Single cell data sets

Warning and instructions

Reference assemblies

On these pages of the NIH website, click on "Send" near the top right; select "Complete Record"; destination "File"; format "FASTA"; and save it.

SAR324 (Deltaproteobacteria) draft assembly

Description Filename Compressed size (bytes) Uncompressed size (bytes)
SAR324 draft assembly sar324_contigs_lane1.fa.bz2 1,262,876 4,384,236
Annotation of SAR324 draft assembly SAR324_MDA_annotation.xlsx   254,647

Reads in .fastq.bz2 format

Description Filename Compressed size (bytes) Uncompressed size (bytes) # reads Read length Insert size μ σ
MD5 sums md5sums.txt   660        
 
Flow cell: E. coli K-12, strain MG1655, standard genomic DNA prepared from culture
E. coli reference, lane 6 ecoli_ref.fastq.bz2 2,066,533,589 6,503,411,804 28,428,648   2 x 100 215.4 10.6
This is available in a slightly different format from the EMBL-EBI Sequence Read Archive, ascension number ERA000206
 
Flow cell: E. coli K-12, strain MG1655, single cell MDA; two single cells, each with technical replicates
E. coli, first single cell, four technical replicates (lanes 1-4)
E. coli, first single cell MDA, lane 1 ecoli_mda_lane1.fastq.bz2 2,208,701,585 6,720,619,310 29,124,078 2 x 100 266.8 56.4
E. coli, first single cell MDA, lane 2 ecoli_mda_lane2.fastq.bz2 2,391,957,740 7,356,522,764 31,880,542 2 x 100 266.9 56.3
E. coli, first single cell MDA, lane 3 ecoli_mda_lane3.fastq.bz2 2,447,195,626 7,555,569,440 32,743,056 2 x 100 267.1 56.1
E. coli, first single cell MDA, lane 4 ecoli_mda_lane4.fastq.bz2 2,426,924,190 7,458,767,056 32,323,444 2 x 100 267.0 56.2
 
Control sample lane
PhiX ecoli_mda_lane5.fastq.bz2 685,601,236 3,071,476,268 13,310,768 2 x 100    
 
E. coli, second single cell MDA, three technical replicates (lanes 6-8)
E. coli, second single cell MDA, lane 6 ecoli_mda_lane6.fastq.bz2 2,033,109,604 6,362,825,516 27,573,794 2 x 100 276.1 60.5
E. coli, second single cell MDA, lane 7 ecoli_mda_lane7.fastq.bz2 1,968,463,324 6,160,355,490 26,695,478 2 x 100 276.1 60.6
E. coli, second single cell MDA, lane 8 ecoli_mda_lane8.fastq.bz2 1,812,059,102 5,683,356,948 24,631,296 2 x 100 276.1 60.5
 
Flow cell: Other bacteria
Deltaproteobacteria, single cell MDA, lane 1   bacteria_mda_lane1.fastq.bz2   2,002,341,888 13,491,072,156 57,853,248 2 x 100    
S. aureus, single cell MDA, lane 7 bacteria_mda_lane7.fastq.bz2 3,134,257,772 15,623,420,978 66,997,488 2 x 100    

NCBI resources for our SAR324 (Deltaproteobacteria) data

Note that the draft assembly and reads deposited at NCBI correspond to the versions provided above for SAR324 (Deltaproteobacteria), but the NCBI pipeline changes the file format and metadata. Our assembly file sar324_contigs_lane1.fa.bz2 posted on this page includes contigs of length at least 110 bp, as reported in the paper, while NCBI filtered out our contigs smaller than 200 bp.
 
Resource ID
Project title SAR324 cluster bacterium JCVI-SC AAA005
Draft assembly AGAU
GenBank ID AGAU00000000.1
BioProject ID PRJNA71321
Taxonomy ID 1073573
Short Read Archive     SRA043956