 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 11, 2018 |
| Title |
Pfal#4_hep |
| Sample type |
SRA |
| |
|
| Source name |
P.fallax_female from aquarium supply
|
| Organism |
Procambarus fallax |
| Characteristics |
strain: female from aquarium supply
tissue: hepatopancreas
|
| 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
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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)
|
| |
|
| Submission date |
Mar 27, 2018 |
| Last update date |
Oct 11, 2018 |
| Contact name |
Fanny Gatzmann |
| E-mail(s) |
f.gatzmann@dkfz.de
|
| Organization name |
DKFZ
|
| Department |
A130 Epigenetics
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| 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 |
|
| 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 |
|
|
|
|
 |
