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Status |
Public on Jun 10, 2016 |
Title |
Co-culture replicate 3, 24 hours after heterotroph addition |
Sample type |
SRA |
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Source name |
Bacterial culture
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Organisms |
Alteromonas macleodii; Prochlorococcus marinus str. NATL2A |
Characteristics |
strain: NATL2A (P. marinus), MIT1002 (A. macleodii) timepoint: 24 hours after heterotroph addition
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Treatment protocol |
The heterotroph Alteromonas MIT1002 was added to one set of biological replicates, at a ~equal cellular abundance to Prochlorococcus. Equivalent amounts of media alone were added to the axenic controls.
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Growth protocol |
Prochlorococcus cells were grown in natural seawater-based PRO99 media under constant light
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Extracted molecule |
total RNA |
Extraction protocol |
Culture samples added to cold RNAlater at each timepoint, cells collected onto a 0.2µm filter, and total RNA extracted with the mirVana kit (Ambion) Strand-specific RNAseq library construction starting with 100ng of total RNA using the dUTP second-strand approach; duplex-specific normalization was performed to reduce ribosomal RNA content in each sample
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
T7Alt_3
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Data processing |
Low quality sequence removed using quality_trim (CLCbio) using default parameters Alignment of paired-end reads to references using the Burrows-Wheeler Aligner V0.7.12 Number of aligned read pairs mapping in the sense orientation to each ORF determined using Python scripts and the samtools package (0.1.19), method after: "Anders, S., Pyl, P. T., & Huber, W. (2014). HTSeq–A Python framework to work with high-throughput sequencing data. Bioinformatics (Oxford, England)." Genome_build: NCBI accessions CP000095 and JXRW01000000 Supplementary_files_format_and_content: tab-delimited text file with the number of reads mapping to each ORF for all timepoints and replicates, as well as associated annotation data
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Submission date |
Sep 28, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Steven Biller |
E-mail(s) |
sbiller@mit.edu
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Organization name |
MIT
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Department |
Civil and Environmental Engineering
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Street address |
15 Vassar St, MIT 48-424
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02139 |
Country |
USA |
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Platform ID |
GPL20972 |
Series (1) |
GSE73511 |
Impact of a heterotroph, Alteromonas MIT1002, on the transcriptome of Prochlorococcus NATL2A |
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Relations |
SRA |
SRX1293060 |
BioSample |
SAMN04122227 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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