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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

JoVE Journal
Genetyka

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JoVE Journal Genetyka

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

9,806 Views

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11:04 min

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May 19, 2019

DOI:

10.3791/59771-v

DOI:

10.3791/59771-v

•

11:04 min

May 19, 2019

•

8 Views

Tiffany Kaul¹, Maria E. Morales¹, Emily Smither¹, Melody Baddoo^1,2, Victoria P. Belancio^1,3, Prescott Deininger^1,4

¹Tulane Cancer Center,Tulane University, ²Department of Pathology,Tulane University, ³Department of Structural and Cellular Biology,Tulane University, ⁴Department of Epidemiology,Tulane University

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Podsumowanie

Here, we present a bioinformatic approach and analyses to identify LINE-1 expression at the locus specific level.

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RNA Next-Generation Sequencing Bioinformatics Pipeline LINE-1s Locus-Specific Level Genetic Instability Mobile Elements L1 Transcripts Cytoplasmic RNA Extraction Sequencing Library Preparation Polyadenylated Transcripts FASTQ Files Bowtie1 Alignment SAMtools Strand Separation Read Counts Bedtools

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