|
| Status |
Public on May 01, 2024 |
| Title |
dek3arp6_17_T0_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
dek3-2/arp6-1 seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
temperature: 17°C
time of the day: T0 (just before lights turn on)
replicate: 2nd
|
| Treatment protocol |
Growing in 17C or 27C
|
| Growth protocol |
Seedlings were grown at 17c or 27C in short days for 10 days and collected at 2 time pointes. ZT0 time point just before the lights are on (End of the night); ZT8-just before the light are off(end of the day)
|
| 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 NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, cat. No. NEB #E7420). Libraries were sequenced in-house on an Illumina NextGen 500 sequencer using paired-end sequencing of 75 bp in length.
|
| |
|
| 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 |
May 14, 2018 |
| Last update date |
May 01, 2024 |
| Contact name |
Anna Brestovitsky |
| Organization name |
Sainsbury Laboratory (SLCU), University of Cambridge
|
| Street address |
Bateman Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1LR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE114418 |
Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors [2 temperatures at 2 time points] |
| GSE114646 |
Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors |
|
| Relations |
| BioSample |
SAMN09207744 |
| SRA |
SRX4082254 |
