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| Status |
Public on Feb 23, 2015 |
| Title |
B-ALL, hyperdiploid |
| Sample type |
SRA |
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| Source name |
B-cell acute lymphoblastic leukemia with hyperdiploid chromosomes
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| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow / peripheral blood
subjects: children with B-ALL (California Childhood Cancer Study)
age: 2.8
gender: F
cytogenetics: hyperdiploid
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions
We sheared the DNA by sonication to 50–500 bp with a Covaris E220, followed by selecting 150- to 300-bp fragments using AMPure XP beads (Agencourt Bioscience).
Genomic DNA libraries were constructed using the TruSeq Sample Preparation kit (Illumina).
Two rounds of sodium bisulfite-conversion of DNA using the EpiTexy Bisulfite kit (Qiagen) was performed to get a conversion efficiency of >99%.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
WGBS data of B-cell acute lymphoblastic leukemia cells
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| Data processing |
From the human genome (GRCh37) and NCBI viral genome (v35), two reference sequences including reference C2T (all Cs were replaced by T) and reference G2A (all Gs were replaced by A) were generated, and to these, each paired-end read was aligned using the GEM software.
Up to four mismatches were allowed, and read pairs with unique compatible mappings (to the same chromosome and in the expected orientation) were selected.
After mapping, most likely genotype and methylation % in each C were estimated, using the software developed at the Centro Nacional de Análisis Genómico, which takes into account the observed bases, base quality scores and the strand origin of each read pair.
The confidence in the genotype call was estimated by the Phred-scaled likelihood. CpG sites were selected where both bases were called as homozygous CC followed by GG with a Phred score of ≥20.
Sites with >500× coverage depth were excluded to avoid highly repetitive regions
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: tab-delimited text file include methylation % estimation for each CpG
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| Submission date |
Apr 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Seung-Tae Lee |
| E-mail(s) |
essere.lee@gmail.com
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| Phone |
+82-10-9933-5465
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| Organization name |
UCSF
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| Street address |
1450 3rd Street
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE56601 |
WGBS data of pediatric B-cell acute leukemias |
| GSE56602 |
Two-Track Epigenetic Remodeling and Backtracking to Embryonic Stem Cell Bivalency in B-cell Acute Lymphoblastic Leukemias |
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| Relations |
| BioSample |
SAMN02721468 |
| SRA |
SRX513207 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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