Lung and heart tissues were processed by slicing approximately 30 mg of tissue from each sample and homogenizing in Buffer RLT Plus for 4 min at 20 Hz using the TissueLyser II (Qiagen). Total RNA was extracted using the AllPrep DNA/RNA/miRNA kit (Qiagen). RNA was quantified with a Nanodrop 1000 spectrophotometer (Thermo Scientific) and quality-verified on a representative subset of 30 samples using the 2200 TapeStation Automated Electrophoresis System (Agilent Technologies). Samples showed RNA integrity numbers (RINs) that greatly exceeded requirements for the employed sequencing technologies, with RINs ≥ 8.8. RNA samples were then analyzed using the TempO-Seq Mouse Whole Transcriptome assay (BioSpyder) with resulting libraries sequenced using the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina). Sequencing data were processed using the Tempo-SeqR pipeline (BioSpyder 2021 ), with QA/QC metrics including the average number of mapped reads in positive controls (i.e., requiring > 6×106 mapped reads), low signal-to-noise ratios (i.e., requiring total number of mapped reads in the positive control divided by the total number of mapped reads in negative controls > 20:1), and the percentage of mapped reads in positive control (i. e., requiring > 80%). Count data were aligned to the Ensemble database v98 and summarized as number of counts per gene.
2200 tapestation automated electrophoresis system
Manufactured by Agilent Technologies
Sourced in United States
The 2200 TapeStation Automated Electrophoresis System is a laboratory instrument designed for automated electrophoresis analysis. It performs size separation and quantification of nucleic acid samples.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (6 mentions)
Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (4 mentions)
Hiseq 2500 ultra high throughput sequencing system, by Illumina (2 mentions)
Allprep dna rna mirna kit, by Qiagen (2 mentions)
Tissuelyser 2, by Qiagen (2 mentions)
Purelink dnase set, by Thermo Fisher Scientific (1 mentions)
Depc treated water, by Thermo Fisher Scientific (1 mentions)
Purelink rna mini kit, by Thermo Fisher Scientific (1 mentions)
Kingfisher instrument, by Thermo Fisher Scientific (1 mentions)
Qubit rna hs assay kit, by Thermo Fisher Scientific (1 mentions)
Truseq stranded total rna with ribo zero gold sample preparation kit, by Illumina (1 mentions)
Mirneasy mini kit, by Qiagen (1 mentions)
5 protocols using 2200 tapestation automated electrophoresis system
1
Transcriptome Profiling of Lung and Heart Tissues
2
Transcriptome Profiling of Lung and Heart Tissues
3
RNA Isolation from Equine ACFC Cell Lines
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
According to the producer’s protocol, RNA was directly isolated from adherent cultures of BPV-E4 and BPV-E1^E4 transgenic equine ACFC-derived neoplastic cell lines that were expanded ex vivo on the bottom of culture dishes. To extract RNA samples, a PureLink™ RNA mini kit (Invitrogen) was used. The procedure was maintained, with the addition of a DNase treatment step (PureLink™ DNase Set, Invitrogen). RNA was eluted with DEPC-treated water (Thermo Fisher Scientific, Waltham, MA, USA).
The quality and quantity of RNA were measured with a 2200 TapeStation Automated Electrophoresis System (Agilent Technologies, Santa Clara, CA, USA), as well as a nanodrop 2000 spectrophotometer (Thermo Scientific) and agarose gel (2% agarose in TBE buffer) electrophoresis.
The quality and quantity of RNA were measured with a 2200 TapeStation Automated Electrophoresis System (Agilent Technologies, Santa Clara, CA, USA), as well as a nanodrop 2000 spectrophotometer (Thermo Scientific) and agarose gel (2% agarose in TBE buffer) electrophoresis.
4
RNA Extraction and Quantification from Nasal Polyps
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The 50 tissue samples from CRSwNP patients and healthy controls were directly put in RNA later medium (Thermo Fisher Scientific Inc., CA, USA) and processed for extraction and purification of total RNA using the Kingfisher RNA kit together with the Kingfisher instrument (Thermo Fisher Scientific Inc., CA, USA) according to the manufacturer’s instructions. The quantity and quality of isolated RNA was determined using the NanoDrop 2000 Spectrophotometer (Thermo Fischer Scientific) and 2200 TapeStation Automated Electrophoresis System (Agilent Technologies). Samples with an RNA integrity number of greater than 6.0 were chosen for sequencing, with the exception of one polyp sample at RIN 4 which was included.
5
Comprehensive RNA Extraction and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA extractions were done on blood using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quantity and quality of isolated RNA were determined using the NanoDrop 2000 Spectrophotometer (Thermo Fischer Scientific, Waltham, USA), Qubit® RNA HS Assay Kit (Invitrogen, Waltham, USA), and 2200 TapeStation Automated Electrophoresis System (Agilent Technologies, Santa Clara, USA). The samples had RNA integrity numbers between 2.2 and 8.8.
Ribosomal RNA was removed, and sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina, San Diego, USA), following the manufacturer’s instructions. Construction of libraries was prepared using the TruSeq Stranded Total RNA Sample Preparation Guide 15,031,048 Rev. E (Illumina, San Diego, USA), using 0.5–1 μg of total RNA input. The Novaseq 6000 platform was used and 100 bp paired-end reads were generated by Clinical Genomics at the University of Gothenburg (Gothenburg, Sweden).
Ribosomal RNA was removed, and sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina, San Diego, USA), following the manufacturer’s instructions. Construction of libraries was prepared using the TruSeq Stranded Total RNA Sample Preparation Guide 15,031,048 Rev. E (Illumina, San Diego, USA), using 0.5–1 μg of total RNA input. The Novaseq 6000 platform was used and 100 bp paired-end reads were generated by Clinical Genomics at the University of Gothenburg (Gothenburg, Sweden).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!