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| Status |
Public on Nov 03, 2022 |
| Title |
10G input |
| Sample type |
SRA |
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| Source name |
Cell Culture
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| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: Cell Culture
parental line: 3D7-A
subclone: Yes
Stage: late trophozoite-early schizont stage
chip antibody: None
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| Growth protocol |
Plasmodium falciparum parasites (3D7 line) were maintained at a 3% hematocrit with B+ erythrocytes in standard parasite culture medium with Albumax II and no human serum, in a 5% CO2, 3% 02, balance N2 atmosphere.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sorbitol-synchronized cultures at the late trophozoite-early schizont stage were saponin lysated and formaldehyde cross-linked. Chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies) and sonicated using a Covaris M220 sonicator.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 4 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 8-10 cycles on the thermocycler.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Quality check was perfomed using FastQC (v.0.11.9) and reads were trimmed and repetitive k-mers removed using BBDUK (v.36.99), with parameters ktrim = r, k = 22, and mink = 6
Reads were aligned to the reference genome (P. falciparum 3D7, plasmoDB release 28) using Bowtie2 (v.2.3.0)
Duplicated reads were excluded using PICARD suite (v.4.1.9.0) with the RemoveDuplicates command
Peak calling was performed using MACS2 (v.2.2.7.1) with parameters “-f BAMPE -B -g 2.41e7 --keep-dup all --fe-cutoff 1.5 -nomodel --extsize 150”.
Coverage as RPKMs was generated for each sample at 10 bp resolution, using DeepTools (v. 3.5.0) BamCoverage command with parameters “--normalizeUsing RPKM -bs 10 --smoothLength 200”
Normalized coverage of enrichment over input (log2-transformed) at 10 bp resolution, we used the DeepTools (v. 3.5.0) BamCompare command with parameters “--normalizeUsing RPKM -bs 10 --smoothLength 200 –pseudocount 10”
Assembly: P. falciparum 3D7, plasmoDB release 28
Supplementary files format and content: Bedgraph: Coverage as RPKMs
Supplementary files format and content: Bedgraph: Coverage as input normalized RPKMs (except input samples)
Supplementary files format and content: narrowPeak: Peaks called using MACS2 (except input samples)
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| Submission date |
Jul 19, 2022 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Lucas Michel-Todó |
| E-mail(s) |
lucas.michel@isglobal.org
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| Organization name |
ISGlobal
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| Department |
Malaria Epigenetics
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| Street address |
Roselló, 149
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| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
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| Platform ID |
GPL21078 |
| Series (2) |
| GSE208560 |
Patterns of heterochromatin distribution alterations linked to transcriptional changes at Plasmodium falciparum clonally variant gene loci [ChIP-seq] |
| GSE208561 |
Patterns of heterochromatin distribution alterations linked to transcriptional changes at Plasmodium falciparum clonally variant gene loci |
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| Relations |
| BioSample |
SAMN29828442 |
| SRA |
SRX16342368 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6351375_10G_in_sort_q5_noDup_rpkmt_bs10_smth200.bedgraph.gz |
16.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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