Search results for the GEO ID: GSE40716  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM999639 | GPL1261 |
|
Female PGCLC, day 3, biological rep1
|
Female PGC-like cell, day 3
|
strain/background: C57BL/6
transgene: BVSC
Sex: female
cell type: primordial germ cell-like cell (PGCLC), day 3
|
PGCLCd3_EA1013_01
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999639
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999639/suppl/GSM999639_EA1013_01.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999640 | GPL1261 |
|
Female PGCLC, day 3, biological rep2
|
Female PGC-like cell, day 3
|
strain/background: C57BL/6
transgene: BVSC
Sex: female
cell type: primordial germ cell-like cell (PGCLC), day 3
|
PGCLCd3_EA1013_05
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999640
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999640/suppl/GSM999640_EA1013_05.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999641 | GPL1261 |
|
Female PGCLC, day 6, biological rep1
|
Female PGC-like cell, day 6
|
strain/background: C57BL/6
transgene: BVSC
Sex: female
cell type: primordial germ cell-like cell (PGCLC), day 6
|
PGCLCd6F_EA1013_02
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999641
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999641/suppl/GSM999641_EA1013_02.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999642 | GPL1261 |
|
Female PGCLC, day 6, biological rep2
|
Female PGC-like cell, day 6
|
strain/background: C57BL/6
transgene: BVSC
Sex: female
cell type: primordial germ cell-like cell (PGCLC), day 6
|
PGCLCd6F_EA1013_06
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999642
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999642/suppl/GSM999642_EA1013_06.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999643 | GPL1261 |
|
Female PGCLC, day 3 agg-day 6, biological rep1
|
Female PGC-like cell, day 3-agg day 6
|
strain/background: C57BL/6
transgene: BVSC
Sex: female
cell type: primordial germ cell-like cell (PGCLC), day 3-agg day 6
|
PGCLCd3ag6_EA1013_03
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999643
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999643/suppl/GSM999643_EA1013_03.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999644 | GPL1261 |
|
Female PGCLC, day 3 agg-day 6, biological rep2
|
Female PGC-like cell, day 3-agg day 6
|
strain/background: C57BL/6
transgene: BVSC
Sex: female
cell type: primordial germ cell-like cell (PGCLC), day 3-agg day 6
|
PGCLCd3ag6_EA1013_07
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999644
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999644/suppl/GSM999644_EA1013_07.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999645 | GPL1261 |
|
Female PGC, embryonic day 12.5, biological rep1
|
Female primordial germ cell (PGC), embryonic day 12.5
|
strain/background: mix (C57BL/6, BDF1)
transgene: stella-EGFP
Sex: female
age: embryonic day 12.5
cell type: primordial germ cell (PGC)
|
PGC12F_EA1013_04
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999645
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999645/suppl/GSM999645_EA1013_04.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999646 | GPL1261 |
|
Female PGC, embryonic day 12.5, biological rep2
|
Female primordial germ cell (PGC), embryonic day 12.5
|
strain/background: mix (C57BL/6, BDF1)
transgene: stella-EGFP
Sex: female
age: embryonic day 12.5
cell type: primordial germ cell (PGC)
|
PGC12F_EA1013_08
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999646
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999646/suppl/GSM999646_EA1013_08.CEL.gz
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999647 | GPL1261 |
|
PGC, embryonic day 9.5, biological rep1
|
Primordial germ cell (PGC), embryonic day 9.5
|
strain/background: mix (C57BL/6, BDF1)
transgene: stella-EGFP
Sex: unknown
age: embryonic day 9.5
cell type: primordial germ cell (PGC)
|
PGC9_EA0831_07
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999647
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999647/suppl/GSM999647_EA0831_07.CEL.gz
| | Sample_relation | Reanalysis of: GSM744103
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999648 | GPL1261 |
|
PGC, embryonic day 9.5, biological rep2
|
Primordial germ cell (PGC), embryonic day 9.5
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strain/background: mix (C57BL/6, BDF1)
transgene: stella-EGFP
Sex: unknown
age: embryonic day 9.5
cell type: primordial germ cell (PGC)
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PGC9_EA0842_07
PGCs were obtained from mating of stella-EGFP reporter male (C57BL/6) and wild-type female (BDF1) mice.
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
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| Sample_geo_accession | GSM999648
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999648/suppl/GSM999648_EA0842_07.CEL.gz
| | Sample_relation | Reanalysis of: GSM744104
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
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GSM999649 | GPL1261 |
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Male PGCLC, day 6, biological rep1
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Male PGC-like cell, day 6
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strain/background: C57BL/6
transgene: BVSC
Sex: male
cell type: primordial germ cell-like cell (PGCLC), day 6
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PGCLCd6M_EA0831_06
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999649
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999649/suppl/GSM999649_EA0831_06.CEL.gz
| | Sample_relation | Reanalysis of: GSM744101
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
| | |
|
GSM999650 | GPL1261 |
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Male PGCLC, day 6, biological rep2
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Male PGC-like cell, day 6
|
strain/background: C57BL/6
transgene: BVSC
Sex: male
cell type: primordial germ cell-like cell (PGCLC), day 6
|
PGCLCd6M_EA0842_06
cDNA, PCR amplified from 5ng total RNA (equivalent to 500 cells).
|
| Sample_geo_accession | GSM999650
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Sep 09 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | PGCLCs and PGCs were purified with FACS based on reporter fluorescence.
| | Sample_growth_protocol_ch1 | PGCLCs were induced from ES cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).
| | Sample_hyb_protocol | Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).
| | Sample_scan_protocol | The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kazuki,,Kurimoto
| | Sample_contact_email | kurimoto@anat2.med.kyoto-u.ac.jp
| | Sample_contact_laboratory | Department of anatomy and cell biology
| | Sample_contact_department | Graduate school of medicine
| | Sample_contact_institute | Kyoto University
| | Sample_contact_address | Yoshida-Konoe-cho, Sakyo-ku
| | Sample_contact_city | Kyoto
| | Sample_contact_zip/postal_code | 606-8501
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM999nnn/GSM999650/suppl/GSM999650_EA0842_06.CEL.gz
| | Sample_relation | Reanalysis of: GSM744102
| | Sample_series_id | GSE40716
| | Sample_data_row_count | 45101
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