Epigenetics
The Single-Cell Omics Platform offers traditional ATAC sequencing. SCOP provides basic bioinformatic support which includes data processing, QC and peak calling.
Assay for Transposase Accessible Chromatin sequencing (ATAC-seq)
Bulk ATACSeq enables the profiling of chromatin accessibility from sorted nuclei, cell lines or tissue.
Guidelines
Please read through our guidelines below.
Viability: The recommended cell viability is >90%, preferably 95%.
If the viability is below 85%, a DNase treatment can be done to remove free-floating DNA.
- Randomize samples (please take the experimental setup into consideration upon randomization)
- Please prepare samples for SCOP as follows:
- Fresh cells or nuclei: Add 50.000 cells or nuclei per sample in a total volume of 100µl
- Cryopreserved cells or nuclei: Add 60.000 cells or nuclei per sample in a total volume of 100µl (accounting for some loss during freeze/thaw).
- Library preparation.
- Quality control of library.
- Library pooling and sequencing on Illumina NovaSeq X+.
- FASTQ files.
- Standard data processing and QC (optional)
Alignment is performed using the nf-core ATACseq pipeline. This pipeline performs extensive quality control, allowing for robust detection of low-quality samples. In addition, samples are visually inspected using SeqMonk to identify quality issues that are difficult to quantify automatically. The final decision to include or exclude samples will, in most cases, be made in collaboration with the user.
Peak calling is performed using the ATACseq pipeline, and the called peaks can be used for differential binding analysis with edgeR. SCOP supports one-way and two-way designs, as well as repeated-measures ANOVA-like setups, and the inclusion of batch-effect variables.
Contrasts of interest are defined in collaboration with the user. Where appropriate, SCOP will attempt to detect missing batch variables and will contact the user if their inclusion is suspected to be necessary.
Alternatively, if visual inspection indicates that peak calling did not perform well, a genome wide analysis can be performed using the csaw package. This is more resource demanding and will only be carried out if requested by the user, or if SCOP staff determine that the peak calling has failed to capture the relevant peaks.
The price for services depends on the technique, number of samples, and sequencing depth. The sequencing price per sample usually becomes cheaper as the number of samples increases. If you would like us to provide a cost estimate, please contact SCOP with information about the number of samples and techniques you are interested in.
Please recognize and acknowledge SCOP’s contributions to the scientific improvements in your project. Being acknowledged in publications is very important as it serves as documentation for the SCOPS's value and performance.