Search results for the GEO ID: GSE27424  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM678008 | GPL570 |
|
scram_lo_1
|
scram_lo_1
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ scramble
treatment: Ca 0.09mM, 72 h
|
no KD, low Ca, rep1
|
| Sample_geo_accession | GSM678008
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678008/suppl/GSM678008.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678008/suppl/GSM678008.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678009 | GPL570 |
|
scram_lo_2
|
scram_lo_2
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ scramble
treatment: Ca 0.09mM, 72 h
|
no KD, low Ca, rep2
|
| Sample_geo_accession | GSM678009
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678009/suppl/GSM678009.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678009/suppl/GSM678009.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678010 | GPL570 |
|
scram_lo_3
|
scram_lo_3
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ scramble
treatment: Ca 0.09mM, 72 h
|
no KD, low Ca, rep3
|
| Sample_geo_accession | GSM678010
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678010/suppl/GSM678010.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678010/suppl/GSM678010.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678011 | GPL570 |
|
n3_lo_4
|
n3_lo_4
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ shNotch3
treatment: Ca 0.09mM, 72 h
|
N3 KD, low Ca, rep1
|
| Sample_geo_accession | GSM678011
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678011/suppl/GSM678011.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678011/suppl/GSM678011.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678012 | GPL570 |
|
n3_lo_5
|
n3_lo_5
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ shNotch3
treatment: Ca 0.09mM, 72 h
|
N3 KD, low Ca, rep2
|
| Sample_geo_accession | GSM678012
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678012/suppl/GSM678012.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678012/suppl/GSM678012.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678013 | GPL570 |
|
n3_lo_6
|
n3_lo_6
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ shNotch3
treatment: Ca 0.09mM, 72 h
|
N3 KD, low Ca, rep3
|
| Sample_geo_accession | GSM678013
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678013/suppl/GSM678013.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678013/suppl/GSM678013.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678014 | GPL570 |
|
scram_hi_7
|
scram_hi_7
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ scramble
treatment: Ca 0.6mM, 72 h
|
no KD, hi Ca, rep1
|
| Sample_geo_accession | GSM678014
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678014/suppl/GSM678014.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678014/suppl/GSM678014.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678015 | GPL570 |
|
scram_hi_8
|
scram_hi_8
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ scramble
treatment: Ca 0.6mM, 72 h
|
no KD, hi Ca, rep2
|
| Sample_geo_accession | GSM678015
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678015/suppl/GSM678015.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678015/suppl/GSM678015.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678016 | GPL570 |
|
scram_hi_9
|
scram_hi_9
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ scramble
treatment: Ca 0.6mM, 72 h
|
no KD, hi Ca, rep3
|
| Sample_geo_accession | GSM678016
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678016/suppl/GSM678016.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678016/suppl/GSM678016.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678017 | GPL570 |
|
n3_hi_10
|
n3_hi_10
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ shNotch3
treatment: Ca 0.6mM, 72 h
|
N3 KD, hi Ca, rep1
|
| Sample_geo_accession | GSM678017
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678017/suppl/GSM678017.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678017/suppl/GSM678017.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678018 | GPL570 |
|
n3_hi_11
|
n3_hi_11
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ shNotch3
treatment: Ca 0.6mM, 72 h
|
N3 KD, hi Ca, rep2
|
| Sample_geo_accession | GSM678018
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678018/suppl/GSM678018.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678018/suppl/GSM678018.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
|
GSM678019 | GPL570 |
|
n3_hi_12
|
n3_hi_12
|
cell type: epithelial cells (keratinocytes)
genotype: hTERT-immortalized, non-transformed
genotype/variation: STR-pGIPZ shNotch3
treatment: Ca 0.6mM, 72 h
|
N3 KD, hi Ca, rep3
|
| Sample_geo_accession | GSM678019
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Feb 18 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.
| | Sample_growth_protocol_ch1 | EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular 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 N3 knockdown 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/GSM678nnn/GSM678019/suppl/GSM678019.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678019/suppl/GSM678019.CHP.gz
| | Sample_series_id | GSE27424
| | Sample_data_row_count | 34955
| | |
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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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