|
| Status |
Public on Nov 19, 2015 |
| Title |
397_MBD_neuroblastoma tumor |
| Sample type |
SRA |
| |
|
| Source name |
primary tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age of the patient at diagnosis (months): 18.4767123287671
inss stage: 2
mycn amplification status: non-amplified
overall survival time (days): 3555
overall survival status: alive
event-free survival time (days): 3555
event-free survival status: no event
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA fragmentation by shearing, followed by MBD capture (MethylCap kit of Diagenode)
NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Quality control by FastQC (version 0.9.2)
Paired-end read mapping to the human reference genome using Bowtie2 (version 2.0.0 beta7) and SAMtools (version 0.1.18)
Marking PCR duplicates by Picard (version 1.79)
Mapping quality control by SAMStat (version 1.08) and bamUtil (version 1.0.2)
Peak calling using MACS (version 1.4.0 beta)
Genome_build: hg19
Supplementary_files_format_and_content: .bam: .bam format was used as output file type for read mapping (Bowtie2; duplicates are removed); .bed: location and score of the identified peaks (MACS); .wig.gz: visualization (MACS); .tdf: visualization of the methyl-seq data in IGV.
|
| |
|
| Submission date |
May 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anneleen Decock |
| E-mail(s) |
a.decock@ugent.be
|
| Organization name |
Ghent University
|
| Lab |
Center for Medical Genetics
|
| Street address |
De Pintelaan 185
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE69224 |
Methyl-CpG-binding domain (MBD) sequencing of 42 primary neuroblastoma tumors |
| GSE69279 |
Methyl-CpG-binding domain (MBD) sequencing of neuroblastoma tumors |
|
| Relations |
| BioSample |
SAMN03734719 |
| SRA |
SRX1038690 |
