|
| Status |
Public on Jan 30, 2017 |
| Title |
HeLa_S3 (WGSBS). |
| Sample type |
SRA |
| |
|
| Source name |
HeLa_S3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
passage: 4
|
| Growth protocol |
Cell were cultured in Dulbecco's Modified Eagle medium supplemented with 4.5 g/L glucose, 10% FBS and 2 nM glutamine in humidified incubator at 37 deg. C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (QIAGEN)
Library construction was performed using the EpiGnome/TruSeq DNA Methylation Kit. Briefly, genomic DNA (50-100 ng) was denatured and bisulfite converted in a reaction containing 0.5 ng of unmethylated lambda DNA (Promega) as a control. Following purification, the BS converted DNA was hybridized with oligonucleotides consisting of random hexamers linked to Illumina P5 adapter sequences and strand replicated using EpiGnome polymerase. Adapter-ligated DNA molecules were enriched by 10 cycles of PCR.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Illumina Genome Analyzer was used for basecalling
The WGSBS fastq data were aligned in Novoalign bisulfite mode using the following parameters: -oSAM -rRandom -t240 -h120 -b2
sam alignments were sorted with the Picard SortSam.jar script and all duplicates removed using the Picard MarkDuplicates.jar script for WGSBS datasets. The results were converted into .bam files and indexed using Samtools
Peak calling was performed with the USeq NovoalignBisulfiteParser to parse the alignments into four binary PointData sets containing the number of observed converted Cyt and non-converted Cyt at each reference Cyt site sequenced in the genome for both the plus and minus strands
Genome_build: hg19
Supplementary_files_format_and_content: read coverage tracks files were built with Useq
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bethany Buck-Koehntop |
| E-mail(s) |
koehntop@chem.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Chemistry
|
| Street address |
315 S 1400 E, rm 2020
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE81779 |
ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner [BiSulfite-seq] |
| GSE81784 |
ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner |
|
| Relations |
| BioSample |
SAMN05163696 |
| SRA |
SRX1793681 |
