nextgen rnaseq Search Results


nextgen rna-seq  (NextGen Sciences)
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Nextgen Rna Seq, supplied by NextGen Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rnaseq methods  (NextGen Sciences)
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Rnaseq Methods, supplied by NextGen Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rnaseq data processing  (NextGen Sciences)
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rnaseq analysis  (NextGen Sciences)
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(A-B) Total <t>RNA</t> was extracted from naïve B cells of spleen of WT or Fancc−/− mice and stimulated 4h in-vitro with 20ug/ml LPS. The mRNAs were analyzed <t>by</t> <t>RNAseq</t> to determine transcript abundance and differential expression using GeneSpring GX (FC≥1.5, p≤0.05). (A) Top 5 deregulated pathways determined by Genespring Pathway analysis module using the Wiki Pathway curated database. (B) Heatmap representation (2 independent experiments) of mean normalized expression values of WNT signaling deregulated genes identify by RNAseq. (C) qPCR validation of candidate WNT deregulated genes from WT and Fancc−/− B cells culture activated 4h by LPS (n=4 mice/genotype, 2 independent experiments). (D) Western blot analysis of β-catenin protein level in whole B cells lysate for indicated time of culture (Representative of 3 independent experiments with pooled B cells of at least 2 mice for each genotype). Values under the blot represent the density ratio of β-catenin/ β-actin. (E-H) LSKs cells were isolated from WT and Fancc−/− BM by Facs sorting, transduced in-vitro with 7TGC reporter lentivirus and transplanted into lethally irradiated Boy/J mice. Donor derived splenocytes (CD45.2+) were analyzed at 4 and 10 weeks post-transplantation. (E) Spleen cellularity of mice at 4 and 10 weeks after BM transplantation with Fancc−/− or WT LSKs. (F) Quantification of proportion of naïve donor B cells percentage at 4 weeks (n=4 mice/genotype, 2 independent experiments) and 10 weeks (n=5 mice/genotype, 2 independent experiments) post-transplantation. (G) Representative overlay histogram of GFP expression from donor derived naïve B cells at 10 weeks post transplantation. (H) Quantification of GFP+ donor derived B cells as indicated in (F) (n=5 mice/genotype, 2 independent experiments). For all graphics, Bar represents mean value ± SD. Evaluation of differences between genotype has been conducted using Student’s T-test (*=p≤0.05, **= p≤0.01).
Rnaseq Analysis, supplied by NextGen Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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next generation rna sequencing nextgen rnaseq  (NextGen Sciences)
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NextGen Sciences next generation rna sequencing nextgen rnaseq
(A-B) Total <t>RNA</t> was extracted from naïve B cells of spleen of WT or Fancc−/− mice and stimulated 4h in-vitro with 20ug/ml LPS. The mRNAs were analyzed <t>by</t> <t>RNAseq</t> to determine transcript abundance and differential expression using GeneSpring GX (FC≥1.5, p≤0.05). (A) Top 5 deregulated pathways determined by Genespring Pathway analysis module using the Wiki Pathway curated database. (B) Heatmap representation (2 independent experiments) of mean normalized expression values of WNT signaling deregulated genes identify by RNAseq. (C) qPCR validation of candidate WNT deregulated genes from WT and Fancc−/− B cells culture activated 4h by LPS (n=4 mice/genotype, 2 independent experiments). (D) Western blot analysis of β-catenin protein level in whole B cells lysate for indicated time of culture (Representative of 3 independent experiments with pooled B cells of at least 2 mice for each genotype). Values under the blot represent the density ratio of β-catenin/ β-actin. (E-H) LSKs cells were isolated from WT and Fancc−/− BM by Facs sorting, transduced in-vitro with 7TGC reporter lentivirus and transplanted into lethally irradiated Boy/J mice. Donor derived splenocytes (CD45.2+) were analyzed at 4 and 10 weeks post-transplantation. (E) Spleen cellularity of mice at 4 and 10 weeks after BM transplantation with Fancc−/− or WT LSKs. (F) Quantification of proportion of naïve donor B cells percentage at 4 weeks (n=4 mice/genotype, 2 independent experiments) and 10 weeks (n=5 mice/genotype, 2 independent experiments) post-transplantation. (G) Representative overlay histogram of GFP expression from donor derived naïve B cells at 10 weeks post transplantation. (H) Quantification of GFP+ donor derived B cells as indicated in (F) (n=5 mice/genotype, 2 independent experiments). For all graphics, Bar represents mean value ± SD. Evaluation of differences between genotype has been conducted using Student’s T-test (*=p≤0.05, **= p≤0.01).
Next Generation Rna Sequencing Nextgen Rnaseq, supplied by NextGen Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sequencing methodologies rnaseq  (NextGen Sciences)
90
NextGen Sciences sequencing methodologies rnaseq
(A-B) Total <t>RNA</t> was extracted from naïve B cells of spleen of WT or Fancc−/− mice and stimulated 4h in-vitro with 20ug/ml LPS. The mRNAs were analyzed <t>by</t> <t>RNAseq</t> to determine transcript abundance and differential expression using GeneSpring GX (FC≥1.5, p≤0.05). (A) Top 5 deregulated pathways determined by Genespring Pathway analysis module using the Wiki Pathway curated database. (B) Heatmap representation (2 independent experiments) of mean normalized expression values of WNT signaling deregulated genes identify by RNAseq. (C) qPCR validation of candidate WNT deregulated genes from WT and Fancc−/− B cells culture activated 4h by LPS (n=4 mice/genotype, 2 independent experiments). (D) Western blot analysis of β-catenin protein level in whole B cells lysate for indicated time of culture (Representative of 3 independent experiments with pooled B cells of at least 2 mice for each genotype). Values under the blot represent the density ratio of β-catenin/ β-actin. (E-H) LSKs cells were isolated from WT and Fancc−/− BM by Facs sorting, transduced in-vitro with 7TGC reporter lentivirus and transplanted into lethally irradiated Boy/J mice. Donor derived splenocytes (CD45.2+) were analyzed at 4 and 10 weeks post-transplantation. (E) Spleen cellularity of mice at 4 and 10 weeks after BM transplantation with Fancc−/− or WT LSKs. (F) Quantification of proportion of naïve donor B cells percentage at 4 weeks (n=4 mice/genotype, 2 independent experiments) and 10 weeks (n=5 mice/genotype, 2 independent experiments) post-transplantation. (G) Representative overlay histogram of GFP expression from donor derived naïve B cells at 10 weeks post transplantation. (H) Quantification of GFP+ donor derived B cells as indicated in (F) (n=5 mice/genotype, 2 independent experiments). For all graphics, Bar represents mean value ± SD. Evaluation of differences between genotype has been conducted using Student’s T-test (*=p≤0.05, **= p≤0.01).
Sequencing Methodologies Rnaseq, supplied by NextGen Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rnaseq data preprocessing pipeline  (NextGen Sciences)
90
NextGen Sciences rnaseq data preprocessing pipeline
Baseline information of patients and PDOX
Rnaseq Data Preprocessing Pipeline, supplied by NextGen Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


