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Sample GSM6124011 Query DataSets for GSM6124011
Status Public on Jan 20, 2023
Title GM12878_FC2
Sample type SRA
 
Source name blood
Organism Homo sapiens
Characteristics tissue: blood
cell line: GM12878
cell type: B-Lymphocyte
genotype: WT
Sex: female
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.
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).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model PromethION
 
Description The read alignment result file contains genome annotation information for HiPore-C reads and ligated fragments.
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
 
Submission date May 09, 2022
Last update date Jan 20, 2023
Contact name Jiayong Zhong
Organization name Zhongshan Ophthalmic Centre, Sun Yat-sen University
Department State Key Laboratory of Ophthalmology, Clinical Research Center for Ocular Disease
Street address Jinsui Road No.7
City Guangzhou
ZIP/Postal code 510632
Country China
 
Platform ID GPL26167
Series (1)
GSE202539 in situ HiPore-C reveals higher-order 3D genome folding principles
Relations
BioSample SAMN28161070
SRA SRX15212799

Supplementary file Size Download File type/resource
GSM6124011_GM12878_FC2_reads_alignment.csv.gz 3.0 Gb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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