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Sample GSM1714868 Query DataSets for GSM1714868
Status Public on Mar 25, 2016
Title J_3-60_4-2-60
Sample type SRA
Source name Jejunum lacking enterocytes
Organism Homo sapiens
Characteristics individual: 3-60
treatment: Bisulfite-converted Padlock
Sex: F
age: 33y
snp c/t-13910: CT
tissue: Jejunum lacking enterocytes
Growth protocol Human jejunum surgical samples, blood and sperm was examined as well as mouse jejunum
Extracted molecule genomic DNA
Extraction protocol DNA from tissues were extracted by standard phenol chloroform extraction
Bisulfite padlock probes technique was used to interrogate the lactase gene region and minichromosome maintenance deficient 6 gene of humans and mice
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
Description Sample name: H4.2/Ind60
Data processing Analysis of the padlock BS-seq data was completed using a custom pipeline based on the Bismark tool
Reads were first trimmed and residual adapter sequences removed using Trimmomatic-0.32.
Reads that did not align to phiX were aligned to the target reference genome (GRCh37/hg19 or GRCm38/mm10).
Percent modification was estimated as the fraction of spanning reads that retained the reference “C”, and were not converted to “T” from the bisulfite treatment.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files with coverage of modified and unmodified cytosines, with fields: chromosome, position, type, # reads with modified cytosine, # reads with unmodified cytosine
Submission date Jun 18, 2015
Last update date May 15, 2019
Contact name Arturas Petronis
Organization name Centre for Addiction and Mental Health
Street address 250 College St Rm606
City Toronto
ZIP/Postal code M5T 1R8
Country Canada
Platform ID GPL16791
Series (2)
GSE69977 Fine-mapping of DNA modifications in the lactase gene region of humans and mice
GSE69979 Epigenetics of lactose intolerance and lactase persistence
BioSample SAMN03781817
SRA SRX1064497

Supplementary file Size Download File type/resource
GSM1714868_R4-p2-ind60_S110.hg19.cov.txt.gz 72.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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