|
Status |
Public on Mar 25, 2016 |
Title |
E_4-31_3-1-54 |
Sample type |
SRA |
|
|
Source name |
Enterocytes
|
Organism |
Homo sapiens |
Characteristics |
individual: 4-31 treatment: Bisulfite-converted Padlock Sex: F age: 39y snp c/t-13910: CT relative lactase mrna expression: 0.878 cell type: 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
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|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Sample name: H3.1/Ind54
|
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 âCâ, and were not converted to âTâ 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
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|
|
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 |
|
Relations |
BioSample |
SAMN03781530 |
SRA |
SRX1064357 |