Journal: Journal of visualized experiments : JoVE
Article Title: RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
doi: 10.3791/59771
Figure Lengend Snippet: Materials
Article Snippet: Centrifuge for 2 min at 1,000 × g and 4 °C, and carefully remove and discard supernatant ( ). table ft1 table-wrap mode="anchored" t5 caption a7 Name Company Catalog Number Comments 1 M HEPES Affymetrix AAJ16924AE 5 M NaCl Invitrogen AM9760G Agilent bioanalyzer 2100 Agilent technologies Agilent RNA 6000 Nano Kit Agilent technologies 5067–1511 bedtools.26.0 https://bedtools.readthedocs.io/en/latest/content/installation.html bowtie-0.12.8 https://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.8/ Cell scraper Olympus plastics 25–270 Chloroform Fisher C298–500 Digitonin Research Products International Corp 50–488-644 Ethanol Fisher A4094 Gibco (Phosphate Buffered Saline) Invitrogen 10–010-049 Homogenizer Thomas Scientific BBI-8541906 IGV 2.4 https://software.broadinstitute.org/software/igv/download Isopropanol Fisher A416–500 mac2unix https://sourceforge.net/projects/cs-cmdtools/files/mac2unix/ Q-tips Fisher 23–400-122 RNAse later solution Invitrogen AM7022 RNaseZap RNase Decontamination Solution Invitrogen AM9780 samtools-1.3 https://sourceforge.net/projects/samtools/files/ sratoolkit.2.9.2 https://github.com/ncbi/sra-tools/wiki/Downloads SUPERaseIn RNase Inhibitor Invitrogen AM2694 Trizol Invitrogen 15–596-018 Water (DNASE, RNASE free) Fisher BP2484100 Open in a separate window Materials Collect cells from tissue specimens. list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare tissue for cytoplasmic RNA extraction within an hour from being dissected and always keep on ice.
Techniques:
