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Sample GSM4074122 Query DataSets for GSM4074122
Status Public on Jun 21, 2020
Title 178RS22
Sample type SRA
 
Source name seedling
Organism Arabidopsis thaliana
Characteristics genotype: ELF3pro::ELF3-Q21 #7
cultivar: Col-0
tissue: seedling
photoperiod: Short day (8L/16D)
temperature: 27C
replicate: single
fragmentation method: NA
chip antibody: NA
Growth protocol Arabidopsis seeds were sterilized and sown on standard half-strength Murashige and Skoog-agar (MS-agar) plates at pH 5.7. Sterilized seeds were stratified for 3 days at 4 ºC in the dark and allowed to germinate for 24 hours at 22 ºC under cool-white fluorescent light at 170 μmol m-2 s-1. The plates were then transferred to short photoperiod conditions (SDs, 8-h light and 16-h dark) at different temperatures. Seedlings were grown on plates for 10 days and harvested at the indicated time points.
Extracted molecule total RNA
Extraction protocol 70 mg of seedlings were pooled per tube and total RNA was extracted using MagMAX™-96 Total RNA Isolation Kit (ThermoFisher) according to the manufacturer‘s instruction.
Libraries were prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep FWD Kit (Illumina) according to manufacturer‘s instruction. The libraries were sequenced on the Illumina NextSeq 500 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Genome_build: TAIR10
Raw fastq were uploaded to Bluebee Genomics Platform and analysed with Quantseq FWD analysis pipeline (https://www.lexogen.com/quantseq-data-analysis/). Briefly, the raw reads were trimmed with BBDuk and aligned to GTF-annotated genome with STAR.
Supplementary_files_format_and_content: *.txt: TSV table containing abundance of transcripts by STAR.
Supplementary_files_format_and_content: *.bam: Genomic alignment by STAR.
 
Submission date Sep 11, 2019
Last update date Jun 21, 2020
Contact name Philip Wigge
E-mail(s) wigge@igzev.de
Organization name Cambridge University
Department Sainsbury Laboratory
Street address 47 Bateman street
City Cambridge
ZIP/Postal code CB2 1LR
Country United Kingdom
 
Platform ID GPL19580
Series (1)
GSE137264 RNA-Seq and ChIP-Seq profiling of ELF3, an prion-like domain-containig in ELF3 that functions as a thermosensor in Arabidopsis.
Relations
BioSample SAMN12727719
SRA SRX6830784

Supplementary file Size Download File type/resource
GSM4074122_178RS22.supp.read_counts.txt.gz 118.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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