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| Status |
Public on Sep 20, 2023 |
| Title |
LagPhase_Rep3_210min |
| Sample type |
SRA |
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| Source name |
cells, 210 min after inoculation on soft-agar, rep.3
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| Organism |
Bacillus subtilis |
| Characteristics |
cell type: Bacteria
genotype: WT chromosome; comI_Q12L in natual plasmid
strain: NCIB3610
time after_inoculation_(min): 210
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| Treatment protocol |
Cells that started swarm expansion were collected into the lysis buffer by our custom sampling robot. Cells before swarm expansion (lag phase) were collected by being suspened in the lysis buffer.
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| Growth protocol |
Bacterial cells were spotted onto the center of a 9 cm petri dish filled with LB soft-agar (0.5% agar) medium and incubated at 30°C for swarm expansion.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods, 2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using DIY method (Culviner et al, mBio, 2020). Integrity of the prepared RNA was tested using a TapeStation.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB, E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing of the cDNA libraries was performed by MPGC (Cologne, Germany) or D-BSSE genomics facilty (Basel, Switzerland)
Sequence reads were trimmed for adaptor sequence/short sequence (<35 nt) using Trimmomatic v0.39
Trimmed sequence reads were mapped to B. subtilis NCIB3610 genome and plasmid (NCBI Accession number: NZ_CP020102 and NZ_CP020103) using HISAT2 v2.2.1 in single-end mode.
Reads mapped to all cetegory of genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, ribonuclease P RNA, tRNA, rRNA) were counted using featureCounts v2.0.1 with fractional counting for multi-mapping and multi-overlapping reads (-OM --fraction) in a strand-specific manner (-s 2). Of those, reads mapped in tRNA and rRNA were removed and the remaining reads were used for the downstream analysis.
All genes for which there were at least 2 samples with a read count of at least 10 were used for the downstream analysis. Samples with remaining reads of < 1 million reads were excluded and the rest of the samples were used for normalization using edgeR (version 3.6.1) and transformed (log2).
Supplementary files format and content: comma-separated files include mapped read count data for each sample
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at expansion phase
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at lag and expansion phase
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| Submission date |
Aug 07, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Kazuki Nosho |
| Organization name |
University of Basel
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| Department |
Biozentrum
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| Street address |
Spitalstrasse 41
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platform ID |
GPL30886 |
| Series (1) |
| GSE224332 |
Spatiotemporal trascriptomics of Bacillus subtilis swarming colony |
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| Relations |
| BioSample |
SAMN36873043 |
| SRA |
SRX21280861 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7689371_LagPhase_Rep3_210min_mappedReads.csv.gz |
82.5 Kb |
(ftp)(http) |
CSV |
| GSM7689371_LagPhase_Rep3_210min_normalizedCounts2.csv.gz |
96.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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