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Status |
Public on May 23, 2021 |
Title |
3_col-0_0h_rep1 |
Sample type |
SRA |
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Source name |
seedlings
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Organism |
Arabidopsis thaliana |
Characteristics |
tissue: seedlings day: 7-day-old genotype: col-0,WT time point: 0h
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Treatment protocol |
1/2 Ms + 100 mM NaCl treatment for 0, 1, 3, 6, 12, 24, 48 and 72 hr
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Growth protocol |
1: 7-day-old Col-0 seedlings liquid grown in 1/2 MS, continuous light; 2: 7-day-old Tak1 gemma liquid grown in 1/2 B5, continuous light; 3: 7-day-old Col-0 and wrky25/33 ko mutant seedlings liquid grown in 1/2 MS, continuous light; 4: 7-day-old NB seedlings grwon on 1/2 MS plates, 16/8 Light/Dark cycle; 5: 7-day-old Tak1 gemma liquid grown in 1/2 B5, continuous light; 6: 14-day-old Tak1 and respecitive WRKY 0E lines gemma liquid grown in 1/2 B5, continuous light
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Extracted molecule |
total RNA |
Extraction protocol |
1-5: Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen); 6: Nuclei was carried out by standard ChIP protocol, pull-down by tagRFP TRAP (Chromotek) 1-5: RNA libraries were prepared for sequencing using standard Illumina protocols; 6: Libraries were prepared according to Illumina's instructions
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
3_raw_reads_counts
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Data processing |
1-5: STAR for genome mapping; 6: Botwie 2 for genome mapping Genome_build: Arabidopisis: TAIR10; Marantica v3.1; Ricd: MSU7 Supplementary_files_format_and_content: 1-5: raw counts; 6: bigwig
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Submission date |
Jun 23, 2020 |
Last update date |
May 23, 2021 |
Contact name |
Daisuke Urano |
Organization name |
Temasek Life Science Laboratory
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Street address |
1 Research Link
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City |
Sinagpore |
ZIP/Postal code |
117604 |
Country |
Singapore |
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Platform ID |
GPL26208 |
Series (1) |
GSE153103 |
Time-course RNA-seq analysis of salt resonse in Arabidopsis and Marchantia |
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Relations |
BioSample |
SAMN15352635 |
SRA |
SRX8604171 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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