|
| Status |
Public on Jun 22, 2016 |
| Title |
IMR90_1 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90, Agilent SureSelect Methyl-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
tissue: lung fibroblast
protocol: Agilent SureSelect Methyl-seq
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
Agilent SureSelect Methyl-Seq libraries were made according to the company’s specifications using 3ug and 1ug of DNA. DNA was sonicated using a Covaris S220 sonicator to obtain products of 150-200bp. DNA was then end-repaired, A-tailed and ligated with methylated adapters to create pre-capture DNA libraries. DNA libraries were then hybridized to the RNA SureSelect Human methyl-seq capture library at 65°C for 16 hrs. Hybridized products were purified by capture with Strepdavin beads and then subjected to bisulfite conversion (64°C for 2.5hr) using the Zymo EZ DNA Gold kit. The bisulfite treated libraries were PCR amplified for 8 cycles with Agilent Taq to get the required amount of DNA library and then indexed by another 6 cycles of PCR amplification to create the final libraries.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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
|
| |
|
| Submission date |
Jun 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thadeous James Kacmarczyk |
| E-mail(s) |
thk2008@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Medicine/Hematology-Oncology
|
| Lab |
Epigenomics Core
|
| Street address |
1300 York Ave
|
| City |
new york |
| State/province |
ny |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE83595 |
“Same Difference”: Comprehensive evaluation of four DNA methylation measurement platforms |
|
| Relations |
| BioSample |
SAMN05277952 |
| SRA |
SRX1869509 |
