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Sample GSM7885663 Query DataSets for GSM7885663
Status Public on Dec 01, 2023
Title DNA methylation data PDO T#1 D61
Sample type genomic
Source name Patient-derived organoid from tumor T#1
Organism Homo sapiens
Characteristics sample type: fresh-frozen
Growth protocol For PDO and PDXO generation, fresh surgically resected tumor samples were disgregated within 24 hours of surgical resection and culured in PDO medium in a 37°C, 5% CO2 incubator (see Methods section for further details)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from FFPE samples using Resnova MagPurix FFPE DNA Extraction Kit according to standard instructions; while PDOs/PDXOs were lysed in lysis buffer (20 mM EDTA, 10 mM Tris, 200 mM NaCl, 0.2% Triton X-100, 100 µg/ml Proteinase K, pH 8.0) for 1h at 37°C under agitation. Genomic DNA was extracted with phenol-chloroform and precipitated with isopropanol.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina HumanMethylation450 BeadChip or Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using Illumina iScan
Data processing RStudio (R package ChAMP v2.26.0)
Submission date Nov 07, 2023
Last update date Dec 01, 2023
Contact name Evelina Miele
Organization name Ospedale Pediatrico Bambino Gesù
Department Oncoematologia
Street address Piazza di Sant'Onofrio 4
City Rome
ZIP/Postal code 00165
Country Italy
Platform ID GPL21145
Series (2)
GSE247231 Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [array]
GSE247381 Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments

Data table header descriptions
VALUE Average beta value normalized with Functional Normalization
Detection Pval PDO T1 D61

Data table
ID_REF VALUE Detection Pval PDO T1 D61
cg00000029 0.56166127 5.8607E-288
cg00000103 0.690757617 0
cg00000109 0.526015344 0
cg00000155 0.906891499 0
cg00000158 0.924630379 0
cg00000165 0.054464518 0
cg00000221 0.787318656 0
cg00000236 0.851020412 0
cg00000289 0.689754615 6.53186E-45
cg00000292 0.272972666 0
cg00000321 0.44393972 0
cg00000363 0.186584285 0
cg00000540 0.898591067 0
cg00000579 0.90576805 0
cg00000596 0.623527375 0
cg00000622 0.038496192 0
cg00000658 0.786813715 0
cg00000714 0.050736775 0
cg00000721 0.888544938 0
cg00000734 0.044950703 0

Total number of rows: 865859

Table truncated, full table size 21727 Kbytes.

Supplementary file Size Download File type/resource
GSM7885663_204875120093_R04C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM7885663_204875120093_R04C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT

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