NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2935172 Query DataSets for GSM2935172
Status Public on Dec 07, 2020
Title T19A [MeDIP-seq]
Sample type SRA
 
Source name Colorectal tumor tissues_well-differentiated
Organism Homo sapiens
Characteristics tissue type: Colorectal tumor tissues
differentiation stage: well-differentiated
tnm: T4NXM0
Extracted molecule genomic DNA
Extraction protocol 1.5µg of original genomic DNA was fragmented to DNA smear between 200bp to 500bp using a Bioruptor NGS (Diagenode) sonication system. End repair, <A> base addition and adaptor ligation steps were performed using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions. Then, the methylated DNA fractions were immunoprecipitated using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode, catalog number: mc-magme-048) with small adjustments. Briefly, 1.5µl of each two control templates (methylated and unmethylated DNA controls) with different sequences were mixed with adapter ligated DNA and heat denatured (95°C, 3min) in a final reaction volume of 90µl within the provided reagents of 24µl MagBuffer A and 6µl MagBuffer B. 7.5µl aliquot of the denatured genomic DNA was saved as input and another 75µl was immunoprecipitated with 5µl of prepared anti-5mC antibody and 20µl of prepared Magbeads. The DNA-antibody-magbeads mixture was incubated overnight at 4°C on a rotating wheel. The DNA-antibody-magbeads mixture was then washed twice using each of 150µl ice-cold MagWash Buffer-1 and washed once with 150µl of ice-cold MagWash Buffer-2. For each buffer, the washing reaction was incubated for 4min at 4°C on a rotating wheel. The input DNA and immunoprecipitated products were then in parallel treated with protease K and purified with ZYMO DNA Clean & Concentrator-5 (ZYMO). The efficiency and sensitivity of immunoprecipitation reaction were detected by qPCR using the enriched DNA and the unbound input DNA. MeDIP-seq library was constructed by PCR amplification with the enriched DNA as template. PCR reaction was performed in 50µl of reaction volume consisting of 20µl MeDIP enriched DNA, 5µl of 2.5mM dNTP, 2µl primers, 5µl of 10X pfx Amplification Buffer, 2µl of 50mM MgSO4, 15.2µl sterilized water and 0.8µl of Platinum pfx DNA polymerase (Invitrogen). The program of amplification was 94°C 2 min, 10 cycles of 94 °C 15s, 62°C 30s and 72°C 30 then prolong with 10min at 72°C. The products could be kept at 12°C. The PCR products were purified using Agencourt Ampure Beads (Beckman Counlter). After analyzing by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR, the prepared library was sequenced using Illumina HiSeq2000 with SE50 read length.
DNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 2000
 
Description MeDIP-seq
Data processing MeDIP-seq raw data were filtered using the following steps. We removed reads with sequence adaptors and reads with more than 10% ‘N’ bases, and further removed reads with more than 50% bases with QA ≤ 20
MeDIP-seq clean data were mapped to hg19 using Bowtie2 (v2.2.5)
DNA methylation abundance were calculated by MEDIPS
Genome_build: hg19
Supplementary_files_format_and_content: DNA methylation abundance measurements
 
Submission date Jan 15, 2018
Last update date Dec 07, 2020
Contact name Zhu Hao
E-mail(s) zhuhao@smu.edu.cn
Phone 8613533979750
Organization name Southern Medical University
Street address Shatai Road
City GuangZhou
ZIP/Postal code 510515
Country China
 
Platform ID GPL11154
Series (2)
GSE109202 The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor [MeDIP-seq]
GSE109204 The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor
Relations
BioSample SAMN08366098
SRA SRX3584930

Supplementary file Size Download File type/resource
GSM2935172_T19A.txt.gz 62.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap