Result

Search results for the GEO ID: GSE16614

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Title

Source name

Description

Characteristics

GSM417274

GPL201

transcriptional effects of LMP3 in MSC_control1

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417274
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	untreated cells
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417274/suppl/GSM417274.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417274/suppl/GSM417274.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417275

GPL201

transcriptional effects of LMP3 in MSC_control2

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417275
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	untreated cells
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417275/suppl/GSM417275.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417275/suppl/GSM417275.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417276

GPL201

transcriptional effects of LMP3 in MSC_control3

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417276
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	untreated cells
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417276/suppl/GSM417276.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417276/suppl/GSM417276.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417277

GPL201

transcriptional effects of LMP3 in MSC_LMP3_replicate2

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417277
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cells treated with AdLMP3
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417277/suppl/GSM417277.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417277/suppl/GSM417277.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417278

GPL201

transcriptional effects of LMP3 in MSC_LMP3_replicate1

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417278
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cells treated with AdLMP3
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417278/suppl/GSM417278.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417278/suppl/GSM417278.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417279

GPL201

transcriptional effects of LMP3 in MSC_LMP3_replicate3

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417279
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cells treated with AdLMP3
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417279/suppl/GSM417279.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417279/suppl/GSM417279.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417280

GPL201

transcriptional effects of LMP3 in MSC_Adψ5_replicate1

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417280
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cells treated with Adψ5
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417280/suppl/GSM417280.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417280/suppl/GSM417280.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417281

GPL201

transcriptional effects of LMP3 in MSC_Adψ5_replicate3

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417281
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cells treated with Adψ5
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417281/suppl/GSM417281.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417281/suppl/GSM417281.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

GSM417282

GPL201

transcriptional effects of LMP3 in MSC_Adψ5_replicate2

bone marrow

gender: male tissue: bone marrow cell type: mesenchymal stem cells

Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

Sample_geo_accession	GSM417282
Sample_status	Public on Dec 31 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Dec 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cells treated with Adψ5
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).
Sample_hyb_protocol	Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.
Sample_scan_protocol	Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.
Sample_platform_id	GPL201
Sample_contact_name	camilla,,bernardini
Sample_contact_email	camilla.bernardini@rm.unicatt.it
Sample_contact_phone	+390630154711
Sample_contact_department	Human Anatomy
Sample_contact_institute	UCSC
Sample_contact_address	L.go F.Vito 1
Sample_contact_city	Rome
Sample_contact_zip/postal_code	00186
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417282/suppl/GSM417282.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417282/suppl/GSM417282.CHP.gz
Sample_series_id	GSE16614
Sample_data_row_count	8793

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