|
| Status |
Public on Sep 04, 2021 |
| Title |
I1-1 |
| Sample type |
SRA |
| |
|
| Source name |
TLE patients with HS ILAE type1
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: temporal lobe epilepsy (TLE) patient
hippocampal sclerosis: With hippocampal sclerosis (HS)
pathological type: International League Against Epilepsy (ILAE) type 1
tissue: Brain; Hippocampus
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After tissue homogenization, DNA was extracted according to the instructions of TIANamp Genomic DNA Kit (Cat#DP304)
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Bismark software was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2.
Sequence reads were transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome.
Genome_build: lambda genome
Supplementary_files_format_and_content: tab-delimited text files include values of methylation level for each Sample.The methylation level of each site equals to mC counts/(mC counts+umC counts).
|
| |
|
| Submission date |
Nov 19, 2019 |
| Last update date |
Sep 04, 2021 |
| Contact name |
wang zhang |
| E-mail(s) |
zhwang_johnson29@outlook.com
|
| Organization name |
First Affiliated hospital of Harbin Medical Univesity
|
| Department |
Neurosurgery
|
| Street address |
No.23, Postal street, Nangang distric
|
| City |
Harbin |
| State/province |
Heilongjiang |
| ZIP/Postal code |
150001 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE140658 |
Differential DNA methylation profiles of HS ILAE type 1 in human temporal lobe epilepsy |
|
| Relations |
| BioSample |
SAMN13327242 |
| SRA |
SRX7182827 |
