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Broad Institute Inc genepattern program

Genepattern Program, supplied by Broad Institute 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/gene+pattern/gene+pattern+program/pmc06249057-615-28-32
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genepattern program - by Bioz Stars, 2026-11
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Images

1) Product Images from "Interleukin-17 producing γδ T cells originate from SOX13 + progenitors that are independent of γδTCR signaling"

Article Title: Interleukin-17 producing γδ T cells originate from SOX13 + progenitors that are independent of γδTCR signaling

Journal: Immunity

doi: 10.1016/j.immuni.2018.09.010


Figure Legend Snippet:

Techniques Used: Clone Assay, Virus, Recombinant, Electron Microscopy, Staining, Reverse Transcription, SYBR Green Assay, RNA Sequencing, Software

Related Articles

Software:

Article Title: Gene expression analysis of biopsy samples reveals critical limitations of transcriptome‐based molecular classifications of hepatocellular carcinoma
Article Snippet: .. The preprocessed data were classified with the Nearest Template Prediction algorithm implementation in the Gene Pattern software (Broad Institute, Boston, MA) using published gene signatures obtained from Molecular Signatures Database . .. For pathway enrichment analysis, we applied the GSEAPreranked algorithm from the javaGSEA software version 2.0.13 (Broad Institute) .

Article Title: Role of LFA-1 integrin in the control of a lymphocytic choriomeningitis virus (LCMV) infection
Article Snippet: .. Unless stated otherwise all data analysis was performed using the Genpattern software (Broad Institute) [ ]. ..

Article Title: Activation of STING in T cells induces type I IFN responses and cell death
Article Snippet: .. Adding TCR stimulation further increased expression of most ISGs, reinforcing the possibility of synergy between these pathways. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 caption a8 STING activation increases B6 T cell expression of apoptosis, cell stress related genes in addition to dramatic increases in ISG expression (A) Gene pathways activated in response to TCR or TCR+DMXAA stimulation as determined using RNA sequencing data clustered based on similarity of samples using GenomePattern software (Broad Institute); (B) Changes in T cell expression of anti- and pro-apoptotic and ER stress-related genes in T cells in response to TCR or TCR+DMXAA activation; (C) STING-dependent upregulation of IFNs and selected ISGs in T cells; (D) STING-dependent activation of pro-apoptotic pathways in T cells versus macrophages. ..

Generated:

Article Title: Immune Chaperone gp96 Drives the Contributions of Macrophages to Inflammatory Colon Tumorigenesis
Article Snippet: .. Heat map was generated demonstrating differential expression of genes in the wild-type and knockout cells, using Gene Pattern program provided by the Broad Institute. ..

Quantitative Proteomics:

Article Title: Immune Chaperone gp96 Drives the Contributions of Macrophages to Inflammatory Colon Tumorigenesis
Article Snippet: .. Heat map was generated demonstrating differential expression of genes in the wild-type and knockout cells, using Gene Pattern program provided by the Broad Institute. ..

Knock-Out:

Article Title: Immune Chaperone gp96 Drives the Contributions of Macrophages to Inflammatory Colon Tumorigenesis
Article Snippet: .. Heat map was generated demonstrating differential expression of genes in the wild-type and knockout cells, using Gene Pattern program provided by the Broad Institute. ..

Expressing:

Article Title: Activation of STING in T cells induces type I IFN responses and cell death
Article Snippet: .. Adding TCR stimulation further increased expression of most ISGs, reinforcing the possibility of synergy between these pathways. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 caption a8 STING activation increases B6 T cell expression of apoptosis, cell stress related genes in addition to dramatic increases in ISG expression (A) Gene pathways activated in response to TCR or TCR+DMXAA stimulation as determined using RNA sequencing data clustered based on similarity of samples using GenomePattern software (Broad Institute); (B) Changes in T cell expression of anti- and pro-apoptotic and ER stress-related genes in T cells in response to TCR or TCR+DMXAA activation; (C) STING-dependent upregulation of IFNs and selected ISGs in T cells; (D) STING-dependent activation of pro-apoptotic pathways in T cells versus macrophages. ..

