Data supporting the 1000 plant (1KP) transcriptomes initiative

Dataset type: Transcriptomic
Data released on October 23, 2019

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):

(PubMed: 31644802)

Related datasets:

doi:10.5524/100627 IsPreviousVersionOf doi:10.5524/100910 (It is a more recent version of this dataset)


There is a new version of this dataset available at: DOI: 10.5524/100910

Accessions (data generated as part of this study):

BioProject: PRJEB4921
BioProject: PRJEB8056
BioProject: PRJEB21674
STUDY: SRP012845
BioProject: PRJNA163187





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
AALA400539  Meliosma cuneifolia Description:RNA extracted from leaves of Meliosma ...
Analyte type:RNA
Tissue:leaf [BTO:0000713]
...
+
ABCD71396  Racomitrium elongatum Description:RNA extracted from gametophyte of Niph...
Analyte type:RNA
Tissue:gametophyte [BTO:0000495]
...
+
ABEH1799584  Heliotropium greggii Description:RNA extracted from mature leaf of Heli...
Analyte type:RNA
Tissue:leaf [BTO:0000713]
...
+
ABIJ59777  Selaginella lepidophylla Description:RNA extracted from Young fronds of Sel...
Analyte type:RNA
Tissue:frond [BTO:0000483]
...
+
ABSS46945white sassafras Sassafras albidum Description:RNA extracted from young leaves of Sas...
Analyte type:RNA
Tissue:juvenile leaf [BTO:0003147]
...
+
ACFP83906Chinese silk-plant Boehmeria nivea Description:RNA extracted from shoot apex includin...
Analyte type:RNA
Tissue:shoot apex [PO:0000037]
...
+
ACWS56990  Agathis macrophylla Description:RNA extracted from Young Leaf of Agath...
Analyte type:RNA
Tissue:juvenile leaf [BTO:0003147]
...
+
ACYX33128Flanders poppy Papaver rhoeas Description:RNA extracted from leaf of Papaver rho...
Analyte type:RNA
Tissue:leaf [BTO:0000713]
...
+
ADHK55362  Galax urceolata Description:RNA extracted from leaves - diploid of...
Analyte type:RNA
Tissue:leaf [BTO:0000713]
...
+
AEKF102169  Penium margaritaceum Description:RNA extracted from algal cells of Peni...
Analyte type:RNA
Tissue:Algae [NCIT:C86587]
...
+
Displaying 1-10 of 1249 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataCSV55.61 KB2019-08-06
Tabular dataCSV55.61 KB2019-07-15
Tabular dataCSV670.26 KB2019-07-15
Tabular dataCSV670.26 KB2019-08-06
Mixed archiveGZIP5.53 GB2019-07-15
AALATranscriptome sequenceFASTA7.26 MB2019-08-06
AALACoding sequenceFASTA2.76 MB2019-08-06
AALAProtein sequenceFASTA1.82 MB2019-08-06
AALATabular dataTSV355.57 KB2019-08-06
AALATabular dataTSV3.29 MB2019-08-06
Displaying 1-10 of 7289 File(s).
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