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| Status |
Public on Feb 15, 2024 |
| Title |
h1_seedling_MNase_rep2 |
| Sample type |
SRA |
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| Source name |
h1 seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype: h1
tissue: ten-day-old seedlings
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| Growth protocol |
Plants were grown under long day (16 hr light; 8 hr dark) conditions at 22 °C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
0.5 g of ten-day-old seedlings were ground with mortar and pestle in liquid nitrogen and homogenized in 10 mL of nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1 X proteinase inhibitors Cocktail) for 15 min on ice. Debris were filtered through two layers of miracloth to get nuclei suspension, which was then cold centrifuged at 4,000 g for 10 min. Nuclei were resuspended in 500 µL of TM2 (50 mM Tris-HCl, 2 mM MgCl2, 0.25 M sucrose, 1 mM PMSF, 1 X proteinase inhibitors Cocktail). After cold centrifugation at 4,000 g for 5 min, nuclei were resuspended in 400 µL of MNase digestion buffer (50 mM Tris-HCl pH 7.5, 5 mM CaCl2, 0.25 M sucrose, 1 mM PMSF, 1X proteinase inhibitors Cocktail) with 1000 U/mL final concentration of MNase (New England Biolabs) and incubated at 37°C with agitation (1000 rpm on Thermomixer) for 10 min. Digestion was stopped by adding 40 µL of 0.5 mM EDTA and 20 µL of 10% SDS. Proteinase K and RNase A were added to remove proteins and RNAs before Phenol-chloroform extraction to get DNA.
follow the instructions of Ovation Ultralow System V2 (Nugen) kit
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
SHXF63D.SDXF84
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| Data processing |
MNase-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. NuMap was then performed to compute nucleosome positions.
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read.
w1: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
w50: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb and 25 kb contact matrix (hic files).
Genome_build: TAIR10
Supplementary_files_format_and_content: MNase-seq: BED files of nucleosome positions.
Supplementary_files_format_and_content: Bisulfite-Seq: GFF files of fractional methylation data either for individual cytosines (w1) or in 50 bp windows (w50).
Supplementary_files_format_and_content: Hi-C: matrix and regions files of different resolutions generated by Fan-C contain genomic contacts and corresponding index information, respectively.
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| Submission date |
Jun 10, 2021 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Xiaoqi Feng |
| E-mail(s) |
xiaoqi.feng@jic.ac.uk
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| Organization name |
John Innes Centre
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| Department |
Cell and Developmental Biology
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| Lab |
Xiaoqi Feng
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| Street address |
Norwich Research Park
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| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE176526 |
Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis |
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| Relations |
| BioSample |
SAMN19655055 |
| SRA |
SRX11110852 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5368655_h1_seedling_nucleosome_rep2.bed.gz |
3.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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