Neb rna ultra directional kit

Manufactured by New England Biolabs

Sourced in United States

The NEB RNA Ultra Directional kit is a laboratory tool designed for the preparation of directional RNA-seq libraries. The kit enables the conversion of RNA samples into cDNA libraries suitable for next-generation sequencing applications.

Automatically generated - may contain errors

Lab products found in correlation

Nextseq 500, by Illumina (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

NEB Ultra II Directional RNA Library Prep Kit NEB Ultra Directional RNA library prep kit RNA Ultra Directional kit NEB kits

2 protocols using neb rna ultra directional kit

RNA-Seq Library Preparation and Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was isolated as described above, and first-strand Illumina-barcoded libraries were generated using the NEB RNA Ultra Directional kit according to the manufacturer’s instructions, including 12 cycles of PCR enrichment. Libraries were subsequently sequenced on an Illumina NextSeq 500 instrument using paired-end 37-bp reads. Trimmomatic pipeline was used to trim data for quality with the following parameters: LEADING, 15; TRAILING, 15; SLIDINGWINDOW, 4; 15 MINLEN, 16. Bowtie2 was used to align data to mouse mm10. HTSeq was used to map aligned reads to genes and to generate a gene count matrix. Technical failure during processing led to the exclusion of samples during analysis. DESeq2 was used to normalize the counts for library depth and perform differential expression analysis between all pairwise comparisons.

Brown F.D., Sen D.R., LaFleur M.W., Godec J., Lukacs-Kornek V., Schildberg F.A., Kim H.J., Yates K.B., Ricoult S.J., Bi K., Trombley J.D., Kapoor V.N., Stanley I.A., Cremasco V., Danial N.N., Manning B.D., Sharpe A.H., Haining W.N, & Turley S.J. (2019). Fibroblastic reticular cells enhance T cell metabolism and survival via epigenetic remodeling. Nature immunology, 20(12), 1668-1680.

+ Open protocol

+ Expand

Mouse Transcriptome Analysis via RNA-seq

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA in the tissue samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA). The mRNA was isolated and purified from the total RNA using Oligo (dT) magnetic beads (Beyotime, Shanghai, China). First‐strand Illumina‐barcoded libraries were generated using the NEB RNA Ultra Directional kit (NEB, Ipswich, Massachusetts, USA) according to the manufacturer's instructions. Sequencing was performed using BGIseq500 platform (BGI, Shenzhen, Guangdong, China). Data were aligned to mouse reference genome NCBI_GCF_000001635.26_GRCm38.p6 (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/) using Bowtie2 (https://github.com/BenLangmead/bowtie2).

Wen Z., Sun H., Zhang Z., Zheng Y., Zheng S., Bin J., Liao Y., Shi M., Zhou R, & Liao W. (2023). High baseline tumor burden‐associated macrophages promote an immunosuppressive microenvironment and reduce the efficacy of immune checkpoint inhibitors through the IGFBP2‐STAT3‐PD‐L1 pathway. Cancer Communications, 43(5), 562-581.

+ Open protocol

+ Expand

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?

Revolutionizing how scientists
search and build protocols!