Activation Assay:

Article Title: Activation of STING in T cells induces type I IFN responses and cell death
Article Snippet: .. Adding TCR stimulation further increased expression of most ISGs, reinforcing the possibility of synergy between these pathways. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 caption a8 STING activation increases B6 T cell expression of apoptosis, cell stress related genes in addition to dramatic increases in ISG expression (A) Gene pathways activated in response to TCR or TCR+DMXAA stimulation as determined using RNA sequencing data clustered based on similarity of samples using GenomePattern software (Broad Institute); (B) Changes in T cell expression of anti- and pro-apoptotic and ER stress-related genes in T cells in response to TCR or TCR+DMXAA activation; (C) STING-dependent upregulation of IFNs and selected ISGs in T cells; (D) STING-dependent activation of pro-apoptotic pathways in T cells versus macrophages. ..

RNA Sequencing:

Article Title: Activation of STING in T cells induces type I IFN responses and cell death
Article Snippet: .. Adding TCR stimulation further increased expression of most ISGs, reinforcing the possibility of synergy between these pathways. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 caption a8 STING activation increases B6 T cell expression of apoptosis, cell stress related genes in addition to dramatic increases in ISG expression (A) Gene pathways activated in response to TCR or TCR+DMXAA stimulation as determined using RNA sequencing data clustered based on similarity of samples using GenomePattern software (Broad Institute); (B) Changes in T cell expression of anti- and pro-apoptotic and ER stress-related genes in T cells in response to TCR or TCR+DMXAA activation; (C) STING-dependent upregulation of IFNs and selected ISGs in T cells; (D) STING-dependent activation of pro-apoptotic pathways in T cells versus macrophages. ..

Amplification:

Article Title: Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology
Article Snippet: .. Class discovery analysis of mutated or amplified genes by unsupervised hierarchical clustering was performed using the Gene Pattern program (Broad Institute, Boston, MA) according to the online instructions. .. Class discovery analysis of mutated or amplified genes by unsupervised hierarchical clustering was performed using the Gene Pattern program (Broad Institute, Boston, MA) according to the online instructions.

other:

Article Title: ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis
Article Snippet: A heat map was created using GSEA or the Gene Pattern program (Broad Institute).

Article Title: Immune chaperone gp96 drives the contributions of macrophages to inflammatory colon tumorigenesis
Article Snippet: Total RNA was extracted from WT and gp96 KO BMDMs using an RNeasy Mini Kit (Qiagen, Valencia, CA).

Article Title: Interleukin-17 producing γδ T cells originate from SOX13 + progenitors that are independent of γδTCR signaling
Article Snippet: Dead cells were excluded from all analyses using propidium iodide (PI), fixable LIVE/DEAD cell stains (both Life Technologies), or 7-aminoactinomycin D (7-AAD, BD).



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Image Search Results


NGS analysis identified the variant c.1088_1089del within the CAPN6 gene ( NM_014289.4 ) in the family examined. ( A ) Both the chromosomal and exon localization of the CAPN6 gene and variant are depicted. ( B ) The Integrative Genomics Viewer (IGV) image displays this variant, with arrows indicating the father, mother, and their three sons. ( C ) Confirmation of the variant through conventional Sanger sequencing is presented for the father, mother, and their three sons, as indicated by the black arrows. Specifically, the variant has been found in hemizygous condition in the affected male offspring while in heterozygous condition for both the mother and daughter.

