NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6351383 Query DataSets for GSM6351383
Status Public on Nov 03, 2022
Title NF54 H3K9me3
Sample type SRA
 
Source name Cell Culture
Organism Plasmodium falciparum
Characteristics tissue: Cell Culture
parental line: NF54
subclone: No
Stage: late trophozoite-early schizont stage
chip antibody: Diagenode, C15410193
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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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)
 
Submission date Jul 19, 2022
Last update date Nov 03, 2022
Contact name Lucas Michel-Todó
E-mail(s) lucas.michel@isglobal.org
Organization name ISGlobal
Department Malaria Epigenetics
Street address Roselló, 149
City Barcelona
State/province Barcelona
ZIP/Postal code 08036
Country Spain
 
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
Relations
BioSample SAMN29828434
SRA SRX16342376

Supplementary file Size Download File type/resource
GSM6351383_NF54_me_Macspeaks_peaks.narrowPeak.gz 19.9 Kb (ftp)(http) NARROWPEAK
GSM6351383_NF54_me_sort_q5_noDup_rpkm_normInput_bs10_smth200_pseudo10.bedgraph.gz 18.9 Mb (ftp)(http) BEDGRAPH
GSM6351383_NF54_me_sort_q5_noDup_rpkmt_bs10_smth200.bedgraph.gz 18.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap