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Status |
Public on May 26, 2019 |
Title |
Single-cell Hi-C data of egg 4 |
Sample type |
SRA |
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Source name |
Single egg of rice
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Organism |
Oryza sativa Japonica Group |
Characteristics |
cell type: Egg isolated from rice non-pollinated florets cultivar: Dongjin
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Growth protocol |
Rice seeds were germinated and grown in a greenhouse or in paddy field.
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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.
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
HiSeq X Ten |
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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.
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Submission date |
Nov 29, 2018 |
Last update date |
May 26, 2019 |
Contact name |
shaoli zhou |
E-mail(s) |
zhoushaoli@mail.hzau.edu.cn
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Organization name |
Huazhong Agricultural University
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Department |
National Key Laboratory of Crop Genetic Improvement
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Street address |
shizishan street
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City |
Wuhan |
State/province |
Hubei |
ZIP/Postal code |
430070 |
Country |
China |
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Platform ID |
GPL23876 |
Series (1) |
GSE123109 |
Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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