Search results for the GEO ID: GSE23325  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM572544 | GPL1261 |
|
NC1
|
regular rodent chow
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572544
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572544/suppl/GSM572544.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572544/suppl/GSM572544.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572545 | GPL1261 |
|
NC2
|
regular rodent chow
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572545
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572545/suppl/GSM572545.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572545/suppl/GSM572545.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572546 | GPL1261 |
|
NC4
|
regular rodent chow
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572546
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572546/suppl/GSM572546.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572546/suppl/GSM572546.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572547 | GPL1261 |
|
NC5
|
regular rodent chow
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572547
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572547/suppl/GSM572547.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572547/suppl/GSM572547.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572548 | GPL1261 |
|
HF21
|
high fat diet
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572548
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572548/suppl/GSM572548.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572548/suppl/GSM572548.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572549 | GPL1261 |
|
HF22
|
high fat diet
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572549
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572549/suppl/GSM572549.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572549/suppl/GSM572549.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572550 | GPL1261 |
|
HF23
|
high fat diet
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572550
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572550/suppl/GSM572550.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572550/suppl/GSM572550.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
GSM572551 | GPL1261 |
|
HF24
|
high fat diet
|
tissue: Pancreatic islets
strain: C57Bl/6J
|
Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA
|
| Sample_geo_accession | GSM572551
| | Sample_status | Public on Nov 20 2011
| | Sample_submission_date | Jul 29 2010
| | Sample_last_update_date | Nov 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_scan_protocol | Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.
| | Sample_data_processing | For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | yumi,,imai
| | Sample_contact_email | imaiy@evms.edu
| | Sample_contact_phone | 757-446-5708
| | Sample_contact_fax | 757-446-7339
| | Sample_contact_institute | Eastern Virginia Medical School
| | Sample_contact_address | 799W Olney Road, LH 2156
| | Sample_contact_city | Norfolk
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23507
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572551/suppl/GSM572551.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM572nnn/GSM572551/suppl/GSM572551.CHP.gz
| | Sample_series_id | GSE23325
| | Sample_data_row_count | 45101
| | |
|
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