primary mouse anti nr2f2 Search Results


95
R&D Systems mouse anti nr2f2 antibody
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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93
Proteintech 1 ap
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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90
OriGene rabbit anti nr2f2
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
Rabbit Anti Nr2f2, supplied by OriGene, 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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R&D Systems mab377 ab 2298772 mouse anti coup tf2 nr2f2 coup tf ii nr2f2
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
Mab377 Ab 2298772 Mouse Anti Coup Tf2 Nr2f2 Coup Tf Ii Nr2f2, supplied by R&D Systems, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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R&D Systems anti coup tfii
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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R&D Systems mouse anti nr2f2 igg
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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Novus Biologicals anti coup tfii
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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Aviva Systems rabbit anti coup tfi
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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Santa Cruz Biotechnology anti nr2f2
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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Biorbyt antibody anti nr2f2
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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Danaher Inc mouse monoclonal anti nr2f2
Eight out of ten constructs successfully modified for expression-pattern characterization in mice
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93
Cell Signaling Technology Inc anti nr2f2 nr2f2 d16c4
Numbers of detected and differential genes from RNA-seq datasets analyzed with Ens95 and RefSeq annotations with matched identifiers.
Anti Nr2f2 Nr2f2 D16c4, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Eight out of ten constructs successfully modified for expression-pattern characterization in mice

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Eight out of ten constructs successfully modified for expression-pattern characterization in mice

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Construct, Modification, Expressing

Eight novel Hprt targeted embryonic stem cell lines successfully generated

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Eight novel Hprt targeted embryonic stem cell lines successfully generated

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Clone Assay, Isolation

Summary of expression pattern from reporter mouse strains

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Summary of expression pattern from reporter mouse strains

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Expressing

Human bacterial artificial chromosomes can be targeted at Hprt by homologous recombination and, if desired, conditionally removed using cre recombinase. (a) Integration into the mouse genome of the bacterial artificial chromosome (BAC)- lacZ -reporter constructs by homologous recombination results in the human gene in either direction relative to the X chromosome; this schematic presents one possible orientation. Regardless of orientation, each insertion resulted in the presence of four loxP sites in the genome (two wild-type and one 511 mutant at one end and one wild-type at the other end of the BAC insert). (b) Crossing the BAC- lacZ- reporter females to ACTB-cre males should result in the generation of two different male offspring; BAC- lacZ -reporter animals, wild-type for the ACTB-cre transgene; and BAC- lacZ- reporter animals carrying the ACTB-cre transgene. Only the reporter animals that are positive for the ACTB-cre gene should recombine the outer most loxP sites, resulting in excision of the BAC construct from the genome and leaving one loxP site. This would result in an absence of lacZ- positive signal. hP , human HPRT promoter; h1, human first exon; m2 and m3, mouse second and third exons; mouse homology arms (dark blue); Hprt coding regions (red); vector backbone (yellow with black edges); Sac B gene from BAC vector backbone (brown); 5′ and 3′ untranslated regions of the human gene (orange); coding region of the human gene (green); lacZ reporter gene (light blue). Schematic, not to scale. (c-f) lacZ expression results from AMOTL1 - lacZ , MAOA - lacZ , NOV - lacZ , and NR2F2 - lacZ females bred to the ACTB-cre males are presented. lacZ -positive staining (blue) was detected in AMOTL1 - lacZ , MAOA - lacZ , NOV - lacZ , and NR2F2 - lacZ males not carrying the ACTB-cre allele whereas absence of staining was detected in males positive for ACTB-cre by genotyping ( AMOTL1 - lacZ , ACTB-cre; MAOA - lacZ , ACTB-cre; NOV - lacZ , ACTB-cre; NR2F2 - lacZ , ACTB-cre), suggesting whole BAC excision from the genome. Scale bar: (c-f) 1 mm. N = 3 animals for all genotypes.

