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| Status |
Public on Sep 29, 2017 |
| Title |
RNA-seq_22c_1hr |
| Sample type |
SRA |
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| Source name |
Col0 WT seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Col0
tissue: seedlings
shift experiment: 22c>27c
temperature: 22c
incubation time: 1hr
replicate: 1st
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
Supplementary_files_format_and_content: text file with gene ID, FPKM, TPM and raw counts.
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| Submission date |
Mar 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sandra Cortijo |
| E-mail(s) |
sandra.cortijo@slcu.cam.ac.uk
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| Organization name |
Sainsbury Laboratory, Cambridge University
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| Street address |
Bateman Street
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1LR |
| Country |
United Kingdom |
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| Platform ID |
GPL19580 |
| Series (2) |
| GSE79353 |
Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-seq I] |
| GSE79355 |
Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana |
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| Relations |
| BioSample |
SAMN04565918 |
| SRA |
SRX1640019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2092764_rna-seq_col0_WT_22to22C_1hr_combined_read.txt.gz |
802.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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