., & Wong, G. K.-S. (2019). Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). GigaScience, 8(10). https://doi.org/10.1093/gigascience/giz126 (PubMed:31644802)
Related datasets:
doi:10.5524/100627 IsPreviousVersionOf doi:10.5524/100910(It is a more recent version of this dataset)
Accessions (data included in GigaDB):
BioProject: PRJEB4921
BioProject: PRJEB8056
BioProject: PRJEB21674
STUDY: SRP012845
BioProject: PRJNA163187
Click on a table column to sort the results.
Table Settings| Sample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
|---|---|---|---|---|---|
| URDJ | Amborella trichopoda | Description:RNA extracted from leaves of Amborella... Analyte type:RNA Tissue:leaf [BTO:0000713] ... |
13333 | ||
| WTKZ | Nuphar advena | Description:RNA extracted from young leaves of Nup... Analyte type:RNA Tissue:juvenile leaf [BTO:0003147] ... |
77108 | ||
| ROAP | Illicium parviflorum | Description:RNA extracted from leaves of Illicium ... Analyte type:RNA Tissue:leaf [BTO:0000713] ... |
13099 | ||
| VZCI | Florida anisetree | Illicium floridanum | Description:RNA extracted from young leaves of Ill... Analyte type:RNA Tissue:juvenile leaf [BTO:0003147] ... |
13098 | |
| NWMY | Kadsura heteroclita | Description:RNA extracted from leaves of Kadsura h... Analyte type:RNA Tissue:leaf [BTO:0000713] ... |
124781 | ||
| FZJL | Austrobaileya scandens | Sample storage condition:RNA extract Description:RNA extracted from young shoot of Aust... Analyte type:RNA ... |
13351 | ||
| NPND | hornwort | Ceratophyllum demersum | Description:RNA extracted from leaves of Ceratophy... Analyte type:RNA Tissue:leaf [BTO:0000713] ... |
4428 | |
| DDEV | barbasco | Canella winterana | Description:RNA extracted from young leaves of Can... Analyte type:RNA Tissue:juvenile leaf [BTO:0003147] ... |
3426 | |
| IFCJ | barbasco | Canella winterana | Description:RNA extracted from young leaves of Can... Analyte type:RNA Tissue:juvenile leaf [BTO:0003147] ... |
3426 | |
| WKSU | Drimys winteri | Alternative accession-SRA Study:ERP023948 Alternative accession-BioSample:SAMEA104170167 Specimen voucher:Soltis and Miles 2843 ... |
3419 |
Click on a table column to sort the results.
Table Settings| File Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
|---|---|---|---|---|---|---|---|---|
| Readme | TEXT | 2.60 kB | 2019-07-15 | |||||
| Clean and contaminant FASTA sequence files for each library | Mixed archive | GZIP | 5.93 GB | 2019-07-15 | MD5 checksum: 05534e4a2d055ccc0d6ebdd48f332daa |
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| Lists whether the sample is overall judged to be validated by the the SILVA based SSU check, i.e. contains the expected 18S sequence, and whether the sample has alignments to any other plant sequences (described as worrisome contamination). | Tabular data | CSV | 56.94 kB | 2019-07-15 | MD5 checksum: a1935744d0b756e18e8bc6407ff5a6fe |
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| Lists each scaffold identified as being an 18S sequence, and which reference sequence it matched against. | Tabular data | CSV | 686.35 kB | 2019-07-15 | MD5 checksum: c7aa46a1a2e981a7a05549fc5bf2aca1 |
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| Listing of the detected contaminant scaffolds and the corresponding original source scaffold | Tabular data | CSV | 5.29 MB | 2019-07-15 | MD5 checksum: 85c140a7d4eb44192449dbc57bb2415d |
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| Lists summary statistics of the prevalence of the apparent contaminants in each sample | Tabular data | CSV | 175.87 kB | 2019-07-15 | MD5 checksum: a2e4f303b21a0be9bb3eb18313b85687 |
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| List of taxonomically close sample pairs which were not compared | Tabular data | CSV | 1.01 MB | 2019-07-15 | MD5 checksum: 3fb48df5f4a92d75b4c611cf21bb31d4 |
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| Corresponding ENA/NCBI references for the source read sequences. | Tabular data | CSV | 556.41 kB | 2019-07-15 | MD5 checksum: 57fc7ba60dc638c755531ef9a06aea1c |
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| Tables with list of samples/assemblies. | Tabular data | CSV | 114.06 kB | 2019-07-15 | MD5 checksum: fbe3cde9a3f1bb3e21d778bd5960f3ab |
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| The SOAPdenovo-Trans assemblies of the sequence reads | Transcriptome sequence | FASTA | 7.61 MB | 2019-08-06 | MD5 checksum: 46da8d45af68ee9519fdd0ff9e61192f |
| Funding body | Awardee | Award ID | Comments |
|---|---|---|---|
| Alberta Ministry of Advanced Education | GKS Wong | RES0010334 | Alberta Innovates - Technology Futures |
| The National Key Research and Development Program of China | |||
| The Ministry of Science and Technology of the People's Republic of China | 2015BAD04B01/2015BAD04B03 | ||
| The Ministry of Science and Technology of the People's Republic of China | 2011DQ782025 | State Key Laboratory of Agricultural Genomics | |
| Guangdong Province | 2011A091000047 | Key Laboratory of core collection of crop genetic resources research and application | |
| Shenzhen Municipal Government of China | CXZZ20140421112021913/ JCYJ20150529150409546/JCYJ20150529150505656 | ||
| National Science Foundation | DBI-1265383 | iPlant Collaborative (CyVerse) | |
| National Science Foundation Grants | CWd | IOS 0922742 | |
| National Science Foundation Grants | MSB | IOS-1339156 | |
| National Science Foundation Grants | JL-M | DEB 0830009 | |
| National Science Foundation Grants | SWG | EF-0629817 | |
| National Science Foundation Grants | MSB | EF-1550838 | |
| National Science Foundation Grants | TW and JL-M) | DEB 0733029 | |
| National Science Foundation Grants | TW | DBI1062335 | |
| National Institutes of Health Grant | TMK | 1R01DA025197 | |
| Natural Sciences and Engineering Research Council of Canada | SWG | Discovery grant |
Protocols.io:
| Date | Action |
|---|---|
| October 23, 2019 | Dataset publish |
| November 6, 2019 | Manuscript Link added : 10.1093/gigascience/giz126 |
| November 7, 2019 | File 1kp_decontamination_libraries.gz updated |
| November 15, 2019 | External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.439gyr6 |
| January 20, 2021 | File format attribute of 1kp_decontamination_libraries.gz updated from archive to gzip |
| June 22, 2021 | Relationship added : DOI 100910 |
| October 14, 2022 | Manuscript Link updated : 10.1093/gigascience/giz126 |
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