Bioinformatics and Genomics Library

Hutch Data Core

Updated: April 15, 2021

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Frame context for this page:

  • curated list of resources for data generation and analysis
  • Relevant wiki pages are linked with each subheading

Genomics

Subheadings from https://www.fredhutch.org/en/research/shared-resources/core-facilities/genomics-bioinformatics/genomics-services.html, some additional listed below “Other services” that may be included eventually (but not now).

Library prep and quality assessment

Sections from wiki, not represented in SR pages

https://sciwiki.fredhutch.org/generation/datagen_platformsData/#library-preparation-for-sequencing

https://sciwiki.fredhutch.org/generation/datagen_assayPrep/

Illumina

https://sciwiki.fredhutch.org/generation/datagen_platformsData/#illumina-sequencers

PacBio

https://sciwiki.fredhutch.org/generation/datagen_platformsData/#pacific-biosciences-pacbio-long-range-sequencer

  • SMRT Sequencing: Resources about the SMRT sequencing technology from PacBio.

https://sciwiki.fredhutch.org/generation/datagen_dnaApproaches/#smrt-sequencing-pacbio

Sanger

10X genomics

https://sciwiki.fredhutch.org/generation/datagen_platformsData/#10x-genomics-single-cell-library-preparation-system

Microarrays

Should we include this? Not mentioned on SR genomics page, but may be listed elsewhere?

https://sciwiki.fredhutch.org/generation/datagen_dnaApproaches/#dna-microarrays

Bioinformatics

Subheadings from https://www.fredhutch.org/en/research/shared-resources/core-facilities/genomics-bioinformatics/bioinformatics-services.html.

RNAseq

https://sciwiki.fredhutch.org/generation/datagen_rnaApproaches/#rna-sequencing

https://sciwiki.fredhutch.org/generation/datagen_rnaApproaches/#qualitative-approaches-transcript-and-splicing-discovery

small RNAs (e.g., miRNA)

Not specifically mentioned in SR pages?

https://sciwiki.fredhutch.org/generation/datagen_rnaApproaches/#example–small-rnas-eg-mirna

  • Genohub guide on small RNA (miRNA): Use this guide to help search for and get accurate pricing and turnaround times for small RNA, microRNA (miRNA) sequencing services. The guide includes considerations you should make before starting your small RNA sequencing project.

Cleavage Under Targets and Release Using Nuclease (CUT&RUN)

Whole exome sequencing

https://sciwiki.fredhutch.org/generation/datagen_dnaApproaches/#capture-based-sequencing—example–whole-exome-sequencing

Targeted sequencing

https://sciwiki.fredhutch.org/generation/datagen_dnaApproaches/#amplicon-based-sequencing—targeted-dna-sequencing

CRISPR screens

ChIPseq

https://sciwiki.fredhutch.org/generation/datagen_dnaApproaches/#chromatin-immunoprecipitation-sequencing-chip-seq

  • Epigenie guide to ChIPseq: An overview of ChIP sequencing. A good starting point with references and resources linking to more information.

ATACseq (DNA accessibility)

PhIPseq

VirScan

10X single-cell analyses

RRBS (Reduced Representation Bisulfite Sequencing)

Should we include this? Not mentioned on SR genomics page, but may be listed elsewhere?

https://sciwiki.fredhutch.org/generation/datagen_dnaApproaches/#reduced-representation-bisulfite-sequencing-rrbs

Nanostring

Should we include this, perhaps with RNAseq under a subheading of “gene expression”? Not mentioned on SR genomics page, but may be listed elsewhere?

https://sciwiki.fredhutch.org/generation/datagen_platformsData/#single-nucleotide-polymorphism-snp-arrays-or-methylation-arrays

https://sciwiki.fredhutch.org/generation/datagen_rnaApproaches/#nanostring-gene-expression-panels

Updated: April 15, 2021

Edit this Page via GitHub       Comment by Filing an Issue      Have Questions? Ask them here.