Result

Search results for the GEO ID: GSE25737

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM632119

GPL1261

E1-GemKD

neurectoderm derived from embryonic stem cells

tissue: neurectoderm derived from embryonic stem cells treatment: Geminin knockdown, shRNAmir #11 cell line origin: derivative of ES-E14TG2a (ATCC) genetic background: 129P2 (formerly 129/Ola)

Doxycycline-induction of Geminin shRNA knockdown

Sample_geo_accession	GSM632119
Sample_status	Public on Mar 18 2011
Sample_submission_date	Dec 01 2010
Sample_last_update_date	Mar 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition
Sample_growth_protocol_ch1	mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.
Sample_platform_id	GPL1261
Sample_contact_name	Kristen,L,Kroll
Sample_contact_email	kkroll@wustl.edu
Sample_contact_laboratory	Kristen Kroll
Sample_contact_department	Developmental Biology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	320 McDonnell Sciences/660 S. Euclid Ave.
Sample_contact_city	Saint Louis
Sample_contact_state	MO
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_contact_web_link	http://devbio.wustl.edu/krolllab/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM632nnn/GSM632119/suppl/GSM632119_E1-GemKD.CEL.gz
Sample_series_id	GSE25737
Sample_data_row_count	45037

GSM632120

GPL1261

E1-uninduced (no Dox) control

neurectoderm derived from embryonic stem cells

tissue: neurectoderm derived from embryonic stem cells treatment: control, shRNAmir #11 cell line origin: derivative of ES-E14TG2a (ATCC) genetic background: 129P2 (formerly 129/Ola)

uninduced (no Dox) control

Sample_geo_accession	GSM632120
Sample_status	Public on Mar 18 2011
Sample_submission_date	Dec 01 2010
Sample_last_update_date	Mar 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition
Sample_growth_protocol_ch1	mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.
Sample_platform_id	GPL1261
Sample_contact_name	Kristen,L,Kroll
Sample_contact_email	kkroll@wustl.edu
Sample_contact_laboratory	Kristen Kroll
Sample_contact_department	Developmental Biology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	320 McDonnell Sciences/660 S. Euclid Ave.
Sample_contact_city	Saint Louis
Sample_contact_state	MO
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_contact_web_link	http://devbio.wustl.edu/krolllab/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM632nnn/GSM632120/suppl/GSM632120_E1-No_Dox_control.CEL.gz
Sample_series_id	GSE25737
Sample_data_row_count	45037

GSM632121

GPL1261

E2-GemKD

neurectoderm derived from embryonic stem cells

tissue: neurectoderm derived from embryonic stem cells treatment: Geminin knockdown, shRNAmir #9 cell line origin: derivative of ES-E14TG2a (ATCC) genetic background: 129P2 (formerly 129/Ola)

Doxycycline-induction of Geminin shRNA knockdown

Sample_geo_accession	GSM632121
Sample_status	Public on Mar 18 2011
Sample_submission_date	Dec 01 2010
Sample_last_update_date	Mar 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition
Sample_growth_protocol_ch1	mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.
Sample_platform_id	GPL1261
Sample_contact_name	Kristen,L,Kroll
Sample_contact_email	kkroll@wustl.edu
Sample_contact_laboratory	Kristen Kroll
Sample_contact_department	Developmental Biology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	320 McDonnell Sciences/660 S. Euclid Ave.
Sample_contact_city	Saint Louis
Sample_contact_state	MO
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_contact_web_link	http://devbio.wustl.edu/krolllab/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM632nnn/GSM632121/suppl/GSM632121_E2-GemKD.CEL.gz
Sample_series_id	GSE25737
Sample_data_row_count	45037

GSM632122

GPL1261

E2-uninduced (no Dox) control

neurectoderm derived from embryonic stem cells

tissue: neurectoderm derived from embryonic stem cells treatment: control, shRNAmir #9 cell line origin: derivative of ES-E14TG2a (ATCC) genetic background: 129P2 (formerly 129/Ola)

uninduced (no Dox) control

Sample_geo_accession	GSM632122
Sample_status	Public on Mar 18 2011
Sample_submission_date	Dec 01 2010
Sample_last_update_date	Mar 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition
Sample_growth_protocol_ch1	mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.
Sample_platform_id	GPL1261
Sample_contact_name	Kristen,L,Kroll
Sample_contact_email	kkroll@wustl.edu
Sample_contact_laboratory	Kristen Kroll
Sample_contact_department	Developmental Biology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	320 McDonnell Sciences/660 S. Euclid Ave.
Sample_contact_city	Saint Louis
Sample_contact_state	MO
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_contact_web_link	http://devbio.wustl.edu/krolllab/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM632nnn/GSM632122/suppl/GSM632122_E2-No_Dox_control.CEL.gz
Sample_series_id	GSE25737
Sample_data_row_count	45037

GSM632123

GPL1261

E3-GemKD

neurectoderm derived from embryonic stem cells

tissue: neurectoderm derived from embryonic stem cells treatment: Geminin knockdown, shRNAmir #11 cell line origin: derivative of ES-E14TG2a (ATCC) genetic background: 129P2 (formerly 129/Ola)

Doxycycline-induction of Geminin shRNA knockdown

Sample_geo_accession	GSM632123
Sample_status	Public on Mar 18 2011
Sample_submission_date	Dec 01 2010
Sample_last_update_date	Mar 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition
Sample_growth_protocol_ch1	mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.
Sample_platform_id	GPL1261
Sample_contact_name	Kristen,L,Kroll
Sample_contact_email	kkroll@wustl.edu
Sample_contact_laboratory	Kristen Kroll
Sample_contact_department	Developmental Biology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	320 McDonnell Sciences/660 S. Euclid Ave.
Sample_contact_city	Saint Louis
Sample_contact_state	MO
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_contact_web_link	http://devbio.wustl.edu/krolllab/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM632nnn/GSM632123/suppl/GSM632123_E3-GemKD.CEL.gz
Sample_series_id	GSE25737
Sample_data_row_count	45037

GSM632124

GPL1261

E3-uninduced (no Dox) control

neurectoderm derived from embryonic stem cells

tissue: neurectoderm derived from embryonic stem cells treatment: control, shRNAmir #11 cell line origin: derivative of ES-E14TG2a (ATCC) genetic background: 129P2 (formerly 129/Ola)

uninduced (no Dox) control

Sample_geo_accession	GSM632124
Sample_status	Public on Mar 18 2011
Sample_submission_date	Dec 01 2010
Sample_last_update_date	Mar 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition
Sample_growth_protocol_ch1	mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.
Sample_platform_id	GPL1261
Sample_contact_name	Kristen,L,Kroll
Sample_contact_email	kkroll@wustl.edu
Sample_contact_laboratory	Kristen Kroll
Sample_contact_department	Developmental Biology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	320 McDonnell Sciences/660 S. Euclid Ave.
Sample_contact_city	Saint Louis
Sample_contact_state	MO
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_contact_web_link	http://devbio.wustl.edu/krolllab/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM632nnn/GSM632124/suppl/GSM632124_E3-No_Dox_control.CEL.gz
Sample_series_id	GSE25737
Sample_data_row_count	45037

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