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| Status |
Public on Jan 05, 2010 |
| Title |
DsigB_replicate1 |
| Sample type |
SRA |
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| Source name |
10403S isogenic mutant
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| Organism |
Listeria monocytogenes |
| Characteristics |
strain: 10403S lacking sigB
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| Treatment protocol |
RNAProtect bacterial reagent (Qiagen, Valencia, CA) was added according to the manufacturer’s instructions to the cultures grown to stationary phase; treated cells were stored at -80ºC (for no longer than 24 h) until RNA isolation was performed.
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| Growth protocol |
Bacteria were grown in 5 ml Brain Heart Infusion (BHI) broth (BD Difco, Franklin Lakes, NJ) at 37ºC with shaking (230 rpm) for 15 h, followed by transfer of a 1% inoculum to 5 ml pre-warmed BHI. After growth to OD600 ~ 0.4, a 1% inoculum was transferred to a 300 ml nephelo flask (Bellco, Vineland, NJ) containing 50 ml pre-warmed BHI. This culture was incubated at 37ºC with shaking until cells reached stationary phase (defined as growth to OD600 = 1.0, followed by incubation for an additional 3 h). Two independent growth replicates and RNA isolations were performed for each strain.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cells were treated with lysozyme followed by 6 sonication cycles at 18W on ice for 30s. Total RNA was isolated and purified using the RNeasy Midi kit (Qiagen) according to the manufacturer’s protocol; RNA molecules <200 nt in length are not recovered well with this procedure, according to the manufacturer. RNA was eluted from the column using RNase-free water. Total RNA was incubated with RQ1 DNase (Promega, Madison, WI) in the presence of RNasin (Promega) to remove remaining DNA. Subsequently, RNA was purified using two phenol-chloroform extractions and one chloroform extraction, followed by RNA precipitation and resuspension of the RNA in RNAse free TE (10 mM Tris, 1 mM EDTA; pH 8.0; Ambion, Austin, TX). UV spectrophotometry (Nanodrop, Wilmington, DE) was used to quantify and assess purity of the RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
10403S lacking sigB
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| Data processing |
Processed data files (eland) contain alignment of short-reads against the 10403S supercontigs.
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| Submission date |
Apr 13, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Lalit Ponnala |
| E-mail(s) |
[email protected]
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| Organization name |
Cornell University
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| Street address |
616 Rhodes Hall
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL9363 |
| Series (1) |
| GSE15651 |
Listeria monocytogenes Transcriptome with RNA-Seq |
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| Relations |
| SRA |
SRX016001 |
| BioSample |
SAMN00008196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM391675_r1s2_eland_out.txt.gz |
55.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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