Search results for the GEO ID: GSE20847  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM521268 | GPL570 |
|
LRPPRC knockdown1, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 1
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 20%
|
Gene expression data from LRPPRC knockdown 1 cell line, with only 20% expression of LRPPRC compared to control.
1.1
|
| Sample_geo_accession | GSM521268
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521268/suppl/GSM521268.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521269 | GPL570 |
|
LRPPRC knockdown1, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 1
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 20%
|
Gene expression data from LRPPRC knockdown 1 cell line, with only 20% expression of LRPPRC compared to control.
1.2
|
| Sample_geo_accession | GSM521269
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521269/suppl/GSM521269.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521270 | GPL570 |
|
LRPPRC knockdown2, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 2
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 33%
|
Gene expression data from LRPPRC knockdown 2 cell line, with only 33% expression of LRPPRC compared to control.
2.1
|
| Sample_geo_accession | GSM521270
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521270/suppl/GSM521270.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521271 | GPL570 |
|
LRPPRC knockdown2, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 2
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 33%
|
Gene expression data from LRPPRC knockdown 2 cell line, with only 33% expression of LRPPRC compared to control.
2.2
|
| Sample_geo_accession | GSM521271
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521271/suppl/GSM521271.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521272 | GPL570 |
|
LRPPRC knockdown3, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 3
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 69%
|
Gene expression data from LRPPRC knockdown 3 cell line, with only 69% expression of LRPPRC compared to control.
3.1
|
| Sample_geo_accession | GSM521272
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521272/suppl/GSM521272.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521273 | GPL570 |
|
LRPPRC knockdown3, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 3
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 69%
|
Gene expression data from LRPPRC knockdown 3 cell line, with only 69% expression of LRPPRC compared to control.
3.2
|
| Sample_geo_accession | GSM521273
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521273/suppl/GSM521273.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521274 | GPL570 |
|
LRPPRC knockdown4, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 4
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 81%
|
Gene expression data from LRPPRC knockdown 4 cell line, with only 81% expression of LRPPRC compared to control.
4.1
|
| Sample_geo_accession | GSM521274
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521274/suppl/GSM521274.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521275 | GPL570 |
|
LRPPRC knockdown4, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 4
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 81%
|
Gene expression data from LRPPRC knockdown 4 cell line, with only 81% expression of LRPPRC compared to control.
4.2
|
| Sample_geo_accession | GSM521275
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521275/suppl/GSM521275.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521276 | GPL570 |
|
LRPPRC knockdown5, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 5
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 100%
|
Gene expression data from LRPPRC knockdown 5 cell line, with only 100% expression of LRPPRC compared to control.
5.1
|
| Sample_geo_accession | GSM521276
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521276/suppl/GSM521276.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521277 | GPL570 |
|
LRPPRC knockdown5, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 5
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 100%
|
Gene expression data from LRPPRC knockdown 5 cell line, with only 100% expression of LRPPRC compared to control.
5.2
|
| Sample_geo_accession | GSM521277
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521277/suppl/GSM521277.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521278 | GPL570 |
|
LRPPRC knockdown6, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 6
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 9%
|
Gene expression data from LRPPRC knockdown 6 cell line, with only 9% expression of LRPPRC compared to control.
6.1
|
| Sample_geo_accession | GSM521278
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521278/suppl/GSM521278.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521279 | GPL570 |
|
LRPPRC knockdown6, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 6
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 9%
|
Gene expression data from LRPPRC knockdown 6 cell line, with only 9% expression of LRPPRC compared to control.
6.2
|
| Sample_geo_accession | GSM521279
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521279/suppl/GSM521279.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521280 | GPL570 |
|
LRPPRC knockdown7, biological replicate 1
|
MCH58 LRPPRC knockdown cell line 7
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 58%
|
Gene expression data from LRPPRC knockdown 7 cell line, with only 58% expression of LRPPRC compared to control.
7.1
|
| Sample_geo_accession | GSM521280
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521280/suppl/GSM521280.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
|
GSM521281 | GPL570 |
|
LRPPRC knockdown7, biological replicate 2
|
MCH58 LRPPRC knockdown cell line 7
|
cell line: MCH58
cell type: fibroblasts
sirna: LRPPRC
lrpprc expression vs. control: 58%
|
Gene expression data from LRPPRC knockdown 7 cell line, with only 58% expression of LRPPRC compared to control.
7.2
|
| Sample_geo_accession | GSM521281
| | Sample_status | Public on Mar 13 2010
| | Sample_submission_date | Mar 11 2010
| | Sample_last_update_date | Mar 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.
| | Sample_growth_protocol_ch1 | MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GCS 3000 from Affymetrix.
| | Sample_data_processing | The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vishal,M,Gohil
| | Sample_contact_laboratory | Vamsi K Mootha
| | Sample_contact_department | Center for Human Genetic Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521281/suppl/GSM521281.CEL.gz
| | Sample_series_id | GSE20847
| | Sample_data_row_count | 54675
| | |
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