Search results for the GEO ID: GSE14434  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM360314 | GPL570 |
|
R1=HeLa_M13_Aug5_2008
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HeLa cell line (human cervical carcinoma)
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HeLaS3
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None
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| Sample_geo_accession | GSM360314
| | Sample_status | Public on Feb 08 2009
| | Sample_submission_date | Jan 14 2009
| | Sample_last_update_date | Jan 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC
| | Sample_treatment_protocol_ch1 | Cells were transfected with 5nM of synthetic oligonucleotides: Sample R1=5nM M13 DNA oligonucleotide, sample R2=5nM anti-PCSK9 siRNA, and sample R3= 5nM UA31D4 Adaptor + 5nM UA31E Adaptor oligonucleotides. Lipofectamine-2000 (Invitrogen) was used as the transfection reagent as per manufacturer's instructions. 24 hours after transfection cells were collected and used to make total RNA.
| | Sample_growth_protocol_ch1 | DMEM + 10% fetal calf serum at 37 degrees 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy kit including Dnase 1 treatment (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.
| | Sample_hyb_protocol | The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.
| | Sample_scan_protocol | Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.
| | Sample_data_processing | Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.
| | Sample_data_processing | The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Samuel,I,Gunderson
| | Sample_contact_email | Gunderson@Biology.Rutgers.Edu
| | Sample_contact_phone | 7324451016
| | Sample_contact_laboratory | Nelson Biology Laboratories
| | Sample_contact_department | Molecular Biology & Biochemistry
| | Sample_contact_institute | Rutgers University
| | Sample_contact_address | 604 Allison Road
| | Sample_contact_city | Piscataway
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 08854
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM360nnn/GSM360314/suppl/GSM360314.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM360nnn/GSM360314/suppl/GSM360314.CHP.gz
| | Sample_series_id | GSE14434
| | Sample_data_row_count | 54675
| | |
|
GSM360315 | GPL570 |
|
R2=HeLa_anti-PCSK9_siRNA_Aug5_2008
|
HeLa cell line (human cervical carcinoma)
|
HeLaS3
|
None
|
| Sample_geo_accession | GSM360315
| | Sample_status | Public on Feb 08 2009
| | Sample_submission_date | Jan 14 2009
| | Sample_last_update_date | Jan 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC
| | Sample_treatment_protocol_ch1 | Cells were transfected with 5nM of synthetic oligonucleotides: Sample R1=5nM M13 DNA oligonucleotide, sample R2=5nM anti-PCSK9 siRNA, and sample R3= 5nM UA31D4 Adaptor + 5nM UA31E Adaptor oligonucleotides. Lipofectamine-2000 (Invitrogen) was used as the transfection reagent as per manufacturer's instructions. 24 hours after transfection cells were collected and used to make total RNA.
| | Sample_growth_protocol_ch1 | DMEM + 10% fetal calf serum at 37 degrees 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy kit including Dnase 1 treatment (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.
| | Sample_hyb_protocol | The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.
| | Sample_scan_protocol | Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.
| | Sample_data_processing | Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.
| | Sample_data_processing | The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Samuel,I,Gunderson
| | Sample_contact_email | Gunderson@Biology.Rutgers.Edu
| | Sample_contact_phone | 7324451016
| | Sample_contact_laboratory | Nelson Biology Laboratories
| | Sample_contact_department | Molecular Biology & Biochemistry
| | Sample_contact_institute | Rutgers University
| | Sample_contact_address | 604 Allison Road
| | Sample_contact_city | Piscataway
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 08854
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM360nnn/GSM360315/suppl/GSM360315.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM360nnn/GSM360315/suppl/GSM360315.CHP.gz
| | Sample_series_id | GSE14434
| | Sample_data_row_count | 54675
| | |
|
GSM360316 | GPL570 |
|
R3=HeLa_anti-PCSK9_Adaptor_Aug5_2008
|
HeLa cell line (human cervical carcinoma)
|
HeLaS3
|
None
|
| Sample_geo_accession | GSM360316
| | Sample_status | Public on Feb 08 2009
| | Sample_submission_date | Jan 14 2009
| | Sample_last_update_date | Jan 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC
| | Sample_treatment_protocol_ch1 | Cells were transfected with 5nM of synthetic oligonucleotides: Sample R1=5nM M13 DNA oligonucleotide, sample R2=5nM anti-PCSK9 siRNA, and sample R3= 5nM UA31D4 Adaptor + 5nM UA31E Adaptor oligonucleotides. Lipofectamine-2000 (Invitrogen) was used as the transfection reagent as per manufacturer's instructions. 24 hours after transfection cells were collected and used to make total RNA.
| | Sample_growth_protocol_ch1 | DMEM + 10% fetal calf serum at 37 degrees 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy kit including Dnase 1 treatment (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.
| | Sample_hyb_protocol | The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.
| | Sample_scan_protocol | Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.
| | Sample_data_processing | Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.
| | Sample_data_processing | The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Samuel,I,Gunderson
| | Sample_contact_email | Gunderson@Biology.Rutgers.Edu
| | Sample_contact_phone | 7324451016
| | Sample_contact_laboratory | Nelson Biology Laboratories
| | Sample_contact_department | Molecular Biology & Biochemistry
| | Sample_contact_institute | Rutgers University
| | Sample_contact_address | 604 Allison Road
| | Sample_contact_city | Piscataway
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 08854
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM360nnn/GSM360316/suppl/GSM360316.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM360nnn/GSM360316/suppl/GSM360316.CHP.gz
| | Sample_series_id | GSE14434
| | Sample_data_row_count | 54675
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