Search results for the GEO ID: GSE28437  |
(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 |
GSM703047 | GPL1261 |
|
γδ IEL, conventional, rep 1
|
pooled small intestinal γδ IEL from conventionally-raised mice
|
mouse strain: C57BL/6J
tissue: small intestine
cell type: γδ intraepithelial lymphocytes (IEL)
age: >8 weeks
intestinal colonization: conventionally-colonized
|
gene expression data from purified small intestinal γδ IEL (flow cytometry-purified IELs)
|
| Sample_geo_accession | GSM703047
| | Sample_status | Public on Apr 06 2011
| | Sample_submission_date | Apr 06 2011
| | Sample_last_update_date | Apr 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Total IEL were isolated from mouse small intestines. γδ IEL were labeled with PE-labeled anti-TCRd. γδ IEL were purified by sorting on a BD moFlo cell sorter.
| | Sample_growth_protocol_ch1 | Mice were raised under germ-free conditions (microorganism-free) or conventional conditions (having intestinal bacteria).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Arcturus PicoPure RNA isolation kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | mRNAs were amplified using the Arcturus RiboAmp HS kit. Biotinylated cRNAs were generated by substituting the Enzo T7 BioArray Transcript kit during the last step.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lora,V,Hooper
| | Sample_contact_email | Lora.Hooper@UTSouthwestern.edu
| | Sample_contact_phone | 214-648-7306
| | Sample_contact_fax | 214-648-7331
| | Sample_contact_department | Center for Immunology
| | Sample_contact_institute | The University of Texas Southwestern Medical Center at Dallas
| | Sample_contact_address | 5323 Harry Hines Blvd.
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390-9093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM703nnn/GSM703047/suppl/GSM703047.CEL.gz
| | Sample_series_id | GSE28437
| | Sample_data_row_count | 45101
| | |
|
GSM703048 | GPL1261 |
|
γδ IEL, conventional, rep 2
|
pooled small intestinal γδ IEL from conventionally-raised mice
|
mouse strain: C57BL/6J
tissue: small intestine
cell type: γδ intraepithelial lymphocytes (IEL)
age: >8 weeks
intestinal colonization: conventionally-colonized
|
gene expression data from purified small intestinal γδ IEL (flow cytometry-purified IELs)
|
| Sample_geo_accession | GSM703048
| | Sample_status | Public on Apr 06 2011
| | Sample_submission_date | Apr 06 2011
| | Sample_last_update_date | Apr 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Total IEL were isolated from mouse small intestines. γδ IEL were labeled with PE-labeled anti-TCRd. γδ IEL were purified by sorting on a BD moFlo cell sorter.
| | Sample_growth_protocol_ch1 | Mice were raised under germ-free conditions (microorganism-free) or conventional conditions (having intestinal bacteria).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Arcturus PicoPure RNA isolation kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | mRNAs were amplified using the Arcturus RiboAmp HS kit. Biotinylated cRNAs were generated by substituting the Enzo T7 BioArray Transcript kit during the last step.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lora,V,Hooper
| | Sample_contact_email | Lora.Hooper@UTSouthwestern.edu
| | Sample_contact_phone | 214-648-7306
| | Sample_contact_fax | 214-648-7331
| | Sample_contact_department | Center for Immunology
| | Sample_contact_institute | The University of Texas Southwestern Medical Center at Dallas
| | Sample_contact_address | 5323 Harry Hines Blvd.
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390-9093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM703nnn/GSM703048/suppl/GSM703048.CEL.gz
| | Sample_series_id | GSE28437
| | Sample_data_row_count | 45101
| | |
|
GSM703049 | GPL1261 |
|
γδ IEL, germ-free, rep 1
|
pooled small intestinal γδ IEL from germ-free mice
|
mouse strain: C57BL/6J
tissue: small intestine
cell type: γδ intraepithelial lymphocytes (IEL)
age: >8 weeks
intestinal colonization: germ-free
|
gene expression data from purified small intestinal γδ IEL (flow cytometry-purified IELs)
|
| Sample_geo_accession | GSM703049
| | Sample_status | Public on Apr 06 2011
| | Sample_submission_date | Apr 06 2011
| | Sample_last_update_date | Apr 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Total IEL were isolated from mouse small intestines. γδ IEL were labeled with PE-labeled anti-TCRd. γδ IEL were purified by sorting on a BD moFlo cell sorter.
| | Sample_growth_protocol_ch1 | Mice were raised under germ-free conditions (microorganism-free) or conventional conditions (having intestinal bacteria).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Arcturus PicoPure RNA isolation kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | mRNAs were amplified using the Arcturus RiboAmp HS kit. Biotinylated cRNAs were generated by substituting the Enzo T7 BioArray Transcript kit during the last step.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lora,V,Hooper
| | Sample_contact_email | Lora.Hooper@UTSouthwestern.edu
| | Sample_contact_phone | 214-648-7306
| | Sample_contact_fax | 214-648-7331
| | Sample_contact_department | Center for Immunology
| | Sample_contact_institute | The University of Texas Southwestern Medical Center at Dallas
| | Sample_contact_address | 5323 Harry Hines Blvd.
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390-9093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM703nnn/GSM703049/suppl/GSM703049.CEL.gz
| | Sample_series_id | GSE28437
| | Sample_data_row_count | 45101
| | |
|
GSM703050 | GPL1261 |
|
γδ IEL, germ-free, rep 2
|
pooled small intestinal γδ IEL from germ-free mice
|
mouse strain: C57BL/6J
tissue: small intestine
cell type: γδ intraepithelial lymphocytes (IEL)
age: >8 weeks
intestinal colonization: germ-free
|
gene expression data from purified small intestinal γδ IEL (flow cytometry-purified IELs)
|
| Sample_geo_accession | GSM703050
| | Sample_status | Public on Apr 06 2011
| | Sample_submission_date | Apr 06 2011
| | Sample_last_update_date | Apr 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Total IEL were isolated from mouse small intestines. γδ IEL were labeled with PE-labeled anti-TCRd. γδ IEL were purified by sorting on a BD moFlo cell sorter.
| | Sample_growth_protocol_ch1 | Mice were raised under germ-free conditions (microorganism-free) or conventional conditions (having intestinal bacteria).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Arcturus PicoPure RNA isolation kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | mRNAs were amplified using the Arcturus RiboAmp HS kit. Biotinylated cRNAs were generated by substituting the Enzo T7 BioArray Transcript kit during the last step.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lora,V,Hooper
| | Sample_contact_email | Lora.Hooper@UTSouthwestern.edu
| | Sample_contact_phone | 214-648-7306
| | Sample_contact_fax | 214-648-7331
| | Sample_contact_department | Center for Immunology
| | Sample_contact_institute | The University of Texas Southwestern Medical Center at Dallas
| | Sample_contact_address | 5323 Harry Hines Blvd.
| | Sample_contact_city | Dallas
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 75390-9093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM703nnn/GSM703050/suppl/GSM703050.CEL.gz
| | Sample_series_id | GSE28437
| | 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 |
|
|
