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Sample GSM7229923 Query DataSets for GSM7229923
Status Public on Mar 04, 2024
Title Proximal-q3C-G1
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
cell type: CML
genotype: with FUCCI knock-in at the AAVS1 locus
cell cycle phase: G1
primer located within a fountain: Proximal
Treatment protocol Asynchronized cells were incubated with 10 uM Hoechst33342 for 45 min and then subjected to FACS analysis. The G1 and S1-S6 cells were collected, fixed by 1% PFA, digested by DpnII, and then ligated in situ.
Growth protocol K562-FUCCI Cells were cultured in RPMI-1640 medium supplemented with 15% fetal bovine serum (FBS), 10 mM HEPES, 100 mM non-essential amino acids (NEAA), 50 U/mL penicillin, 50 mg/mL streptomycin, and 50 mM b-mercaptoethanol without further indication.
Extracted molecule genomic DNA
Extraction protocol Standard protocols for genomic DNA extraction.
Genomic DNA was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description G1 phased cells
Data processing Illumina RTA software used for basecalling.
Both Illumina adapter sequences and ending low quality sequences (QC < 30) were trimmed by cutadapt (http://cutadapt.readthedocs.io/en/stable/); remaining reads shorter than 25bp were discarded.
The reported pipeline used in q3C-seq, termed PEM-Q (https://github.com/liumz93/PEM-Q), was applied to perform reads alignment and translocation break point detection.
The reported pipeline, PEM-Q, was applied to perform duplicates identification.
All samples were downsample to 16351 translocations by using bedtools sample -n .
Assembly: hg19
Supplementary files format and content: tab files indicating the junction site of chromatin interaction that downsampled from the original translocations
Library strategy: q3C-seq
 
Submission date Apr 26, 2023
Last update date Mar 04, 2024
Contact name Yang Liu
E-mail(s) liu.y@pku.edu.cn
Organization name School of life sciences, Peking University
Lab Jiazhi Hu lab
Street address Yiheyuan Road, No. 5
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL20795
Series (1)
GSE230613 Chromatin contacts within a fountain-like structure
Relations
BioSample SAMN34376328
SRA SRX20102993

Supplementary file Size Download File type/resource
GSM7229923_Proximal-q3C-G1.tab.gz 36.4 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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