|
| Status |
Public on Sep 23, 2015 |
| Title |
Rings_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Ring stage Plasmodium falciparum
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
Stage: Rings
antibody: H3K4me3
antibody catalog/vendor: 07-473 (upstate)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Plasmodium falciparum strain 3D7 was cultured cultured in RPMI1640 medium supplemented with 25 mM HEPES, 0.5% AlbuMAX I, 1.77 mM sodium bicarbonate, 100 μM hypoxanthine and 12.5 μg ml-1 gentamicin sulfate at 37 °C. RBCs were prepared from fresh whole blood obtained from a healthy donor and stored at 4 °C for at least 1 day. Increased yields were obtained by subculturing every 2 days for 6–8 h before invasion. This was done by equally dividing the contents of each flask into two or more flasks and quickly restoring the hematocrit and medium volume in each of the flasks with fresh erythrocytes and fresh medium to keep the hematocrit between 1 and 1.5% in the required volume of culture medium. The culture was synchronized with 5% sorbitol and the parasites were collected at 18, 30 and 40 hpi for chromatin immunoprecipitation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and antibody-DNA complexes were isolated with antibody.
ChIP-seq libraries for all the samples were prepared from around 5 ng of DNA using fragment library construction kit from life technolofies for SoLiD sequencing. Briefly ChIPed DNA samples were end repaired and adapters were ligated using T4 DNA ligase. Ligated DNA were subsequently amplified using adapter specific barcoded primers for 15 cycles. DNA purification at every step was performed using Agencourt XP beads. Library profiles were assessed using Agilent bioanalyzer 2100 high sensitivityDNA kit. Equimolar amount of libraries were pooled and 50 bp reads were sequenced in-house using SoLiD 4.0.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
Chromatin IP using specific antibody
|
| Data processing |
Reference genome was converted to color-space using bowtie-build
ChIP-seq data were mapped using the Bowtie allowing two mismatches.
Bed files generated using Samtools
Genome_build: plasFalc1
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Nov 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Krishanpal Karmodiya |
| E-mail(s) |
krish@iiserpune.ac.in
|
| Organization name |
Indian Institute of Science Education and Research
|
| Department |
Center of Excellence in Epigenetics
|
| Street address |
Dr. Homi Bhabha Road
|
| City |
Pune |
| State/province |
Maharashtra |
| ZIP/Postal code |
411008 |
| Country |
India |
| |
|
| Platform ID |
GPL19422 |
| Series (1) |
| GSE63369 |
A comprehensive epigenome map of Plasmodium falciparum reveals unique mechanisms of transcriptional regulation |
|
| Relations |
| BioSample |
SAMN03198548 |
| SRA |
SRX761220 |
