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| Status |
Public on May 07, 2023 |
| Title |
A1b-A2_37 |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: young seedlings
treatment: 37°C for 45min
genotype: Col-0
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from young seedlings of Col-0 using CTAB method, and digested with RNase A and cleaned using phenol: chloroform: isoamylalcohol.
Isolated genomic DNA was sonicated to an average length of 200 bp in Covaris sonicator and quantified. After sonication, fragmented genomic DNA was end prepared and adaptor ligated according to the protocol of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645), and purified using NaOAc and ethanol. The DNA was diluted in Elution buffer (10 mM Tris-HCl, pH 8.5) and measured using Qubit dsDNA HS Assay Kit. 200-300 ng prepared DNA was used for each binding reaction. cDNA sequences of HSFA1b, HSFA2 and HSFA3 were subcloned into pIX-HALO. HALO-tagged HSFs were expressed in the TNT wheat germ expression system (Promega). Different combinations of HSFs or HALO (negative control) were incubated with prepared DNA overnight at room temperature, respectively. For 37°C treatment, the samples were treated at 37°C for 45 min before overnight incubation at room temperature. Washing and DNA recovery steps were as described (Bartlett et al., 2017). The recovered DNA was amplified using Q5 Master Mix and different index primers in NEBNext® Ultra™ II DNA Library Prep Kit, then pooled and size selected (200-700 bp) by gel fractionation. 10 nM DNA library was sequenced using NextSeq 500/550 Mid output Kit (300 cycles), 150 bp SE reads.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: DAP-seq
Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using bwa mem (Li, 2013; http://arxiv.org/abs/1303.3997) version 0.7.12-r1044.
Mappings were sorted and indexed using samtools (Li et al., 2009; http://doi.org/10.1093/bioinformatics/btp352) version 1.3.1.
RPGC normalized coverage tracks were generated using the deepTools (Ramírez et al., 2016; http://doi.org/10.1093/nar/gkw257) version 1.50 bamCoverage function.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Normalized coverage files in bigWig format.
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| Submission date |
Dec 21, 2021 |
| Last update date |
May 07, 2023 |
| Contact name |
Isabel Bäurle |
| E-mail(s) |
[email protected]
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| Phone |
+49 331 9772647
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| Organization name |
Universität Potsdam
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| Department |
Institut für Biochemie und Biologie
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| Street address |
Karl-Liebknecht-Str. 24-25
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| City |
Potsdam |
| ZIP/Postal code |
14476 |
| Country |
Germany |
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| Platform ID |
GPL19580 |
| Series (2) |
| GSE192407 |
HSFA2 and HSFA3 binding after heat acclimation [DAP-seq] |
| GSE192431 |
HSFA2 and HSFA3 binding after heat acclimation |
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| Relations |
| BioSample |
SAMN24287273 |
| SRA |
SRX13474988 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5746471_A1b-A2-37_ATTCCT_S13.SeqDepthNorm.bw |
32.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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