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Status |
Public on Mar 04, 2024 |
Title |
Proximal-q3C-G1 |
Sample type |
SRA |
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Source name |
K562
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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
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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.
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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.
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
HiSeq X Ten |
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Description |
G1 phased cells
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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
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Submission date |
Apr 26, 2023 |
Last update date |
Mar 04, 2024 |
Contact name |
Yang Liu |
E-mail(s) |
liu.y@pku.edu.cn
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Organization name |
School of life sciences, Peking University
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Lab |
Jiazhi Hu lab
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Street address |
Yiheyuan Road, No. 5
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City |
Beijing |
ZIP/Postal code |
100871 |
Country |
China |
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Platform ID |
GPL20795 |
Series (1) |
GSE230613 |
Chromatin contacts within a fountain-like structure |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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