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| Status |
Public on Aug 22, 2014 |
| Title |
LB_WT |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Listeria monocytogenes EGD-e |
| Characteristics |
strain: BUG1600
genotype/variation: wild type
growth medium supplemented with: none (LB control)
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| Growth protocol |
Listeria monocytogenes strains were grown in LB broth with shaking at 200 rpm in Erlenmeyer flasks at 37° C
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| Extracted molecule |
total RNA |
| Extraction protocol |
10µg of total RNA was ribodepleted and non-directional libraries were constructed using a random hexamer priming approach fully described in the manuscript
For all RNA isolations, 25 ml cultures of L. monocytogenes were grown to an OD600 of 0.3 – 0.5 and subsequently pelleted by centrifugation at 4000 rpm for 20 mins in 50 ml Falcon tubes with swing bucket rotor. Pellets were resuspended in 1ml Tri Reagent (Sigma, 93289), transferred to 2 ml Lysing Matrix Tubes (MP Biomedicals, 6911) and mechanically lysed by bead beating in a FastPrep apparatus (45 secs, speed 6.5 followed by an additional 30 secs, speed 6.5). Subsequently tubes were centrifuged for 5 min at 8000 X G, 4° C in a tabletop centrifuge to separate beads from lysates. Lysates were drawn off and transferred to 2 ml Eppendorf tubes. RNA isolation proceeded according to the manufacturers instructions. Briefly, 200 μl Chloroform (Carlo Erba Reagents, 438601) was added to the lysate, shaken and incubated for 10 minutes at room temperature followed by centrifugation for 15 min at 13,000 X G, 4° C. The upper aqueous phase was removed and transferred to a new 1.5 ml Eppendorf tube and RNA was precipitated by the addition of 500 μl Isopropanol and incubation at room temperature for 5-10 mins. RNA was pelleted by centrifuging for 10 mins at 13,000 X G, 4° C. The supernatant was discarded and the pellet was washed twice with 75% ethanol. RNA pellets were resuspended in 50 μl water.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
For RNA-seq; Reads were mapped to the corresponding reference genome (NC_003210) using Novoalign (Novocraft V3.02.02) and RPM were calculated with in-house perl scripts
For CLIP-Seq; Raw sequence files (fastq) were cleaned of 3' Adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG), and low quality (cutoff 28) and short sequence (15nt) reads were removed using AdapterRemoval v1.5.2 (Lindgreen et. al, 2012) software. Reads were aligned against the reference genome (NC_003210) with bowtie v1.0.0 (Langmead et al., 2009) using default parameters, counted with HTSeq v0.6.0 and normalized to reads per million.
Genome_build: NC_003210
Supplementary_files_format_and_content: The *cov.txt contains three columns; the 1st column describes the concerned chromosome/contig, the 2nd the position on the specified region and the last the normalised coverage (in reads per million)
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| Submission date |
Aug 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Mellin |
| E-mail(s) |
[email protected]
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| Organization name |
Institut Pasteur
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| Street address |
25 rue Docteur Roux
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| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL19075 |
| Series (1) |
| GSE60363 |
Sequestration of a two-component response regulator by a riboswitch regulated non-coding RNA |
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| Relations |
| BioSample |
SAMN02985680 |
| SRA |
SRX676055 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1477268_LB_WT.cov.txt.gz |
10.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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