|
| Status |
Public on Aug 02, 2021 |
| Title |
Sample 43 |
| Sample type |
SRA |
| |
|
| Source name |
Solanum lycopersicum cv. M82 and Capsicum annuum variety Big Dipper
|
| Organisms |
Capsicum annuum; Solanum lycopersicum |
| Characteristics |
tissue: Stem graft junction
timepoint: 5 days after grafting
library: Pepper:tomato graft junction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol total RNA extraction
mRNA was extracted following the NEBNext Poly(A) mRNA Magnetic Isolation Module protocol and libraries were prepared using the NEBNext mRNA Library Prep set for Illumina (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FastQC Preprocessing: nohup ./ fastqc <Fastq.gz location> <Fastq.gz location> <As many fasrq.gz files as you want> --outdir=/<output directory location> &
adaptor trimming using rimmomatic version 0.36: ohup java -jar <location of trimmomatic.jar> SE -phred33 <location of fastq.gz file> <output name/location>
aligned to tomato and pepper genome using bowtie2: nohup bowtie2 -x <Index Name> -U <Fastq file> -S <Alignment Name.sam> --no-unal &
convert from *.sam to *.bam files using samtools: samtools view -Sb <alignment.sam> > <alignment.bam>
sort using samtools: nohup samtools sort <file.bam> -o <sorted file.bam> &
index using samtools: nohup samtools index <sorted file.bam> <sorted file.bai> &
analyze alignments using Bedtools Multicov: bedtools multicov -D -bams <sorted bam file.bam> -bed <GFF filed.gff> > <Text file.txt> &
Supplementary_files_format_and_content: Sorted, indexed alignments (*.bai). Alignments to tomato genome are named without prefix to the file name. Alignments against pepper genome have "Pepper_" prior to the file name.
|
| |
|
| Submission date |
May 23, 2019 |
| Last update date |
Aug 02, 2021 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
|
| Phone |
314-587-1422
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Meyers lab
|
| Street address |
975 N Warson Road
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL26701 |
| Series (1) |
| GSE131700 |
Graft junction transcriptome between tomato and pepper over time |
|
| Relations |
| BioSample |
SAMN11841162 |
| SRA |
SRX5889065 |
