Search results for the GEO ID: GSE29485  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM729412 | GPL1261 |
|
Cbx2_KO_XX_1
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Cbx2_KO_XX
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729412
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729412/suppl/GSM729412.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729413 | GPL1261 |
|
Cbx2_KO_XX_2
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Cbx2_KO_XX
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729413
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729413/suppl/GSM729413.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729414 | GPL1261 |
|
Cbx2_KO_XX_3
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Cbx2_KO_XX
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729414
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729414/suppl/GSM729414.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729415 | GPL1261 |
|
Cbx2_KO_XY_1
|
Cbx2_KO_XY gonads at E11.5
|
genotype/variation: Cbx2_KO_XY
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729415
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729415/suppl/GSM729415.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729416 | GPL1261 |
|
Cbx2_KO_XY_2
|
Cbx2_KO_XY gonads at E11.5
|
genotype/variation: Cbx2_KO_XY
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729416
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729416/suppl/GSM729416.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729417 | GPL1261 |
|
Cbx2_KO_XY_3
|
Cbx2_KO_XY gonads at E11.5
|
genotype/variation: Cbx2_KO_XY
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729417
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729417/suppl/GSM729417.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729418 | GPL1261 |
|
Wildtype_XX_1
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Wildtype_XX
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729418
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729418/suppl/GSM729418.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729419 | GPL1261 |
|
Wildtype_XX_2
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Wildtype_XX
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729419
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729419/suppl/GSM729419.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729420 | GPL1261 |
|
Wildtype_XX_3
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Wildtype_XX
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729420
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729420/suppl/GSM729420.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729421 | GPL1261 |
|
Wildtype_XY_1
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Wildtype_XY
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729421
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729421/suppl/GSM729421.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729422 | GPL1261 |
|
Wildtype_XY_2
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Wildtype_XY
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729422
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729422/suppl/GSM729422.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
GSM729423 | GPL1261 |
|
Wildtype_XY_3
|
Cbx2_KO_XX gonads at E11.5
|
genotype/variation: Wildtype_XY
tissue: gonads
age: E11.5
|
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.
|
| Sample_geo_accession | GSM729423
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.
| | Sample_growth_protocol_ch1 | Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Yuko,,Katoh-Fukui
| | Sample_contact_email | yfukui@ncgg.go.jp
| | Sample_contact_institute | National Inastitute for Longevity Sciences
| | Sample_contact_address | 35genngo ,moriokamachi
| | Sample_contact_city | Oobu
| | Sample_contact_zip/postal_code | 4748511
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729423/suppl/GSM729423.CEL.gz
| | Sample_series_id | GSE29485
| | Sample_data_row_count | 45101
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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