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Sample GSM2398358 Query DataSets for GSM2398358
Status Public on Aug 10, 2017
Title Genomc DNA from 293T-TET3-RUNX1
Sample type genomic
Source name 293T-TET3-RUNX1
Organism Homo sapiens
Characteristics cell li ne: 293T
gender: Female
tissue: Kidney
developmental stage: Embryo
transduced with: TET3 and RUNX1
Treatment protocol 293T cells were transduced genes of interest by using lentivirus vector system. Transduced cells were purified by antibiotics
Growth protocol 293T cells were provided from RIKEN Bioresource Center (BRC) and were cultured in Dulbecco's modified Eagle's medium (DMEM) (Wako), supplemented with 10% FBS and penicillin/streptomycin (100 U/ml, 100 µg/ml) (Life Technologies) on Poly-D-lysine courted dish (Becton Dickinson).
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted and purified using NucleoSpin Tissue (Macherey-Nagel) according to standard instructions
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description TET3 and RUNX1 transduced
Data processing Signal intensities were measured by GenomeStudio software v2010.3. Color balance adjustment, quantile normalization and M-value calculation were done by lumi, a bioconductor package.
Submission date Nov 21, 2016
Last update date Aug 10, 2017
Contact name Takahiro Suzuki
Phone 81-45-503-9222
Organization name RIKEN
Department Center for Integrative Medical Sciences
Lab Laboratory for Cellular Function Conversion Technologies
Street address 1-7-22 Suehiro-cho, Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
Platform ID GPL13534
Series (1)
GSE60316 RUNX1-Mediated Binding Site Directed DNA Demethylation is a Novel Mechanism of Hematopoietic Gene Activation.

Data table header descriptions
VALUE M-value (log2 intensity of methylated probe/ intensity of unmethylated probe)

Data table
cg00000029 1.866901613
cg00000108 3.789210522
cg00000109 2.770088528
cg00000165 3.022070399
cg00000236 2.854103952
cg00000289 1.868648269
cg00000292 1.754464006
cg00000321 1.587155869
cg00000363 3.323633732
cg00000622 -4.565739381
cg00000658 2.601669245
cg00000714 -1.162912344
cg00000721 3.435169896
cg00000734 -2.896222256
cg00000769 -3.681945356
cg00000807 2.369826338
cg00000884 1.24959781
cg00000905 -1.643863502
cg00000924 0.29925936
cg00000948 2.775614575

Total number of rows: 485577

Table truncated, full table size 11066 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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