(Coming soon, but the tutorials 1-7 above are geared to
ChIP-Seq and RNA-Seq) Isolation and sequencing of genomic
DNA "bound" by a specific transcription factor, covalently
modified histone, or other nuclear protein. This
methodology provides genome-wide maps of factor
binding. Most of HOMER's routines cater to the
analysis of ChIP-Seq data.
(This one is currently only a quick-recipe driven list of
commands, but the tutorials 1-3, & 8 above are geared
to ChIP-Seq and RNA-Seq) Extraction, fragmentation, and
sequencing of RNA populations within a sample. The
replacement for gene expression measurements by
microarray. There are many variants on this, such as
Ribo-Seq (isolation of ribosomes translating RNA), small
RNA-Seq (to identify miRNAs), etc.
: RNA-Seq of nascent
RNA. Transcription is halted, nuclei are isolated,
labeled nucleotides are added back, and transcription
briefly restarted resulting in labeled RNA
molecules. These newly created, nascent RNAs are
isolated and sequenced to reveal "rates of transcription"
as opposed to the total number of stable transcripts
measured by normal RNA-seq.
: Sequencing only the 5'
cap-protected fragments of RNA can be used to define sites
of transcriptional initiation at nucleotide
resolution. This section covers the identification
of TSS from 5' RNA sequencing data.
Genomic interaction assay for understanding genome 3D
structure. This assay is much more specialized - For
more information about how to use HOMER to analyze Hi-C
data, check out the Hi-C
: Treatment of nuclei with
a restriction enzyme such as DNase I will result in
cleavage of DNA at accessible regions. Isolation of
these regions and their detection by sequencing allows the
creation of DNase hypersensitivity maps, providing
information about which regulatory elements are accessible
in the genome.
Profiling of cytosine methylation in genomic DNA.