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| Status |
Public on Jul 04, 2018 |
| Title |
Cp_immature_DNase-seq |
| Sample type |
SRA |
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| Source name |
immature fruit flesh
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| Organism |
Carica papaya |
| Characteristics |
cultivar: Tainong1
tissue: fruit flesh
developmental stage: immature
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase-Seq was performed as described in 1. Grøntved, L. et al., Epigenetics Chromatin 5, 10 (2012). The purified nuclei were suspended in 500 ul of nuclease digestion buffer (30 mM Tris-HCl pH 8.0, 14 mM MgCl2, 0.5% NP-40, 0.2% BSA) containing different concentration of DNase (Cyanase, RiboSolutions). After a short incubation at 37°C for 3 min, the digestion was immediately terminated by adding EDTA and SDS. RNase A was then added to digest the RNA. The DNA was purified by Phenol/Chloroform extraction and ethanol precipitation. The purified total DNA was run on a 2% agarose gel and the small fragments released by the DNase digestion were purified and converted to Illumina TruSeq libraries as described in He, H.H. et al., Nat. Methods, 2014.
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Cp_immature
sequencing instrument(s): Illumina HiSeq 4000,HiSeq X Ten
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| Data processing |
Most of the sequencing and base-calling services were provide by CloudHealth Genomics, Ltd. (Shanghai).
For RNA-Seq dataset, raw data was aligned to a home maintained rDNA database using Bowtie2 (version 2.1.0) with default parameters to filter out any rRNA sequence. Retained reads were then mapped to genome reference using TopHat2 (v2.1.1) with parameters: --read-realign-edit-dist 0 --max-intron-length 10000 --max-segment-intron 10000 --prefilter-multihits. FPKM value of each gene was calculated using StringTie (v1.3.1c) with parameters: -e -j 3 -f 0.2 -A. Raw read counts of genes were calculated using HTSeq (version 0.9.1) with parameters: --nonunique all.
For DNase-Seq and ChIP-Seq dataset, raw reads were mapped to the genome reference using Bowtie2 (version 2.1.0) with option: -3 100. For DNase-Seq and transcription factor ChIP-Seq datasets, peaks were called using MACS (ver 2.1.1.20160309), with the parameters: --nomodel -q 0.01 and -q 0.01, respectively. For H3K27me3 ChIP-Seq dataset, peaks were called using SICER (version 1.1) with the settings: window size 150, gap size 300, FDR 0.01. H3K27me3 candidate peaks were filtered further by their length, fold of enrichment and FDR: 1. peaks shorter than 300 bp was discarded; 2. for peaks shorter than 1kb, fold of enrichment and FDR requirement cutoff were setted as 5 and 1e-50, respectively for apple and tomato datasets, 4 and 1e-50 repectively for banana, grape and pear datasets, 3 and 1e-5 for datasets of other species; 3. for peaks longer than 1kb, fold of enrichment cutoff were setted as 4 for apple and tomato datasets, 3 for banana, grape and pear datasets, 2 for datasets of other species; Alignments with mapping score less than 10 and PCR duplicates were discarded using samtools before peak calling. bedgraph file generated by MACS with --SPMR enabled was converted to bw file using bedGraphToBigWig.
For Bisulfite-Seq dataset, raw data was mapped to genome reference using BSMAP (version 2.90) with the parameters: -A AGATCGGAAGAGC -w 100 -r 0 -q 10. Methylation ratio of each cytosine was calculated using methratio.py with the parameters: -z -r. The result file was compressed using bgzip and index using tabix.
Genome_build: Arabidopsis thaliana: genome release 9 (assembly), TAIR10 (annotation), https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Athaliana
Genome_build: Apple: GDDH13 Version 1.1 (assembly), GDDH13 Version 1.1 (annotation), https://iris.angers.inra.fr/gddh13/
Genome_build: Banana: DH-Pahang v2 (assembly), DH-Pahang v2 (annotation), http://banana-genome.cirad.fr/content/download-dh-pahang
Genome_build: Cucumber: Chinese long v2 (assembly), Chinese long v2 (annotation), ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/
Genome_build: Grape: Genoscope (12X) (assembly), CRIBI V2.1 (annotation), http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Genome_build: Melon: v3.5 (assembly), v3.5 (annotation), https://melonomics.net/files/Genome/Melon_genome_v3.5_Garcia-Mas_et_al_2012/
Genome_build: Papaya: ASGPBv0.4 (assembly), ASGPBv0.4 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Cpapaya
Genome_build: Peach: v1.0 (assembly), v1.0 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ppersica
Genome_build: Pear: Pbr_v1.0 (assembly), NCBI Annotation Release 101 (annotation), https://www.ncbi.nlm.nih.gov/genome/12793
Genome_build: Strawberry: v1.1 (assembly), v1.1 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Fvesca
Genome_build: Watermelon: v1 (assembly), v1 (annotation), ftp://www.icugi.org/pub/genome/watermelon/97103/v1/
Genome_build: Tomato: v2.5 (assembly), ITAG2.4 (annotation), ftp://ftp.solgenomics.net/tomato_genome/assembly/build_2.50/
Genome_build: Rice: Os-Nipponbare-Reference-IRGSP-1.0 (assembly), MSU release 7.0 (annotation), https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Osativa
Supplementary_files_format_and_content: For RNA-Seq dataset, tab delimited abundance file gives FPKM of each gene, tab delimited count file gives read counts of each gene
Supplementary_files_format_and_content: For Dnase-Seq dataset, bw file shows the read density across the entile genome, tab delimited file in narrowPeak format shows peak calling information generated by MACS2
Supplementary_files_format_and_content: For Bisulfite-Seq dataset, bgzip compressed tab delimited file gives all and mC counts of each genomic cytosine across the entile genome. Index file are also provided, so one can fast retrieve the data randomly using tabix.
Supplementary_files_format_and_content: For ChIP-Seq dataset, bw file shows the read density across the entile genome. For transcription factor ChIP-Seq dataset, tab delimited file in narrowPeak format shows peak calling information generated by MACS2. For H3K27me3 ChIP-Seq dataset, tab delimited file shows peak calling information generated by SICER.
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| Submission date |
Jul 03, 2018 |
| Last update date |
Jul 04, 2018 |
| Contact name |
Silin Zhong |
| E-mail(s) |
zhonglab.cuhk@gmail.com
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| Organization name |
CUHK
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| Department |
School of Life Sciences
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| Street address |
Shatin, N.T.
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| City |
Hong Hong |
| ZIP/Postal code |
NA |
| Country |
China |
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| Platform ID |
GPL25274 |
| Series (1) |
| GSE116581 |
fruitENCODE: An encyclopedia of DNA elements for fruit ripening |
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| Relations |
| BioSample |
SAMN06673735 |
| BioSample |
SAMN06673734 |
| SRA |
SRX2697833 |
| SRA |
SRX2697834 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3243330_Cp_immature_DNase-seq.bw |
55.8 Mb |
(ftp)(http) |
BW |
| GSM3243330_Cp_immature_DNase-seq.narrowPeak.gz |
545.2 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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