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Sample GSM4764869 Query DataSets for GSM4764869
Status Public on Apr 14, 2021
Title HiC_Pfhmgb1_KO_rep3
Sample type SRA
 
Source name HiC_Pfhmgb1_KO_rep3
Organism Plasmodium falciparum
Characteristics development stage: Ring
strain: Pf 3D7
digestion enzyme: DpnII
genotype: Pfhmgb1 Knock Down
host: Homo sapiens
Treatment protocol Synchronized parasites at ring stage were cross-linked with 1% paraformaldehyde for 10 min, stopped with 0.125 M glycine for 5min and released with 0.15% saponin.
Growth protocol P. falciparum 3D7strain with 2% hematocrit was cultured in medium containing 10.44g/L RPMI-1640, 25mM HEPES, 10% Albumax I, 20μg/ml gentamicin, 0.1 mM hypoxanthine, a gas phase with 5% O2, 3% CO2 at 37 °C. Parasites were synchronized by 5% sorbitol and a 40%/70% Percoll gradient centrifugation.
Extracted molecule genomic DNA
Extraction protocol Parasites were lysed in 5 ml ice-cold lysis buffer with rotation for 1 h at 4 °C and washed twice with PBS and once with 1×NEBuffer 2. Pelleted nuclei was resuspended with 300 μl H2O, 44 μl of 10×NEBuffer 2 and 38 μl of 1% SDS at 65 °C water bath 10 minutes and reaction was terminated by addition of T44 μl of 10% Triton X-100. To fragment DNA, 350 U endonucleases DpnII (NEB,R0543M) was added to the reaction at 37 °C overnight. Digested DNA was filled in the restriction fragment overhangs with Klenow (NEB,M0210L) and marked the DNA ends with biotin. Chromatin was then ligated with T4 DNA ligase(NEB) for 4 h at 16 °C, reversed with proteinase K and purified with phenol:chloroform and ethanol protocol. After removal of biotin from un-ligated ends with T4 DNA polymerase (NEB, M0203L), DNA was sonicated to reduce their size to 300-500 bp.
To prepare biotinylated DNA, sheared DNA were immobilized on Dynabeads M-280 Streptavidin at room temperature for 1 h with rotation. The process of ends repair, A-tailing and adaptor ligation referring to ChIP library, the Hi-C library was amplified 6-10 cycles and the PCR product was loaded to 2% agarose and size selected 300-600bp band.
The library were sequenced on an Illumina HiSeq Xten system with PE150 strategy.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description HiC_Pfhmgb1_KO_rep3
KO_2000_iced.matrix
Data processing The adaptor and low-quality sequences were trimmed from the reads using cutadapt(v1.18). Then the clean reads were processed (i.e., mapping, filtering, pairing, removing duplicates and normalizing) using HiC-Pro package(v2.11.1) as described. In brief, each end of read pairs was mapped to Plasmodium falciparum 3D7 genome (Pf 3D7 v32) using bowtie2 with default parameters in HiC-Pro configure files. The alignment results were saved in a bam format file, respectively. On the basis of the alignment results, the reads were re-paired to remove singleton, multi-hits, low-MAPQ and unmapped reads. The pairable reads were assigned to DpnII restriction fragments for filtering dangling-end, self-circle ligation and PCR duplicates. The raw contact matrix was generated for each sample of each replicate at a resolution of 10-kb and then normalized using the iterative correction and eigenvector decomposition (ICE) method to correct for experimental and technical biases.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: *matrix: Normalized contact matrix at 2kb resolution of HiC sequencing data for different samples.
Supplementary_files_format_and_content: 2k_abs.bed: Contact region.
 
Submission date Sep 03, 2020
Last update date Apr 14, 2021
Contact name meng liu
E-mail(s) 1710949@tongji.edu.cn
Organization name TongJi University
Street address 1239,SiPing Road
City shanghai
ZIP/Postal code 20082
Country China
 
Platform ID GPL26835
Series (2)
GSE141759 HMGB1 is required for virulence gene expression via configuration of genome architecture in Plasmodium falciparum [HiC]
GSE141762 HMGB1 is required for virulence gene expression via configuration of genome architecture in Plasmodium falciparum
Relations
BioSample SAMN16053467
SRA SRX9069544

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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