Result

Search results for the GEO ID: GSE16856

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM423908

GPL570

LNCaP untreated cells

LNCaP cell line

cell line: prostate cancer cell line LNCaP treatment protocol: untreated (control)

Affymetrix gene expression

Sample_geo_accession	GSM423908
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423908/suppl/GSM423908.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423909

GPL570

LNCaP cells treated with caffeine

LNCaP cell line

cell line: prostate cancer cell line LNCaP treatment protocol: treated with caffeine

Affymetrix gene expression

Sample_geo_accession	GSM423909
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423909/suppl/GSM423909.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423910

GPL570

LNCaP cells treated with both actinomycin D and caffeine after treatment with caffeine

LNCaP cell line

cell line: prostate cancer cell line LNCaP treatment protocol: treated with both caffeine and actinomycin D after treatment with caffeine

Affymetrix gene expression

Sample_geo_accession	GSM423910
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423910/suppl/GSM423910.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423911

GPL570

LNCaP cells treated with actinomycin D only after treatment with caffeine

LNCaP cell line

cell line: prostate cancer cell line LNCaP treatment protocol: treated with actinomycin D alone after treatment with caffeine

Affymetrix gene expression

Sample_geo_accession	GSM423911
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423911/suppl/GSM423911.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423912

GPL570

22Rv1 untreated cells

22Rv1 cell line

cell line: prostate cancer cell line 22RV1 treatment protocol: untreated (control)

Affymetrix gene expression

Sample_geo_accession	GSM423912
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423912/suppl/GSM423912.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423913

GPL570

22Rv1 cells treated with caffeine

22Rv1 cell line

cell line: prostate cancer cell line 22Rv1 treatment protocol: treated with caffeine

Affymetrix gene expression

Sample_geo_accession	GSM423913
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423913/suppl/GSM423913.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423914

GPL570

22Rv1 cells treated with both actinomycin D and caffeine after treatment with caffeine

22Rv1 cell line

cell line: prostate cancer cell line 22Rv1 treatment protocol: treated with both caffeine and actinomycin D after treatment with caffeine

Affymetrix gene expression

Sample_geo_accession	GSM423914
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423914/suppl/GSM423914.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

GSM423915

GPL570

22RV1 cells treated with actinomycin D only after treatment with caffeine

22Rv1 cell line

cell line: prostate cancer cell line 22Rv1 treatment protocol: treated with actinomycin D alone after treatment with caffeine

Affymetrix gene expression

Sample_geo_accession	GSM423915
Sample_status	Public on Jun 30 2009
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Jun 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription
Sample_growth_protocol_ch1	Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA). To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.
Sample_platform_id	GPL570
Sample_contact_name	Yurij,,Ionov
Sample_contact_email	yurij.ionov@roswellpark.org
Sample_contact_phone	(716)8459535
Sample_contact_fax	9716)8451698
Sample_contact_department	Cancer Genetics
Sample_contact_institute	Roswell Park Cancer Institute
Sample_contact_address	Elm and Carlton streets
Sample_contact_city	Buffalo
Sample_contact_state	NY
Sample_contact_zip/postal_code	14263
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423915/suppl/GSM423915.CEL.gz
Sample_series_id	GSE16856
Sample_data_row_count	54675

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