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| Status |
Public on Apr 19, 2021 |
| Title |
WT-1 |
| Sample type |
SRA |
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| Source name |
Wild Type
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| Organism |
Bacillus subtilis |
| Characteristics |
genotype: rpoC-10His amyE::Physpank-nusA lacIq nusA::Spr
iptg: 2 mM
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| Treatment protocol |
None
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| Growth protocol |
cells were plated on LB plates at 37°C +2 mM IPTG +20 µg/ml chloramphenicol -> single colonies isolated and grown O/N at 37°C standing culture in +0.4 mM IPTG +20 µg/ml chloramphenicol -> next day, cells were grown at in 25 mL of LB at 37°C +20 µg/ml chloramphenicol and +2 mM IPTG in cases where NusA production was to be sustained
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from collected cell paste via RNeasy mini-kit (Qiagen, cat # 74104)
total RNA was dephosphorylated using CIP (NEB, discontinued), rRNA was depleted via ribo-zero Gram-positive rRNA depletion kits (Illumina, discontinued), remaining RNA was ligated to custom unique 2', 3’ dideoxy RNA oligonucleotide (IDT), Illumina sequencing libraries were generated from ligation products using TruSeq Stranded mRNA kit (Illumina, cat # 20020594)
Term-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Wild Type
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| Data processing |
base calling and quality scoring conducted via BaseSpace
adaptor trimming and low quality read removal via Trimmomatic v. 0.38 for RNA-seq .fastq dataset
all reads containing custom oligo were extracted via Cutadapt v. 1.16 for Term-seq .fastq dataset
both RNA-seq and Term-seq .fastq files were mapped to B. subtilis genome using bwa-mem v.0.7.12-r1034
sam -> bam, and bam files split by strand via samtools v. 0.1.19-44428cd
coverage files (.cov) for 3' end mapping and .bedgraph files to illustrate coverage were generated using bedtools v. 2.26.0
2 custom python (python v. 3.8.3) scripts were used to identify 3' ends from Term-seq .fastq derived .cov files (located at: https://github.com/zfmandell/Term-seq)
RNA-seq coverage files generated using bedtools v. 2.26.0
Genome_build: Refseq : NC_000964.3
Supplementary_files_format_and_content: .bedgraph files, containing either RNA-seq coverage information, and list of called 3' ends with associated Cv values
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| Submission date |
Jul 15, 2020 |
| Last update date |
Apr 19, 2021 |
| Contact name |
Paul Babitzke |
| E-mail(s) |
pxb28@psu.edu
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| Organization name |
Pennsylvania State University
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| Street address |
203 Althouse Laboratory
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| City |
State College |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL24109 |
| Series (1) |
| GSE154522 |
NusG is an intrinsic transcription termination factor that stimulates motility and cooperatively coordinates global gene expression with NusA |
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| Relations |
| BioSample |
SAMN15545441 |
| SRA |
SRX8740592 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4672499_WT_1_final_coverage.bedgraph.gz |
12.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM4672499_WT_1_final_peaks.bedgraph.gz |
27.6 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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