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Sample GSM5966661 Query DataSets for GSM5966661
Status Public on Mar 23, 2022
Title TRAP_DMSO_3
Sample type SRA
 
Source name roots
Organism Arabidopsis thaliana
Characteristics genotype: transgenic line ubiquitously expressing a GFP-tagged RPL30
assay: TRAP
treatment: DMSO
tissue: roots
replicate: 3
Treatment protocol At 7 DAG, samples were treated for 16h with either with 10 µM AZD8055 or DMSO control media before being transferred to DMSO, 10 µM IAA, 10 µM AZD8055 or 10 µM AZD8055 + 10 µM IAA.
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.
Extracted molecule total RNA
Extraction protocol Root tissues were dissected after 6h. All sampling were performed in triplicate. For each sample, about 1500 segments of the lower two-thirds of the seedling roots were pooled, flash frozen in liquid nitrogen and later homogenised with a polysome-extraction buffer (Thellmann et al, 2020). The suspension was centrifuged for 15 min (16 000 g, 4°C). An aliquot of the homogenate was used for Bulk-RNA-extraction by use of TRIzol reagent (Invitrogen). The remaining supernatant was incubated with GFP-Trap® Magnetic Agarose beads (Chromotek, Munich, Germany). Ribosomal bound RNA was obtained by immunoprecipitation with magnetic anti-GFP beads in accordance with the manufacturer’s instructions and subsequently purified by use of TRIzol reagent (Invitrogen).
Illumina NextSeq libraries were prepared from 2 µg of total RNA (bulk) or 100ng (Ribosome bound) after depleting the rRNA via Ribo-Zero Plus rRNA Depletion Kit (Illumina) and sequencing performed on NextSeq 500 flow cells (12 samples per cell).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description total RNA - RiboZero
TRAP_10
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 23, 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)
GSE199203 Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]
GSE199211 TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana
Relations
BioSample SAMN26886318
SRA SRX14574424

Supplementary file Size Download File type/resource
GSM5966661_TRAP_010_trimmed_counts.tab.gz 186.7 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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