Search results for the GEO ID: GSE21833  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM543406 | GPL1261 |
|
Stomach_control_rep1
|
Gastric mucosa
|
tissue: gastric mucosa
infection: uninfected
|
n/a
|
| Sample_geo_accession | GSM543406
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543406/suppl/GSM543406_Bassa_1_1_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543407 | GPL1261 |
|
Stomach_control_rep2
|
Gastric mucosa
|
tissue: gastric mucosa
infection: uninfected
|
n/a
|
| Sample_geo_accession | GSM543407
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543407/suppl/GSM543407_Bassa_2_3_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543408 | GPL1261 |
|
Stomach_control_rep3
|
Gastric mucosa
|
tissue: gastric mucosa
infection: uninfected
|
n/a
|
| Sample_geo_accession | GSM543408
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543408/suppl/GSM543408_Bassa_9_14_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543409 | GPL1261 |
|
Stomach_Hpmutant_rep1
|
Gastric mucosa
|
tissue: gastric mucosa
infection: H. pylori strain 99-305 (mutant, HpcagA-)
|
n/a
|
| Sample_geo_accession | GSM543409
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543409/suppl/GSM543409_Bassa_3_7_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543410 | GPL1261 |
|
Stomach_Hpmutant_rep2
|
Gastric mucosa
|
tissue: gastric mucosa
infection: H. pylori strain 99-305 (mutant, HpcagA-)
|
n/a
|
| Sample_geo_accession | GSM543410
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543410/suppl/GSM543410_Bassa_4_8_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543411 | GPL1261 |
|
Stomach_Hpmutant_rep3
|
Gastric mucosa
|
tissue: gastric mucosa
infection: H. pylori strain 99-305 (mutant, HpcagA-)
|
n/a
|
| Sample_geo_accession | GSM543411
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543411/suppl/GSM543411_Bassa_8_9_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543412 | GPL1261 |
|
Stomach_HpWT_rep1
|
Gastric mucosa
|
tissue: gastric mucosa
infection: H. pylori strain 98-325 (wild-type, HpcagA+)
|
n/a
|
| Sample_geo_accession | GSM543412
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543412/suppl/GSM543412_Bassa_7_2_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543413 | GPL1261 |
|
Stomach_HpWT_rep2
|
Gastric mucosa
|
tissue: gastric mucosa
infection: H. pylori strain 98-325 (wild-type, HpcagA+)
|
n/a
|
| Sample_geo_accession | GSM543413
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543413/suppl/GSM543413_Bassa_5_11_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
|
GSM543414 | GPL1261 |
|
Stomach_HpWT_rep3
|
Gastric mucosa
|
tissue: gastric mucosa
infection: H. pylori strain 98-325 (wild-type, HpcagA+)
|
n/a
|
| Sample_geo_accession | GSM543414
| | Sample_status | Public on Nov 13 2010
| | Sample_submission_date | May 14 2010
| | Sample_last_update_date | May 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to the standard target labeling protocols.
| | Sample_hyb_protocol | The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_scan_protocol | The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Saroj,K,Mohapatra
| | Sample_contact_email | skmohapatra@yahoo.com
| | Sample_contact_department | VBI
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | washington Street
| | Sample_contact_city | blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24060
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543414/suppl/GSM543414_Bassa_6_12_stomach.CEL.gz
| | Sample_series_id | GSE21833
| | Sample_data_row_count | 45101
| | |
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