|
| Status |
Public on Mar 16, 2016 |
| Title |
PCR-BS replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mixed blood stages of malaria parasites
|
| Organism |
Plasmodium berghei ANKA |
| Characteristics |
extract_protocol: PCR-BS (standard Bisulfite-Seq)
strain: Plasmodium berghei 2.34 ANKA strain
|
| Growth protocol |
6-10 week old Thieler‟s original mice were injected intraperitoneally with 0.2 mL of 6 mg/mL phenylhydrazine, and three days later infected with 5x107 parasites (Plasmodium berghei ANKA strain, clone 233). From day 6 onwards tail smears were taken to assay parasitaemia. Mice were bled by cardiac puncture
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted following standard protocols (Doolan, D. L. Methods in Molecular Medicine Volume 72: Malaria Methods and Protocols ed. Humana Press, Inc., Totowa, New Jersey, USA, pp. 25-40)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Standard Bisulfite-Seq replicate
grm037_BS_plasb2_AD04
|
| Data processing |
bcl files were converted to fastq using bcl2fastq v2.15.0.4 with defaut options.
Fastq reads where trimmed using trimugalore version 0.3.7 with cutadapt version 1.4.2. Option --stringency was set to 3.
Trimmed reads were aligned using bwameth.py (wrapper around bwa mem)
Mapping quality of reads with more then 10% mismatches was set to 0 using resetHighMismatchReads.py (https://code.google.com/p/bioinformatics-misc/source/browse/#svn%2Ftrunk)
Overlapping read pairs were clipped using clipOverlap in the BamUtil suite version 1.0.12.
The counts of converted and unconverted cytosine, i.e. the methylation status, in the P.berghei genome were obtained from the alignment files using bam2methylation.py (https://code.google.com/p/bioinformatics-misc/source/browse/#svn%2Ftrunk). Only reads with mapping quality 15 or above were considered and read bases with quality less than 13 were excluded from methylation calling. In addition, at each cytosine position the number of mismatches, i.e. the number of reads not A or C, was recorded.
Genome_build: The reference sequence for alignment was mouse genome version mm9 (UCSC) concatenated to Plasmodium berghei genome version 11 (http://plasmodb.org/common/downloads/release-11.0/PbergheiANKA/fasta/data/PlasmoDB-11.0_PbergheiANKAugenome.fasta)
Supplementary_files_format_and_content: 20140710.grm.met.txt.gz is a table of methylation calls in the Plasmodium berghei genome for each of the five libraries. The columns are:
chrom: Chromosome name
start: Cytosine position start (0 based)
end: Cytosine position end (always start+1)
strand: Strand of the cytosine
pct_met.<library id>: Percentage methylation (cnt_met / cnt_tot * 100) for sample <library id>
cnt_met.<library id>: Count of methylated (uncoverted) reads for sample <library id>
cnt_tot.<library id>: Total read depth for sample <library id> after filtering low quality reads and base calls.
p.fisher.<library id>: P-value from Fisher test for the null hypothesis that the observed methylation is not different from the error rate. Error rate is estimated from the number of calls different from C or T.
...
cnt_tot.all_rebuilt: Total read count for the ReBuilT libraries
cnt_met.all_rebuilt: Total methylation count for the ReBuilT libraries
p.all_rebuilt: Combined p value using Stouffer method from the individial ReBuilT libraries.
fdr.all_rebuilt: P-value in p.all_rebuilt adjusted using false discovery rate method.
cnt_tot.all_BS: Same as cnt_tot.all_rebuilt for the PCR-BS libraries
cnt_met.all_BS: Same as cnt_met.all_rebuilt for the PCR-BS libraries
p.all_BS: : Same as p.all_rebuilt for the PCR-BS libraries
fdr.all_BS: Same as fdr.all_rebuilt for the PCR-BS libraries
states: State inferred from the HMM model to identify runs of methylated cytosines. "u": Unmetylated run. "M": Methylated run
pct_met.all_rebuilt: Percentage methylation for the ReBuilT libraries (cnt_met.all_rebuilt / cnt_tot.all_rebuilt * 100)
|
| |
|
| Submission date |
Jan 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Beraldi |
| E-mail(s) |
[email protected]
|
| Organization name |
Cambridge Research Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19670 |
| Series (1) |
| GSE65116 |
Enhanced methylome sequencing by recovery of unsequenceable fragments |
|
| Relations |
| BioSample |
SAMN03288253 |
| SRA |
SRX848666 |
