Result

Search results for the GEO ID: GSE34002

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GSM840281

GPL1261

DKK1-treated ESC-RPCs, biological rep1

DKK1-treated ESC-RPCs

cell type: ESC-derived retinal progenitor cells treatment: DKK1 parental cell line: ESC-RPCs were differentiated from 46C ES cell line, which was generated by gene targeting in E14Tg2a.IV ES cells

Gene expression data from DKK-treated ESC-RPCs

Sample_geo_accession	GSM840281
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840281/suppl/GSM840281_BH11150-2_D1_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840282

GPL1261

DKK1-treated ESC-RPCs, biological rep2

DKK1-treated ESC-RPCs

cell type: ESC-derived retinal progenitor cells treatment: DKK1 parental cell line: ESC-RPCs were differentiated from 46C ES cell line, which was generated by gene targeting in E14Tg2a.IV ES cells

Gene expression data from DKK-treated ESC-RPCs

Sample_geo_accession	GSM840282
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840282/suppl/GSM840282_BH11150-2_D2_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840283

GPL1261

DKK1-treated ESC-RPCs, biological rep3

DKK1-treated ESC-RPCs

cell type: ESC-derived retinal progenitor cells treatment: DKK1 parental cell line: ESC-RPCs were differentiated from 46C ES cell line, which was generated by gene targeting in E14Tg2a.IV ES cells

Gene expression data from DKK-treated ESC-RPCs

Sample_geo_accession	GSM840283
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840283/suppl/GSM840283_BH11150-2_D3_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840284

GPL1261

Normal control ESC-RPCs, biological rep1

Normal control ESC-RPCs

cell type: ESC-derived retinal progenitor cells treatment: untreated parental cell line: ESC-RPCs were differentiated from 46C ES cell line, which was generated by gene targeting in E14Tg2a.IV ES cells

Gene expression data from normal control ESC-RPCs

Sample_geo_accession	GSM840284
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840284/suppl/GSM840284_BH11150-2_N1_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840285

GPL1261

Normal control ESC-RPCs, biological rep2

Normal control ESC-RPCs

Gene expression data from normal control ESC-RPCs

Sample_geo_accession	GSM840285
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840285/suppl/GSM840285_BH11150-2_N2_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840286

GPL1261

Normal control ESC-RPCs, biological rep3

Normal control ESC-RPCs

Gene expression data from normal control ESC-RPCs

Sample_geo_accession	GSM840286
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840286/suppl/GSM840286_BH11150-2_N3_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840287

GPL1261

Primary RPCs, biological rep1

Primary cultured RPCs

cell type: Retinal progenitor cells from newborn C57 mice genetic background: C57 treatment: untreated

Gene expression data from primary RPCs

Sample_geo_accession	GSM840287
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840287/suppl/GSM840287_BH11150-2_R1_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840288

GPL1261

Primary RPCs, biological rep2

Primary cultured RPCs

cell type: Retinal progenitor cells from newborn C57 mice genetic background: C57 treatment: untreated

Gene expression data from primary RPCs

Sample_geo_accession	GSM840288
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840288/suppl/GSM840288_BH11150-2_R2_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

GSM840289

GPL1261

Primary RPCs, biological rep3

Primary cultured RPCs

cell type: Retinal progenitor cells from newborn C57 mice genetic background: C57 treatment: untreated

Gene expression data from primary RPCs

Sample_geo_accession	GSM840289
Sample_status	Public on Apr 16 2013
Sample_submission_date	Nov 29 2011
Sample_last_update_date	Apr 16 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .
Sample_growth_protocol_ch1	For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Sample_hyb_protocol	Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Sample_scan_protocol	Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Sample_data_processing	Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Sample_platform_id	GPL1261
Sample_contact_name	Lu,,Cui
Sample_contact_email	lcui@sibs.ac.cn
Sample_contact_institute	Institue of Health Sciences
Sample_contact_address	225 South Chongqing road
Sample_contact_city	Shanghai
Sample_contact_zip/postal_code	200025
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM840nnn/GSM840289/suppl/GSM840289_BH11150-2_R3_Mouse430_2_.CEL.gz
Sample_series_id	GSE34002
Sample_data_row_count	45101

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