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| Status |
Public on Feb 05, 2019 |
| Title |
Si_nkd |
| Sample type |
SRA |
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| Source name |
Whole leaf
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| Organism |
Setaria italica |
| Characteristics |
tissue: Leaf
developmental stage: Fully expanded
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| Growth protocol |
S. bicolor, S. italica and Z. mays were grown under controlled conditions at the University of Cambridge in a chamber set to 12 h/12 h light/dark; 28 ºC light/20 ºC dark; 400µmol m-2 s-1 photon flux density, 60% humidity. For germination, S. bicolor and Z. mays seeds were imbibed in H2O for 48 h, S. italica seeds were incubated on wet filter paper at 30 ºC overnight in the dark. Z. mays, S. bicolor and S. italica were grown on 3:1 (v/v) M3 compost to medium vermiculite mixture, with a thin covering of soil. Seedlings were hand-watered. For B. distachyon plants were grown under controlled conditions at the Sainsbury Laboratory Cambridge University, first under short day conditions 14 h/10 h, light/dark for 2 weeks and then shifted to long day 20 h/4 h, light/dark, for 1 week and harvested at ZT20. Temperature was set at 20 ºC, humidity 65% and light intensity 350 µmol m-2 s-1.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Deproteinated DNA was extracted using a QIAGEN DNeasy Plant Mini Kit (QIAGEN, UK) according to the manufacturer’s instructions.
The extracted DNA samples were quantified fluorometrically using Qubit 3.0 Fluorometer (Life technologies), and a total of 1 ng of digested DNA was used for library construction. Sequencing ready libraries were prepared using a KAPA Hyper Prep Kit (KAPA Biosystems, London UK) according to the manufacturer’s instructions.
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
DNAse I digestion on deproteinated DNA
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| Data processing |
Reads were mapped to genomes using bowtie2 (Langmead and Salzberg, 2012) and processed using samtools (Li et al., 2009) to remove those with a MAPQ score <42.
Genome_build: The following genome assemblies were used: Bdistachyon_283_assembly_v2.0; Sbicolor_255_v2.0; Sitalica_164_v2; Zmays_284_AGPv3.
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| Submission date |
Feb 04, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Steven James Burgess |
| E-mail(s) |
[email protected]
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| Organization name |
University of Cambridge
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| Department |
Plant Sciences
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| Lab |
Molecular physiology
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| Street address |
Department of Plant Sciences, Downing College
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| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 3EA |
| Country |
United Kingdom |
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| Platform ID |
GPL23255 |
| Series (1) |
| GSE97369 |
DNase-SEQ analysis of whole leaf and bundle sheath tissues in Zea mays, Sorghum bicolor, Setaria italica and Brachypodium distachyon. |
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| Relations |
| BioSample |
SAMN10869584 |
| SRA |
SRX5330820 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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