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| Status |
Public on Mar 21, 2013 |
| Title |
SB2B MM |
| Sample type |
SRA |
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| Source name |
Shewanella amazonensis SB2B grown in D,L-lactate medium till mid-log-phase
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| Organism |
Shewanella amazonensis SB2B |
| Characteristics |
treatment: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7
strain: SB2B
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| Growth protocol |
Aerobic growth to mid-log phase at 30C with shaking at 200 rpm
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes. Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment. RNA quality was confirmed with an Agilent Bioanalyze. Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends, blocked the 3' ends with sodium periodate and we added a sequencing adaptor onto the 5' end with Ambion T4 RNA ligase. We used random hexamer primers with a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR amplified the library to enrich for products that contained both adaptors and to complete the 5' adaptor. 6-mer index GATCAG was incorporated into the reverse PCR primer. We purified the PCR products and removed unincorporated nucleotides, primers, and adaptor-only products with AMPure XP Beads (Agencourt).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Indexed and sequenced on Illumina HiSeq sharing with seven other samples in one lane
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| Data processing |
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to Shewanella amazonensis SB2B genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella amazonensis SB2B/ASM1524v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand
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| Submission date |
Mar 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Wenjun Shao |
| E-mail(s) |
[email protected]
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| Organization name |
University of California
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| Department |
Molecular and Cell Biology
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| Lab |
Adam Arkin
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| Street address |
2151 Berkeley Way
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94704-5230 |
| Country |
USA |
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| Platform ID |
GPL16842 |
| Series (2) |
| GSE45317 |
Transcript structures in Shewanella amazonensis SB2B |
| GSE58337 |
Conservation of transcription start sites within genes across a bacterial genus |
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| Relations |
| SRA |
SRX252380 |
| BioSample |
SAMN01984753 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1101896_RNASeq5_SB_MM_main_chromosome_FWD.wig.gz |
475.4 Kb |
(ftp)(http) |
WIG |
| GSM1101896_RNASeq5_SB_MM_main_chromosome_REV.wig.gz |
435.4 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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