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Series GSE139201 Query DataSets for GSE139201
Status Public on Oct 22, 2019
Title Differential gene expression at shoot apices between Wild Type and vip3-1-null allele
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The aim of this study was to evaluate gene expression defects at the shoot apical meristem and young flower meristems of the vip3-1 null allele. VIP3 belongs to polymerase II-associated factor 1 complex (Paf1c), which is involved in several RNA polymerase II-dependent transcriptional processes. Arabidopsis vip3 mutants exhibit phylotactic defects and strong floral indeterminacy phenotypes.
 
Overall design Material for the RNA-seq was collected from the primary inflorescence of vip3-1 and Col-0 shoot apices (from plants grown in short day 21°C then continuous light 16°C conditions). Apices were dissected, by removing flower older than stage 4. Samples were collected into liquid nitrogen-cooled eppendorf tubes directly after dissection, each tube containing between 30 and 35 apices, 6 samples for each genotype. RNA extraction was performed using the PicoPure RNA Isolation kit Arcturus (ThermoFisher, KIT0204) with an on column DNAase treatment (Qiagen, catalog#79254). After elution, 2 samples were combined together, obtaining the final technical triplicates for each genotype. Isolated RNA was subjected to high throughput sequencing analyses to identify differentially expressed transcripts.
 
Contributor(s) Fal K
Citation(s) 31540913
Submission date Oct 21, 2019
Last update date Mar 26, 2020
Contact name Christophe TREHIN
E-mail(s) christophe.trehin@ens-lyon.fr
Organization name ENS Lyon
Department Biology
Lab Reproduction et Développement des Plantes
Street address 46, Allée d'Italie
City Lyon
ZIP/Postal code 69364 Cedex 07
Country France
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (6)
GSM4133877 WT RNA-Seq - replicate 1
GSM4133878 WT RNA-Seq - replicate 2
GSM4133879 WT RNA-Seq - replicate 3
Relations
BioProject PRJNA578729
SRA SRP226506

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139201_Fal_et_al_TAIR10_gene_exp_diff_filt.txt.gz 188.8 Kb (ftp)(http) TXT
GSE139201_Fal_et_al_TAIR10_genes-countsMatrix.txt.gz 379.1 Kb (ftp)(http) TXT
GSE139201_Fal_et_al_TAIR10_genes-fpkmsMatrix.txt.gz 663.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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