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Human bacterial artificial chromosomes can be targeted at Hprt by homologous recombination and, if desired, conditionally removed using cre recombinase. (a) Integration into the mouse genome of the bacterial artificial chromosome (BAC)- lacZ -reporter constructs by homologous recombination results in the human gene in either direction relative to the X chromosome; this schematic presents one possible orientation. Regardless of orientation, each insertion resulted in the presence of four loxP sites in the genome (two wild-type and one 511 mutant at one end and one wild-type at the other end of the BAC insert). (b) Crossing the BAC- lacZ- reporter females to ACTB-cre males should result in the generation of two different male offspring; BAC- lacZ -reporter animals, wild-type for the ACTB-cre transgene; and BAC- lacZ- reporter animals carrying the ACTB-cre transgene. Only the reporter animals that are positive for the ACTB-cre gene should recombine the outer most loxP sites, resulting in excision of the BAC construct from the genome and leaving one loxP site. This would result in an absence of lacZ- positive signal. hP , human HPRT promoter; h1, human first exon; m2 and m3, mouse second and third exons; mouse homology arms (dark blue); Hprt coding regions (red); vector backbone (yellow with black edges); Sac B gene from BAC vector backbone (brown); 5′ and 3′ untranslated regions of the human gene (orange); coding region of the human gene (green); lacZ reporter gene (light blue). Schematic, not to scale. (c-f) lacZ expression results from AMOTL1 - lacZ , MAOA - lacZ , NOV - lacZ , and NR2F2 - lacZ females bred to the ACTB-cre males are presented. lacZ -positive staining (blue) was detected in AMOTL1 - lacZ , MAOA - lacZ , NOV - lacZ , and NR2F2 - lacZ males not carrying the ACTB-cre allele whereas absence of staining was detected in males positive for ACTB-cre by genotyping ( AMOTL1 - lacZ , ACTB-cre; MAOA - lacZ , ACTB-cre; NOV - lacZ , ACTB-cre; NR2F2 - lacZ , ACTB-cre), suggesting whole BAC excision from the genome. Scale bar: (c-f) 1 mm. N = 3 animals for all genotypes.

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Homologous Recombination, Construct, Mutagenesis, Plasmid Preparation, Expressing, Staining

Human NR2F2 - lacZ expressed in mature neurons populating the basolateral and corticolateral amygdaloid nuclei that are immunoreactive for the Nr2f2 mouse protein. Expression analysis of the human NR2F2 - lacZ strain was undertaken by examination of β-galactosidase (β-gal) staining (blue). (a) E12.5 whole embryos revealed staining in the rostral secondary prosencephalon (black arrow) that extended throughout all three prosomeric regions of the diencephalon (black arrowhead). Staining was present in the nasal cavity (white arrow), the vestibulochochlear ganglion (red arrowhead) and mesenchyme of the posterior limbs (white arrowhead). (b) E12.5 cleared embryos additionally demonstrated staining in the developing bladder (black arrow). (c) P7 brains stained in the amygdala nuclei (white arrows), and the subthalamic nuclei (black arrows). (d) Adult brains revealed strong staining extending from the posterior basolateral amygdaloid nuclei (BLP) (black arrows) to the posterolateral cortical amygdaloid nuclei (PLCo) (white arrows), and the posteroventral part of the medial amygdaloid nuclei (MePV) (white arrowheads). Broad staining was detected in the ventral thalamic area, excluding the cerebral peduncle (cp). (e) Colocalization experiment using β-gal staining and a neuronal nuclei (NeuN) antibody (brown) performed on adult brain cryosections revealed strong expression of NR2F2 - lacZ in mature neurons populating the BLP, and the basomedial amygdaloid nuclei (BMP) (red arrows). Colocalization was found in the PLCo, and the posteromedial cortical amygdaloid nuclei (PMCo) (black arrows), and the MePV (black arrowhead). Lower level of β-gal staining was detected in mature neurons in the anterolateral amygdalohippocampal area (AHiAL) (red arrowhead). Boxed region in (e) is shown in (f) . (f) Higher magnification revealed strong expression of β-gal in mature neurons in the PMCo and sparse expression in mature neurons in the AHiAL. (g) Colocalization experiment, using an anti-β-gal antibody (green), and an NR2F2 antibody (red), performed on adult brain cryosections revealed strong β-gal labeling in cells expressing the Nr2f2 mouse gene in brain regions extending from the PMCo (white arrowhead) to the MePV (white arrow). Lower levels of β-gal were detected in the AHiAL (red arrow). Boxed region in (g) is shown in (h) . (h) Higher magnification revealed strong expression of β-gal (green) in Nr2f2 -positive cells (red) in the PMCo (white arrow) and lower expression in the AHiAL (white arrowhead). LV, lateral ventricle. Scale bar: (a - d) 1 mm; (e , g) 100 μm; (f , h) 20 μm.

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Human NR2F2 - lacZ expressed in mature neurons populating the basolateral and corticolateral amygdaloid nuclei that are immunoreactive for the Nr2f2 mouse protein. Expression analysis of the human NR2F2 - lacZ strain was undertaken by examination of β-galactosidase (β-gal) staining (blue). (a) E12.5 whole embryos revealed staining in the rostral secondary prosencephalon (black arrow) that extended throughout all three prosomeric regions of the diencephalon (black arrowhead). Staining was present in the nasal cavity (white arrow), the vestibulochochlear ganglion (red arrowhead) and mesenchyme of the posterior limbs (white arrowhead). (b) E12.5 cleared embryos additionally demonstrated staining in the developing bladder (black arrow). (c) P7 brains stained in the amygdala nuclei (white arrows), and the subthalamic nuclei (black arrows). (d) Adult brains revealed strong staining extending from the posterior basolateral amygdaloid nuclei (BLP) (black arrows) to the posterolateral cortical amygdaloid nuclei (PLCo) (white arrows), and the posteroventral part of the medial amygdaloid nuclei (MePV) (white arrowheads). Broad staining was detected in the ventral thalamic area, excluding the cerebral peduncle (cp). (e) Colocalization experiment using β-gal staining and a neuronal nuclei (NeuN) antibody (brown) performed on adult brain cryosections revealed strong expression of NR2F2 - lacZ in mature neurons populating the BLP, and the basomedial amygdaloid nuclei (BMP) (red arrows). Colocalization was found in the PLCo, and the posteromedial cortical amygdaloid nuclei (PMCo) (black arrows), and the MePV (black arrowhead). Lower level of β-gal staining was detected in mature neurons in the anterolateral amygdalohippocampal area (AHiAL) (red arrowhead). Boxed region in (e) is shown in (f) . (f) Higher magnification revealed strong expression of β-gal in mature neurons in the PMCo and sparse expression in mature neurons in the AHiAL. (g) Colocalization experiment, using an anti-β-gal antibody (green), and an NR2F2 antibody (red), performed on adult brain cryosections revealed strong β-gal labeling in cells expressing the Nr2f2 mouse gene in brain regions extending from the PMCo (white arrowhead) to the MePV (white arrow). Lower levels of β-gal were detected in the AHiAL (red arrow). Boxed region in (g) is shown in (h) . (h) Higher magnification revealed strong expression of β-gal (green) in Nr2f2 -positive cells (red) in the PMCo (white arrow) and lower expression in the AHiAL (white arrowhead). LV, lateral ventricle. Scale bar: (a - d) 1 mm; (e , g) 100 μm; (f , h) 20 μm.

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Expressing, Staining, Labeling

Comparative genomics delineated the DNA boundaries that were sufficient for adult brain-specific expression of NOV and NR2F2 . Coordinates corresponding to the human bacterial artificial chromosome (BAC) constructs used in this study were retrieved and visualized using the University of California Santa Cruz (UCSC) genome browser. (a) DNA alignment of the human NOV BAC (RP11-840I14) (black), against both the RP23-235B13 BAC construct used in the Gene Expression Nervous System Atlas (GENSAT) mouse model (blue), and the mouse genome, delineated the genomic DNA boundaries sufficient for proper expression of this human gene in the basolateral amygdaloid nuclei, cortical layers, and pyramidal neurons in the cornu ammonis 1 (CA1) regions in the adult brain. One hypothesis suggested by our results was that additional functionally conserved regulatory elements homologous to the large non-overlapping 3′ mouse-BAC region are necessary for proper human-gene expression in the developing cortical layers at P7. (b) DNA alignment of the human NR2F2 BAC (RP11-134D15) (black), against both the RP23-109L9 BAC construct used in the GENSAT mouse model (blue) and the mouse genome, delineated the genomic DNA boundaries sufficient for region-specific expression of this human gene in the basolateral, and corticolateral amygdaloid nuclei in the adult brain. One hypothesis suggested by our results was that additional functionally-conserved regulatory elements homologous to the non-overlapping 5′ mouse-BAC region are necessary for proper expression in the developing hypothalamus at P7. Black rectangle box in (b) is shown in (c) . (c) Sequence alignment using the coordinates of the primers used in the BAC lacZ retrofitting process (grey bars) and the cDNA sequence used to generate an anti-NR2F2 antibody (black bar), suggested that the absence of expression of the NR2F2 - lacZ constructs in retinal amacrine cells was not attributable to detection of different isoforms of NR2F2 .

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Comparative genomics delineated the DNA boundaries that were sufficient for adult brain-specific expression of NOV and NR2F2 . Coordinates corresponding to the human bacterial artificial chromosome (BAC) constructs used in this study were retrieved and visualized using the University of California Santa Cruz (UCSC) genome browser. (a) DNA alignment of the human NOV BAC (RP11-840I14) (black), against both the RP23-235B13 BAC construct used in the Gene Expression Nervous System Atlas (GENSAT) mouse model (blue), and the mouse genome, delineated the genomic DNA boundaries sufficient for proper expression of this human gene in the basolateral amygdaloid nuclei, cortical layers, and pyramidal neurons in the cornu ammonis 1 (CA1) regions in the adult brain. One hypothesis suggested by our results was that additional functionally conserved regulatory elements homologous to the large non-overlapping 3′ mouse-BAC region are necessary for proper human-gene expression in the developing cortical layers at P7. (b) DNA alignment of the human NR2F2 BAC (RP11-134D15) (black), against both the RP23-109L9 BAC construct used in the GENSAT mouse model (blue) and the mouse genome, delineated the genomic DNA boundaries sufficient for region-specific expression of this human gene in the basolateral, and corticolateral amygdaloid nuclei in the adult brain. One hypothesis suggested by our results was that additional functionally-conserved regulatory elements homologous to the non-overlapping 5′ mouse-BAC region are necessary for proper expression in the developing hypothalamus at P7. Black rectangle box in (b) is shown in (c) . (c) Sequence alignment using the coordinates of the primers used in the BAC lacZ retrofitting process (grey bars) and the cDNA sequence used to generate an anti-NR2F2 antibody (black bar), suggested that the absence of expression of the NR2F2 - lacZ constructs in retinal amacrine cells was not attributable to detection of different isoforms of NR2F2 .

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Expressing, Construct, Gene Expression, Sequencing

Primers used for reporter-gene retrofitting

Journal: BMC Biology

Article Title: Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

doi: 10.1186/1741-7007-11-106

Figure Lengend Snippet: Primers used for reporter-gene retrofitting

Article Snippet: Colocalization experiments were performed using chicken anti-β-gal antibody (Abcam, San Francisco, CA, USA; ab9361) 1:5,000, mouse anti-NR2F2 antibody (R&D systems, Minneapolis, MN, USA; PP-H7147-00) 1:100, and incubated overnight at 4°C.

Techniques: Sequencing

Numbers of detected and differential genes from RNA-seq datasets analyzed with Ens95 and RefSeq annotations with matched identifiers.

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet: Numbers of detected and differential genes from RNA-seq datasets analyzed with Ens95 and RefSeq annotations with matched identifiers.

Article Snippet: Antibody , anti-NR2F2 NR2F2 D16C4, rabbit monoclonal , Cell Signaling Technology , Cat #6434; RRID: AB_11220428 , used at 1:100.

Techniques:

( A, B ) Log 10 average expression as quantified using indicated annotation for ( A ) kdrl pos - or ( B ) pdgfrb pos -enriched genes identified as such only in RefSeq and lacking an Ens95 3' UTR annotation. Expression levels for genes from each annotation with matched NCBI ID are shown in each case. Data are normally distributed (Shapiro-Wilks test), paired t-test, p values are indicated; n = 3 (i.e. each point represents an average value from three separate RNA-seq replicates). ( C ) UCSC browser image of slc7a5 locus on the minus strand showing 3' UTR annotations from Ens95 and RefSeq. Mapped read depth from kdrl pos cells on the genome, or assigned to each annotation are indicated, as is a 3P-seq feature. The GSE32900 track is consolidated RNA-seq reads from all stages indicated in . The location of a putative missing 3' UTR is indicated. ( D ) Pie chart showing numbers of reference genes with the same or longer 3' UTRs in each indicated annotation. ( E ) Pie charts showing the proportion of reference genes selectively identified as kdrl pos - or pdgfrb pos -enriched by Ens95 and RefSeq with indicated relative 3' UTR length. ( F, G ) Correlation plots showing log 10 average expression from kdrl pos RNA-seq (n = 3) quantified with each annotation for matched reference genes with ( F ) longer Ens95 (maroon) or RefSeq (light blue) 3' UTR, or ( G ) same 3' UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. ( H, I ) UCSC browser images of ( H ) sox17 and ( I ) cspg4 loci, both on the minus strand, showing 3' UTR annotations from Ens95 and RefSeq. Mapped read depth of RNA-seq from ( H ) kdrl pos or ( I ) pdgfrb pos cells captured for each annotation is indicated. Consolidated reads from GSE32900 and location of 3P-Seq features are indicated, as is putative missing 3' UTR in cspg4 . Figure 2—source data 1. Missing 3' UTR annotations in RefSeq and Ens95. This file includes lists of Ens95 (worksheet 1) and RefSeq (worksheet 2) genes indicating annotation as coding sequence (CDS) and whether there is an annotated stop codon and 3' UTR. Data from RNA-seq-based quantification for Ens95 genes missing a 3' UTR that is present in RefSeq is included for kdrl pos (worksheet 3), pdgfrb pos (worksheet 4), and Nr2f2 pos (worksheet 5) cells. These data were used to generate and graphs in ; . Figure 2—source data 2. Reference gene set for 3' UTR comparisons. IDs for representative Ens95, RefSeq, and V4.3 transcript ID, along with V4.3 gene symbols are shown with respective 3' UTR lengths (worksheet 1). Average median ratio normalized expression and log 2 fold change (pos/neg) values quantified with Ens95, RefSeq, and V4.3 annotations from kdrl pos (worksheet 2), pdgfrb pos (worksheet 3), and Nr2f2 pos (worksheet 4) RNA-seq for reference genes are included. Data directly used to generate , , and incorporated into source data as indicated below. Figure 2—source data 3. RNA-seq analysis of Nr2f2 pos and NR2f2 neg cells. Output from DESeq2 analysis comparing Nr2f2 pos and Nr2f2 neg RNA-seq from gene expression levels quantified using RSEM with Ens95 (worksheet 1) or RefSeq (worksheet 2). Median ratio normalized expression values are shown for each sample, along with adjusted p-value, p-value, log 2 fold change, fold change, and log 10 adjusted p-value. Intersection of genesets identified as significantly enriched in Nr2f2 pos cells using Ens95 or RefSeq (worksheet 3). Figure 2—source data 4. Transcript based-comparison of RefSeq and Ensembl annotations. Worksheet one is a list of Ens95 genes missing from RefSeq with Ensembl gene ID, matching ZFIN ID and biotype annotation. Worksheet two is a list of RefSeq genes missing from Ensembl with NCBI gene ID, matching ZFIN ID, and coding sequence annotation. Transcript level matching output from gffcompare is included using Ens95 (worksheet 3) or RefSeq (worksheet 4) as a reference. Worksheet five is a transcript level comparison of Ens95 and Ens99. In this case, all transcripts exhibit a complete intron/exon chain match (designated by a ‘=

