Search results for the GEO ID: GSE21806  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM543036 | GPL1355 |
|
sham control, biological rep 1
|
rat initial segment of epididymis, sham operation
|
time point: 0
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - sham control
|
| Sample_geo_accession | GSM543036
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543036/suppl/GSM543036.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543037 | GPL1355 |
|
sham control, biological rep 2
|
rat initial segment of epididymis, sham operation
|
time point: 0
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - sham control
|
| Sample_geo_accession | GSM543037
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543037/suppl/GSM543037.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543038 | GPL1355 |
|
sham control, biological rep 3
|
rat initial segment of epididymis, sham operation
|
time point: 0
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - sham control
|
| Sample_geo_accession | GSM543038
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543038/suppl/GSM543038.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543039 | GPL1355 |
|
sham control, biological rep 4
|
rat initial segment of epididymis, sham operation
|
time point: 0
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - sham control
|
| Sample_geo_accession | GSM543039
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543039/suppl/GSM543039.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543040 | GPL1355 |
|
6 hour EDL, biological rep 1
|
rat initial segment of epididymis, EDL operation
|
time point: 6h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 6 hours EDL
|
| Sample_geo_accession | GSM543040
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543040/suppl/GSM543040.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543041 | GPL1355 |
|
6 hour EDL, biological rep 2
|
rat initial segment of epididymis, EDL operation
|
time point: 6h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 6 hours EDL
|
| Sample_geo_accession | GSM543041
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543041/suppl/GSM543041.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543042 | GPL1355 |
|
6 hour EDL, biological rep 3
|
rat initial segment of epididymis, EDL operation
|
time point: 6h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 6 hours EDL
|
| Sample_geo_accession | GSM543042
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543042/suppl/GSM543042.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543043 | GPL1355 |
|
6 hour EDL, biological rep 4
|
rat initial segment of epididymis, EDL operation
|
time point: 6h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 6 hours EDL
|
| Sample_geo_accession | GSM543043
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543043/suppl/GSM543043.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543044 | GPL1355 |
|
12 hour EDL, biological rep 1
|
rat initial segment of epididymis, EDL operation
|
time point: 12h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 12 hours EDL
|
| Sample_geo_accession | GSM543044
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543044/suppl/GSM543044.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543045 | GPL1355 |
|
12 hour EDL, biological rep 2
|
rat initial segment of epididymis, EDL operation
|
time point: 12h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 12 hours EDL
|
| Sample_geo_accession | GSM543045
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543045/suppl/GSM543045.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543046 | GPL1355 |
|
12 hour EDL, biological rep 3
|
rat initial segment of epididymis, EDL operation
|
time point: 12h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 12 hours EDL
|
| Sample_geo_accession | GSM543046
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543046/suppl/GSM543046.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543047 | GPL1355 |
|
12 hour EDL, biological rep 4
|
rat initial segment of epididymis, EDL operation
|
time point: 12h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 12 hours EDL
|
| Sample_geo_accession | GSM543047
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543047/suppl/GSM543047.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543048 | GPL1355 |
|
18 hour EDL, biological rep 1
|
rat initial segment of epididymis, EDL operation
|
time point: 18h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 18 hours EDL
|
| Sample_geo_accession | GSM543048
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543048/suppl/GSM543048.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543049 | GPL1355 |
|
18 hour EDL, biological rep 2
|
rat initial segment of epididymis, EDL operation
|
time point: 18h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 18 hours EDL
|
| Sample_geo_accession | GSM543049
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543049/suppl/GSM543049.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543050 | GPL1355 |
|
18 hour EDL, biological rep 3
|
rat initial segment of epididymis, EDL operation
|
time point: 18h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 18 hours EDL
|
| Sample_geo_accession | GSM543050
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543050/suppl/GSM543050.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
| | |
|
GSM543051 | GPL1355 |
|
18 hour EDL, biological rep 4
|
rat initial segment of epididymis, EDL operation
|
time point: 18h
gender: male
strain: Sprague-Dawley
tissue: initial segment of epididymis
age: adult
|
Gene expression data from adult male rat epididymis - 18 hours EDL
|
| Sample_geo_accession | GSM543051
| | Sample_status | Public on Mar 11 2011
| | Sample_submission_date | May 13 2010
| | Sample_last_update_date | Mar 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal. After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.
| | Sample_growth_protocol_ch1 | Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.
| | Sample_hyb_protocol | Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.
| | Sample_scan_protocol | The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).
| | Sample_data_processing | Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2. Analyses were performed in R release 2.9 and BioConductor release 2.4
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Michael,Bruce,Black
| | Sample_contact_email | mblack@thehamner.org
| | Sample_contact_phone | (919) 558-1200
| | Sample_contact_laboratory | Center for Genomic Biology and Bioinformatics
| | Sample_contact_department | Chemical Safety Sciences
| | Sample_contact_institute | The Hamner Institutes for Health Sciences
| | Sample_contact_address | 6 Davis Dr., P.O. Box 12137
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | N.C.
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM543nnn/GSM543051/suppl/GSM543051.CEL.gz
| | Sample_series_id | GSE21806
| | Sample_data_row_count | 31099
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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