|
| Status |
Public on Jul 24, 2023 |
| Title |
HCI-005 Vehicle 1 |
| Sample type |
SRA |
| |
|
| Source name |
HCI005 Vehicle tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer PDX model HCI005
treatment: Vehicle
replicate: 1
|
| Treatment protocol |
Mice were randomly assigned to treatment groups and treated with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).
|
| Growth protocol |
A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for WGBS experiments. Using a cryostat (Leica, #CM3050-S), 15x 30 µm sections were cut from each tumour at -20 ̊C and these samples were subjected to DNA extraction.
Library preparation and indexing were carried out as described in the CEGX TruMethyl WG user guide v2 wih minor improvements as described in Nair et al., 2018.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads from WGBS data were aligned to the human genome using version 1.2 of an internally developed pipeline Meth10X. It is publicly available and can be downloaded fromhttps://github.com/luuloi/Meth10X(Nair et al., 2018). The pipeline backbone is built based on workflow control Bpipe (Sadedin SP at el. 2012) version 0.9.9.2 which mainly help to make automation, parallelism, restarting jobs and integration with cluster resource managers easier following the pipeline structure ofP3BSseq (Luu PL, et al., 2017). Meth10X takes raw bisulphite reads in fastq files as inputs and produces a html report of all necessary metrics of bisulphite quality control and a tsv file of DNA methylation of 28 million CpG as rows and samples as columns. Briefly, adaptor sequences were removed using in-house bash script in paired end mode following prep kit guide. Bwa-meth verion 0.20 (https://github.com/brentp/bwa-meth) was then used to align reads to hg38 using bwa version 0.7.13 (https://github.com/lh3/bwa). The generated bam files are merged and marked duplication by Picard tools 2.3.0 (http://broadinstitute.github.io/picard). The merged bam files are checked with Qualimap 2.2.1 (Konstantin Okonechnikov at el. 2015) for quality as well as all metrics of WGBS. MethylDackel (https://github.com/dpryan79/MethylDackel) and Biscuit (https://github.com/zwdzwd/biscuit) are used to call DNA methylation and SNP. Samtools version 1.2 (Li H.et al. 2009) is used to manipulate bam files and all the plots are done with ggplot2 in R (H. Wickham. 2009).
Assembly: hg38
Supplementary files format and content: BigWig file containing counts of methylated (C) and coverage (cov, methylated Cs + unmethylated Ts) at each CpG site assayed.
|
| |
|
| Submission date |
Jul 19, 2023 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
j.achinger@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Lab |
Epigenetics Research Laboratory
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE171074 |
The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer |
| GSE237768 |
Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer [WGBS] |
|
| Relations |
| Reanalyzed by |
GSE240481 |
| BioSample |
SAMN36617457 |
| SRA |
SRX21082214 |
