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smart-seq2 library preparation  (Illumina Inc)


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    Illumina Inc smart-seq2 library preparation
    Smart Seq2 Library Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/smart-seq2+libraries/smart+seq2+libraries/pmc11001867-115-0-26
    Average 90 stars, based on 1 article reviews
    smart-seq2 library preparation - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Reverse Transcription:

    Article Title:
    Article Snippet: .. G en es scRNAseq Reverse transcription was conducted with a CEL-Seq2 primer containing T7 promoter, Illumina 5’ adaptor, unique molecule identifier (UMI), barcode and polyT stretch followed by second strand synthesis. .. Sequencing was performed on Illumina NextSeq500 with the following run parameters: Read1 = 14 nt, Read2 = 78 nt, 2% phiX.

    other:

    Article Title: lncRNAlyzr: Enrichment Analysis for lncRNA Sets.
    Article Snippet: lncRNAs make up a large portion of the human genome affecting many biological processes in normal physiology and diseases.. However, human lncRNAs are understudied compared to protein-coding genes.. While there are many tools for performing gene set enrichment analysis for coding genes, few tools exist for lncRNA enrichment analysis. lncRNAlyzr is a webserver application designed for lncRNAs enrichment analysis. lncRNAlyzr has a database containing 33 lncRNA set libraries created by computing correlations between lncRNAs and annotated coding gene sets.

    Article Title: Metabolic Adaptations in Cancer and the Host Using Drosophila Models and Advanced Tools
    Article Snippet: Salivary gland ( Ras V12 ) , Non-tumour tissue: haemolymph bleeding larvae and capillary suction , Smart-seq2/Illumina (San Diego, CA, USA) , [ ] .

    Article Title: High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome
    Article Snippet: UMI: Unique molecular identifiers. (C) smRandom-seq2 sequencing library preparation scheme for Illumina platforms.

    Article Title: Aneuploidy-driven gene expression profiling in human blastocysts: insights from RNA-Seq analysis.
    Article Snippet: Purpose Preimplantation aneuploidy in humans is one of the primary causes of implantation failure and embryo miscarriage.. This study was conducted to gain insight into gene expression changes that may result from aneuploidy in blastocysts through RNA-Seq analysis.. Methods The surplus embryos of preimplantation genetic testing for aneuploidy (PGT-A) candidate couples with normal karyotype and maternal age < 38 were collected following identical ovarian stimulation protocol.

    Article Title: Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data
    Article Snippet: Platform , Illumina , Smart-seq2 , Illumina.

    Article Title: Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.
    Article Snippet: As part of this optimization, we modified the adaptor sequences of the CEL-Seq2 primers to ensure compatibility with both Illumina and BGI platforms for sequencing.

    Article Title: Gut bacterial L-lysine alters metabolism and histone methylation to drive dendritic cell tolerance
    Article Snippet: CD103+ cDC1s (CD103+ CD11b ) and CD103+ cDC2s (CD103+ CD11b+) were sorted from CD11c+ cells enriched from MLNs of mice using CD11c MicroBeads UltraPure (Miltenyi Biotec).



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    Increased chromatin accessibility in knockout round spermatids. A).Volcano plot of DEGs between control and Eif5a SKO samples.FDR<0.05. B.The average tag density plot(top pannel) and heatmaps (bottom pannel)around TSS (±3 kb) for the enrichment of ATAC‐seq reads in control and Eif5a SKO round spermatids. C).Plot shows Gain and Loss sites in all control and Eif5a SKO sample replicates. D).Venn diagram showing the overlap of differential peaks identified by CUT&Tag and ATAC‐seq between WT and CKO groups. E).Four‐quadrant scatter plot comparing the log 2 fold changes of significantly differential peaks (FDR < 0.05) from H3K4me3 CUT&Tag (x‐axis) and ATAC‐seq (y‐axis). The Pearson correlation coefficient for the compared data is 0.468. Pearson's *r* = 0.468. F) Venn diagram show shared genes between ATAC‐seq (FDR<0.05) <t>and</t> <t>Smart‐seq2</t> (FDR<0.05, FC>1.5).
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    Increased chromatin accessibility in knockout round spermatids. A).Volcano plot of DEGs between control and Eif5a SKO samples.FDR<0.05. B.The average tag density plot(top pannel) and heatmaps (bottom pannel)around TSS (±3 kb) for the enrichment of ATAC‐seq reads in control and Eif5a SKO round spermatids. C).Plot shows Gain and Loss sites in all control and Eif5a SKO sample replicates. D).Venn diagram showing the overlap of differential peaks identified by CUT&Tag and ATAC‐seq between WT and CKO groups. E).Four‐quadrant scatter plot comparing the log 2 fold changes of significantly differential peaks (FDR < 0.05) from H3K4me3 CUT&Tag (x‐axis) and ATAC‐seq (y‐axis). The Pearson correlation coefficient for the compared data is 0.468. Pearson's *r* = 0.468. F) Venn diagram show shared genes between ATAC‐seq (FDR<0.05) <t>and</t> <t>Smart‐seq2</t> (FDR<0.05, FC>1.5).
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    Increased chromatin accessibility in knockout round spermatids. A).Volcano plot of DEGs between control and Eif5a SKO samples.FDR<0.05. B.The average tag density plot(top pannel) and heatmaps (bottom pannel)around TSS (±3 kb) for the enrichment of ATAC‐seq reads in control and Eif5a SKO round spermatids. C).Plot shows Gain and Loss sites in all control and Eif5a SKO sample replicates. D).Venn diagram showing the overlap of differential peaks identified by CUT&Tag and ATAC‐seq between WT and CKO groups. E).Four‐quadrant scatter plot comparing the log 2 fold changes of significantly differential peaks (FDR < 0.05) from H3K4me3 CUT&Tag (x‐axis) and ATAC‐seq (y‐axis). The Pearson correlation coefficient for the compared data is 0.468. Pearson's *r* = 0.468. F) Venn diagram show shared genes between ATAC‐seq (FDR<0.05) and Smart‐seq2 (FDR<0.05, FC>1.5).

