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Htseq2000

Manufactured by Illumina
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The HTSeq2000 is a high-throughput sequencing platform designed to generate large volumes of genomic data. It utilizes advanced sequencing technology to enable rapid and accurate DNA sequencing. The core function of the HTSeq2000 is to provide a robust and efficient solution for large-scale genomic analysis projects.

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Lab products found in correlation

Truseq stranded mrna sample prep kit, by Illumina (4 mentions) Artseq ribosome profiling kit, by Illumina (2 mentions) Smarter ultra low input rna v4 and smarter low input library prep kit v2, by Takara Bio (2 mentions) Truseq rna sample preparation kit, by Illumina (1 mentions)

5 protocols using htseq2000

1

Transcriptomic and Translational Profiling of B Cells

Cited 1 time
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mRNAseq libraries were obtained using TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc). Splenic B cells from individual HuRf/f control or HuR-cKO mice were independently processed for RNA extraction (ex vivo samples, n=4 per genotype) or were stimulated with LPS for 48 hours in RPMI media plus 1 mM NaPyr (n=3-4 per genotype).
Previously published mRNAseq libraries were used to analyse the expression of genes involved in glycolysis, TCA cycle and electron transport in naive and GC B cells (GEO deposition number - GSE47705)54 (link).
Ribosome footprinting profiling (Ribo-Seq) assays were performed using ARTseq™ Ribosome Profiling Kit (Epicentre, Illumina). Ex vivo or LPS-activated B cells (n=4-5 per genotype and condition) were treated with cyclohexamide (CHX, 100 μg/ml) three minutes prior cell extract preparation. cDNA libraries were sequenced using either GAIIX (iCLIP) or HTSeq2000 (mRNAseq and Ribo-Seq) Illumina technology. The type of sequencing performed was: iCLIP, 40 bp SE; mRNAseq, 100 bp SE; and Ribo-seq, 50 bp SE.
Diaz-Muñoz M.D., Bell S.E., Fairfax K., Monzon-Casanova E., Cunningham A.F., Gonzalez-Porta M., Andrews S.R., Bunik V.I., Zarnack K., Curk T., Heggermont W.A., Heymans S., Gibson G.E., Kontoyiannis D.L., Ule J, & Turner M. (2015). The RNA-binding protein HuR (Elavl1) is essential for the B cell antibody response. Nature immunology, 16(4), 415-425.
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2

Bulk RNA-seq of Sorted B Cells

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Sorted MZ or FO B cells from individual control mice were independently processed for RNA extraction. RNAseq libraries were obtained using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) or SMARTer Ultra Low Input RNA v4 and SMARTer Low Input Library Prep Kit V2 (Clontech). Low input libraries were prepared and sequenced from total RNA at Aros Applied Biotechnology A/S. RNAseq libraries were sequenced using the HTSeq2000 (Illumina). 100bp single end or paired end sequencing was performed on all libraries.
Newman R., Ahlfors H., Saveliev A., Galloway A., Hodson D.J., Williams R., Besra G.S., Cook C.N., Cunningham A.F., Bell S.E, & Turner M. (2017). Maintenance of the marginal zone B cell compartment specifically requires the RNA-binding protein ZFP36L1. Nature immunology, 18(6), 683-693.
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3

Transcriptomic and Translational Profiling of B Cells

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
mRNAseq libraries were obtained using TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc). Splenic B cells from individual HuRf/f control or HuR-cKO mice were independently processed for RNA extraction (ex vivo samples, n=4 per genotype) or were stimulated with LPS for 48 hours in RPMI media plus 1 mM NaPyr (n=3-4 per genotype).
Previously published mRNAseq libraries were used to analyse the expression of genes involved in glycolysis, TCA cycle and electron transport in naive and GC B cells (GEO deposition number - GSE47705)54 (link).
Ribosome footprinting profiling (Ribo-Seq) assays were performed using ARTseq™ Ribosome Profiling Kit (Epicentre, Illumina). Ex vivo or LPS-activated B cells (n=4-5 per genotype and condition) were treated with cyclohexamide (CHX, 100 μg/ml) three minutes prior cell extract preparation. cDNA libraries were sequenced using either GAIIX (iCLIP) or HTSeq2000 (mRNAseq and Ribo-Seq) Illumina technology. The type of sequencing performed was: iCLIP, 40 bp SE; mRNAseq, 100 bp SE; and Ribo-seq, 50 bp SE.
Diaz-Muñoz M.D., Bell S.E., Fairfax K., Monzon-Casanova E., Cunningham A.F., Gonzalez-Porta M., Andrews S.R., Bunik V.I., Zarnack K., Curk T., Heggermont W.A., Heymans S., Gibson G.E., Kontoyiannis D.L., Ule J, & Turner M. (2015). The RNA-binding protein HuR (Elavl1) is essential for the B cell antibody response. Nature immunology, 16(4), 415-425.
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4

RNA-seq analysis of BRAF-induced senescence

Cited 2 times
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RNA-seq libraries on biological triplicate vector and BRAFV600E-transduced Tig3 cells and senescent Tig3 cells were generated from 1 µg total RNA using the Illumina TruSeq RNA Sample Preparation kit, following the manufacturer's instruction. Libraries were single-end sequenced on the Illumina HTSeq 2000 platform. The reads were aligned to the human genome build GTC37.75 using TopHat 2.012 (Kim et al. 2013 (link)). HTSeq-count (Anders et al. 2015 (link)) was used to determine expression per gene using the default union mode. Differentially expressed genes were determined in R using edgeR (Robinson et al. 2010 (link)) and voom (Law et al. 2014 (link)) and were considered differentially expressed if they had a P-value <0.05 after Benjamini-Hochberg adjustment (Hochberg and Benjamini 1990 (link)). Relative expression of fragments per kilobase per million reads (FPKM) of each gene was calculated by normalizing the reads for each gene-by-gene length (kb) and library size (million reads).
Lenain C., de Graaf C.A., Pagie L., Visser N.L., de Haas M., de Vries S.S., Peric-Hupkes D., van Steensel B, & Peeper D.S. (2017). Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence. Genome Research, 27(10), 1634-1644.
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5

Bulk RNA-seq of Sorted B Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
Sorted MZ or FO B cells from individual control mice were independently processed for RNA extraction. RNAseq libraries were obtained using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) or SMARTer Ultra Low Input RNA v4 and SMARTer Low Input Library Prep Kit V2 (Clontech). Low input libraries were prepared and sequenced from total RNA at Aros Applied Biotechnology A/S. RNAseq libraries were sequenced using the HTSeq2000 (Illumina). 100bp single end or paired end sequencing was performed on all libraries.
Newman R., Ahlfors H., Saveliev A., Galloway A., Hodson D.J., Williams R., Besra G.S., Cook C.N., Cunningham A.F., Bell S.E, & Turner M. (2017). Maintenance of the marginal zone B cell compartment specifically requires the RNA-binding protein ZFP36L1. Nature immunology, 18(6), 683-693.
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