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| Status |
Public on Feb 15, 2024 |
| Title |
h1_seedling |
| 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 |
DNA was extracted from ten-day-old seedlings by CTAB method
follow the instructions of NEBNext® Ultra™ II DNA Library Prep Kit and EZ DNA Methylation-Lightning Kit
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
SHXF64B.SDXF86
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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 |
SAMN19655049 |
| SRA |
SRX11110858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5368661_SHXF64B.SDXF86_w1_CG.gff.gz |
38.6 Mb |
(ftp)(http) |
GFF |
| GSM5368661_SHXF64B.SDXF86_w1_CHG.gff.gz |
42.2 Mb |
(ftp)(http) |
GFF |
| GSM5368661_SHXF64B.SDXF86_w1_CHH.gff.gz |
196.0 Mb |
(ftp)(http) |
GFF |
| GSM5368661_SHXF64B.SDXF86_w50_CG.gff.gz |
19.1 Mb |
(ftp)(http) |
GFF |
| GSM5368661_SHXF64B.SDXF86_w50_CHG.gff.gz |
18.5 Mb |
(ftp)(http) |
GFF |
| GSM5368661_SHXF64B.SDXF86_w50_CHH.gff.gz |
23.1 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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