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| Status |
Public on Jul 06, 2017 |
| Title |
Yersinia pestis transposon mutant library cultured at 28ºC (replicate 1) |
| Sample type |
SRA |
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| Source name |
970-Input_NoIndex_L005_R1_001.fastq
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| Organism |
Yersinia pestis |
| Characteristics |
strain: CO92
growth conditions: cultured at 28ºC
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| Treatment protocol |
Growth at 28ºC or 37ºC
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| Growth protocol |
Grown in blood agar base (BAB) broth
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted using the Gentra Puregene kit (Qiagen)
The gDNA was fragmented to <500 base pairs (bp) using 2 x 15 minute cycles at 4ºC in a BioRuptor sonicator (medium intensity, 30s on/90s off). A NEBNext DNA library preparation for Illumina kit (NEB) was used according to the manufacturer’s instructions, to end repair, A-tail and ligate adapters to the fragments. Parallel polymerase chain reaction (PCR) samples were set up with 10 μl JumpStart 10x buffer, 6 μl MgCl2, 2 μl 10mM nucleoside triphosphates (dNTPs), 0.6 μl 100 μM PE_PCR_V3.3 primer, 0.6 μl 100 μM Yp_EzTn_PCR primer, 1 μl JumpStart Taq DNA polymerase and 28.8 μl nuclease-free water per reaction. Primer sequences are listed in Additional file 2, Table S2. The reactions were amplified at 94oC for 2 minutes, (94oC for 30 seconds, 60oC for 20 seconds, 72oC for 30 seconds) for 22 cycles, 72oC for 10 minutes, then held at 12oC. PCR products were pooled and ethanol precipitated before being size selected on a 2% (w/v) agarose tris-borate-EDTA (TBE) gel. Agarose blocks corresponding to 350-500 bp were excised, and the DNA extracted using a Qiagen MinElute Gel Extraction kit as per the manufacturer’s instructions
The DNA was quantified by qPCR and on an Agilent BioAnalyzer before being submitted for sequencing as 100 bp single end reads on an Illumina HiSeq 2500 standard model.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Yersinia pestis mutant library cultured at 28ºC (replicate 1)
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| Data processing |
BWA was used to align the data
RD values - Relative distance to distal ends for each transposon insertion in genes
Supplementary_files_format_and_content: RD
Genome_build: Yersinia pestis CO92 complete genome - AL590842
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| Submission date |
Jun 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
ZhengRong Yang |
| E-mail(s) |
z.r.yang@exeter.ac.uk
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| Phone |
0044 1392 263448
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| Organization name |
University of Exeter
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| Street address |
Prince of Wales Road
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| City |
Exeter |
| ZIP/Postal code |
EX4 4PS |
| Country |
United Kingdom |
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| Platform ID |
GPL23606 |
| Series (1) |
| GSE100226 |
An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions |
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| Relations |
| BioSample |
SAMN07257404 |
| SRA |
SRX2935076 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2674959_input1.RD.gz |
29.7 Mb |
(ftp)(http) |
RD |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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