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet: ( A, B ) Log 10 average expression as quantified using indicated annotation for ( A ) kdrl pos - or ( B ) pdgfrb pos -enriched genes identified as such only in RefSeq and lacking an Ens95 3' UTR annotation. Expression levels for genes from each annotation with matched NCBI ID are shown in each case. Data are normally distributed (Shapiro-Wilks test), paired t-test, p values are indicated; n = 3 (i.e. each point represents an average value from three separate RNA-seq replicates). ( C ) UCSC browser image of slc7a5 locus on the minus strand showing 3' UTR annotations from Ens95 and RefSeq. Mapped read depth from kdrl pos cells on the genome, or assigned to each annotation are indicated, as is a 3P-seq feature. The GSE32900 track is consolidated RNA-seq reads from all stages indicated in . The location of a putative missing 3' UTR is indicated. ( D ) Pie chart showing numbers of reference genes with the same or longer 3' UTRs in each indicated annotation. ( E ) Pie charts showing the proportion of reference genes selectively identified as kdrl pos - or pdgfrb pos -enriched by Ens95 and RefSeq with indicated relative 3' UTR length. ( F, G ) Correlation plots showing log 10 average expression from kdrl pos RNA-seq (n = 3) quantified with each annotation for matched reference genes with ( F ) longer Ens95 (maroon) or RefSeq (light blue) 3' UTR, or ( G ) same 3' UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. ( H, I ) UCSC browser images of ( H ) sox17 and ( I ) cspg4 loci, both on the minus strand, showing 3' UTR annotations from Ens95 and RefSeq. Mapped read depth of RNA-seq from ( H ) kdrl pos or ( I ) pdgfrb pos cells captured for each annotation is indicated. Consolidated reads from GSE32900 and location of 3P-Seq features are indicated, as is putative missing 3' UTR in cspg4 . Figure 2—source data 1. Missing 3' UTR annotations in RefSeq and Ens95. This file includes lists of Ens95 (worksheet 1) and RefSeq (worksheet 2) genes indicating annotation as coding sequence (CDS) and whether there is an annotated stop codon and 3' UTR. Data from RNA-seq-based quantification for Ens95 genes missing a 3' UTR that is present in RefSeq is included for kdrl pos (worksheet 3), pdgfrb pos (worksheet 4), and Nr2f2 pos (worksheet 5) cells. These data were used to generate and graphs in ; . Figure 2—source data 2. Reference gene set for 3' UTR comparisons. IDs for representative Ens95, RefSeq, and V4.3 transcript ID, along with V4.3 gene symbols are shown with respective 3' UTR lengths (worksheet 1). Average median ratio normalized expression and log 2 fold change (pos/neg) values quantified with Ens95, RefSeq, and V4.3 annotations from kdrl pos (worksheet 2), pdgfrb pos (worksheet 3), and Nr2f2 pos (worksheet 4) RNA-seq for reference genes are included. Data directly used to generate , , and incorporated into source data as indicated below. Figure 2—source data 3. RNA-seq analysis of Nr2f2 pos and NR2f2 neg cells. Output from DESeq2 analysis comparing Nr2f2 pos and Nr2f2 neg RNA-seq from gene expression levels quantified using RSEM with Ens95 (worksheet 1) or RefSeq (worksheet 2). Median ratio normalized expression values are shown for each sample, along with adjusted p-value, p-value, log 2 fold change, fold change, and log 10 adjusted p-value. Intersection of genesets identified as significantly enriched in Nr2f2 pos cells using Ens95 or RefSeq (worksheet 3). Figure 2—source data 4. Transcript based-comparison of RefSeq and Ensembl annotations. Worksheet one is a list of Ens95 genes missing from RefSeq with Ensembl gene ID, matching ZFIN ID and biotype annotation. Worksheet two is a list of RefSeq genes missing from Ensembl with NCBI gene ID, matching ZFIN ID, and coding sequence annotation. Transcript level matching output from gffcompare is included using Ens95 (worksheet 3) or RefSeq (worksheet 4) as a reference. Worksheet five is a transcript level comparison of Ens95 and Ens99. In this case, all transcripts exhibit a complete intron/exon chain match (designated by a ‘=" in class code). Data used to generate .

