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Sample GSM7916802 Query DataSets for GSM7916802
Status Public on Dec 08, 2023
Title sr34a-1 germinated seeds submitted to ABA treatment biol rep 2
Sample type SRA
 
Source name 44h germinated seeds + 2h ABA treatment
Organism Arabidopsis thaliana
Characteristics tissue: 44h germinated seeds + 2h ABA treatment
genotype: sr34a-1
treatment: ABA 0.5 µM
Treatment protocol 44h germinated seeds were transferred to MS medium (Control) or MS medium supplemented with 0.5 µM ABA during 2h
Growth protocol Stratified seeds were grown on MS medium in continuous white light (100 µmol/m2) at 21 ºC for 44h
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA kit (Analytik Jena BioSolutions).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description M2A2
Data processing Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Alternative splicing (AS) quantification is performed using vast-tools. vast-tools maps the RNA-seq data to the araTha10 library, based on Ensembl Plants v31 and composed of an extended annotation with all exon-exon and exon-intron junction sequences found in the Arabidopsis thaliana genome. vast-tools then quantifies intron retention, exon skipping, alternative 5' splice site and alterntive 3' splice site events and provides the percentage of inclusion (PSI) of the putative alternative sequence using only exon-exon (or exon-intron for IR) junction reads.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file including cRPKM values for each gene
Supplementary files format and content: Tab-delimited text file including PSI values for each alternative splicing event
 
Submission date Nov 24, 2023
Last update date Dec 08, 2023
Contact name Tom Laloum
E-mail(s) tomlaloum@gmail.com
Phone 918995207
Organization name Instituto Gulbenkian de Ciencia
Lab Plant Molecular Biology
Street address Rua da Quinta Grande, 6
City Oeiras
ZIP/Postal code 2780-156
Country Portugal
 
Platform ID GPL26208
Series (2)
GSE248561 RNA-seq experiment of wild-type (WT) and sr34a-1 mutant germinated seeds grown for 44 hours and exposed or not to ABA for 2 hours.
GSE248563 sr34a-1 mutant germinated seeds and exposure to ABA
Relations
BioSample SAMN38412807
SRA SRX22635932

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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