Search results for the GEO ID: GSE15652  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM391678 | GPL1355 |
|
Rat SSC GDNF Control Rep1
|
Rat SSC + GDNF
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF Control Rep1
|
| Sample_geo_accession | GSM391678
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391678/suppl/GSM391678.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391678/suppl/GSM391678.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391679 | GPL1355 |
|
Rat SSC GDNF Control Rep2
|
Rat SSC + GDNF
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF Control Rep2
|
| Sample_geo_accession | GSM391679
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391679/suppl/GSM391679.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391679/suppl/GSM391679.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391680 | GPL1355 |
|
Rat SSC GDNF Control Rep3
|
Rat SSC + GDNF
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF Control Rep3
|
| Sample_geo_accession | GSM391680
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391680/suppl/GSM391680.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391680/suppl/GSM391680.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391681 | GPL1355 |
|
Rat SSC GDNF Withdrawal Rep1
|
Rat SSC GDNF Withdrawal
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF Withdrawal Rep1
|
| Sample_geo_accession | GSM391681
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391681/suppl/GSM391681.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391681/suppl/GSM391681.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391682 | GPL1355 |
|
Rat SSC GDNF Withdrawal Rep2
|
Rat SSC GDNF Withdrawal
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF Withdrawal Rep2
|
| Sample_geo_accession | GSM391682
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391682/suppl/GSM391682.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391682/suppl/GSM391682.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391683 | GPL1355 |
|
Rat SSC GDNF Withdrawal Rep3
|
Rat SSC GDNF Withdrawal
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF Withdrawal Rep3
|
| Sample_geo_accession | GSM391683
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391683/suppl/GSM391683.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391683/suppl/GSM391683.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391684 | GPL1355 |
|
Rat SSC GDNF 2hr Replacement Rep1
|
Rat SSC GDNF 2hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 2hr Replacement Rep1
|
| Sample_geo_accession | GSM391684
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391684/suppl/GSM391684.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391684/suppl/GSM391684.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391685 | GPL1355 |
|
Rat SSC GDNF 2hr Replacement Rep2
|
Rat SSC GDNF 2hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 2hr Replacement Rep2
|
| Sample_geo_accession | GSM391685
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391685/suppl/GSM391685.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391685/suppl/GSM391685.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391686 | GPL1355 |
|
Rat SSC GDNF 2hr Replacement Rep3
|
Rat SSC GDNF 2hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 2hr Replacement Rep3
|
| Sample_geo_accession | GSM391686
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391686/suppl/GSM391686.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391686/suppl/GSM391686.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391687 | GPL1355 |
|
Rat SSC GDNF 4hr Replacement Rep1
|
Rat SSC GDNF 4hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 4hr Replacement Rep1
|
| Sample_geo_accession | GSM391687
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391687/suppl/GSM391687.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391687/suppl/GSM391687.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391688 | GPL1355 |
|
Rat SSC GDNF 4hr Replacement Rep2
|
Rat SSC GDNF 4hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 4hr Replacement Rep2
|
| Sample_geo_accession | GSM391688
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391688/suppl/GSM391688.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391688/suppl/GSM391688.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391689 | GPL1355 |
|
Rat SSC GDNF 4hr Replacement Rep3
|
Rat SSC GDNF 4hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 4hr Replacement Rep3
|
| Sample_geo_accession | GSM391689
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391689/suppl/GSM391689.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391689/suppl/GSM391689.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391690 | GPL1355 |
|
Rat SSC GDNF 8hr Replacement Rep1
|
Rat SSC GDNF 8hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 8hr Replacement Rep1
|
| Sample_geo_accession | GSM391690
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391690/suppl/GSM391690.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391690/suppl/GSM391690.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391691 | GPL1355 |
|
Rat SSC GDNF 8hr Replacement Rep2
|
Rat SSC GDNF 8hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 8hr Replacement Rep2
|
| Sample_geo_accession | GSM391691
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391691/suppl/GSM391691.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391691/suppl/GSM391691.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
| | |
|
GSM391692 | GPL1355 |
|
Rat SSC GDNF 8hr Replacement Rep3
|
Rat SSC GDNF 8hr Replacement
|
cell type: Cultured spermatogonial stem cells
|
Rat SSC GDNF 8hr Replacement Rep3
|
| Sample_geo_accession | GSM391692
| | Sample_status | Public on Apr 14 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Cultured rat SSCs were subjected to 1 of 5 treatments. Each treatment was replicated 3 times with independent cultures. Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.
| | Sample_growth_protocol_ch1 | Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF. After 1 month of culture, which included self-renewal expansion, treatments were applied.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol + RNeasy Column
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
| | Sample_hyb_protocol | The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays. Each sample (n=15) was hybridized to its own array. Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.
| | Sample_scan_protocol = The average signal from two sequential scans was calculated for each microarray. For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes. The default values were provided by Affymetrix and were applied to all analysis parameters. For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed. The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector. Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau | 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.
| | Sample_data_processing | For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm. The newly generated probeset signal values were exported into GeneSpring (Agilent). Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis. The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed. In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets). This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation. To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets). Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jonathan,A,Schmidt
| | Sample_contact_email | andyschmidt26@hotmail.com
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 3850 Baltimore Avenue
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391692/suppl/GSM391692.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391692/suppl/GSM391692.CHP.gz
| | Sample_series_id | GSE15652
| | Sample_data_row_count | 31099
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