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Sample GSM6025427 Query DataSets for GSM6025427
Status Public on Jul 30, 2023
Title non-treated PIF4-L.1 seedlings rep3
Sample type SRA
 
Source name whole seedlings
Organism Arabidopsis thaliana
Characteristics developmental stage: 3 day-old
growth conditions: darkness (D)
genotype: PIF4pro:PIF4-3xFlag
genetic backgroung: Columbia
Growth protocol Stratified seeds were irradiated with white light at 22ºC for 3 hours to induce germination, grown in darkness at 22ºC for 3 days, and then either placed at 37ºC or kept at 22ºC for 3 hours.
Extracted molecule polyA RNA
Extraction protocol Total RNA (1 µg) 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 NextSeq 500
 
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).
Supplementary files format and content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript
 
Submission date Apr 05, 2022
Last update date Jul 30, 2023
Contact name Guiomar Martín
E-mail(s) guiomarm@igc.gulbenkian.pt
Organization name Instituto Gulbenkian de Ciência
Department Plant Molecular Biology
Street address Rua da Quinta Grande, 6
City Oeiras
State/province Lisboa
ZIP/Postal code 2780-156
Country Portugal
 
Platform ID GPL19580
Series (1)
GSE200247 RNA-seq experiment of wild-type (WT) and pif4 mutant seedlings grown for 3 days in darkness and exposed or not to heat stress for 3 hours.
Relations
BioSample SAMN27355587
SRA SRX14752184

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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