Pricing

Organization CCBB Hourly Rate
Scripps Internal $125.00
External non-profit $250.00
External for-profit $312.50

CCBB services Epigenomics:

  • ChIP-Seq / eCLIP-Seq / CUT&RUN / CUT&TAG / RIP-Seq

  • ATAC-Seq

ChIP-Seq / eCLIP-Seq / CUT&RUN / CUT&TAG / RIP-Seq

Requirements:

  1. Read targets reached (e.g. ~ 10 million reads per sample; human genome for each of your samples in the study)

  2. Number of sample submitted are less than 10

  3. Sample metadata (description of ChIP and INPUT samples shared with CCBB prior to sequencing)

  4. Biological replicates if any for your ChIP samples

  5. Reference genomes considered as standard: human, mouse, rat

Standard analysis (CCBB effort level - 5 hours; 3-5 business days)

  • Alignment to reference genome using BWA

  • peak calling (using protocol specific peak callers)

  • BigWig files

  • HOMER to annotate peaks relative to gene features along with QC plots/tables.

Additional analysis (consult CCBB for effort level and timeline for completion)

  • Integration analysis (e.g. ChIP-Seq and RNA-Seq)

  • Contribution to writing a scientific paper including Methods section

  • Motif discovery

  • Help with visualization etc.

ATAC-Seq

Standard analysis (CCBB effort level - 5 hours; 3-5 business days)

  • Alignment to reference genome using BWA

  • MACS2 for peak-calling

  • bed and BigWig files

  • HOMER to annotate peaks relative to gene features.

Additional analysis (consult CCBB for effort level and timeline for completion)

  • Motif searching

  • ATAC_ChIP and RNA-Seq

  • TF Footprinting

  • DE analysis

Additional services:

Consult CCBB to get a quote/estimation of effort in hours. CCBB service hourly charges apply.

  • Software development, custom pipeline implementation

  • Re-analysis of older dataset

  • Analysis for public dataset

  • Specific figures/tables for publications; writing methods section or contribution for scientific papers/grant proposals

  • Functional Analysis using Advaita/GSEA/SetRank

  • Letter of Support for grants

  • GEO/SRA submissions

Email ccbb.at.scripps.edu to set up a consultation meeting for additional service(s)