(A-B) Total RNA was extracted from naïve B cells of spleen of WT or Fancc−/− mice and stimulated 4h in-vitro with 20ug/ml LPS. The mRNAs were analyzed by RNAseq to determine transcript abundance and differential expression using GeneSpring GX (FC≥1.5, p≤0.05). (A) Top 5 deregulated pathways determined by Genespring Pathway analysis module using the Wiki Pathway curated database. (B) Heatmap representation (2 independent experiments) of mean normalized expression values of WNT signaling deregulated genes identify by RNAseq. (C) qPCR validation of candidate WNT deregulated genes from WT and Fancc−/− B cells culture activated 4h by LPS (n=4 mice/genotype, 2 independent experiments). (D) Western blot analysis of β-catenin protein level in whole B cells lysate for indicated time of culture (Representative of 3 independent experiments with pooled B cells of at least 2 mice for each genotype). Values under the blot represent the density ratio of β-catenin/ β-actin. (E-H) LSKs cells were isolated from WT and Fancc−/− BM by Facs sorting, transduced in-vitro with 7TGC reporter lentivirus and transplanted into lethally irradiated Boy/J mice. Donor derived splenocytes (CD45.2+) were analyzed at 4 and 10 weeks post-transplantation. (E) Spleen cellularity of mice at 4 and 10 weeks after BM transplantation with Fancc−/− or WT LSKs. (F) Quantification of proportion of naïve donor B cells percentage at 4 weeks (n=4 mice/genotype, 2 independent experiments) and 10 weeks (n=5 mice/genotype, 2 independent experiments) post-transplantation. (G) Representative overlay histogram of GFP expression from donor derived naïve B cells at 10 weeks post transplantation. (H) Quantification of GFP+ donor derived B cells as indicated in (F) (n=5 mice/genotype, 2 independent experiments). For all graphics, Bar represents mean value ± SD. Evaluation of differences between genotype has been conducted using Student’s T-test (*=p≤0.05, **= p≤0.01).

