BUSCADOR RECOLECTA

[Organism] Homo sapiens, [Experiment type] Expression profiling by array, [Overall design] Two-condition experiment, Progressing vs regressing metastases. 3 progressing and 2 regressing metastases extracted from the same patient after M-VAX immunotherapy. One replicate per array., [Platforms (1)] GPL7088 CCDTM Hs_CCDTM36k - version 1, [Relations] BioProject PRJNA130231, 1. Sample GSM592226. Title: melanoma progressing 1. Sample type: RNA. Platform ID: GPL7088. Series: GSE24067 Progressing vs regressing melanoma metastases; GSE26383 Response to immunotherapy in melanoma metastasis., Channel 1: [Source name] melanoma, progressing [Organism] Homo sapiens [Characteristics] tissue: melanoma treatment protocol: M-VAX preservation: cryopreservation patient: 1 [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy5 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., Channel 2: [Source name] Total RNA from pooled PBMC [Organism] Homo sapiens [Characteristics] tissue: Blood preservation: cryopreservation reference: Total RNA from pooled PBMC [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy3 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., [Hybridization protocol] 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x) [Scan protocol] Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3). [Description] metastasis non responding after M-VAX immunotherapy 1 [Data processing] LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction., 2. Sample GSM592227. Title: melanoma progressing 2. Sample type: RNA. Platform ID: GPL7088. Series (2): GSE24067 Progressing vs regressing melanoma metastases. GSE26383 Response to immunotherapy in melanoma metastasis., Channel 1 [Source name] melanoma, progressing [Organism] Homo sapiens [Characteristics] tissue: melanoma treatment protocol: M-VAX preservation: cryopreservation patient: 1 [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy5 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., Channel 2 [Source name] Total RNA from pooled PBMC [Organism] Homo sapiens [Characteristics] tissue: Blood preservation: cryopreservation reference: Total RNA from pooled PBMC [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy3 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., [Hybridization protocol] 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x) [Scan protocol] Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3). [Description] metastasis non responding after M-VAX immunotherapy 2 [Data processing] LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction., 3. Sample GSM592228. Title: melanoma progressing 3. Sample type: RNA. Platform ID: GPL7088. Series (2): GSE24067 Progressing vs regressing melanoma metastases; GSE26383 Response to immunotherapy in melanoma metastasis, Channel 1 [Source name] melanoma, progressing [Organism] Homo sapiens [Characteristics] tissue: melanoma treatment protocol: M-VAX preservation: cryopreservation patient: 1 [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy5 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., Channel 2 [Source name] Total RNA from pooled PBMC [Organism] Homo sapiens [Characteristics] tissue: Blood preservation: cryopreservation reference: Total RNA from pooled PBMC [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy3 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., [Hybridization protocol] 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x) [Scan protocol] Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3). [Description] metastasis non responding after M-VAX immunotherapy 3 [Data processing] LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction., 4. Sample GSM592229. Title: melanoma regressing 1. Sample type: RNA. Platform ID: GPL7088. Series (2): GSE24067 Progressing vs regressing melanoma metastases; GSE26383 Response to immunotherapy in melanoma metastasis., Channel 1 [Source name] melanoma, regressing [Organism] Homo sapiens [Characteristics] tissue: melanoma treatment protocol: M-VAX preservation: cryopreservation patient: 1 [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy5 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., Channel 2 [Source name] Total RNA from pooled PBMC [Organism] Homo sapiens [Characteristics] tissue: Blood preservation: cryopreservation reference: Total RNA from pooled PBMC [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy3 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., Hybridization protocol 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x) [Scan protocol] Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3). [Description] metastasis responding after M-VAX immunotherapy 1 [Data processing] LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction., 5. Sample GSM592230. Title: melanoma regressing 2. Sample type: RNA. Platform ID: GPL7088. Series (2): GSE24067 Progressing vs regressing melanoma metastases; GSE26383 Response to immunotherapy in melanoma metastasis., Channel 1 [Source name] melanoma, regressing [Organism] Homo sapiens [Characteristics] tissue: melanoma treatment protocol: M-VAX preservation: cryopreservation patient: 1 [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy5 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., Channel 2 [Source name] Total RNA from pooled PBMC [Organism] Homo sapiens [Characteristics] tissue: Blood preservation: cryopreservation reference: Total RNA from pooled PBMC [Extracted molecule] total RNA [Extraction protocol] Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions [Label] Cy3 [Label protocol] 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion)., [Hybridization protocol] 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x) [Scan protocol] Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3). [Description] metastasis responding after M-VAX immunotherapy 2 [Data processing] LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction., We documented the transcriptional pattern of 3 progressing and 2 regressing synchronous melanoma metastases from the same patient following M-VAX treatment.

Inscripción grabada en los sillares de un contrafuerte en la fachada sur de la iglesia, debajo de un reloj de sol. Contiene los nombres de la Sagrada Familia, entre dos escudos, el último de los cuales contiene el nombre de José. El nombre de Jesús y el de María están separados por un círculo con tres flechas que parten de él hacia arriba. En una segunda línea, con tamaño más pequeño de letra, está la datación., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Dos inscripciones es un escudo incrustado en el muro del callejón del arco de la Iglesia de la trinidad. Una inscripción es un lema; en latín; el otro es el nombre del linaje: "Briones"., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Inscripción en una cruz de piedra incrustada en el muro de una casa situada en la calle de San Millán. La inscripción contiene el lema "INRI" y la fecha., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Inscripción en los sillares del dintel de la puerta de la capilla de la Dolorosa. Contiene una serie de símbolos , entre ellos una corona y pequeños corazones, los anagramas de Jesús y María y la datación., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Inscripción en cartela moldurada que ocupa la cara lateral de un sillar de piedra bajo el escudo que corona el muro frontal de la fuente de la plaza del Pilar, actualmente plaza de Enrique Hernández. La piedra se encuentra en muy mal estado de conservación, sobre todo por efectos del salitre, lo que ha afectado especialmente a la inscripción, que es casi completamente ilegible., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Pequeña inscripción en un tondo de piedra debajo del escudo que corona la portada del antigua Hospital de San Andrés, edificio actualmente en estado ruinoso, situado en la calle de San Andrés, número 4. Son legibles dos líneas, con un nombre propio, Domingo Simón, aunque hay rastros de otra, sobre ellas, ilegible. El hospital fue fundado en el siglo XV (1415) por Juan Fernández Pacheco, marqués de Villena; la portada es del XVI, pero la inscripción corresponde al XVIII., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Breves inscripciones en un escudo situado en la portada de la fachada suroriental del antiguo Convento hospital del Padre Eterno. Contiene las palabras de la Anunciación a María, y el término exalto, con el pelícano, como símbolo de Jesucristo, en el centro, y el anagrama del nombre de Jesucristo en un tondo en su cuerpo. El edificio se encuentra actualmente en estado ruinoso, pero deja entrever aún su extraordinario valor arquitectónico y artístico., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Breve inscripción en castellano que da cuenta de la realización de una obra, probablemente de la sacristía, sobre el dintel de cuya ventana se encuentra grabado el texto, orientado al sur., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Inscripción en una lápida de piedra, situada en una capilla lateral. Muy tosca de factura. Las dos últimas líneas, en el extremo inferior de la lápida, están escritas en letra más pequeña que el resto, y en su mayor parte son ilegibles., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed