Search results for the GEO ID: GSE17353 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM433796 | GPL570 |
|
EPC2-hTERT_ Normoxia_ Exp1_rep1
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433796
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433796/suppl/GSM433796.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433797 | GPL570 |
|
EPC2-hTERT_Normoxia_Exp1_rep2
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433797
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433797/suppl/GSM433797.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433798 | GPL570 |
|
EPC2-hTERT_Hypoxia_Exp1_rep1
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433798
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433798/suppl/GSM433798.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433799 | GPL570 |
|
EPC2-hTERT_Hypoxia_Exp1_rep2
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433799
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433799/suppl/GSM433799.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433800 | GPL570 |
|
EPC2-hTERT_Normoxia_Exp2_rep1
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433800
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433800/suppl/GSM433800.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433801 | GPL570 |
|
EPC2-hTERT_Normoxia_Exp2_rep2
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433801
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433801/suppl/GSM433801.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433802 | GPL570 |
|
EPC2-hTERT_Hypoxia_Exp2_rep1
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433802
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433802/suppl/GSM433802.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
|
GSM433803 | GPL570 |
|
EPC2-hTERT_Hypoxia_Exp2_rep2
|
esophageal epithelial cells (keratinocytes)
|
cells: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
|
none
|
Sample_geo_accession | GSM433803
| Sample_status | Public on Sep 01 2009
| Sample_submission_date | Jul 27 2009
| Sample_last_update_date | Jul 27 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | EPC2-hTERT cells were exposed to either 21% O2 (normoxia) or 0.2% O2 (severe hypoxia) for 24 hrs. in experiment 1 (Exp 1) and either 21% O2 (normoxia) or 1% O2 (moderate hypoxia) for 24 hrs. in experiment 2 (Exp 2).
| Sample_growth_protocol_ch1 | EPC2-hTERT cells were grown under normoxic conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| Sample_hyb_protocol | Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions
| Sample_scan_protocol | Scanning of Affymetrix chips were performed according manufacturer's instructions
| Sample_data_processing | .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the hypoxia-exposed cell experiments
| Sample_platform_id | GPL570
| Sample_contact_name | Hiroshi,,Nakagawa
| Sample_contact_email | nakagawh@mail.med.upenn.edu
| Sample_contact_phone | 215-573-1867
| Sample_contact_fax | 215-573-2024
| Sample_contact_laboratory | Nakagawa
| Sample_contact_department | Gastroenterology Division
| Sample_contact_institute | University of Pennsylvania
| Sample_contact_address | 415 Curie Blvd.
| Sample_contact_city | Philadelphia
| Sample_contact_state | PA
| Sample_contact_zip/postal_code | 19104
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433803/suppl/GSM433803.CEL.gz
| Sample_series_id | GSE17353
| Sample_data_row_count | 35166
| |
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