Result

Search results for the GEO ID: GSE23119

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM573579

GPL1261

Normal spermatogonia control, rep1

Normal spermatogonia

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: normal diet

Gene expression data from normal spermatogonia.

Sample_geo_accession	GSM573579
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573579/suppl/GSM573579.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573579/suppl/GSM573579.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573580

GPL1261

Normal spermatogonia control, rep2

Normal spermatogonia

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: normal diet

Gene expression data from normal spermatogonia.

Sample_geo_accession	GSM573580
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573580/suppl/GSM573580.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573580/suppl/GSM573580.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573581

GPL1261

Normal spermatogonia control, rep3

Normal spermatogonia

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: normal diet

Gene expression data from normal spermatogonia.

Sample_geo_accession	GSM573581
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573581/suppl/GSM573581.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573581/suppl/GSM573581.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573582

GPL1261

VAD spermatogonia at 18 weeks, rep1

VAD spermatogonia at 18 weeks

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: vitamin A-deficient diet treatment time: 18 weeks

Gene expression data from VAD spermatogonia at 18 weeks.

Sample_geo_accession	GSM573582
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573582/suppl/GSM573582.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573582/suppl/GSM573582.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573583

GPL1261

VAD spermatogonia at 18 weeks, rep2

VAD spermatogonia at 18 weeks

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: vitamin A-deficient diet treatment time: 18 weeks

Gene expression data from VAD spermatogonia at 18 weeks.

Sample_geo_accession	GSM573583
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573583/suppl/GSM573583.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573583/suppl/GSM573583.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573584

GPL1261

VAD spermatogonia at 18 weeks, rep3

VAD spermatogonia at 18 weeks

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: vitamin A-deficient diet treatment time: 18 weeks

Gene expression data from VAD spermatogonia at 18 weeks.

Sample_geo_accession	GSM573584
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573584/suppl/GSM573584.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573584/suppl/GSM573584.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573585

GPL1261

VAD spermatogonia at 25 weeks, rep1

VAD spermatogonia at 25 weeks

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: vitamin A-deficient diet treatment time: 25 weeks

Gene expression data from VAD spermatogonia at 25 weeks.

Sample_geo_accession	GSM573585
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573585/suppl/GSM573585.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573585/suppl/GSM573585.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573586

GPL1261

VAD spermatogonia at 25 weeks, rep2

VAD spermatogonia at 25 weeks

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: vitamin A-deficient diet treatment time: 25 weeks

Gene expression data from VAD spermatogonia at 25 weeks.

Sample_geo_accession	GSM573586
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573586/suppl/GSM573586.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573586/suppl/GSM573586.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

GSM573587

GPL1261

VAD spermatogonia at 25 weeks, rep3

VAD spermatogonia at 25 weeks

strain: Balb/C developmental stage: adult tissue: testes cell type: spermatogonia treatment: vitamin A-deficient diet treatment time: 25 weeks

Gene expression data from VAD spermatogonia at 25 weeks.

Sample_geo_accession	GSM573587
Sample_status	Public on Aug 03 2010
Sample_submission_date	Aug 02 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were fed a control or VAD diet. Spermatogonial stem cells were selected from animals at 18 and 25 weeks of VAD. The vitamin A status of the mice was determined by measurement of serum RBP levels using the Dual Mouse/Rat RBP4 EIA Kit.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Spermatogonia were isolated by the STATPUT procedure. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat-inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%.
Sample_extract_protocol_ch1
Sample_extract_protocol_ch1	Total RNA was extracted from the isolated germ cells using TRIzol Reagent and cleaned with RNeasy mini-columns.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle amplification protocol from 100ng total RNA.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix Scanner G3000 7G.
Sample_data_processing	Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	TIN-LAP,,LEE
Sample_contact_laboratory	Laboratory of Clincal Genomics
Sample_contact_department	NICHD
Sample_contact_institute	National Institutes of Health
Sample_contact_address	2C08 Building 49
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573587/suppl/GSM573587.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573587/suppl/GSM573587.CHP.gz
Sample_series_id	GSE23119
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes