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Sample GSM2472780 Query DataSets for GSM2472780
Status Public on Nov 15, 2017
Title cyc-mock1
Sample type SRA
 
Source name inflorescence
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia-0
tissue: inflorescence
age: 30 days after germination
developmental stage: until flower stage 3-4
Treatment protocol 10µM cycloheximide, 0.01% ethanol,0.015% Silwet, with or without 10µM dexamethasone,
Growth protocol 23°C; 65% humidity; 16h light/8h dark; LED lights 200µE
Extracted molecule total RNA
Extraction protocol RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg inout was used.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Quality control: FastQC
Read alignment: TOPHAT2
BAM SAM conversion: samtools
Read table reconstruction: HT-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with normalized read count table
 
Submission date Jan 31, 2017
Last update date May 15, 2019
Contact name Jan Lohmann
E-mail(s) jan.lohmann@cos.uni-heidelberg.de
Phone +49186784234
Organization name Centre for Organismal Studies
Department Stem Cell Biology
Lab Jan Lohmann
Street address Im Neuenheimer Feld, 230
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL19580
Series (2)
GSE94308 Control of plant cell fate transitions by transcriptional and hormonal signals [RNA-seq: cyc-mock_vs_cyc-dex_3h]
GSE94311 Control of plant cell fate transitions by transcriptional and hormonal signals
Relations
BioSample SAMN06284172
SRA SRX2529380

Supplementary file Size Download File type/resource
GSM2472780_ht_count_CYC-MOCK1_cat.txt.gz 105.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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