|
| Status |
Public on Feb 22, 2021 |
| Title |
Pst-kb1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Pseudomonas syringae |
| Characteristics |
strain: pv. tomato DC3000
genotype/variation: wild type
media: kings_B_media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
rRNA was depleted from purified total RNA using the Ribo-Zero Gram-Negative Bacteria kit (Illumina). rRNA-depleted samples were then cleaned up with the RNA Clean & Concentrator-5 (Zymo Research) and eluted in 15ul. library strategy RNA-Seq. RNA-Seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420; New England BioLabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
General read quality was evaluated using FastQC v0.11.2
Genome and GTF files were downloaded from NCBI and indexed using bowtie2-build (Bowtie2 v2.3.1).
FASTQs were filtered and trimmed using fastq-mcf (ea-utils v1.1.2) using paramteres "-q 20 -x 0.5" and adapter sequences from the NEBNext manual.
Filtered and trimmed reads were mapped using tophat2 (v2.1.1) using parameters "--library-type fr-firststrand --max-intron-length 5 --min-intron-length 4 --transcriptome-max-hits 1 --max-multihits 1 --no-coverage-search --no-novel-juncs --no-sort-bam
samtools v0.1.19 was used to merge and sort the accepted_hits.bam and unmapped.bam files output by tophat using commands "samtools merge -n" and "samtools sort -n"
htseq-count (htseq v0.6.1) was used to count reads per gene with the parameters "--order=name --format=bam --stranded=reverse --type=gene --idattr=locus_tag" $TH_DIR/${SAMPLE}/merged.name.bam
A Jupyter notebook containing the analysis pipeline is available at <https://gitlab.oit.duke.edu/Biostatistics_and_Bioinformatics/HTS_SummerCourse_2017/-/blob/master/Materials/Computation/Wk4_Day4_AM/analysis_nb/2017_generate_pilot_counts.ipynb>
Genome_build: GCF_000007805.1_ASM780v1
Supplementary_files_format_and_content: tab-delimited text files containing raw read counts per gene
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Feb 24, 2021 |
| Contact name |
Joshua Aaron Granek |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University School of Medicine
|
| Department |
Department of Biostatistics and Bioinformatics
|
| Street address |
Box 3568, 213 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL29316 |
| Series (1) |
| GSE160315 |
Nutritional regulation of pathogenesis gene expression in Pseudomonas syringae |
|
| Relations |
| BioSample |
SAMN16581739 |
| SRA |
SRX9389477 |
