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| Status |
Public on Oct 17, 2016 |
| Title |
L10-15-Control |
| Sample type |
SRA |
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| Source name |
Biopsy of Uninfected Non-neoplastic
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| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
disease state: Control
Sex: F
age: 70
hcv_viral_load: 0
hcv_activity: NA
staging: 1
interface_necrosis: NA
confluent_necrosis: NA
focal_lytic_nec_apop: NA
portal_inflammation: NA
total_grade: NA
hcv_genotype: NA
cea: 72
ca19_9: NA
afp: 2.5
sgot: 20
sgpt: 13
batch: 0
race: B
differentiation: 0
hcv_activity: 0
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We extracted genomic DNA using proteinase K and RNase A digestion followed by phenol/chloroform extraction and ethanol precipitation.
We characterized DNA methylation patterns using the HELP-tagging assay, a massively parallel sequencing-based restriction enzyme approach described previously. To minimize potential batch effects, HELP-tagging libraries were processed in batches that balanced by patient age, disease grade, HIV viral load, and HPV genotype. Genomic DNA was digested with the methylation sensitive restriction enzyme, HpaII for comparison with a reference genome digested with the methylation insensitive restriction enzyme, MspI. Digested DNA was ligated to a custom Illumina sequencing adapter containing a T7 transcriptional promoter and an EcoP15I restriction site at the 3’ end, allowing digestion with EcoP15I. A second Illumina sequencing adapter with a unique sequencing index was then added and after in vitro transcription, reverse transcription, and PCR amplification, the library was sequenced on the Illumina HiSeq 2000 platform.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: HELP-tagging
Libraries were multiplexed for 50 bp single-end sequencing on the Illumina HiSeq 2000 platform. Illumina CASAVA pipeline 1.8 was used to generate fastq files.
Alignment was completed with ELAND allowing at most 3 mismatches. Reads flanking HpaII sites were quantified with a custom script.
The read counts were log transformed and normalized before taking the ratio of the normalized HpaII count to normalized MspI count at each assayed HpaII site. The CDF of the Cauchy distribution was used to obtain methylation probabilities.
Mixture modeling of the distribution assuming three composite distributions was performed to scale the probabilities between 0 and 1. HpaII sites with less than 5 read counts were removed from the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Combined_processed_HELP_tagging_data.txt.gz: Matrix with columns corresponding to each sample and rows corresponding to assayed HpaII sites.
Supplementary_files_format_and_content: Hcount files: Quantification of the number reads with an end located at a HpaII site for the positive strand, negative strand, and total.
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| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Neil Ari Wijetunga |
| Organization name |
Albert Einstein College of Medicine
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| Department |
Genetics
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| Lab |
John Greally Price 214
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| Street address |
1301 Morris Park Ave
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE82176 |
Human liver HELP-tagging cytosine methylation data corresponding to uninfected non-malignant, HCV+ non-malignant, and HCV+ HCC tissue |
| GSE82178 |
Human liver RNA-seq and HELP-tagging data corresponding to uninfected non-malignant, HCV+ non-malignant, and HCV+ HCC tissue |
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| Relations |
| BioSample |
SAMN05199344 |
| SRA |
SRX1817221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2185637_hg19.L10_15_Control.A81M65ABXX.lane_6.hcount.txt.gz |
5.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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