Search results for the GEO ID: GSE11407  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM287846 | GPL570 |
|
Ac4ManNLev-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287846
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with Ac4ManNLev (75 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287846/suppl/GSM287846.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287846/suppl/GSM287846.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287847 | GPL570 |
|
Ac4ManNLev-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287847
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with Ac4ManNLev (75 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287847/suppl/GSM287847.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287847/suppl/GSM287847.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287848 | GPL570 |
|
C1OH-Ac3ManNAc-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287848
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-Ac3ManNAc (100 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287848/suppl/GSM287848.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287848/suppl/GSM287848.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287849 | GPL570 |
|
C1OH-Ac3ManNAc-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287849
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-Ac3ManNAc (100 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287849/suppl/GSM287849.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287849/suppl/GSM287849.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287850 | GPL570 |
|
C1OH-But3GalNAc-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287850
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3GalNAc (50 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287850/suppl/GSM287850.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287850/suppl/GSM287850.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287851 | GPL570 |
|
C1OH-But3GalNAc-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287851
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3GalNAc (50 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0(GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287851/suppl/GSM287851.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287851/suppl/GSM287851.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287862 | GPL570 |
|
C1OH-But3GlcNAc-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287862
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3GlcNAc (40 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287862/suppl/GSM287862.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287862/suppl/GSM287862.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287863 | GPL570 |
|
C1OH-But3GlcNAc-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287863
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3GlcNAc (40 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287863/suppl/GSM287863.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287863/suppl/GSM287863.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287864 | GPL570 |
|
C1OH-But3ManNAc-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287864
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3ManNAc (30 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287864/suppl/GSM287864.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287864/suppl/GSM287864.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287865 | GPL570 |
|
C1OH-But3ManNAc-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287865
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C1OH-But3ManNAc (30 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287865/suppl/GSM287865.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287865/suppl/GSM287865.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287905 | GPL570 |
|
C6OH-But3ManNAc-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287905
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C6OH-But3ManNAc (30 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287905/suppl/GSM287905.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287905/suppl/GSM287905.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287906 | GPL570 |
|
C6OH-But3ManNAc-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287906
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with C6OH-But3ManNAc (30 uM) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287906/suppl/GSM287906.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287906/suppl/GSM287906.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287907 | GPL570 |
|
EtOH-1
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287907
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with EtOH (final percentage | 0.40%) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287907/suppl/GSM287907.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287907/suppl/GSM287907.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287909 | GPL570 |
|
EtOH-2
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287909
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with EtOH (final percentage | 0.40%) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287909/suppl/GSM287909.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287909/suppl/GSM287909.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
| | |
|
GSM287910 | GPL570 |
|
EtOH-3
|
MDA-MB-231 breast cancer cells
|
no additional information
|
none
|
| Sample_geo_accession | GSM287910
| | Sample_status | Public on May 08 2009
| | Sample_submission_date | May 09 2008
| | Sample_last_update_date | May 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = Cells were plated and grown for 3 days before being harvested for microarray analysis. Growth medium (RPMI 1640 with 10% FBS) was supplemented with EtOH (final percentage | 0.40%) at the time of plating.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using Trizol reagent (Invitrogen), following manufacturer's instructions. Isolated RNA was purified using Turbo DNase (Ambion) and Mini Spin columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA from control and experimental cells was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).
| | Sample_hyb_protocol | 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_data_processing | Image analysis of each GeneChip was done through the GeneChip Operating System 1.4.0 (GCOS) software from Affymetrix, using the standard default settings. For comparison between different chips, global scaling was used following MAS5.0 algorithm, scaling all probesets to a user defined target intensity (TGT) of 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Yarema
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 3400 N. Charles St., Clark Hall 106A
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21218
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287910/suppl/GSM287910.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287910/suppl/GSM287910.CHP.gz
| | Sample_series_id | GSE11407
| | Sample_data_row_count | 54675
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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