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| Status |
Public on Jun 23, 2023 |
| Title |
pif_emb48 (biol rep 3) |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: embryo
genotype: pif3-1 mutant
treatment: 30C for 48 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated from 200 mature endosperms or embryos
cDNA libraries were prepared from 200 ng total RNA using a TruSeq mRNA Library Prep Kit (Illumina, Switzerland).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Low-quality reads were filtered out by the fastqc program (RRID:SCR_005539) with the option –q 20 and –p 90.
The reads were mapped to the Col-0 genome (TAIR10) with the TopHat program (RRID:SCR_013035)
Assembly: Transcript assembly and normalization was performed with the Cufflinks program (RRID:SCR_ 013307), and gene expression levels were calculated in FPKM (Fragments Per Kilobase of exon per Million mapped fragments) units.
Supplementary files format and content: Differential gene expression analysis was performed by Cuffdiff (RRID:SCR_001647), a part of the Cufflinks package
Supplementary files format and content: tab-delimited text files include average FPKM values
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| Submission date |
Feb 09, 2023 |
| Last update date |
Jun 23, 2023 |
| Contact name |
Urszula Piskurewicz |
| E-mail(s) |
urszula.piskurewicz@unige.ch
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| Organization name |
University of Geneva
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| Department |
30, Quai Ernest-Ansermet
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| Street address |
30, Quai Ernest-Ansermet
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| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE224926 |
PIF3 regulates different genes in the endosperm and embryo |
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| Relations |
| BioSample |
SAMN33225027 |
| SRA |
SRX19321651 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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