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Items: 1 to 20 of 97

1.

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Takahashi H, Lassmann T, Murata M, Carninci P.

Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005.

2.

CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks.

Takahashi H, Kato S, Murata M, Carninci P.

Methods Mol Biol. 2012;786:181-200. doi: 10.1007/978-1-61779-292-2_11.

3.

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

Faulkner GJ, Forrest AR, Chalk AM, Schroder K, Hayashizaki Y, Carninci P, Hume DA, Grimmond SM.

Genomics. 2008 Mar;91(3):281-8. doi: 10.1016/j.ygeno.2007.11.003.

4.

Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference.

de Hoon M, Hayashizaki Y.

Biotechniques. 2008 Apr;44(5):627-8, 630, 632. doi: 10.2144/000112802. Review.

5.

Detecting expressed genes using CAGE.

Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Carninci P, Hayashizaki Y, Itoh M.

Methods Mol Biol. 2014;1164:67-85. doi: 10.1007/978-1-4939-0805-9_7.

PMID:
24927836
6.

Digital gene expression by tag sequencing on the illumina genome analyzer.

Morrissy S, Zhao Y, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Prabhu AL, Tam A, Hirst M, Marra M.

Curr Protoc Hum Genet. 2010 Apr;Chapter 11:Unit 11.11.1-36. doi: 10.1002/0471142905.hg1111s65.

PMID:
20373513
7.

NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes.

Poulain S, Kato S, Arnaud O, Morlighem JÉ, Suzuki M, Plessy C, Harbers M.

Methods Mol Biol. 2017;1543:57-109. doi: 10.1007/978-1-4939-6716-2_4.

PMID:
28349422
8.

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y.

Genome Res. 2003 Jun;13(6B):1273-89.

9.

cDNA library construction for next-generation sequencing to determine the transcriptional landscape of Legionella pneumophila.

Sahr T, Buchrieser C.

Methods Mol Biol. 2013;954:555-66. doi: 10.1007/978-1-62703-161-5_34.

PMID:
23150420
10.

NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.

Salimullah M, Sakai M, Plessy C, Carninci P.

Cold Spring Harb Protoc. 2011 Jan 1;2011(1):pdb.prot5559. doi: 10.1101/pdb.prot5559. Erratum in: Cold Spring Harb Protoc. 2011 Feb;(2). doi: 10.1101/pdb.erratum2011_01. Mizuho, Sakai [corrected to Sakai, Mizuho].

11.

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.

Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P; FANTOM Consortium.

Genome Res. 2014 Apr;24(4):708-17. doi: 10.1101/gr.156232.113. Epub 2014 Mar 27.

12.

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.

Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project.

Nature. 2009 Feb 19;457(7232):1028-32. doi: 10.1038/nature07759. Epub 2009 Jan 25.

13.

Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.

Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P, Suzuki H.

Biotechniques. 2008 Jul;45(1):95-7. doi: 10.2144/000112814.

14.

[Cap analysis gene expression: CAGE].

Nakamura M, Carninci P.

Tanpakushitsu Kakusan Koso. 2004 Dec;49(17 Suppl):2688-93. Review. Japanese. No abstract available.

PMID:
15669240
15.

Next-generation sequencing and potential applications in fungal genomics.

Sanmiguel P.

Methods Mol Biol. 2011;722:51-60. doi: 10.1007/978-1-61779-040-9_4.

PMID:
21590412
16.

Library preparation and data analysis packages for rapid genome sequencing.

Pomraning KR, Smith KM, Bredeweg EL, Connolly LR, Phatale PA, Freitag M.

Methods Mol Biol. 2012;944:1-22. doi: 10.1007/978-1-62703-122-6_1.

17.

Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.

Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R.

J Vis Exp. 2011 Oct 27;(56):e3340. doi: 10.3791/3340.

18.

Paired-end diTagging for transcriptome and genome analysis.

Ng P, Wei CL, Ruan Y.

Curr Protoc Mol Biol. 2007 Jul;Chapter 21:Unit 21.12. doi: 10.1002/0471142727.mb2112s79.

PMID:
18265396
19.

CAGE: cap analysis of gene expression.

Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, Hayashizaki Y, Carninci P.

Nat Methods. 2006 Mar;3(3):211-22. No abstract available.

PMID:
16489339
20.

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.

Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y.

PLoS One. 2012;7(1):e30809. doi: 10.1371/journal.pone.0030809. Epub 2012 Jan 30.

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