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Sample GSM6047744 Query DataSets for GSM6047744
Status Public on Apr 21, 2022
Title PTB7-Th:IEICO-4F, PC3
Sample type SRA
 
Source name leaf
Organism Solanum lycopersicum
Characteristics tissue: leaf
genotype: wildtype
cultivar: Moneymaker
intensity experiment: PPFD Controlled (PC)
osc filter: PTB7-Th:IEICO-4F
treatment: PI_PC
Treatment protocol OSC filter vs spectrally neutral control
Growth protocol growth chamber under ceramic metal halide + incandescent bulbs
Extracted molecule total RNA
Extraction protocol PureLink RNA Mini on-column kit with TRIzol with on-column DNAse treatment
mRNA library was prepped by BGI Genomics Co., Ltd. with polyA selection by an oligo dT library
All 31 samples were multiplexed, pooled and loaded together onto a DNBSEQ Technology Platform
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description DNBSEQ Technology Platform
Data processing QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to RefSeq GCF_000188115.4 using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to RefSeq GCF_000188115.4 annotations using featureCounts and read abundances quantified at the gene-level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Assembly: RefSeq GCF_000188115.4
Supplementary files format and content: Text files with counts for each sample by gene
 
Submission date Apr 18, 2022
Last update date Apr 23, 2022
Contact name Heike Sederoff
E-mail(s) hwsedero@ncsu.edu
Organization name North Carolina State University
Department Plant & Microbial Biology
Lab Sederoff Lab
Street address 851 Main Campus Dr
City Raleigh
State/province NC
ZIP/Postal code 27695-7612
Country USA
 
Platform ID GPL28981
Series (1)
GSE200978 Transcriptome of tomato leaf tissue grown under OSC filters
Relations
BioSample SAMN27621196
SRA SRX14891682

Supplementary file Size Download File type/resource
GSM6047744_B3-8_counts.txt.gz 4.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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