Protocols
Caron Lab protocols can be found at our protocols.io page: https://www.protocols.io/groups/caron-lab-protistan-ecology.
Sequence Data
Koid, AE, A Jones, Z Liu, DA Caron, KB Heidelberg. 2014. Comparative transcriptome analysis of four prymnesiophytes. PLoS ONE. 6: e97801 pdf
- The sequences for the four transcriptomes were deposited in CAMERA (Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis) with the following accession numbers: CAM_ASM_000151 (P. parvum), CAM_ASM_000808 (C. brevifilum), CAM_ASM_000453 (C. ericina), CAM_ASM_000460 (P. antarctica).
Liu, Z, AC Jones, V Campbell, KD Hambright, KB Heidelberg, DA Caron. 2015. Gene expression in the mixotrophic haptophyte, Prymnesium parvum, responds to prey availability. Front. Microbiol. 6:319. pdf
- Sequence data deposited into the NCBI Sequence Read Archive under accession number SRA166613 and sample IDs MMETSP0006_2, MMETSP0815, and MMETSP0008_2, for axenic, bacterized and ciliate treatment, respectively.
Lie, AAY, Z Liu, S Hu, AC Jones, DY Kim, PD Countway, LA Amaral-Zettler, RJ Gast, EB Sherr, BF Sherr, SC Cary and DA Caron. 2014. Investigating microbial eukaryote diversity: Insights from a comparison of pyrotag and full-length sequences of 18S rDNA from a global survey. App. Env. Microbiol. 80: 4363-4373 pdf
- The full-length 18S rRNA gene sequences were submitted to GenBank under accession numbers KJ757035 to KJ759741, KJ760393 to KJ762454, and KJ762829 to KJ764638.
Hu, S, Z Liu, AA Lie, PD Countway, DY Kim, AC Jones, RJ Gast, SC Cary, EB Sherr, BF Sherr, and DA Caron. 2015. Estimating protistan diversity using high-throughput sequencing. J. Eukayot. Microbiol. 62:688-693. doi: 10.1111/jeu.12217. pdf
- Sequences were submitted to GenBank with accession numbers: KJ757035–KJ764638.
Liu, Z, AE Koid, R Terrado, V Campbell, DA Caron, KB Heidelberg. 2015. Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation. Front Microbiol. 6:631. doi: 10.3389/fmicb.2015.00631. pdf
- Original sequence data were deposited in NCBI Sequence Read Archive under accession number SRA166613 and sample IDs MMETSP0006_2, MMETSP0007 and MMETSP0814, for axenic, P-limited and N-limited treatment, respectively.
Ochromonas sp. str. BG-1 transcriptomes
We sequenced transcriptomes of three treatments, three replicates for each treatment, totaling 176.8 Gb of data.
Original sequences have been deposited at NCBI Sequence Read Archive (SRA) under the accession numbers SRX965527 (exponential phase samples), SRX968591 (stationary phase samples), and SRX970036 (dark treatment samples).
Protist single-cell transcriptomes
We sequenced single-cell transcriptomes of two species, Karlodium veneficum (10 cells) and Prymnesium parvum(18 cells), isolated using two methods, and their batch culture transcriptomes for comparison, totaling 121.2 Gb of data.
Original sequences have been deposited at NCBI SRA under the accession numbers SRX1430089 (P. parvum batch culture), SRX1430091 (P. parvum single cells isolated manually), SRX1431799 (P. parvum single cells isolated using microfluidics), SRX1434822 (K. veneficum batch culture), SRX1434823 (K. veneficum single cells isolated manually).
Transcriptome assemblies generated using these data are being uploaded to NCBI Transcriptome Shotgun Assembly Database.
For more information, please see:
Publications related to this project