Search results for the GEO ID: GSE37655  |
(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 |
GSM925103 | GPL1261 |
|
WT
|
wild type mouse
|
genotype/variation: wild type
age: 16 weeks old
tissue: normal lung tissue
|
|
| Sample_geo_accession | GSM925103
| | Sample_status | Public on May 01 2012
| | Sample_submission_date | Apr 30 2012
| | Sample_last_update_date | May 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Fresh lungs were harvested into RNA later (Ambion).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from lung homogenates by using TRIzol (Invitrogen). RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.
| | Sample_hyb_protocol | Four replicates of cDNA sample were hybridized to Affymetrix Mouse Genome Mo430 2.0 GeneChips, using Affymetrix GeneChip Hybridization, Wash, and Stain Kit following manufacturer’s protocol.
| | Sample_scan_protocol | GeneChips were scanned on Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix AGCC software.
| | Sample_data_processing | Analysis was performed by using standard Partek Genomics Gene expression analysis workflow as well as using R package PUMA.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Qun,,Jiang
| | Sample_contact_email | jiangq2@mail.nih.gov
| | Sample_contact_laboratory | Jiang
| | Sample_contact_institute | NCI-Frederick
| | Sample_contact_address | 1050 boyles street
| | Sample_contact_city | frederick
| | Sample_contact_state | Maryland
| | Sample_contact_zip/postal_code | 21702
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM925nnn/GSM925103/suppl/GSM925103_WT_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM925nnn/GSM925103/suppl/GSM925103_WT_Mouse430_2.mas5.CHP.gz
| | Sample_series_id | GSE37655
| | Sample_data_row_count | 45101
| | |
|
GSM925104 | GPL1261 |
|
KA2
|
KA/KA-Lori-Ikkα mouse
|
genotype/variation: KA/KA-Lori-Ikkα
age: 16 weeks old
tissue: mixture tissue of lung SCC and tumor neighbor
|
|
| Sample_geo_accession | GSM925104
| | Sample_status | Public on May 01 2012
| | Sample_submission_date | Apr 30 2012
| | Sample_last_update_date | May 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Fresh lungs were harvested into RNA later (Ambion).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from lung homogenates by using TRIzol (Invitrogen). RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.
| | Sample_hyb_protocol | Four replicates of cDNA sample were hybridized to Affymetrix Mouse Genome Mo430 2.0 GeneChips, using Affymetrix GeneChip Hybridization, Wash, and Stain Kit following manufacturer’s protocol.
| | Sample_scan_protocol | GeneChips were scanned on Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix AGCC software.
| | Sample_data_processing | Analysis was performed by using standard Partek Genomics Gene expression analysis workflow as well as using R package PUMA.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Qun,,Jiang
| | Sample_contact_email | jiangq2@mail.nih.gov
| | Sample_contact_laboratory | Jiang
| | Sample_contact_institute | NCI-Frederick
| | Sample_contact_address | 1050 boyles street
| | Sample_contact_city | frederick
| | Sample_contact_state | Maryland
| | Sample_contact_zip/postal_code | 21702
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM925nnn/GSM925104/suppl/GSM925104_KA2_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM925nnn/GSM925104/suppl/GSM925104_KA2_Mouse430_2.mas5.CHP.gz
| | Sample_series_id | GSE37655
| | Sample_data_row_count | 45101
| | |
|
GSM925105 | GPL1261 |
|
KAT
|
KA/KA-Lori-Ikkα mouse with macrophage depletion treatment
|
genotype/variation: KA/KA-Lori-Ikkα
age: 16 weeks old
tissue: lung tissue with some inflammation and no tumor observed
|
|
| Sample_geo_accession | GSM925105
| | Sample_status | Public on May 01 2012
| | Sample_submission_date | Apr 30 2012
| | Sample_last_update_date | May 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Fresh lungs were harvested into RNA later (Ambion).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from lung homogenates by using TRIzol (Invitrogen). RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.
| | Sample_hyb_protocol | Four replicates of cDNA sample were hybridized to Affymetrix Mouse Genome Mo430 2.0 GeneChips, using Affymetrix GeneChip Hybridization, Wash, and Stain Kit following manufacturer’s protocol.
| | Sample_scan_protocol | GeneChips were scanned on Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix AGCC software.
| | Sample_data_processing | Analysis was performed by using standard Partek Genomics Gene expression analysis workflow as well as using R package PUMA.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Qun,,Jiang
| | Sample_contact_email | jiangq2@mail.nih.gov
| | Sample_contact_laboratory | Jiang
| | Sample_contact_institute | NCI-Frederick
| | Sample_contact_address | 1050 boyles street
| | Sample_contact_city | frederick
| | Sample_contact_state | Maryland
| | Sample_contact_zip/postal_code | 21702
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM925nnn/GSM925105/suppl/GSM925105_KAT_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM925nnn/GSM925105/suppl/GSM925105_KAT_Mouse430_2.mas5.CHP.gz
| | Sample_series_id | GSE37655
| | Sample_data_row_count | 45101
| | |
|
| |
| |
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 |
|
|
