Search results for the GEO ID: GSE31474  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM782017 | GPL570 |
|
H5N2-F189 infected A549 at 10H, biological rep1
|
H5N2 (F189) infected A549 10 hpi rep 1
|
cell type: Human aveolar basal epithelial cells
cell line: A549
infection: H5N2-F189
time: 10 hpi
|
Gene expression data from H5N2 (F189) infected A549 10 hpi rep 1
|
| Sample_geo_accession | GSM782017
| | Sample_status | Public on Jan 03 2013
| | Sample_submission_date | Aug 18 2011
| | Sample_last_update_date | Jan 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The cells were infected with A/duck/Malaysia/F189/07/2004(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
| | Sample_growth_protocol_ch1 | The cells were grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Richard,J,Sugrue
| | Sample_contact_email | RJSUGRUE@ntu.edu.sg
| | Sample_contact_department | Divison of Molecular and Cell Biology
| | Sample_contact_institute | Nanyang Technological University
| | Sample_contact_address | 60 Nanyang Drive
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 637551
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM782nnn/GSM782017/suppl/GSM782017_A549_H5N2-F189_10H-1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM782nnn/GSM782017/suppl/GSM782017_A549_H5N2-F189_10H-1.CHP.gz
| | Sample_series_id | GSE31474
| | Sample_series_id | GSE31524
| | Sample_data_row_count | 54675
| | |
|
GSM782018 | GPL570 |
|
H5N2-F189 infected A549 at 10H, biological rep2
|
H5N2 (F189) infected A549 10 hpi rep 2
|
cell type: Human aveolar basal epithelial cells
cell line: A549
infection: H5N2-F189
time: 10 hpi
|
Gene expression data from H5N2 (F189) infected A549 10 hpi rep 2
|
| Sample_geo_accession | GSM782018
| | Sample_status | Public on Jan 03 2013
| | Sample_submission_date | Aug 18 2011
| | Sample_last_update_date | Jan 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The cells were infected with A/duck/Malaysia/F189/07/2004(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
| | Sample_growth_protocol_ch1 | The cells were grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Richard,J,Sugrue
| | Sample_contact_email | RJSUGRUE@ntu.edu.sg
| | Sample_contact_department | Divison of Molecular and Cell Biology
| | Sample_contact_institute | Nanyang Technological University
| | Sample_contact_address | 60 Nanyang Drive
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 637551
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM782nnn/GSM782018/suppl/GSM782018_A549_H5N2-F189_10H-2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM782nnn/GSM782018/suppl/GSM782018_A549_H5N2-F189_10H-2.CHP.gz
| | Sample_series_id | GSE31474
| | Sample_series_id | GSE31524
| | Sample_data_row_count | 54675
| | |
|
GSM782019 | GPL570 |
|
H5N2-F189 infected A549 at 10H, biological rep3
|
H5N2 (F189) infected A549 10 hpi rep 3
|
cell type: Human aveolar basal epithelial cells
cell line: A549
infection: H5N2-F189
time: 10 hpi
|
Gene expression data from H5N2 (F189) infected A549 10 hpi rep 3
|
| Sample_geo_accession | GSM782019
| | Sample_status | Public on Jan 03 2013
| | Sample_submission_date | Aug 18 2011
| | Sample_last_update_date | Jan 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The cells were infected with A/duck/Malaysia/F189/07/2004(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
| | Sample_growth_protocol_ch1 | The cells were grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Richard,J,Sugrue
| | Sample_contact_email | RJSUGRUE@ntu.edu.sg
| | Sample_contact_department | Divison of Molecular and Cell Biology
| | Sample_contact_institute | Nanyang Technological University
| | Sample_contact_address | 60 Nanyang Drive
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 637551
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM782nnn/GSM782019/suppl/GSM782019_A549_H5N2-F189_10H-3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM782nnn/GSM782019/suppl/GSM782019_A549_H5N2-F189_10H-3.CHP.gz
| | Sample_series_id | GSE31474
| | Sample_series_id | GSE31524
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
Select expression type |
| Transcripts profile based on; |
A. Differential status (Up/Down regulation) |
|
|
Regulation type |
|
Fold change |
|
p-value |
|
|
|
B. Absolute calls (Transcribed/Not-detected) |
|
|
| Derive calls within/across groups |
Within groups |
|
|
Detection status |
|
Percentage detection |
|
|
Across groups |
|
|
Detection status |
First group: |
- |
Second group:
|
Percentage detection |
First group: |
- |
Second group:
|
|
|
| |
Filter results by number of probes |
|
|
