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Status |
Public on May 01, 2018 |
Title |
Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 40 |
Sample type |
SRA |
|
|
Source name |
Bacterial co-culture, extended darkness, 40hr
|
Organisms |
Alteromonas macleodii; Prochlorococcus marinus str. NATL2A |
Characteristics |
p. marinus strain/background: NATL2A a. macleodii strain/background: MIT1002 condition: 13:11 light:dark light cycle -> extended darkness timepoint: 40 hours
|
Treatment protocol |
Cultures were split after 24 hours of sampling under the day:night light cycle; at 'sundown', half experienced the normal light regime, the other half stayed in the dark.
|
Growth protocol |
Cultures were grown in natural seawater-based PRO99 media under a 13:11 day:night light cycle.
|
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 RNA-seq 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 |
H40D_2 Processed data file: extended_darkness_counts.txt
|
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 HTSeq (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 CP000095.2 (Prochlorococcus marinus) and JXRW01000000.1 (Alteromonas macleodii). Supplementary_files_format_and_content: extended_darkness_counts.txt: 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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|
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Submission date |
Jan 05, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Steven Biller |
E-mail(s) |
sbiller@mit.edu
|
Organization name |
MIT
|
Department |
Civil and Environmental Engineering
|
Street address |
15 Vassar St, MIT 48-424
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02139 |
Country |
USA |
|
|
Platform ID |
GPL20972 |
Series (1) |
GSE93197 |
What happens to Prochlorococcus when the sun does not come up? |
|
Relations |
BioSample |
SAMN06205948 |
SRA |
SRX2464659 |