Journal: International Journal of Molecular Sciences

Article Title: Potential Link Between a Disruptive CAPN6 Variant and Neurodevelopmental Disorders

doi: 10.3390/ijms27031140

Figure Lengend Snippet: NGS analysis identified the variant c.1088_1089del within the CAPN6 gene ( NM_014289.4 ) in the family examined. ( A ) Both the chromosomal and exon localization of the CAPN6 gene and variant are depicted. ( B ) The Integrative Genomics Viewer (IGV) image displays this variant, with arrows indicating the father, mother, and their three sons. ( C ) Confirmation of the variant through conventional Sanger sequencing is presented for the father, mother, and their three sons, as indicated by the black arrows. Specifically, the variant has been found in hemizygous condition in the affected male offspring while in heterozygous condition for both the mother and daughter.

Article Snippet: CAPN6 gene expression patterns of placenta tissues were obtained from the Human Protein Atlas (HPA) database ( https://www.proteinatlas.org/ ) (accessed on 26 May 2025).

Techniques: Variant Assay, Sequencing

Pedigree analysis of the examined family with an X-linked genetic disorder associated with the mutation c.1088_1089del (p.Asp363GlyfsTer2) in the CAPN6 ( NM_014289.4 ) gene. Both the mother and the daughter exhibited mild intellectual disability. Furthermore, both the male sons exhibited severe neurodevelopmental and mild motor coordination disorders. Red arrows indicate the specific position of the variant. Blue and red asterisks indicate wild type and mutated sequence, respectively.

Journal: International Journal of Molecular Sciences

Article Title: Potential Link Between a Disruptive CAPN6 Variant and Neurodevelopmental Disorders

doi: 10.3390/ijms27031140

Figure Lengend Snippet: Pedigree analysis of the examined family with an X-linked genetic disorder associated with the mutation c.1088_1089del (p.Asp363GlyfsTer2) in the CAPN6 ( NM_014289.4 ) gene. Both the mother and the daughter exhibited mild intellectual disability. Furthermore, both the male sons exhibited severe neurodevelopmental and mild motor coordination disorders. Red arrows indicate the specific position of the variant. Blue and red asterisks indicate wild type and mutated sequence, respectively.

Article Snippet: CAPN6 gene expression patterns of placenta tissues were obtained from the Human Protein Atlas (HPA) database ( https://www.proteinatlas.org/ ) (accessed on 26 May 2025).

Techniques: Mutagenesis, Variant Assay, Sequencing

Domain organization and structural prediction of wild-type CAPN6. ( A ) Schematic representation of the functional domains of CAPN6, annotated according to the ProRule and InterPRO databases. A black arrow marks the mutation site at position 363 in the amino acid sequence. ( B ) Structural model generated using AlphaFold3, with domains colored according to panel. ( A ) The mutation site (Asp363) is highlighted in turquoise and indicated by a black square. ( C ) Close-up view of the wild-type residue (turquoise) and its hydrogen-bonding interactions with Asp365 and Asn369. Structural visualization and modeling were performed using UCSF ChimeraX.

Journal: International Journal of Molecular Sciences

Article Title: Potential Link Between a Disruptive CAPN6 Variant and Neurodevelopmental Disorders

doi: 10.3390/ijms27031140

Figure Lengend Snippet: Domain organization and structural prediction of wild-type CAPN6. ( A ) Schematic representation of the functional domains of CAPN6, annotated according to the ProRule and InterPRO databases. A black arrow marks the mutation site at position 363 in the amino acid sequence. ( B ) Structural model generated using AlphaFold3, with domains colored according to panel. ( A ) The mutation site (Asp363) is highlighted in turquoise and indicated by a black square. ( C ) Close-up view of the wild-type residue (turquoise) and its hydrogen-bonding interactions with Asp365 and Asn369. Structural visualization and modeling were performed using UCSF ChimeraX.

Article Snippet: CAPN6 gene expression patterns of placenta tissues were obtained from the Human Protein Atlas (HPA) database ( https://www.proteinatlas.org/ ) (accessed on 26 May 2025).

Techniques: Structural Proteomics, Functional Assay, Mutagenesis, Sequencing, Generated, Residue