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Techniques: Expressing, RNA Sequencing, Sequencing, Gene Expression, Comparison

( A,B ) Volcano plots of differentially expressed genes from Nr2f2-positive and -negative (Nr2f2 pos and Nr2f2 neg ) endothelial cells identified using RNA-seq reads quantified with ( A ) RefSeq or ( B ) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log 2 fold change >1 or <-1, respectively). Grey dots are genes that fall below statistical cutoffs. ( A, B ) Green dots are selected known vein-specific genes. ( C ) Venn diagram of genes with a common NCBI ID in Ens95 and RefSeq identified as significantly Nr2f2 pos -enriched using either annotation. ( D ) Correlation of log 10 average expression levels (n = 3) from indicated annotation for Nr2f2 pos -enriched genes identified selectively as such by Ens95 or RefSeq only (left plot) or both annotations (right plot). Data are not normally distributed, Spearman correlation, r values are indicated. ( E ) Log 10 average expression (n = 3) for Nr2f2 pos -enriched genes as quantified by each indicated annotation. Separate plots shown for genes selectively identified as Nr2f2 pos -enriched using Ens95 or RefSeq. Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. ( F ) Plots of commonly annotated genes identified as Nr2f2 pos -enriched only by Ens95 with indicated values from Ens95 (left plot) or RefSeq (right plot). ( G ) Pie charts showing the proportion of reference genes identified as Nr2f2 pos -enriched by Ens95 and RefSeq with indicated relative 3' UTR length. ( H ) Correlation of log 10 average expression from Nr2f2 pos RNA-seq (n = 3) quantified with each annotation for matched reference genes with same 3' UTR length or longer Ens95 or RefSeq 3' UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. ( I ) Log 10 average expression (n = 3) as quantified by Ens95 or RefSeq for Nr2f2 pos -enriched genes lacking an Ens95 3' UTR annotation. Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p value is indicated. ( J ) UCSC browser image of the erg gene (on minus strand) showing 3' UTR annotation and lack thereof from RefSeq and Ens95, respectively. Mapped depth of RNA-seq reads from Nr2f2 pos cells captured for each annotation is indicated. Genome-mapped consolidated reads from GSE32900 are also shown as is the location of 3P-seq feature, also on the minus strand.

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet: ( A,B ) Volcano plots of differentially expressed genes from Nr2f2-positive and -negative (Nr2f2 pos and Nr2f2 neg ) endothelial cells identified using RNA-seq reads quantified with ( A ) RefSeq or ( B ) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log 2 fold change >1 or <-1, respectively). Grey dots are genes that fall below statistical cutoffs. ( A, B ) Green dots are selected known vein-specific genes. ( C ) Venn diagram of genes with a common NCBI ID in Ens95 and RefSeq identified as significantly Nr2f2 pos -enriched using either annotation. ( D ) Correlation of log 10 average expression levels (n = 3) from indicated annotation for Nr2f2 pos -enriched genes identified selectively as such by Ens95 or RefSeq only (left plot) or both annotations (right plot). Data are not normally distributed, Spearman correlation, r values are indicated. ( E ) Log 10 average expression (n = 3) for Nr2f2 pos -enriched genes as quantified by each indicated annotation. Separate plots shown for genes selectively identified as Nr2f2 pos -enriched using Ens95 or RefSeq. Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. ( F ) Plots of commonly annotated genes identified as Nr2f2 pos -enriched only by Ens95 with indicated values from Ens95 (left plot) or RefSeq (right plot). ( G ) Pie charts showing the proportion of reference genes identified as Nr2f2 pos -enriched by Ens95 and RefSeq with indicated relative 3' UTR length. ( H ) Correlation of log 10 average expression from Nr2f2 pos RNA-seq (n = 3) quantified with each annotation for matched reference genes with same 3' UTR length or longer Ens95 or RefSeq 3' UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. ( I ) Log 10 average expression (n = 3) as quantified by Ens95 or RefSeq for Nr2f2 pos -enriched genes lacking an Ens95 3' UTR annotation. Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p value is indicated. ( J ) UCSC browser image of the erg gene (on minus strand) showing 3' UTR annotation and lack thereof from RefSeq and Ens95, respectively. Mapped depth of RNA-seq reads from Nr2f2 pos cells captured for each annotation is indicated. Genome-mapped consolidated reads from GSE32900 are also shown as is the location of 3P-seq feature, also on the minus strand.

