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Status |
Public on Oct 11, 2018 |
Title |
Pfal#4_hep |
Sample type |
SRA |
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Source name |
P.fallax_female from aquarium supply
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Organism |
Procambarus fallax |
Characteristics |
strain: female from aquarium supply tissue: hepatopancreas
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Extracted molecule |
genomic DNA |
Extraction protocol |
Samples of organs and tissues from adult crayfish for DNA and RNA preparation were taken under a dissection microscope, snap-frozen in liquid nitrogen and stored at -80°C until extraction of nucleic acids. Embryonized eggs and juveniles were frozen in liquid nitrogen as a whole. Genomic DNA was isolated using the Blood & Cell Culture DNA Kit (Qiagen, Hilden, Germany) The TruSeq PCR-Free Library Prep Kit (LT) was used for library preparation, and the Epitect Kit (Qiagen) for bisulfite conversion. Library amplification was performed using the Kapa HiFi HotStart Uracil+ ReadyMix (2X). WGBS on an Illumina HiSeq platform
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Illumina Casava1.8.1 software used for basecalling. Preprocessing, read trimming: Trimmomatic 0.35 Preprocessing, quality filtering: Trimmomatic 0.35 WGBS mapping: BSMAP 2.73 methylation calling: BSMAP-provided script methratio.py select for CpGs and calculate total coverage and ratio at each CpG site Genome_build: Pvir0.4 Supplementary_files_format_and_content: sample_cov.bed: bed file for each CpG site with chrom, start, end, coverage Supplementary_files_format_and_content: sample_ratio.bed: bed file for each CpG site with chrom, start, end, methylation ratio (#methylated reads/#total reads at this position)
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Submission date |
Mar 27, 2018 |
Last update date |
Oct 11, 2018 |
Contact name |
Fanny Gatzmann |
E-mail(s) |
f.gatzmann@dkfz.de
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Organization name |
DKFZ
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Department |
A130 Epigenetics
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Street address |
Im Neuenheimer Feld 580
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City |
Heidelberg |
ZIP/Postal code |
69120 |
Country |
Germany |
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Platform ID |
GPL22798 |
Series (2) |
GSE112409 |
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [WGBS] |
GSE112411 |
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish |
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Relations |
BioSample |
SAMN08802936 |
SRA |
SRX3854650 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3069677_Pfal4_hep_cov.bed.gz |
319.1 Mb |
(ftp)(http) |
BED |
GSM3069677_Pfal4_hep_ratio.bed.gz |
305.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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