|
| Status |
Public on Jul 30, 2023 |
| Title |
non-treated PIF4-L.1 seedlings rep2 |
| 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) |
guiomar.martin@cragenomica.es
|
| Organization name |
Centre for Research in Agricultural Genomics
|
| Street address |
Vall Moronta
|
| City |
Cerdanyola del Vallès |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| 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 |
SAMN27355588 |
| SRA |
SRX14752183 |
