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| Status |
Public on Jun 19, 2019 |
| Title |
Single-cell Hi-C data of shoot cell 4 |
| Sample type |
SRA |
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| Source name |
Single shoot cell of rice
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cell type: Shoot cell isolated from 12-day-after-germination seedling
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 |
Jun 19, 2019 |
| Last update date |
Jun 20, 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 |
SAMN12094988 |
| SRA |
SRX6093639 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3897719_Shoot_cell_4.ncc.txt.gz |
53.8 Kb |
(ftp)(http) |
TXT |
| GSM3897719_Shoot_cell_4.pdb.gz |
1.4 Mb |
(ftp)(http) |
PDB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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