Search results for the GEO ID: GSE16486  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM414369 | GPL1261 |
|
m.Gas: sham surgery, placebo pellet implantation; biological rep1
|
m.Gas: sham surgery, placebo pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: sham
testosterone supplementation: placebo pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; sham surgery, placebo pellet implantation
|
| Sample_geo_accession | GSM414369
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414369/suppl/GSM414369.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414370 | GPL1261 |
|
m.Gas: sham surgery, placebo pellet implantation; biological rep2
|
m.Gas: sham surgery, placebo pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: sham
testosterone supplementation: placebo pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; sham surgery, placebo pellet implantation
|
| Sample_geo_accession | GSM414370
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414370/suppl/GSM414370.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414371 | GPL1261 |
|
m.Gas: sham surgery, placebo pellet implantation; biological rep3
|
m.Gas: sham surgery, placebo pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: sham
testosterone supplementation: placebo pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; sham surgery, placebo pellet implantation
|
| Sample_geo_accession | GSM414371
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414371/suppl/GSM414371.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414372 | GPL1261 |
|
m.Gas: castration, placebo pellet implantation; biological rep1
|
m.Gas: castration, placebo pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: castration
testosterone supplementation: placebo pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, placebo pellet implantation
|
| Sample_geo_accession | GSM414372
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414372/suppl/GSM414372.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414373 | GPL1261 |
|
m.Gas: castration, placebo pellet implantation; biological rep2
|
m.Gas: castration, placebo pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: castration
testosterone supplementation: placebo pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, placebo pellet implantation
|
| Sample_geo_accession | GSM414373
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414373/suppl/GSM414373.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414374 | GPL1261 |
|
m.Gas: castration, placebo pellet implantation; biological rep3
|
m.Gas: castration, placebo pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: castration
testosterone supplementation: placebo pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, placebo pellet implantation
|
| Sample_geo_accession | GSM414374
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414374/suppl/GSM414374.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414375 | GPL1261 |
|
m.Gas: castration, 2.5 mg testosterone pellet implantation; biological rep1
|
m.Gas: castration, 2.5 mg testosterone pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: castration
testosterone supplementation: 2.5 mg testosterone pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, 2.5 mg testosterone pellet implantation
|
| Sample_geo_accession | GSM414375
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414375/suppl/GSM414375.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414376 | GPL1261 |
|
m.Gas: castration, 2.5 mg testosterone pellet implantation; biological rep2
|
m.Gas: castration, 2.5 mg testosterone pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: castration
testosterone supplementation: 2.5 mg testosterone pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, 2.5 mg testosterone pellet implantation
|
| Sample_geo_accession | GSM414376
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414376/suppl/GSM414376.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
|
GSM414377 | GPL1261 |
|
m.Gas: castration, 2.5 mg testosterone pellet implantation; biological rep3
|
m.Gas: castration, 2.5 mg testosterone pellet implantation
|
tissue: gastrocnemius muscle (m.Gas) in young adult CD-1 mice
castration surgery: castration
testosterone supplementation: 2.5 mg testosterone pellet implantation
|
Gene expression data from gastrocnemius muscle (m.Gas) in young adult mice; castration, 2.5 mg testosterone pellet implantation
|
| Sample_geo_accession | GSM414377
| | Sample_status | Public on Jun 08 2009
| | Sample_submission_date | Jun 08 2009
| | Sample_last_update_date | Jun 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 = Mice were randomized into three treatment groups, referred to as Sham, Castration, and Testosterone (N | 12/group, total 36 mice). Mice first underwent castration or sham surgery (Sham). Castrated animals were then implanted, sub-cutaneously, with either placebo (Castration) or testosterone (2.5 mg pellet, 60-day release, Innovative Research of America, Sarasota, FL) (Testosterone). Sham animals were implanted with placebo pellets. Pellet implantation was performed immediately after surgery. After 14-days, blood was sampled from the carotid artery of anesthetized animals, and the non-fasted animals were sacrificed by decapitation. The gastrocnemius (m.Gas) and levator ani (m.L ani) muscles were carefully dissected, trimmed of fat and non-muscle connective tissue, weighed and stored in RNAlater until being processed for RNA, or immediately frozen on dry ice and stored at -80oC for Western blotting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction and purification of total RNA with Qiagen Rneasy Minelute Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were normalized using Robust Multichip Average (RMA) algorithms, which consist of background adjustment, quantile normalization, and a robust probe-set summary of the log-transformed probe-level data by median polishing; executed using the R statistical environment and the BioConductor package. The balanced design of this study enabled the use of a 1-way ANOVA, which was used to statistically determine which of the >34,000 genes (>45,000 probes) were differentially expressed between groups (34). The three pair-wise comparisons were: Castration vs. Sham (castration (C) effect); Testosterone vs. Castration (testosterone replacement (T) effect); and Testosterone vs. Sham (overall effects). The 212 probes with a P ≤ 0.01 in at least one of the two primary pair-wise comparisons were grouped into 6 distinct expression profile categories: (1) increased by castration and decreased by testosterone (C↑T↓) (negative regulation by testosterone), (2) decreased by castration and increased by testosterone (C↓T↑) (positive regulation by testosterone), increased by castration only (C↑), decreased by castration only (C↓), increased by testosterone only (T↑), and decreased by testosterone only (T↓). Grouping of the 212 differentially expressed probes was conducted using P < 0.05 for the appropriate pair-wise comparisons.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Harvey,J,Armbrecht
| | Sample_contact_email | hjarmbrec@aol.com
| | Sample_contact_phone | (314) 894-6511
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology
| | Sample_contact_institute | St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine
| | Sample_contact_address | #1 Jefferson Barracks Drive
| | Sample_contact_city | St. Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM414nnn/GSM414377/suppl/GSM414377.CEL.gz
| | Sample_series_id | GSE16486
| | Sample_data_row_count | 45101
| | |
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