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Techniques: RNA Sequencing, Expressing

( A ) Schematic outline for generating a new zebrafish transcriptome annotation. See Results and Materials and methods sections for details. ( B ) Pie charts showing the proportion of reference genes with same, longer or shorter 3' UTR in the V4.3 annotation compared to relative 3' UTR length between Ens95 and RefSeq. ( C, E ) Venn diagrams showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in ( C ) kdrl pos - or ( E ) pdgfrb pos -cells in each indicated annotation. ( D, F ) Volcano plots of reference genes with common NCBI ID identified as ( D ) kdrl pos - or ( F ) pdgfrb pos -enriched only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log 2 fold change >1 and adjp <0.05. ( G ) 3' UTR lengths and ( H ) log 10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. ( G, H ) Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Error bars denote mean and standard deviation. ( I ) Log 10 average expression (n = 3) and ( J ) 3' UTR lengths across all annotations for reference genes uniquely identified as enriched in indicated transgene-positive cell type using V4.3 (log 2 fold change >1, padj <0.05). Data are not normally distributed. Friedman test to assess variance (p<0.0001 in all cases). Dunn's multiple comparison test was used for pairwise comparisons, p values are indicated. Error bars denote mean and standard deviation. Figure 3—source data 1. List of SRA accession numbers, stages, and read numbers from GSE32900 for associated RNA-seq datasets used in this study. Figure 3—source data 2. List of manually-identified discrepancies in Ensembl gene annotation due to spurious fusionor overlapping transcripts. Table includes Ens95 gene symbol, gene ID, and spurious transcript ID. Persistence of observed discrepancy in Ens99 is indicated, as is previous status of curation in ZFIN. All of these have been reported to ZFIN. Figure 3—source data 3. RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. Figure 3—source data 4. Novel genes from V4.2 genome annotation. This table includes information regarding blastx hits against zebrafish and human proteins, matches with lincRNAs, number of exons per gene, and whether the novel locus was included in the V4.3 annotation. Figure 3—source data 5. V4.3 gene information table, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene symbols, and gene names. Annotation notes are also included regarding the relative strength of coordinate-based incorporation of NCBI (Entrez) and Ens99 gene identifiers. Figure 3—source data 6. Output from DESeq2 analysis comparing kdrl pos and kdrl neg RNA-seq. Gene expression levels were quantified using RSEM with the V4.3 annotation. Median ratio normalized expression values are shown for each sample, along with adjusted p-value and log 2 fold change. Matching Ensembl and NCBI gene IDs are included. Figure 3—source data 7. Output from DESeq2 analysis comparing pdgfrb pos and pdgfrb neg RNA-seq. Gene expression levels were quantified using RSEM with the V4.3 annotation. Median ratio normalized expression values are shown for each replicate, along with adjusted p-value and log 2 fold change. Matching Ensembl and NCBI gene IDs are included. Figure 3—source data 8. Worksheet 1 - Output from DESeq2 analysis comparing Nr2f2 pos and Nr2f2 neg RNA-seq. Gene expression levels were quantified using RSEM with the V4.3 annotation. Median ratio normalized expression values are shown for each replicate, along with adjusted p-value and log 2 fold change. Matching Ensembl and NCBI gene IDs are included. Worksheet 2 – Nr2f2 pos -enriched genes with matched entries from reference gene set and associated 3' UTR lengths .

