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| Status |
Public on Apr 26, 2019 |
| Title |
nasT_2 |
| Sample type |
SRA |
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| Source name |
B. diazoeficiens ΔnasT mutant
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| Organism |
Bradyrhizobium diazoefficiens |
| Characteristics |
genotype/variation: delta nasT
strain: USDA 110
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| Growth protocol |
Cells of B. diazoefficiens were inoculated into 20 mL (optical density ~0.01 at 660 nm) of HMM medium wth 10 mM KNO3 in 100-mL bottles and reciprocally shaken (100 rpm, 30°C) for 24 h under anaerobic conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using hot phenol extraction. Digestion with DNase I (RQ1; Promega), purification with the RNeasy Mini Kit (Qiagen), and First-strand cDNA synthesis (SuperScript II reverse transcriptase; Invitrogen) were performed according to the manufacturer’s instructions.
Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). For each cDNA sample (four in total), 5 μg were used for RNA-seq analysis. Ribosomal RNAs was removed with the Ribo-Zero Magnetic Kit for Gram-negative Bacteria (Epicentre) and cDNA library was prepared with the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). These steps were performed by Hokkaido System Science Co., Ltd. (http://www.hssnet.co.jp/).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Original files generated by the sequencing instrument were imported to the CLC Genomic Workbench software 9.5.3., with a library size of 200-500 bp.
Trimming of reads was performed with default values (except for with a minimum number of nucleotides on reads of 70) using the CLC Genomic Workbench software 9.5.3.
Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3.
Genome_build: GenBank accession number NC_004463
Supplementary_files_format_and_content: A tab-delimited text file including the mapping reports (for WT_1, nasT_1, WT_2, and nasT_2)
Supplementary_files_format_and_content: Four tab-delimited text files including read counts and RPKM values for each sample
Supplementary_files_format_and_content: A tab-delimited text file including the differential expression analysis WT vs. ΔnasT
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| Submission date |
Apr 25, 2019 |
| Last update date |
Apr 26, 2019 |
| Contact name |
Cristina Sanchez |
| E-mail(s) |
[email protected]
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| Organization name |
Tohoku University
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| Department |
Graduate School of Life Sciences
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| Street address |
2-1-1 Katahira, Aoba-ku
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| City |
Sendai |
| ZIP/Postal code |
980-8577 |
| Country |
Japan |
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| Platform ID |
GPL26569 |
| Series (1) |
| GSE130301 |
Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens. |
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| Relations |
| BioSample |
SAMN11494917 |
| SRA |
SRX5734925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3735697_nasT_2.txt.gz |
228.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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