    Journal: Advanced Science

    Article Title: EIF5A Couples Translational Control With Transcriptional Reprogramming Through Chromocenter Reorganization During Spermiogenesis

    doi: 10.1002/advs.202517423

    Figure Lengend Snippet: Increased chromatin accessibility in knockout round spermatids. A).Volcano plot of DEGs between control and Eif5a SKO samples.FDR<0.05. B.The average tag density plot(top pannel) and heatmaps (bottom pannel)around TSS (±3 kb) for the enrichment of ATAC‐seq reads in control and Eif5a SKO round spermatids. C).Plot shows Gain and Loss sites in all control and Eif5a SKO sample replicates. D).Venn diagram showing the overlap of differential peaks identified by CUT&Tag and ATAC‐seq between WT and CKO groups. E).Four‐quadrant scatter plot comparing the log 2 fold changes of significantly differential peaks (FDR < 0.05) from H3K4me3 CUT&Tag (x‐axis) and ATAC‐seq (y‐axis). The Pearson correlation coefficient for the compared data is 0.468. Pearson's *r* = 0.468. F) Venn diagram show shared genes between ATAC‐seq (FDR<0.05) and Smart‐seq2 (FDR<0.05, FC>1.5).

    Article Snippet: The Smart‐seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired‐end reads.

    Techniques: Knock-Out, Control

    Proteomic alterations associated with transcriptional changes induced by Eif5a deletion. A).Venn diagram of shared genes between Smart‐seq2 (P value<0.05, FC>1.5) and Proteomics (P<0.05, FC>1.5) analyses. B).GO enrichment analysis based on the 119 commonly upregulated genes. C).QRT‐PCR analysis of candidate genes that were consistently dysregulated in both the transcriptome and proteome of Eif5a SKO testes. Data are presented as mean ± SD from three independent biological replicates (n = 3). Statistical significance was determined using a two‐tailed, unpaired Student's t‐test (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). D). Western blots show SPATA1, SPACA3 and SPACA9 proteins in Eif5a SKO and control mice. β‐Actin served as the loading control. E). IGV visualization of genomic regions harboring acrosome‐related ( Spaca3, Ly6K,Spaca9,Spata1,Lamp2 ) and microtubule‐associated ( Ccdc169, Dynlt3 ) genes. Top: ATAC‐seq tracks showing chromatin accessibility in control (blue) versus SKO (red) round spermatids. Bottom: Corresponding Smart‐seq2 coverage.

    Journal: Advanced Science

    Article Title: EIF5A Couples Translational Control With Transcriptional Reprogramming Through Chromocenter Reorganization During Spermiogenesis

    doi: 10.1002/advs.202517423

    Figure Lengend Snippet: Proteomic alterations associated with transcriptional changes induced by Eif5a deletion. A).Venn diagram of shared genes between Smart‐seq2 (P value<0.05, FC>1.5) and Proteomics (P<0.05, FC>1.5) analyses. B).GO enrichment analysis based on the 119 commonly upregulated genes. C).QRT‐PCR analysis of candidate genes that were consistently dysregulated in both the transcriptome and proteome of Eif5a SKO testes. Data are presented as mean ± SD from three independent biological replicates (n = 3). Statistical significance was determined using a two‐tailed, unpaired Student's t‐test (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). D). Western blots show SPATA1, SPACA3 and SPACA9 proteins in Eif5a SKO and control mice. β‐Actin served as the loading control. E). IGV visualization of genomic regions harboring acrosome‐related ( Spaca3, Ly6K,Spaca9,Spata1,Lamp2 ) and microtubule‐associated ( Ccdc169, Dynlt3 ) genes. Top: ATAC‐seq tracks showing chromatin accessibility in control (blue) versus SKO (red) round spermatids. Bottom: Corresponding Smart‐seq2 coverage.

    Article Snippet: The Smart‐seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired‐end reads.

    Techniques: Quantitative RT-PCR, Two Tailed Test, Western Blot, Control