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| Status |
Public on Apr 14, 2021 |
| Title |
HiC_Pfhmgb1_KO_rep3 |
| Sample type |
SRA |
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| Source name |
HiC_Pfhmgb1_KO_rep3
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| Organism |
Plasmodium falciparum |
| Characteristics |
development stage: Ring
strain: Pf 3D7
digestion enzyme: DpnII
genotype: Pfhmgb1 Knock Down
host: Homo sapiens
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| 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.
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| 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.
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| 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.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
HiC_Pfhmgb1_KO_rep3
KO_2000_iced.matrix
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| 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.
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| Submission date |
Sep 03, 2020 |
| Last update date |
Apr 14, 2021 |
| Contact name |
meng liu |
| E-mail(s) |
1710949@tongji.edu.cn
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| Organization name |
TongJi University
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| Street address |
1239,SiPing Road
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| City |
shanghai |
| ZIP/Postal code |
20082 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN16053467 |
| SRA |
SRX9069544 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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