Result

Search results for the GEO ID: GSE6593

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM152271

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MKP

Mouse primary Megakaryocytes stage MKP

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4

none

Sample_geo_accession	GSM152271
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152271/suppl/GSM152271.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152272

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MKP replicate

Mouse primary Megakaryocytes stage MKP

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4

none

Sample_geo_accession	GSM152272
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152272/suppl/GSM152272.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152273

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MK3

Mouse primary Megakaryocytes stage MK3

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 3

none

Sample_geo_accession	GSM152273
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152273/suppl/GSM152273.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152274

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MK3 replicate

Mouse primary Megakaryocytes stage MK3

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 3

none

Sample_geo_accession	GSM152274
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152274/suppl/GSM152274.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152275

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MK4

Mouse primary Megakaryocytes stage MK4

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4

none

Sample_geo_accession	GSM152275
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152275/suppl/GSM152275.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152276

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MK4 replicate

Mouse primary Megakaryocytes stage MK4

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4

none

Sample_geo_accession	GSM152276
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152276/suppl/GSM152276.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152277

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MK6

Mouse primary Megakaryocytes stage MK6

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 6

none

Sample_geo_accession	GSM152277
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152277/suppl/GSM152277.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

GSM152278

GPL339

Expression analysis of primary mouse megakaryocyte differentiation-MK6 replicate1

Mouse primary Megakaryocytes stage MK6

mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 6

none

Sample_geo_accession	GSM152278
Sample_status	Public on Jan 08 2007
Sample_submission_date	Dec 21 2006
Sample_last_update_date	Jan 08 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol reagents
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
Sample_label_protocol_ch1	The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
Sample_label_protocol_ch1	The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample
Sample_hyb_protocol	The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
Sample_hyb_protocol	The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
Sample_hyb_protocol	The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
Sample_data_processing	Affymetrix MAS 5.0
Sample_platform_id	GPL339
Sample_contact_name	Ramesh,A,Shivdasani
Sample_contact_email	ramesh_shivdasani@dfci.harvard.edu
Sample_contact_phone	617 632-5746
Sample_contact_fax	617 632-5417
Sample_contact_laboratory	Shivdasani
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	44 Binney St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_contact_web_link	http://research.dfci.harvard.edu/shivdasani
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM152nnn/GSM152278/suppl/GSM152278.CEL.gz
Sample_series_id	GSE6593
Sample_data_row_count	22690

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