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| Status |
Public on Jul 14, 2023 |
| Title |
GM12878_low |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
cell type: lymphoblast cell
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| Growth protocol |
GM12878 (HG001) cell line and GM24385 (HG002) cell line were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 15%fetal bovine serum (FBS,Gibco,cat#26140079) and Penicillin/Streptomycin (PS; Gibco, cat#15140122). K562 cell line was cultured in RPMI-1640 supplemented with 10% FBS and 1% PS. COLO320DM cell line was cultured RPMI-1640 supplemented with 10% FBS and 1% PS. Wild-type V6.5 murine embryonic stem cells (mESCs) were cultured on 0.25% gelatin-coated 6-well plate in Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco, cat#11320033) containing 15%FBS,1%Glutamax(Gibco, cat#35050061),0.1mM 2-mercaptoethanol (Gibco, cat#21985023),1%MEM nonessential amino acids(Gibco, cat#11140050),1%nuleoside (Millipore, cat#ES-008-D), 1%PS and 10000× 107 units/ml Leukemia Inhibitory Factor (LIF; Millipore, cat#ESG1107). The other male mouse ES cell line (named F15) was cultured in serum-free 2i/LIF medium, with in equal volume of DMEM (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 131 21103049) maintained in 2i (3 uM CHIR99021 and 1 uM PD0325901), LIF (1 000 U/ml), as previously described. These cell lines were all cultured at 37 ˚C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Resuspended ligated nuclei pellets in 200μL 0.25%BSA in PBS each tube and added 0.2μL 1000×DAPI for sorting nuclei. Single nucleus was flow sorted into each well of 96-well plate containing 2 μL lysis buffer(0.04 μL 1M Tris-HCl (pH 8.0),0.08μL 500 mM NaCl,0.03μL10% Triton X-100 (Sigma), 0.0004μL 0.5 M EDTA,0.05μL 20mg/mL QIAGEN protease). And then to decrosslinking and digest, incubated at 50°C, 3h; 70°C, 20 min; 68°C, 45 min; 4°C pause. After digesting, 96-well plates were stored at −80 ˚C.
A total amount of 1 g DNA per sample was used as input material for the DNA library preparations. SQK-LSK109 Kit (Nanopore, UK) was used to construct 1D library. The DNA library was constructed by standard ligation method without DNA fragmentation, after end repaired, added the sequencing adaptor, motor protein and tether protein were connected to prepare the DNA library. After that, each amplicon fragment library was loaded into 1 R9 flow cell and sequenced on PromethION HAC (high accuracy) model.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
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| Description |
scNanoHi-C
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| Data processing |
Sequencing data were first demultiplexed to single cells by Nanoplexer using default parameters. Adapter sequences were trimmed by Cutadapt and reads shorter than 500bp were also removed. These cleaned reads of each cell were then fed into the Pore-C snakemake pipeline to align to reference genome using the bwasw algorithm, tag haplotype by whatshap using known phased SNV sites, assign to restriction fragments and identify high-order concatemers. The resulting single cells concatemer sets were further filtered to remove single-cell artifacts according to previous single-cell Hi-C methods, which included duplicated, promiscuous and isolated contacts. The final single-cell concatemer sets then could be decomposed into virtual pair-wise contacts (VPCs) to store in a parquet format and assigned to genomic bins for contacts map visualization with cooler in mcool format.
Assembly: GRh38 or mm10
Supplementary files format and content: .parquet: filtered pair-wise contacts file of scNanoHi-C single cells with metadata
Supplementary files format and content: .mcool scNanoHi-C pair-wise multi-resolution cooler contacts matrcies
Library strategy: scNanoHi-C
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| Submission date |
Nov 03, 2022 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Jiansen Lu |
| E-mail(s) |
jiansenlu@pku.edu.cn
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| Organization name |
Peking University
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| Department |
Biomedical Pioneering Innovation Center (BIOPIC)
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| Lab |
Fuchou Tang
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| Street address |
No. 5 Yiheyuan Road, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE217189 |
scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order structures within individual cells |
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| Relations |
| BioSample |
SAMN31589870 |
| SRA |
SRX18158267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6706396_GM12878_low_clean_parquet.tar.gz |
2.4 Gb |
(ftp)(http) |
TAR |
| GSM6706396_GM12878_low_mcool.tar.gz |
1.1 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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