|
| Status |
Public on Mar 25, 2016 |
| Title |
J_4-8_3-1-20 |
| Sample type |
SRA |
| |
|
| Source name |
Jejunum lacking enterocytes
|
| Organism |
Homo sapiens |
| Characteristics |
individual: 4-8
treatment: Bisulfite-converted Padlock
Sex: M
age: 51y
snp c/t-13910: CC
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: H3.1/Ind20
|
| 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
|
| |
|
| 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 |
SAMN03781504 |
| SRA |
SRX1064331 |
