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Simultaneous generation of many RNA-seq libraries in a single reaction

Shishkin, Alexander A. and Giannoukos, Georgia and Kucukural, Alper and Ciulla, Dawn and Busby, Michele and Surka, Christine and Chen, Jenny and Bhattacharyya, Roby P. and Rudy, Robert F. and Patel, Milesh M. and Novod, Nathaniel and Hung, Deborah T. and Gnirke, Andreas and Garber, Manuel and Guttman, Mitchell and Livny, Jonathan (2015) Simultaneous generation of many RNA-seq libraries in a single reaction. Nature Methods, 12 (4). pp. 323-325. ISSN 1548-7091. PMCID PMC4712044. https://resolver.caltech.edu/CaltechAUTHORS:20150106-114459354

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[img] PDF (Supplementary Figures 1–6 and Supplementary Protocol) - Supplemental Material
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[img] MS Excel (Supplementary Table 1 (58 KB). Metrics for RNAtagSeq and dUTP data) - Supplemental Material
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[img] MS Excel (Supplementary Table 2 (41 KB) . Validated sets of RNAtag-Seq adapters used in this study) - Supplemental Material
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[img] MS Excel (Supplementary Table 4 (3,580 KB). Normalized expression values (TPM) for 11 mouse tissues) - Supplemental Material
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[img] MS Excel (Supplementary Table 5 (60 KB). Lists of genes differentially expressed in mouse tissues) - Supplemental Material
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[img] MS Excel (Supplementary Table 6 (1,617 KB). Normalized expression values (fragments per kb of gene per million of reads mapped to ORFs) for 32 E. coli clinical isolates in culture with and without ciprofloxacin) - Supplemental Material
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[img] MS Excel (Supplementary Table 7 (37 KB). Lists of genes up- and downregulated in cipro susceptible strains following exposure to cipro for the indicated times) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 1: Comparison of replicate data sets generated by dUTP and RNAtag-Seq for K562 and three bacterial species) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 2: Read coverage in RNAtag-Seq and dUTP data sets over the same genomic region of E. coli) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 3: Distribution of reads per barcode in a single pool) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 4: Correlation of normalized reads per gene among 32 individually barcoded RNAtag-Seq libraries in a single pool) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 5: Comparison of RNAtag-Seq data generated with 54 RNA and 32 DNA adaptors) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 6: Additional results from differential gene expression analysis of E. coli using RNAtag-Seq) - Supplemental Material
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Abstract

Although RNA-seq is a powerful tool, the considerable time and cost associated with library construction has limited its utilization for various applications. RNAtag-Seq, an approach to generate multiple RNA-seq libraries in a single reaction, lowers time and cost per sample, and it produces data on prokaryotic and eukaryotic samples that are comparable to those generated by traditional strand-specific RNA-seq approaches.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nmeth.3313DOIArticle
http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3313.htmlPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712044/PubMed CentralArticle
http://rdcu.be/cIMWPublisherFree ReadCube access
ORCID:
AuthorORCID
Chen, Jenny0000-0002-6664-2597
Guttman, Mitchell0000-0003-4748-9352
Additional Information:© 2015 Macmillan Publishers Limited. Received 27 October 2014. Accepted 08 February 2015. Published online 02 March 2015. Accession codes. NCBI Sequence Read Archive: SRP051252. We thank all members of Lander and Guttman labs for their help, especially J.M. Engreitz, P. McDonel and K. Sirokman; L. Gaffney for assistance with figures; and C. Nusbaum for helpful suggestions on the manuscript. We thank I. Antoshechkin and the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. This work was supported by a US National Institutes of Health (NIH) Director's Early Independence Award (DP5OD012190 to M. Guttman), funds from the Broad Institute of MIT and Harvard and the California Institute of Technology (M. Guttman) and funds from the US National Institute of Allergy and Infectious Diseases, NIH, Department of Health and Human Services, under contract no. HHSN272200900018C.
Funders:
Funding AgencyGrant Number
NIHDP50D012190
Broad Institute of MIT and HarvardUNSPECIFIED
CaltechUNSPECIFIED
National Institute of Allergy and Infectious DiseasesUNSPECIFIED
Department of Health and Human ServicesHHSN272200900018C
Issue or Number:4
PubMed Central ID:PMC4712044
Record Number:CaltechAUTHORS:20150106-114459354
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20150106-114459354
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:53208
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2015 01:49
Last Modified:09 Mar 2020 13:18

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