Search results for the GEO ID: GSE16555  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM415922 | GPL1261 |
|
OE-Control 1
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415922
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415922/suppl/GSM415922.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415923 | GPL1261 |
|
OE-Control 2
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415923
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415923/suppl/GSM415923.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415924 | GPL1261 |
|
OE-Control 3
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415924
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415924/suppl/GSM415924.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415925 | GPL1261 |
|
OE 1
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415925
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415925/suppl/GSM415925.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415926 | GPL1261 |
|
OE 2
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415926
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415926/suppl/GSM415926.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415927 | GPL1261 |
|
OE 3
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415927
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415927/suppl/GSM415927.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415928 | GPL1261 |
|
KO-Control 1
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415928
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415928/suppl/GSM415928.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415929 | GPL1261 |
|
KO-Control 2
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415929
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415929/suppl/GSM415929.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415930 | GPL1261 |
|
KO-Control 3
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415930
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415930/suppl/GSM415930.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415931 | GPL1261 |
|
KO 1
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415931
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415931/suppl/GSM415931.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415932 | GPL1261 |
|
KO 2
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415932
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415932/suppl/GSM415932.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
GSM415933 | GPL1261 |
|
KO 3
|
H441 cell Line
|
cell line: H441
|
none
|
| Sample_geo_accession | GSM415933
| | Sample_status | Public on Jun 23 2010
| | Sample_submission_date | Jun 11 2009
| | Sample_last_update_date | Jun 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The cells were supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomyocin, and 1% Glutamine. All cell lines were incubated in a humidified incubator at 37º C supplied with 5% carbon dioxide. Cells were routinely maintained in 75 cm2 tissue culture flasks (BD Biosciences Discovery Labware) and harvested when they were in the logarithmic phase of growth.
| | Sample_growth_protocol_ch1 | The human lung adenocarcinoma cell line H441 was obtained from the American Type Culture Collection (ATCC), and maintained in RPMI 1640 medium (Life Technologies)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the RNeasy Mini Kit (QIAGEN), digested with DNase1 (Ambion) to remove DNA contamination
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | According to manufacture's protocol (Affymetrix)
| | Sample_hyb_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_scan_protocol | According to manufacture's protocol (Affymetrix)
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings. Hybridization data were sequentially subjected to normalization, transformation, filtration, and functional classification and pathway analysis as previously described (Xu et al., 2007; Xu et al., 2006). Data analysis was performed with BRB Array Tools software package (http://linus.nci.nih.gov/BRBArrayTools.html). Differentially expressed genes between KD vs. NT, OE vs. NT and KD vs. OE were identified using a random-variance t-test (Wright and Simon, 2003). Genes were considered statistically significant if their p value was less than 0.01 and fold change great than 1.5. The maximum proportion of false discovery rate was set to 0.1. In addition, Affymetrix Present Call in at least two of three replicates and coefficient of variation among replicates 50% were set as a requirement for gene selection.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Avinash ,Manmohan,Baktula
| | Sample_contact_email | avinash.baktula@cchmc.org
| | Sample_contact_phone | 513-636-6096
| | Sample_contact_laboratory | Grimes lab
| | Sample_contact_department | Immunobiology
| | Sample_contact_institute | Cincinnati Childrens Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45219
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415933/suppl/GSM415933.CEL.gz
| | Sample_series_id | GSE16555
| | Sample_data_row_count | 45101
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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