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| Status |
Public on Oct 03, 2013 |
| Title |
MID5_GBM_100U |
| Sample type |
SRA |
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| Source name |
glioblastoma cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: glioblastoma tumor cells
m.cvipi activity: 100U
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| Treatment protocol |
Nuclei were prepared and probed with 0U or 100U M.CviPI activity according to standard MAPit protocol.
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| Growth protocol |
Cells were grown in serum-free spheroid suspension culture (i.e. neurosphere culture conditions)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with phenol:chloroform:isoamylalcohol and perceipitated with ethanol and salt.
Libraries were prepared for each sample using bisulfite-patch-PCR protocol. Briefly, purified genomic DNA is digested by a restriction enzyme into fragments with defined ends. After denaturation, in a multiplexed reaction, both ends of selected target loci are hybridized and ligated to specific patch oligonucleotides and universal priming sequences. After enzymatic enrichment of ligated loci, PCR is performed using primers with platform-specific adapter and universal sequences. Barcoded products are then pooled, purified and sequenced.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
454 GS FLX Titanium |
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| Description |
deaminated
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| Data processing |
library strategy: Bisulfite-seq (amplicon)
Base and quality scores from instrument software
Barcodes called by fastools called through Python
Sequences aligned to references by blastn following in silico deamination by Python
Images generated by MethylMapper
(Python pipeline software, fastools, MethylMapper available on request)
Genome_build: AluBIpatch (amplicon reference library). There is no a publication reference or URL for the AluBI patch. Rather, sequences have been provided as AluBIpatch.fa (linked as supplementary file on Series record). AluBIpatch.fa is a database of reference sequences (no reads are aligned to them in this ".fa" file).
Supplementary_files_format_and_content: report.tsv table reporting reads assigned to each sample/locus/strand (linked as supplementary file on Series record), *.tsv tables reporting methylation/accessiblity of sites/patches on indivdiual molecules.
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| Submission date |
Aug 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Nancy H Nabilsi |
| Phone |
325-273-8145
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| Organization name |
University of Florida
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| Department |
Biochemistry and Mol Bio
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL14603 |
| Series (1) |
| GSE50047 |
Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma |
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| Relations |
| BioSample |
SAMN02324140 |
| SRA |
SRX337515 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1213140_processed_MID5.tsv.gz |
586.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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