Result

Search results for the GEO ID: GSE20841

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GSM ID

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Title

Source name

Description

Characteristics

GSM521108

GPL1261

day 5 FACS sorted CXCR4+/ FLK+ cells, biological rep1

CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

strain: CGR8 cell type: embryonic stem cell

Gene expression data from day 5 sorted biomarker positive progenitors

Sample_geo_accession	GSM521108
Sample_status	Public on Mar 11 2011
Sample_submission_date	Mar 11 2010
Sample_last_update_date	Mar 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000
Sample_data_processing	Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.
Sample_data_processing
Sample_data_processing	To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Sample_data_processing	Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values
Sample_platform_id	GPL1261
Sample_contact_name	Anca,,Chiriac
Sample_contact_email	chiriac.anca@mayo.edu
Sample_contact_phone	507-266-7915
Sample_contact_laboratory	Andre Terzic-Cardiovascular Research Lab
Sample_contact_department	Molecular Pharmacology and Experimental Therapeutics
Sample_contact_institute	Mayo Clinic
Sample_contact_address	Stabile 5, 200 First Street SW
Sample_contact_city	Rochester
Sample_contact_state	MN
Sample_contact_zip/postal_code	55905
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521108/suppl/GSM521108.CEL.gz
Sample_series_id	GSE20841
Sample_data_row_count	45101

GSM521109

GPL1261

day 5 FACS sorted CXCR4+/ FLK+ cells, biological rep2

CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

strain: CGR8 cell type: embryonic stem cell

Gene expression data from day 5 sorted biomarker positive progenitors

Sample_geo_accession	GSM521109
Sample_status	Public on Mar 11 2011
Sample_submission_date	Mar 11 2010
Sample_last_update_date	Mar 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000
Sample_data_processing	Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.
Sample_data_processing
Sample_data_processing	To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Sample_data_processing	Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values
Sample_platform_id	GPL1261
Sample_contact_name	Anca,,Chiriac
Sample_contact_email	chiriac.anca@mayo.edu
Sample_contact_phone	507-266-7915
Sample_contact_laboratory	Andre Terzic-Cardiovascular Research Lab
Sample_contact_department	Molecular Pharmacology and Experimental Therapeutics
Sample_contact_institute	Mayo Clinic
Sample_contact_address	Stabile 5, 200 First Street SW
Sample_contact_city	Rochester
Sample_contact_state	MN
Sample_contact_zip/postal_code	55905
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521109/suppl/GSM521109.CEL.gz
Sample_series_id	GSE20841
Sample_data_row_count	45101

GSM521110

GPL1261

day 5 FACS sorted CXCR4+/ FLK+ cells, biological rep3

CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

strain: CGR8 cell type: embryonic stem cell

Gene expression data from day 5 sorted biomarker positive progenitors

Sample_geo_accession	GSM521110
Sample_status	Public on Mar 11 2011
Sample_submission_date	Mar 11 2010
Sample_last_update_date	Mar 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000
Sample_data_processing	Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.
Sample_data_processing
Sample_data_processing	To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Sample_data_processing	Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values
Sample_platform_id	GPL1261
Sample_contact_name	Anca,,Chiriac
Sample_contact_email	chiriac.anca@mayo.edu
Sample_contact_phone	507-266-7915
Sample_contact_laboratory	Andre Terzic-Cardiovascular Research Lab
Sample_contact_department	Molecular Pharmacology and Experimental Therapeutics
Sample_contact_institute	Mayo Clinic
Sample_contact_address	Stabile 5, 200 First Street SW
Sample_contact_city	Rochester
Sample_contact_state	MN
Sample_contact_zip/postal_code	55905
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521110/suppl/GSM521110.CEL.gz
Sample_series_id	GSE20841
Sample_data_row_count	45101

GSM521111

GPL1261

day 5 FACS sorted CXCR4-/ FLK- cells, biological rep1

CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

strain: CGR8 cell type: embryonic stem cell

Gene expression data from day 5 sorted biomarker negative progenitors

Sample_geo_accession	GSM521111
Sample_status	Public on Mar 11 2011
Sample_submission_date	Mar 11 2010
Sample_last_update_date	Mar 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000
Sample_data_processing	Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.
Sample_data_processing
Sample_data_processing	To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Sample_data_processing	Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values
Sample_platform_id	GPL1261
Sample_contact_name	Anca,,Chiriac
Sample_contact_email	chiriac.anca@mayo.edu
Sample_contact_phone	507-266-7915
Sample_contact_laboratory	Andre Terzic-Cardiovascular Research Lab
Sample_contact_department	Molecular Pharmacology and Experimental Therapeutics
Sample_contact_institute	Mayo Clinic
Sample_contact_address	Stabile 5, 200 First Street SW
Sample_contact_city	Rochester
Sample_contact_state	MN
Sample_contact_zip/postal_code	55905
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521111/suppl/GSM521111.CEL.gz
Sample_series_id	GSE20841
Sample_data_row_count	45101

GSM521112

GPL1261

day 5 FACS sorted CXCR4-/ FLK- cells, biological rep2

CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

strain: CGR8 cell type: embryonic stem cell

Gene expression data from day 5 sorted biomarker negative progenitors

Sample_geo_accession	GSM521112
Sample_status	Public on Mar 11 2011
Sample_submission_date	Mar 11 2010
Sample_last_update_date	Mar 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000
Sample_data_processing	Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.
Sample_data_processing
Sample_data_processing	To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Sample_data_processing	Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values
Sample_platform_id	GPL1261
Sample_contact_name	Anca,,Chiriac
Sample_contact_email	chiriac.anca@mayo.edu
Sample_contact_phone	507-266-7915
Sample_contact_laboratory	Andre Terzic-Cardiovascular Research Lab
Sample_contact_department	Molecular Pharmacology and Experimental Therapeutics
Sample_contact_institute	Mayo Clinic
Sample_contact_address	Stabile 5, 200 First Street SW
Sample_contact_city	Rochester
Sample_contact_state	MN
Sample_contact_zip/postal_code	55905
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521112/suppl/GSM521112.CEL.gz
Sample_series_id	GSE20841
Sample_data_row_count	45101

GSM521113

GPL1261

day 5 FACS sorted CXCR4-/ FLK- cells, biological rep3

CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

strain: CGR8 cell type: embryonic stem cell

Gene expression data from day 5 sorted biomarker negative progenitors

Sample_geo_accession	GSM521113
Sample_status	Public on Mar 11 2011
Sample_submission_date	Mar 11 2010
Sample_last_update_date	Mar 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000
Sample_data_processing	Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.
Sample_data_processing
Sample_data_processing	To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Sample_data_processing	Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values
Sample_platform_id	GPL1261
Sample_contact_name	Anca,,Chiriac
Sample_contact_email	chiriac.anca@mayo.edu
Sample_contact_phone	507-266-7915
Sample_contact_laboratory	Andre Terzic-Cardiovascular Research Lab
Sample_contact_department	Molecular Pharmacology and Experimental Therapeutics
Sample_contact_institute	Mayo Clinic
Sample_contact_address	Stabile 5, 200 First Street SW
Sample_contact_city	Rochester
Sample_contact_state	MN
Sample_contact_zip/postal_code	55905
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM521nnn/GSM521113/suppl/GSM521113.CEL.gz
Sample_series_id	GSE20841
Sample_data_row_count	45101

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