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Sample GSM1896834 Query DataSets for GSM1896834
Status Public on Jun 10, 2016
Title Co-culture replicate 3, 2 hours after heterotroph addition
Sample type SRA
 
Source name Bacterial culture
Organisms Alteromonas macleodii; Prochlorococcus marinus str. NATL2A
Characteristics strain: NATL2A (P. marinus), MIT1002 (A. macleodii)
timepoint: 2 hours after heterotroph addition
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.
Growth protocol Prochlorococcus cells were grown in natural seawater-based PRO99 media under constant light
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description T3Alt_3
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
 
Submission date Sep 28, 2015
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)
GSE73511 Impact of a heterotroph, Alteromonas MIT1002, on the transcriptome of Prochlorococcus NATL2A
Relations
SRA SRX1293036
BioSample SAMN04122025

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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