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| Status |
Public on Oct 13, 2020 |
| Title |
variant F |
| Sample type |
SRA |
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| Source name |
Bacterial culture, P. polymyxa E681, F
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| Organism |
Paenibacillus polymyxa |
| Characteristics |
strain: E681
genotype/variation: variant F
morphology: Flat colony
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from ‘B’ and ‘F’ type cells of P. polymyxa E681 were isolated from 2-day-old cultures grown in TSA using the RNeasy mini kit with on-column DNase I treatment (Qiagen Inc., Hilden, Germany). After DNase I treatment, a MICROBExpress bacterial mRNA enrichment kit (Ambion, Carlsbad, CA) was used to remove bacterial rRNA from the total RNA sample.
RNA-sequencing libraries were prepared using an Illumina TruSeqTM RNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq2000 instrument using the reagents provided in the Illumina TruSeq PE Cluster kits (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
F_TTCGCT
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| Data processing |
Raw data derived from RNA-seq was filtered to a minimum phred quality score of 28 using FASTX-Toolkit.
The filtered reads were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bamtoreadcount.
Reads per kilobase of gene per million mapped sequence reads were calculated for normalization.
Genome_build: ASM14687v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 03, 2017 |
| Last update date |
Oct 13, 2020 |
| Contact name |
Jungwook Park |
| E-mail(s) |
jjuwoogi@pusan.ac.kr
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| Organization name |
Pusan National University
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| Department |
Microbiology
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| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
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| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
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| Platform ID |
GPL22875 |
| Series (1) |
| GSE93062 |
RNA-seq analyses of phase variation-dependent genes in Paenibacillus polymyxa E681 |
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| Relations |
| BioSample |
SAMN06198143 |
| SRA |
SRX2457734 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2443167_F.txt.gz |
94.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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