iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
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iRNA-seq : computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. / Madsen, Jesper Grud Skat; Schmidt, Søren Fisker; Larsen, Bjørk Ditlev; Loft, Anne; Nielsen, Ronni; Mandrup, Susanne.
In: Nucleic Acids Research, Vol. 43, No. 6, e40, 31.03.2015, p. 1-9.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - iRNA-seq
T2 - computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
AU - Madsen, Jesper Grud Skat
AU - Schmidt, Søren Fisker
AU - Larsen, Bjørk Ditlev
AU - Loft, Anne
AU - Nielsen, Ronni
AU - Mandrup, Susanne
N1 - © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2015/3/31
Y1 - 2015/3/31
N2 - RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, IRNA-SEQ: , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
AB - RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, IRNA-SEQ: , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
KW - Cell Line
KW - Chromatin Immunoprecipitation
KW - Gene Expression Profiling
KW - Gene Expression Regulation
KW - Genome, Human
KW - Humans
KW - Introns
KW - Sequence Analysis, RNA
U2 - 10.1093/nar/gku1365
DO - 10.1093/nar/gku1365
M3 - Journal article
C2 - 25564527
VL - 43
SP - 1
EP - 9
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 6
M1 - e40
ER -
ID: 150711674