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| Status |
Public on Jan 20, 2023 |
| Title |
GM12878_FC4 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell line: GM12878
cell type: B-Lymphocyte
genotype: WT
Sex: female
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| Growth protocol |
Human B lymphocytes GM12878 cells(Coriell Institue) and K562 cells were incubated in 1 × RPMI1640 media supplemented with 15%(GM12878) or 10%(K562) fetal bovine serum at 37 °C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
15 million GM12878 or K562 cells were spun down and resuspended in 10 ml fresh medium. Cells were fixed with 1% formaldehyde and incubating for 10 minutes at room temperature (RT). After quenching, cell were lysed and cell nuclei were collected, then chromatin was digested with DpnII restriction enzyme and ligated with T4 DNA ligase, and recrosslinking reversal was performed with Proteinase K or Pronase. Finally DNA was purified using Phenol-Chloroform Isoamyl alcohol method.
A total amount of 3-4ug purified DNA per sample was used as input material for the ONT library preparations. After the sample was qualified, size select of ligation DNA > 3kb were performed using the PippinHT system(Sage Science, USA). Next, the ends of DNA were repaired, and A-ligation reaction were conducted with NEBNext Ultra II End Repair/dA-tailing Kit(Cat# E7546). The adapter in the SQK-LSK109(Oxford Nanopore Technologies, UK) was used for further ligation reaction and DNA library was measured by Qubit 4.0 Fluorometer(Invitrogen, USA).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
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| Description |
The read alignment result file contains genome annotation information for HiPore-C reads and ligated fragments.
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| Data processing |
Basecalls were performed using Guppy v4.5.3 with high-accuracy basecalling model “dna_r9.4.1_450bps_hac_prom.cfg”, and reads with quality score less than 7 were filtered.
HiPore-C reads were aligned and annotated with our in-house developed MapPore-C pipeline.
The 5mC methylation were called using Megalodon v2.0.3 with model “res_dna_r941_prom_modbases_5mC_v001.cfg” in GPU servers.
Genome pairwise-contacts were generated by in-house python scripts, and cool/mool, hic files were generated using cooler v0.8.6.post0 and juice tools v1.22.1, respectively.
Assembly: hg38
Supplementary files format and content: alignment_csv
Library strategy: in situ HiPore-C Seq
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| Submission date |
May 09, 2022 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Jiayong Zhong |
| Organization name |
Zhongshan Ophthalmic Centre, Sun Yat-sen University
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| Department |
State Key Laboratory of Ophthalmology, Clinical Research Center for Ocular Disease
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| Street address |
Jinsui Road No.7
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| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE202539 |
in situ HiPore-C reveals higher-order 3D genome folding principles |
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| Relations |
| BioSample |
SAMN28161068 |
| SRA |
SRX15212801 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6124013_GM12878_FC4_reads_alignment.csv.gz |
5.2 Gb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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