Search results for the GEO ID: GSE27393  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM677390 | GPL1355 |
|
HIVTg_3mo_lung_replicate1
|
lung (right superior lobe) tissue RNA
|
strain: HIV Tg rat, Hsd:HIV-1 (F344)
gender: male
tissue: lung
age: 3 months
|
|
| Sample_geo_accession | GSM677390
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_growth_protocol_ch1 | All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
| | Sample_hyb_protocol | The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
| | Sample_scan_protocol | Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
| | Sample_data_processing | GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using 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 | GPL1355
| | Sample_contact_name | Amie,K,Lund
| | Sample_contact_email | alund@lrri.org
| | Sample_contact_phone | 505-348-9649
| | Sample_contact_fax | 505-348-9480
| | Sample_contact_department | Environmental and Cardiopulmonary Toxicology
| | Sample_contact_institute | Lovelace Respiratory Research Institute
| | Sample_contact_address | 2425 Ridgecrest Dr. SE
| | Sample_contact_city | Albquerque
| | Sample_contact_state | NM
| | Sample_contact_zip/postal_code | 87108
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677390/suppl/GSM677390.CEL.gz
| | Sample_series_id | GSE27393
| | Sample_data_row_count | 31099
| | |
|
GSM677391 | GPL1355 |
|
HIVTg_3mo_lung_replicate2
|
lung (right superior lobe) tissue RNA
|
strain: HIV Tg rat, Hsd:HIV-1 (F344)
gender: male
tissue: lung
age: 3 months
|
|
| Sample_geo_accession | GSM677391
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_growth_protocol_ch1 | All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
| | Sample_hyb_protocol | The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
| | Sample_scan_protocol | Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
| | Sample_data_processing | GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using 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 | GPL1355
| | Sample_contact_name | Amie,K,Lund
| | Sample_contact_email | alund@lrri.org
| | Sample_contact_phone | 505-348-9649
| | Sample_contact_fax | 505-348-9480
| | Sample_contact_department | Environmental and Cardiopulmonary Toxicology
| | Sample_contact_institute | Lovelace Respiratory Research Institute
| | Sample_contact_address | 2425 Ridgecrest Dr. SE
| | Sample_contact_city | Albquerque
| | Sample_contact_state | NM
| | Sample_contact_zip/postal_code | 87108
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677391/suppl/GSM677391.CEL.gz
| | Sample_series_id | GSE27393
| | Sample_data_row_count | 31099
| | |
|
GSM677392 | GPL1355 |
|
HIVTg_3mo_lung_replicate3
|
lung (right superior lobe) tissue RNA
|
strain: HIV Tg rat, Hsd:HIV-1 (F344)
gender: male
tissue: lung
age: 3 months
|
|
| Sample_geo_accession | GSM677392
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_growth_protocol_ch1 | All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
| | Sample_hyb_protocol | The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
| | Sample_scan_protocol | Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
| | Sample_data_processing | GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using 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 | GPL1355
| | Sample_contact_name | Amie,K,Lund
| | Sample_contact_email | alund@lrri.org
| | Sample_contact_phone | 505-348-9649
| | Sample_contact_fax | 505-348-9480
| | Sample_contact_department | Environmental and Cardiopulmonary Toxicology
| | Sample_contact_institute | Lovelace Respiratory Research Institute
| | Sample_contact_address | 2425 Ridgecrest Dr. SE
| | Sample_contact_city | Albquerque
| | Sample_contact_state | NM
| | Sample_contact_zip/postal_code | 87108
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677392/suppl/GSM677392.CEL.gz
| | Sample_series_id | GSE27393
| | Sample_data_row_count | 31099
| | |
|
GSM677393 | GPL1355 |
|
F344_3mo_lung_replicate1
|
lung (right superior lobe) tissue RNA
|
strain: F344
gender: male
tissue: lung
age: 3 months
|
|
| Sample_geo_accession | GSM677393
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_growth_protocol_ch1 | All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
| | Sample_hyb_protocol | The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
| | Sample_scan_protocol | Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
| | Sample_data_processing | GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using 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 | GPL1355
| | Sample_contact_name | Amie,K,Lund
| | Sample_contact_email | alund@lrri.org
| | Sample_contact_phone | 505-348-9649
| | Sample_contact_fax | 505-348-9480
| | Sample_contact_department | Environmental and Cardiopulmonary Toxicology
| | Sample_contact_institute | Lovelace Respiratory Research Institute
| | Sample_contact_address | 2425 Ridgecrest Dr. SE
| | Sample_contact_city | Albquerque
| | Sample_contact_state | NM
| | Sample_contact_zip/postal_code | 87108
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677393/suppl/GSM677393.CEL.gz
| | Sample_series_id | GSE27393
| | Sample_data_row_count | 31099
| | |
|
GSM677394 | GPL1355 |
|
F344_3mo_lung_replicate2
|
lung (right superior lobe) tissue RNA
|
strain: F344
gender: male
tissue: lung
age: 3 months
|
|
| Sample_geo_accession | GSM677394
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_growth_protocol_ch1 | All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
| | Sample_hyb_protocol | The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
| | Sample_scan_protocol | Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
| | Sample_data_processing | GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using 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 | GPL1355
| | Sample_contact_name | Amie,K,Lund
| | Sample_contact_email | alund@lrri.org
| | Sample_contact_phone | 505-348-9649
| | Sample_contact_fax | 505-348-9480
| | Sample_contact_department | Environmental and Cardiopulmonary Toxicology
| | Sample_contact_institute | Lovelace Respiratory Research Institute
| | Sample_contact_address | 2425 Ridgecrest Dr. SE
| | Sample_contact_city | Albquerque
| | Sample_contact_state | NM
| | Sample_contact_zip/postal_code | 87108
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677394/suppl/GSM677394.CEL.gz
| | Sample_series_id | GSE27393
| | Sample_data_row_count | 31099
| | |
|
GSM677395 | GPL1355 |
|
F344_3mo_lung_replicate 3
|
lung (right superior lobe) tissue RNA
|
strain: F344
gender: male
tissue: lung
age: 3 months
|
|
| Sample_geo_accession | GSM677395
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_growth_protocol_ch1 | All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity). Rats had access to chow and water ad libitum throughout the study period.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).
| | Sample_hyb_protocol | The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).
| | Sample_scan_protocol | Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software
| | Sample_data_processing | GeneSpringGX11.1 software (Agilent Technologies). The data were analyzed with MAS 5.0 using 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 | GPL1355
| | Sample_contact_name | Amie,K,Lund
| | Sample_contact_email | alund@lrri.org
| | Sample_contact_phone | 505-348-9649
| | Sample_contact_fax | 505-348-9480
| | Sample_contact_department | Environmental and Cardiopulmonary Toxicology
| | Sample_contact_institute | Lovelace Respiratory Research Institute
| | Sample_contact_address | 2425 Ridgecrest Dr. SE
| | Sample_contact_city | Albquerque
| | Sample_contact_state | NM
| | Sample_contact_zip/postal_code | 87108
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677395/suppl/GSM677395.CEL.gz
| | Sample_series_id | GSE27393
| | Sample_data_row_count | 31099
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