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Sample GSM2446219 Query DataSets for GSM2446219
Status Public on May 01, 2018
Title Co-culture replicate 3, 13:11 day:night cycle, Time 28
Sample type SRA
 
Source name Bacterial co-culture, normal light regime, 28hr
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
timepoint: 28 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description H28L_3
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.
 
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 SAMN06205894
SRA SRX2464636

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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