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Sample GSM5966638 Query DataSets for GSM5966638
Status Public on Mar 23, 2022
Title UB10pro_amiR-TOR_IAA_Es_2
Sample type SRA
 
Source name roots
Organism Arabidopsis thaliana
Characteristics genotype: UB10pro_amiR-TOR
treatment: IAA_Es
replicate: 2
tissue: roots
Treatment protocol Samples were then transfered either to 10 µM NPA and 10 µM Estradiol (NPA_Es) or DMSO control (NPA) for additional 24 h before being shifted to either 10 µM IAA + 10 µM Estradiol (IAA_Ees) or DMSO (IAA) for LR induction or maintained on the same plates. Root tissue was harvested after 6 h. All sampling points were performed in triplicate.then transferred to plates containing 10µM IAA, and 10µM DEX and DMSO control. Root tissue was harvested at 0, 2, 4 and 6 h after transfer onto auxin plates. All sampling points were performed in triplicate. For each sample, app. 200 segments of the lower two-thirds of the seedling roots were pooled.
Growth protocol Seeds were germinated on Nitex membranes (Sefar) on 0.5X MS medium and transferred 7d after germination under 16h light/8h dark conditions to 10µM NPA for 24h.
Extracted molecule total RNA
Extraction protocol Root samples were flash frozen in liquid nitrogen, RNA was extracted with the Universal RNA purification kit.
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 Reads were mapped onto the Arabidopsis thaliana genome (TAIR10) and numbers of reads per transcripts computed using STAR (version 2.5.2b) with options: --runThreadN 36 --quantMode TranscriptomeSAM GeneCounts
Subsequent analysis of differentially expressed genes was performed in R using the DEseq2 package (Love, M. I. et al. Genome Biology 15, (2014))
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include counts values per transcript for each Sample
 
Submission date Mar 23, 2022
Last update date Mar 24, 2022
Contact name Alexis Maizel
E-mail(s) alexis.maizel@cos.uni-heidelberg.de
Organization name Heidelberg University
Department Center for Organismal Studies
Street address Im Neuenheimer Feld 230
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL19580
Series (2)
GSE199202 Transcriptome profiling of Arabidopsis roots upon lateral root induction in WT and TOR knock down [dataset1]
GSE199211 TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana
Relations
BioSample SAMN26886341
SRA SRX14574451

Supplementary file Size Download File type/resource
GSM5966638_HV2WVBGX2_AlMa_May1_17_17s002655-1-1_Ibberson_lane114_sequence_counts.tab.gz 204.6 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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