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet: ( A ) Schematic outline for generating a new zebrafish transcriptome annotation. See Results and Materials and methods sections for details. ( B ) Pie charts showing the proportion of reference genes with same, longer or shorter 3' UTR in the V4.3 annotation compared to relative 3' UTR length between Ens95 and RefSeq. ( C, E ) Venn diagrams showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in ( C ) kdrl pos - or ( E ) pdgfrb pos -cells in each indicated annotation. ( D, F ) Volcano plots of reference genes with common NCBI ID identified as ( D ) kdrl pos - or ( F ) pdgfrb pos -enriched only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log 2 fold change >1 and adjp <0.05. ( G ) 3' UTR lengths and ( H ) log 10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. ( G, H ) Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Error bars denote mean and standard deviation. ( I ) Log 10 average expression (n = 3) and ( J ) 3' UTR lengths across all annotations for reference genes uniquely identified as enriched in indicated transgene-positive cell type using V4.3 (log 2 fold change >1, padj <0.05). Data are not normally distributed. Friedman test to assess variance (p<0.0001 in all cases). Dunn's multiple comparison test was used for pairwise comparisons, p values are indicated. Error bars denote mean and standard deviation. Figure 3—source data 1. List of SRA accession numbers, stages, and read numbers from GSE32900 for associated RNA-seq datasets used in this study. Figure 3—source data 2. List of manually-identified discrepancies in Ensembl gene annotation due to spurious fusionor overlapping transcripts. Table includes Ens95 gene symbol, gene ID, and spurious transcript ID. Persistence of observed discrepancy in Ens99 is indicated, as is previous status of curation in ZFIN. All of these have been reported to ZFIN. Figure 3—source data 3. RefSeq (worksheet 1) and Ens99 (worksheet 2) genes missing from the V4.2 annotation. Figure 3—source data 4. Novel genes from V4.2 genome annotation. This table includes information regarding blastx hits against zebrafish and human proteins, matches with lincRNAs, number of exons per gene, and whether the novel locus was included in the V4.3 annotation. Figure 3—source data 5. V4.3 gene information table, including unique LL ID numbers, associated Ens99 gene ID, NCBI ID, and ZFIN gene ID numbers, gene symbols, and gene names. Annotation notes are also included regarding the relative strength of coordinate-based incorporation of NCBI (Entrez) and Ens99 gene identifiers. Figure 3—source data 6. Output from DESeq2 analysis comparing kdrl pos and kdrl neg RNA-seq. Gene expression levels were quantified using RSEM with the V4.3 annotation. Median ratio normalized expression values are shown for each sample, along with adjusted p-value and log 2 fold change. Matching Ensembl and NCBI gene IDs are included. Figure 3—source data 7. Output from DESeq2 analysis comparing pdgfrb pos and pdgfrb neg RNA-seq. Gene expression levels were quantified using RSEM with the V4.3 annotation. Median ratio normalized expression values are shown for each replicate, along with adjusted p-value and log 2 fold change. Matching Ensembl and NCBI gene IDs are included. Figure 3—source data 8. Worksheet 1 - Output from DESeq2 analysis comparing Nr2f2 pos and Nr2f2 neg RNA-seq. Gene expression levels were quantified using RSEM with the V4.3 annotation. Median ratio normalized expression values are shown for each replicate, along with adjusted p-value and log 2 fold change. Matching Ensembl and NCBI gene IDs are included. Worksheet 2 – Nr2f2 pos -enriched genes with matched entries from reference gene set and associated 3' UTR lengths .

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Techniques: Comparison, Expressing, Standard Deviation, RNA Sequencing, Gene Expression

Numbers of genes identified as enriched in indicated genotype with each annotation.

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet: Numbers of genes identified as enriched in indicated genotype with each annotation.

Article Snippet: Antibody , anti-NR2F2 NR2F2 D16C4, rabbit monoclonal , Cell Signaling Technology , Cat #6434; RRID: AB_11220428 , used at 1:100.

Techniques:

( A ) Volcano plot of RNA-seq data from Nr2f2 pos and Nr2f2 neg cells quantified using V4.3. Numbers of differentially expressed genes are shown. Selected known venous endothelial genes are indicated with green dots, as is erg , which is not detected as differentially expressed by Ens95. Genes with significant differences (padj <0.05) are red (log 2 fold change pos/neg > 1) or blue (Nr2f2 pos -enriched, log 2 fold change pos/neg <-1). ( B ) Venn diagram showing intersection of reference genes (using commonly annotated NCBI ID) that are significantly enriched in Nr2f2 pos -cells in each indicated annotation. ( C ) Volcano plot of Nr2f2 pos -enriched reference genes identified only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log 2 fold change<-1 and adjp <0.05. ( D ) 3' UTR lengths and ( E ) log 10 average expression (n = 3) for reference genes in Ens95 and V4.3 for the indicated dataset. ( D, E ) Data are normally distributed, paired t-test, p values are indicated. Error bars denote mean and standard deviation.

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet: ( A ) Volcano plot of RNA-seq data from Nr2f2 pos and Nr2f2 neg cells quantified using V4.3. Numbers of differentially expressed genes are shown. Selected known venous endothelial genes are indicated with green dots, as is erg , which is not detected as differentially expressed by Ens95. Genes with significant differences (padj <0.05) are red (log 2 fold change pos/neg > 1) or blue (Nr2f2 pos -enriched, log 2 fold change pos/neg <-1). ( B ) Venn diagram showing intersection of reference genes (using commonly annotated NCBI ID) that are significantly enriched in Nr2f2 pos -cells in each indicated annotation. ( C ) Volcano plot of Nr2f2 pos -enriched reference genes identified only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log 2 fold change<-1 and adjp <0.05. ( D ) 3' UTR lengths and ( E ) log 10 average expression (n = 3) for reference genes in Ens95 and V4.3 for the indicated dataset. ( D, E ) Data are normally distributed, paired t-test, p values are indicated. Error bars denote mean and standard deviation.

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Techniques: RNA Sequencing, Comparison, Expressing, Standard Deviation

Journal: eLife

Article Title: An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

doi: 10.7554/eLife.55792

Figure Lengend Snippet:

Article Snippet: Antibody , anti-NR2F2 NR2F2 D16C4, rabbit monoclonal , Cell Signaling Technology , Cat #6434; RRID: AB_11220428 , used at 1:100.

Techniques: Software