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Loss of Fancc impairs antibody secreting cell differentiation in mice through deregulating Wnt signaling pathway

doi: 10.4049/jimmunol.1501056

Figure Lengend Snippet: (A-B) Total RNA was extracted from naïve B cells of spleen of WT or Fancc−/− mice and stimulated 4h in-vitro with 20ug/ml LPS. The mRNAs were analyzed by RNAseq to determine transcript abundance and differential expression using GeneSpring GX (FC≥1.5, p≤0.05). (A) Top 5 deregulated pathways determined by Genespring Pathway analysis module using the Wiki Pathway curated database. (B) Heatmap representation (2 independent experiments) of mean normalized expression values of WNT signaling deregulated genes identify by RNAseq. (C) qPCR validation of candidate WNT deregulated genes from WT and Fancc−/− B cells culture activated 4h by LPS (n=4 mice/genotype, 2 independent experiments). (D) Western blot analysis of β-catenin protein level in whole B cells lysate for indicated time of culture (Representative of 3 independent experiments with pooled B cells of at least 2 mice for each genotype). Values under the blot represent the density ratio of β-catenin/ β-actin. (E-H) LSKs cells were isolated from WT and Fancc−/− BM by Facs sorting, transduced in-vitro with 7TGC reporter lentivirus and transplanted into lethally irradiated Boy/J mice. Donor derived splenocytes (CD45.2+) were analyzed at 4 and 10 weeks post-transplantation. (E) Spleen cellularity of mice at 4 and 10 weeks after BM transplantation with Fancc−/− or WT LSKs. (F) Quantification of proportion of naïve donor B cells percentage at 4 weeks (n=4 mice/genotype, 2 independent experiments) and 10 weeks (n=5 mice/genotype, 2 independent experiments) post-transplantation. (G) Representative overlay histogram of GFP expression from donor derived naïve B cells at 10 weeks post transplantation. (H) Quantification of GFP+ donor derived B cells as indicated in (F) (n=5 mice/genotype, 2 independent experiments). For all graphics, Bar represents mean value ± SD. Evaluation of differences between genotype has been conducted using Student’s T-test (*=p≤0.05, **= p≤0.01).

Article Snippet: RNA isolation, RNA NextGen sequencing (RNAseq) analysis and real-time quantitative PCR (qPCR) Total RNA was purified with RNeasy plus mini kit from B cells ex-vivo, after culture or after CFSE peak based cell sorting by FACSAria (3 division peak).

Techniques: In Vitro, Quantitative Proteomics, Expressing, Biomarker Discovery, Western Blot, Isolation, Irradiation, Derivative Assay, Transplantation Assay

Baseline information of patients and PDOX

Journal: Acta Neuropathologica Communications

Article Title: Metabolic and transcriptomic profiles of glioblastoma invasion revealed by comparisons between patients and corresponding orthotopic xenografts in mice

doi: 10.1186/s40478-021-01232-4

Figure Lengend Snippet: Baseline information of patients and PDOX

Article Snippet: Preprocessing of RNA sequencing (RNAseq) data was performed following the standard pipeline and recommendations from bcbio-nextgen (version 1.0.4, http://bcbio-nextgen.readthedocs.org/en/latest/ ).

Techniques: