| |
RNA-seq |
Isolate RNA followed by HT sequencing |
(Waern et al, 2011) |
| Transcripts, small RNA and transcribed regions |
CAGE |
HT sequencing of 5'-methylated RNA |
(Kodzius et al, 2006) |
| |
RNA-PET |
CAGE combined with HT sequencing of poly-A tail |
(Fullwood et al, 2009c) |
| |
ChIRP-Seq |
Antibody-based pull down of DNA bound to lncRNAs followed by HT sequencing |
(Chu et al, 2011) |
| |
GRO-Seq |
HT sequencing of bromouridinated RNA to identify transcriptionally engaged PolII and determine direction of transcription |
(Core et al, 2008) |
| |
NET-seq |
Deep sequencing of 3′ ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution |
(Churchman and Weissman, 2011) |
| |
Ribo-Seq |
Quantification of ribosome-bound regions revealed uORFs and non-ATG codons |
(Ingolia et al, 2009) |
| |
|
|
|
| Transcriptional machinery and protein–DNA interactions |
ChIP-seq |
Antibody-based pull down of DNA bound to protein followed by HT sequencing |
(Robertson et al, 2007) |
| |
DNAse footprinting |
HT sequencing of regions protected from DNAse1 by presence of proteins on the DNA |
(Hesselberth et al, 2009) |
| |
DNAse-seq |
HT sequencing of hypersensitive non-methylated regions cut by DNAse1 |
(Crawford et al, 2006) |
| |
FAIRE |
Open regions of chromatin that is sensitive to formaldehyde is isolated and sequenced |
(Giresi et al, 2007) |
| |
Histone modification |
ChIP-seq to identify various methylation marks |
(Wang et al, 2009a) |
| |
|
|
|
| DNA methylation |
RRBS |
Bisulfite treatment creates C to U modification that is a marker for methylation |
(Smith et al, 2009) |
| Chromosome-interacting sites |
5C |
HT sequencing of ligated chromosomal regions |
(Dostie et al, 2006) |
| |
ChIA-PET |
Chromatin-IP of formaldehyde cross-linked chromosomal regions, followed by HT sequencing |
(Fullwood et al, 2009a) |
