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Sample GSM3495876 Query DataSets for GSM3495876
Status Public on May 26, 2019
Title Single-cell Hi-C data of egg 4
Sample type SRA
 
Source name Single egg of rice
Organism Oryza sativa Japonica Group
Characteristics cell type: Egg isolated from rice non-pollinated florets
cultivar: Dongjin
Growth protocol Rice seeds were germinated and grown in a greenhouse or in paddy field.
Extracted molecule genomic DNA
Extraction protocol After isolation, cells were immediately aspirated with a glass micropipette and blown out to 0.53 M mannitol (pH 5.7, adjusted with 0.1 M MES) containing 2% (v/v) formaldehyde by using a glass micropipette system. After 15 minutes, the cells were aspirated and blown out to fresh 0.53 M mannitol without formaldehyde for washing, Finally, the fixed clean cells were aspirated one by one, and blown into a 200 μl PCR well containing 7.7 μl Dpn II buffer (1X), at 4°C and kept on ice for next steps.
For the precise protocol for library construction, please see the paper of this data linked to. Briefly,7.7 μl 1×Dpn II buffer containing single cell was heated in 62 °C for 7 min to directly lyse cell and to loosen the nuclear membrane.For each well, 0.3 μl (3 U) Dpn II (R0543, NEB) was added after cooling, and incubate at 37 °C for 14 hours.Denature Dpn II at 62 °C for 10 min. Add 2 μl ligation mixture (1 μl 10×T4 ligase buffer, 1 μl (400 U) T4 DNA ligase, M0202, NEB),hold at 16 °C for 4.5 hours, then at room temperature for 30 min.Denature ligase and de-crosslink at 65 °C for 6 hours. DNA amplification was applied with REPLI-g Single Cell Kit (150345, QIAGEN).Shear DNA to 150-500 bp range by sonication.Finally,contruct the library for illumina sequencing by following the classic steps including end repairing, adaptor ligation, and DNA amplification.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing Library strategy: Single cell Hi-C
The Nuc_processing software was used to take paired sequenced fastq files to create processed single-cell Hi-C contact files (ncc). The Nuc_dymanic software (parameter: -s 8 2 1 0.5 0.2 0.1 0.05 0.02 0.01 0.005) was used to calculated single cell genome structure, the output files (pdb) were for viewing the 3D genome structures in pymol.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: For ncc and pdb file were all blank-delimited text files of output of Nuc_processing and Nuc_dynamic softwares, respectively.
 
Submission date Nov 29, 2018
Last update date May 26, 2019
Contact name shaoli zhou
E-mail(s) zhoushaoli@mail.hzau.edu.cn
Organization name Huazhong Agricultural University
Department National Key Laboratory of Crop Genetic Improvement
Street address shizishan street
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
 
Platform ID GPL23876
Series (1)
GSE123109 Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote
Relations
BioSample SAMN10497977
SRA SRX5078298

Supplementary file Size Download File type/resource
GSM3495876_Egg_4.ncc.txt.gz 147.8 Kb (ftp)(http) TXT
GSM3495876_Egg_4.pdb.gz 1.5 Mb (ftp)(http) PDB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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