RNA-seq expression studies were independently performed in two laboratories (Accession #GSE128696 , #GSE129044 ). For the FI-NK vs. IL-21-NKAES/IL-15-NKAES comparisons, extraction of total RNA was done using the RNeasy mini kit (Qiagen) and Total RNA Purification Plus Kit (Norgen Biotek), respectively. The quality of RNA was verified with 2100 Bioanalyzer (Agilent) prior to preparation of sequencing libraries with the TruSeq RNA Sample Prep v2 Kit. Quality of libraries was verified via Agilent 4200 Tapestation using a High Sensitivity D1000 ScreenTape Assay kit. For the IL-15 NKAES analysis, approximately 60–80 million paired-end 150 bp sequence reads per library were generated, whereas for the IL-21 NKAES analysis, 30 million single-end 101 bp sequence reads per library were generated, both using Illumina HiSeq4000 platform. Kallisto, an RNA quantification program based on pseudoalignment was used to obtain read count estimates per gene (14 (link)). The differential gene expression analysis was done using DESeq2, edgeR, and limma R packages.
D1000 screentape assay kit
Manufactured by Agilent Technologies
The D1000 ScreenTape Assay kit is a lab equipment product from Agilent Technologies. It is designed for the automated analysis of DNA and RNA samples using the Agilent 2200 TapeStation system. The kit provides pre-prepared reagents and consumables necessary for the assessment of sample quality and quantity.
Automatically generated - may contain errors
Lab products found in correlation
Tapestation 4200, by Agilent Technologies (1 mentions)
Total rna purification plus kit, by Norgen Biotek (1 mentions)
Hiseq 4000 platform, by Illumina (1 mentions)
Rneasy mini kit, by Qiagen (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Novaseq 6000 s1 reagent kit 200 cycle, by Illumina (1 mentions)
Novaseq 6000 sequencing system, by Illumina (1 mentions)
Direct zol rna microprep kit, by Zymo Research (1 mentions)
2 protocols using d1000 screentape assay kit
1
Transcriptomic Profiling of Activated NK Cells
2
Microglial RNA-Seq on SPI-collagen Membranes
Check if the same lab product or an alternative is used in the 5 most similar protocols
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As described in Section 2.1, SPI-collagen or collagen membranes were created in 6-well plates by coating the wells with the appropriate solution followed by EDC and NHS crosslinking. Human microglial cells were seeded on the membranes at 200,000 cells per well. The microglial cells were cultured for 3 days and then RNA was extracted from the cultured cells with the Direct-zol RNA Microprep kit (Zymo Research, Irvine, CA).
RNA-Seq was performed at the Kansas University Medical Center Genome Sequencing Center. RNA libraries were prepared using the Universal Plus mRNA-Seq with NuQuant kit (Tecan Genomics 0520-A01). Libraries were validated using the D1000 ScreenTape Assay kit (Agilent Technologies 5067-5582) followed by concentration determination with a Qubit fluorometer. A concentration of 2.125 nM was used for multiplexed sequencing. Adapter ligation was verified by qPCR. The NovaSeq 6000 S1 Reagent Kit (200 cycle) (Illumina 20012864) was used to run the pooled libraries on an Illumina NovaSeq 6000 Sequencing System using 2 × 101 cycle sequencing with dual indexes. A one percent spike-in of PhIX Illumina Control library was included in the sequencing runs to allow measurement of error rates.
RNA-Seq was performed at the Kansas University Medical Center Genome Sequencing Center. RNA libraries were prepared using the Universal Plus mRNA-Seq with NuQuant kit (Tecan Genomics 0520-A01). Libraries were validated using the D1000 ScreenTape Assay kit (Agilent Technologies 5067-5582) followed by concentration determination with a Qubit fluorometer. A concentration of 2.125 nM was used for multiplexed sequencing. Adapter ligation was verified by qPCR. The NovaSeq 6000 S1 Reagent Kit (200 cycle) (Illumina 20012864) was used to run the pooled libraries on an Illumina NovaSeq 6000 Sequencing System using 2 × 101 cycle sequencing with dual indexes. A one percent spike-in of PhIX Illumina Control library was included in the sequencing runs to allow measurement of error rates.
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