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| Status |
Public on Jun 22, 2016 |
| Title |
IMR90_Roche_0_25ug |
| Sample type |
SRA |
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| Source name |
IMR90, Roche, 0.25ug starting material
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| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
tissue: lung fibroblast
protocol: Roche NimbleGen SeqCap Epi CpGiant
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
Roche NimbleGen SeqCap Epi CpGiant libraries were made using 1ug and 0.25ug of starting material, according to the company’s specifications. DNA was sonicated using a Covaris S220 sonicator to obtain products of 180-220bp. DNA was then end-repaired, A-tailed and ligated with methylated indexed-adapters to create pre-capture DNA libraries. The pre-capture libraries were bisulfite converted at 54°C for 1 hour using the Zymo EZ DNA Lightening kit. The bisulfite treated pre-capture libraries were PCR amplified with HiFi HotSart polymerase. The amplified, bisulfite converted sample libraries were then hybridized to the probe pool of fully-, partially- and un-methylated cytosines from both strands of DNA oligos at 42° C for 72 hrs. Hybridized products were purified by capture with Capture Beads and PCR amplified for 15 cycles to create the final libraries.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalling performed by CASAVA version 1.8.2
filtered for pass filter reads by unix tool grep with a command: zcat sample_R1.fastq.gz | grep --no-group-separator -A 3 '^@.* [^:]*:N:[^:]*:' > sample_R1_PF.fastq
adapter trimming performed by Flexbar v2.4 with command: flexbar -r sample_R1_PF.fastq -p sample_R2_PF.fastq -t sample_trimmed -a peadapters.fa -f i1.5 -ao 6 -m 21 -at 2 -ae RIGHT -n 10 -u 2 -j -am 3 -ai -3 -ag -20
align to human genome hg19 performed by Bismark v0.5.4, Bowtie v0.12.7 with command: bismark -q -un -X 400 -l 100 --phred33-quals --directional hg19 -1 sample_trimmed_1.fastq -2 sample_trimmed_2.fastq
methylation extraction by custom PERL script
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files include for each CpG: chromosome, base, strand, coverage, frequency C, and frequency T
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| Submission date |
Jun 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thadeous James Kacmarczyk |
| E-mail(s) |
thk2008@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Department |
Medicine/Hematology-Oncology
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| Lab |
Epigenomics Core
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| Street address |
1300 York Ave
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| City |
new york |
| State/province |
ny |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE83595 |
“Same Difference”: Comprehensive evaluation of four DNA methylation measurement platforms |
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| Relations |
| BioSample |
SAMN05277954 |
| SRA |
SRX1869511 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2210595_methylcall.CpG.IMR90_Roche_0_25ug.mincov0.txt.gz |
170.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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