Search results for the GEO ID: GSE16447 |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM413505 | GPL570 |
|
IV_1
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: female
|
no further description
|
Sample_geo_accession | GSM413505
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413505/suppl/GSM413505.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413505/suppl/GSM413505.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413506 | GPL570 |
|
IV_2
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: female
|
no further description
|
Sample_geo_accession | GSM413506
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413506/suppl/GSM413506.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413506/suppl/GSM413506.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413507 | GPL570 |
|
IV_3
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: male
|
no further description
|
Sample_geo_accession | GSM413507
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413507/suppl/GSM413507.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413507/suppl/GSM413507.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413508 | GPL570 |
|
IV_4
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: female
|
no further description
|
Sample_geo_accession | GSM413508
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413508/suppl/GSM413508.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413508/suppl/GSM413508.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413509 | GPL570 |
|
IV_5
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: male
|
no further description
|
Sample_geo_accession | GSM413509
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413509/suppl/GSM413509.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413509/suppl/GSM413509.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413510 | GPL570 |
|
IV_6
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: male
|
no further description
|
Sample_geo_accession | GSM413510
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413510/suppl/GSM413510.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413510/suppl/GSM413510.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413511 | GPL570 |
|
IV-9
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: female
|
no further description
|
Sample_geo_accession | GSM413511
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413511/suppl/GSM413511.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413511/suppl/GSM413511.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413512 | GPL570 |
|
Male Control
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: male
|
no further description
|
Sample_geo_accession | GSM413512
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413512/suppl/GSM413512.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413512/suppl/GSM413512.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
|
GSM413513 | GPL570 |
|
Female Control
|
skin fibroblasts
|
tissue: skin
cell type: fibroblasts
gender: female
|
no further description
|
Sample_geo_accession | GSM413513
| Sample_status | Public on Dec 11 2009
| Sample_submission_date | Jun 05 2009
| Sample_last_update_date | Dec 11 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturers’ protocols.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Briefly, 5 µg of total RNA was used to prepare double-stranded cDNA. Biotinylated cRNA was synthesized with an RNA transcript labeling kit and 20 µg of the cRNA product was chemically fragmented to approximately 50-200 nucleotides.
| Sample_hyb_protocol | The fragmented cRNA was hybridized to an Affymetrix HG U133 Plus 2.0 chip. Chips were washed and stained using the EukGE-WS2v5 protocol on an Affymetrix fluidics 450 station. The stain included streptavidin-phycoerythrin (10 µg/mL) and biotinylated goat anti-streptavidin (3 µg/mL).
| Sample_scan_protocol | Fluorescence intensities were captured with an argonion laser confocal scanner.
| Sample_data_processing | Scanned output files were analyzed with GeneChip Operating Software 1.4 (GCOS; Affymetrix, Santa Clara, CA, USA). To examine the quality of the arrays the R function AffyQC was run on the CEL files.
| Sample_data_processing | Data was normalized in R program using RMA (Robust Multichip Average) normalization. Data analysis was done using Omniviz software version 5.0.1 (Omniviz, Biowisdom USA Maynard, MA) software.
| Sample_platform_id | GPL570
| Sample_contact_name | J.,,Verkerk
| Sample_contact_laboratory | Bioinformatics
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015GE
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://www.erasmusmc.nl/bioinformatica/?lang=en
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413513/suppl/GSM413513.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413513/suppl/GSM413513.CHP.gz
| Sample_series_id | GSE16447
| Sample_data_row_count | 54675
| |
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