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Sample GSM2491656 Query DataSets for GSM2491656
Status Public on Sep 29, 2017
Title RNA-seq_TK_17c_15min
Sample type SRA
 
Source name TK Wild Type
Organism Arabidopsis thaliana
Characteristics shift experiment: 17c>27c
temperature: 17c
incubation time: 15min
replicate: 1st
Growth protocol Seedlings were grown at 17c in long days for 10 days and collected after 15min, 1hr or 4hrs of shift at 17c, 27c or 37c. Shifts were done at ZT1
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 30 mg of grinded seedlings using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using 1 ug of high integrity total RNA (RIN>8) using the TruSeq Stranded mRNA library preparation kit and TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2101 and RS-122-2001), following manufacturer’s instruction. The libraries were sequenced on a HiSeq2000 using paired-end sequencing of 100 bp in length at Max Planck Institute (MPI) Tubingen and the Beijing Genomics Institute (BGI) sequencing centres.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed.
Genome_build: TAIR10
 
Submission date Feb 14, 2017
Last update date May 15, 2019
Contact name Sandra Cortijo
E-mail(s) sandra.cortijo@slcu.cam.ac.uk
Organization name Sainsbury Laboratory, Cambridge University
Street address Bateman Street
City Cambridge
ZIP/Postal code CB2 1LR
Country United Kingdom
 
Platform ID GPL19580
Series (2)
GSE79355 Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana
GSE94900 Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-Seq II]
Relations
BioSample SAMN06334873
SRA SRX2563429

Supplementary file Size Download File type/resource
GSM2491656_RNA-seq_TK_17c_15min_4mismatches_combined_read.txt.gz 793.7 Kb (ftp)(http) TXT
GSM2491656_RNA-seq_TK_17c_15min_combined_read.txt.gz 792.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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