RNA-seq analysis was performed with Ion Proton, Ion PI Template OT2 200 Kit v3, and Ion PI sequencing 200 Kit v3 (Thermo Fisher Scientific)53 (link)–55 (link). A549 cells were treated with or without TGF-β1 for 3 days. cDNA libraries were prepared using the RNeasy Mini Kit with the On-Column DNase Digestion Set (QIAGEN, Venlo, The Netherlands), Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific), and the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific). Sequence data were analysed with the GSEA software56 (link) and GSEApy (https://github.com/zqfang/GSEApy ).
On column dnase digestion set
Manufactured by Qiagen
Sourced in Netherlands
The On-Column DNase Digestion Set is a laboratory equipment product designed for the removal of DNA contamination from RNA samples. It provides a convenient and effective method to eliminate DNA during the RNA purification process.
Automatically generated - may contain errors
Lab products found in correlation
Ion total rna seq kit v2, by Thermo Fisher Scientific (4 mentions)
Dynabeads mrna direct purification kit, by Thermo Fisher Scientific (4 mentions)
Rneasy mini kit, by Qiagen (4 mentions)
Ion proton, by Thermo Fisher Scientific (1 mentions)
Ion pi template ot2 200 kit v3, by Thermo Fisher Scientific (1 mentions)
Ion pi sequencing 200 kit v3, by Thermo Fisher Scientific (1 mentions)
Ion pi chip v3, by Thermo Fisher Scientific (1 mentions)
Dynabeads mrna direct micro purification kit, by Thermo Fisher Scientific (1 mentions)
Ion pi hi q chef kit, by Thermo Fisher Scientific (1 mentions)
Hiseq 2000, by Illumina (1 mentions)
5 protocols using on column dnase digestion set
1
RNA-seq Analysis of TGF-β1 Effects
2
RNA-seq Library Preparation and Analysis
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RNA-seq analysis was performed as described previously [47 (link)]. A complementary DNA library was prepared using the RNeasy Mini Kit with the On-Column DNase Digestion Set (Qiagen, Venlo, Netherlands), Dynabeads mRNA DIRECT Micro Purification kit and Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific). Samples were then amplified with Ion PI Hi-Q Chef Kit and applied to an Ion PI Chip v3 in Ion Chef (Thermo Fisher Scientific). DAVID [48 (link), 49 (link)] was used for gene functional classification. Raw and processed data are available at GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106719 ).
3
Transcriptome Analysis of DENV-2 Infection
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Total RNA was collected from DENV-2 infected (or non-infected) 293T cells at 48h post-infection. cDNA libraries were prepared through the sequential use of the RNeasy Mini Kit with On-Column DNase Digestion Set (QIAGEN, Venlo, Netherlands), Dynabeads mRNA DIRECT purification Kit and Total RNA-Seq Kit v2 (Thermo Fisher Scientific). The transcription sequences were sequenced using an Illumina Hiseq2000, and the total base number was more than 20 Gb per sample. RNA-Seq de novo assembly was performed using Trinity. Get ORF in EBOSS were used to find protein from contigs.
4
RNA-seq Library Preparation Protocol
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RNA‐seq was performed as described previously (Isogaya et al., 2014 ; Mizutani et al., 2016 ). cDNA libraries were prepared using the RNeasy Mini Kit with the On‐Column DNase Digestion Set (QIAGEN, Venlo, The Netherlands), Dynabeads mRNA DIRECT Purification Kit, and the Ion Total RNA‐Seq Kit v2 (Thermo Fisher Scientific).
5
RNA-seq Library Preparation Protocol
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cDNA libraries were prepared through the sequential use of the RNeasy Mini Kit with On-Column DNase Digestion Set (QIAGEN, Venlo, Netherlands), Dynabeads mRNA DIRECT Purification Kit and Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) and were sequenced and analyzed as in RIP-seq.
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