Search results for the GEO ID: GSE41459  |
(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 |
GSM1017646 | GPL570 |
|
trophoblast_control_1
|
ACH-3P cells
|
cell line: ACH-3P cells
treatment: control
|
|
| Sample_geo_accession | GSM1017646
| | Sample_status | Public on Oct 11 2012
| | Sample_submission_date | Oct 10 2012
| | Sample_last_update_date | Oct 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.
| | Sample_growth_protocol_ch1 | First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.
| | Sample_data_processing | The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katherine,,Gates
| | Sample_contact_email | kcmcb@colostate.edu
| | Sample_contact_department | Biomedical Sciences
| | Sample_contact_institute | Colorado State University
| | Sample_contact_address | 3107 Rampart Rd
| | Sample_contact_city | Fort Collins
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80523
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1017nnn/GSM1017646/suppl/GSM1017646_L1.CEL.gz
| | Sample_series_id | GSE41459
| | Sample_data_row_count | 54675
| | |
|
GSM1017647 | GPL570 |
|
trophoblast_control_2
|
ACH-3P cells
|
cell line: ACH-3P cells
treatment: control
|
|
| Sample_geo_accession | GSM1017647
| | Sample_status | Public on Oct 11 2012
| | Sample_submission_date | Oct 10 2012
| | Sample_last_update_date | Oct 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.
| | Sample_growth_protocol_ch1 | First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.
| | Sample_data_processing | The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katherine,,Gates
| | Sample_contact_email | kcmcb@colostate.edu
| | Sample_contact_department | Biomedical Sciences
| | Sample_contact_institute | Colorado State University
| | Sample_contact_address | 3107 Rampart Rd
| | Sample_contact_city | Fort Collins
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80523
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1017nnn/GSM1017647/suppl/GSM1017647_L2.CEL.gz
| | Sample_series_id | GSE41459
| | Sample_data_row_count | 54675
| | |
|
GSM1017648 | GPL570 |
|
trophoblast_control_3
|
ACH-3P cells
|
cell line: ACH-3P cells
treatment: control
|
|
| Sample_geo_accession | GSM1017648
| | Sample_status | Public on Oct 11 2012
| | Sample_submission_date | Oct 10 2012
| | Sample_last_update_date | Oct 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.
| | Sample_growth_protocol_ch1 | First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.
| | Sample_data_processing | The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katherine,,Gates
| | Sample_contact_email | kcmcb@colostate.edu
| | Sample_contact_department | Biomedical Sciences
| | Sample_contact_institute | Colorado State University
| | Sample_contact_address | 3107 Rampart Rd
| | Sample_contact_city | Fort Collins
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80523
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1017nnn/GSM1017648/suppl/GSM1017648_L3.CEL.gz
| | Sample_series_id | GSE41459
| | Sample_data_row_count | 54675
| | |
|
GSM1017649 | GPL570 |
|
trophoblast_shRNA_1
|
ACH-3P cells
|
cell line: ACH-3P cells
treatment: shRNA
|
|
| Sample_geo_accession | GSM1017649
| | Sample_status | Public on Oct 11 2012
| | Sample_submission_date | Oct 10 2012
| | Sample_last_update_date | Oct 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.
| | Sample_growth_protocol_ch1 | First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.
| | Sample_data_processing | The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katherine,,Gates
| | Sample_contact_email | kcmcb@colostate.edu
| | Sample_contact_department | Biomedical Sciences
| | Sample_contact_institute | Colorado State University
| | Sample_contact_address | 3107 Rampart Rd
| | Sample_contact_city | Fort Collins
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80523
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1017nnn/GSM1017649/suppl/GSM1017649_H1.CEL.gz
| | Sample_series_id | GSE41459
| | Sample_data_row_count | 54675
| | |
|
GSM1017650 | GPL570 |
|
trophoblast_shRNA_2
|
ACH-3P cells
|
cell line: ACH-3P cells
treatment: shRNA
|
|
| Sample_geo_accession | GSM1017650
| | Sample_status | Public on Oct 11 2012
| | Sample_submission_date | Oct 10 2012
| | Sample_last_update_date | Oct 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.
| | Sample_growth_protocol_ch1 | First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.
| | Sample_data_processing | The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katherine,,Gates
| | Sample_contact_email | kcmcb@colostate.edu
| | Sample_contact_department | Biomedical Sciences
| | Sample_contact_institute | Colorado State University
| | Sample_contact_address | 3107 Rampart Rd
| | Sample_contact_city | Fort Collins
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80523
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1017nnn/GSM1017650/suppl/GSM1017650_H2.CEL.gz
| | Sample_series_id | GSE41459
| | Sample_data_row_count | 54675
| | |
|
GSM1017651 | GPL570 |
|
trophoblast_shRNA_3
|
ACH-3P cells
|
cell line: ACH-3P cells
treatment: shRNA
|
|
| Sample_geo_accession | GSM1017651
| | Sample_status | Public on Oct 11 2012
| | Sample_submission_date | Oct 10 2012
| | Sample_last_update_date | Oct 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ACH-3P cells were infected with lentivirus expressing no shRNA (control) or shRNA to target PRR15 mRNA for degradation (shRNA) at an MOI~100, with three biological replicates per treatment.
| | Sample_growth_protocol_ch1 | First trimester human trophoblast cells (ACH-3P) were grown in plastic cell culture dishes at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy Mini Kit (Qiagen) was used to extract RNA from cell pellets according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA were prepared from 500 ng RNA according to the standard Affymetrix protocol (Affymetrix User Manual, GeneChip 3' IVT Express Kit)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of aRNA were hybridized for 16 hours at 40C to GeneChip Human Genome U133 Plus 2.0 Arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip 3000 7G Scanner using GCOS version 1.4 software and system controls.
| | Sample_data_processing | The data were analyzed in ArrayTrack and normalized to the geometric mean intensities of each chip. Groups were compared by Welch's T-test on log base 2 expression values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katherine,,Gates
| | Sample_contact_email | kcmcb@colostate.edu
| | Sample_contact_department | Biomedical Sciences
| | Sample_contact_institute | Colorado State University
| | Sample_contact_address | 3107 Rampart Rd
| | Sample_contact_city | Fort Collins
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80523
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1017nnn/GSM1017651/suppl/GSM1017651_H3.CEL.gz
| | Sample_series_id | GSE41459
| | 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 |
|
|
