Search results for the GEO ID: GSE41035  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1007032 | GPL570 |
|
control-plusDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: EGFP shRNA
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007032
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007032/suppl/GSM1007032_20914_a_Control_shRNAplusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007033 | GPL570 |
|
control-plusDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: EGFP shRNA
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007033
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007033/suppl/GSM1007033_20916_c_Control_shRNAplusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007034 | GPL570 |
|
shRNA2-4-noDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 2-4
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007034
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007034/suppl/GSM1007034_20918_b_shRNA2-4noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007035 | GPL570 |
|
shRNA2-4-plusDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 2-4
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007035
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007035/suppl/GSM1007035_20920_a_shRNA2-4plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007036 | GPL570 |
|
shRNA2-4-plusDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 2-4
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007036
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007036/suppl/GSM1007036_20922_c_shRNA2-4plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007037 | GPL570 |
|
shRNA4-1-noDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 4-1
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007037
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007037/suppl/GSM1007037_20924_b_shRNA4-1noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007038 | GPL570 |
|
shRNA4-1-plusDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 4-1
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007038
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007038/suppl/GSM1007038_20926_a_shRNA4-1plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007039 | GPL570 |
|
shRNA4-1-plusDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 4-1
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007039
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007039/suppl/GSM1007039_20928_c_shRNA4-1plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007040 | GPL570 |
|
shRNA6-16-noDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 6-16
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007040
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007040/suppl/GSM1007040_20930_b_shRNA6-16noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007041 | GPL570 |
|
shRNA6-16-plusDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 6-16
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007041
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007041/suppl/GSM1007041_20932_a_shRNA6-16plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007042 | GPL570 |
|
shRNA6-16-plusDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 6-16
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007042
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007042/suppl/GSM1007042_20934_c_shRNA6-16plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007043 | GPL570 |
|
control-noDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: EGFP shRNA
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007043
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007043/suppl/GSM1007043_20935_a_Control_shRNAnoDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007044 | GPL570 |
|
control-noDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: EGFP shRNA
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007044
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007044/suppl/GSM1007044_20912_b_Control_shRNAnoDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007045 | GPL570 |
|
control-noDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: EGFP shRNA
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007045
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007045/suppl/GSM1007045_20913_c_Control_shRNAnoDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007046 | GPL570 |
|
control-plusDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: EGFP shRNA
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007046
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007046/suppl/GSM1007046_20915_b_Control_shRNAplusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007047 | GPL570 |
|
shRNA2-4-noDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 2-4
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007047
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007047/suppl/GSM1007047_20917_a_shRNA2-4noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007048 | GPL570 |
|
shRNA2-4-noDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 2-4
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007048
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007048/suppl/GSM1007048_20919_c_shRNA2-4noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007049 | GPL570 |
|
shRNA2-4-plusDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 2-4
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007049
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007049/suppl/GSM1007049_20921_b_shRNA2-4plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007050 | GPL570 |
|
shRNA4-1-noDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 4-1
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007050
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007050/suppl/GSM1007050_20923_a_shRNA4-1noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007051 | GPL570 |
|
shRNA4-1-noDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 4-1
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007051
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007051/suppl/GSM1007051_20925_c_shRNA4-1noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007052 | GPL570 |
|
shRNA4-1-plusDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 4-1
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007052
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007052/suppl/GSM1007052_20927_b_shRNA4-1plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007053 | GPL570 |
|
shRNA6-16-noDox-rep1
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 6-16
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007053
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007053/suppl/GSM1007053_20929_a_shRNA6-16noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007054 | GPL570 |
|
shRNA6-16-noDox-rep3
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 6-16
doxycycline treatment: no
|
|
| Sample_geo_accession | GSM1007054
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007054/suppl/GSM1007054_20931_c_shRNA6-16noDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
GSM1007055 | GPL570 |
|
shRNA6-16-plusDox-rep2
|
bladder cancer cells treated 48 hr
|
cell line: RT112
transduced: FGFR3 shRNA 6-16
doxycycline treatment: yes
|
|
| Sample_geo_accession | GSM1007055
| | Sample_status | Public on Nov 07 2012
| | Sample_submission_date | Sep 20 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.
| | Sample_growth_protocol_ch1 | RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol
| | Sample_scan_protocol | HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol
| | Sample_data_processing | Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jinfeng,,Liu
| | Sample_contact_email | jinfengl@gene.com
| | Sample_contact_department | Bioinformatics and Computational Biology
| | Sample_contact_institute | Genentech Inc.
| | Sample_contact_address | 1 DNA Way, MS93
| | Sample_contact_city | South San Francisco
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94080
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1007nnn/GSM1007055/suppl/GSM1007055_20933_b_shRNA6-16plusDox_SPR557_HGU133P.CEL.gz
| | Sample_series_id | GSE41035
| | Sample_data_row_count | 54675
| | |
|
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