Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW

Date Published: April 25, 2014

DOI: http://dx.doi.org/10.5061/dryad.9r0p6

 

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Title Mapping between ITS and MDA names
Description This files maps between the ITS sequence name and the MDA sequence name. ITS sequence names are described by their well in the ITS sanger sequencing plates (96-well plates) MDA sequence names are described by their well in the MDA reactions plates (384-well plates) ITS sequence name format is as follows: <cruise name><MDA plate number><ITS plate well><ITS plate number> for example: >B245a_520_F02_p18 means BATS cruise 245a, MDA plate 520, ITS plate 18 well F02. To find the relavant MDA well use the mapping file ITS_to_MDA_mapping_final.xls In this example the MDA well is thus plate 520 well O2
Download ITS_to_MDA_mapping_final.xlsx (43.62 Kb)
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Title ITS-rRNA multi-alignment of all single cells
Description Alignment of all ITS sequences used to build the trees and heatmaps in Fig. 1. The format of sequence names is as follows: <cruise name><MDA plate number><ITS plate well><ITS plate number>
Download ITS_all_algn.fasta (821.0 Kb)
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Title ITS-rRNA multi-alignment of the 96 single cells
Description Multi-alignment of the ITS of the 96 single cells (as well as of 5 HLII strains) used to generate the tree in Fig 2A.
Download ITS_96_algn.fasta (58.96 Kb)
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Title Mapping between ITS and MDA names (96 single cells)
Description ITS names and MDA names of the 96 single cells.
Download ITS_to_MDA_96cells.xlsx (16.47 Kb)
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Title C1 composite genome
Description Used as a reference genome for the reference-guided assembly. Was built from large overlapping contigs of single-cells within the cN2-C1 clade.
Download C1_composite_genome.gbk (3.140 Mb)
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Title Whole genome alignment of the 96 single cell partial genomes
Description Multi-alignment of the partial genomes of the 96 single cells used to generate the tree in Fig 2B.
Download WG_96_algn.fasta (162.9 Mb)
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Title Whole genome alignment of 8 clonal E. coli partial genomes
Description Multi-alignment of the partial genomes of the 8 clonal E. coli single cells used as a control to estimate the error rate involved in single cell genomics.
Download Ecoli_WG_8_algn.fasta (38.17 Mb)
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Title Classification of genes into Clusters of Orthologous Genes (COGs).
Description Classification of genes into Clusters of Orthologous Genes (COGs). Each entry is a gene (or partial gene sequence) in one of the 96 single cells denovo assembled genomes or in a genome of a cultured strains. The number in the beginnig of each header is the COG ID. The fatsa headers for genes in a single cell genome has the following format: >COG ID|MDA name|Detailed name|contig_<Number>_<Gene index on the contig>|Start bp|End bp|+/- Strand|Method|Description The fatsa headers for genes in a complete genome of a cultured strain has the following format: >COG ID|Short name|Detailed name|Start bp|End bp|+/- Strand|Method|
Download README.txt (2.972 Kb)
Download COGS.fasta (148.7 Mb)
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When using this data, please cite the original publication:

Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344(6182): 416-420. http://dx.doi.org/10.1126/science.1248575

Additionally, please cite the Dryad data package:

Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW (2014) Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.9r0p6
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