Result

Search results for the GEO ID: GSE27206

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM672181

GPL570

SMA-iPS-01

iPS cells, SMA patient

genotype/variation: SMN1D7;SMN2+/+ cell type: induced pluripotent stem cells (iPS cells)

DNA9252-001

Sample_geo_accession	GSM672181
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672181/suppl/GSM672181.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672182

GPL570

SMA-iPS-02

iPS cells, SMA patient

genotype/variation: SMN1D7;SMN2+/+ cell type: induced pluripotent stem cells (iPS cells)

DNA9252-002

Sample_geo_accession	GSM672182
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672182/suppl/GSM672182.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672183

GPL570

WT-iPS-01

iPS cells father

genotype/variation: SMN1D7/+;SMN2+/+ cell type: induced pluripotent stem cells (iPS cells)

DNA9252-004

Sample_geo_accession	GSM672183
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672183/suppl/GSM672183.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672184

GPL570

iPS-19.9-01

iPS cells-CTR

genotype/variation: SMN1+/+;SMN2+/+ cell type: induced pluripotent stem cells (iPS cells)

DNA9252-006

Sample_geo_accession	GSM672184
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672184/suppl/GSM672184.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672185

GPL570

iPS-19.9-02

iPS cells-CTR

genotype/variation: SMN1+/+;SMN2+/+ cell type: induced pluripotent stem cells (iPS cells)

DNA9252-007

Sample_geo_accession	GSM672185
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672185/suppl/GSM672185.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672186

GPL570

iPS-19.9-03

iPS cells-CTR

genotype/variation: SMN1+/+;SMN2+/+ cell type: induced pluripotent stem cells (iPS cells)

DNA9252-008

Sample_geo_accession	GSM672186
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672186/suppl/GSM672186.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672187

GPL570

SMA-Fibro-01

Fibroblasts, SMA patient

genotype/variation: SMN1D7;SMN2+/+ cell type: fibroblasts

DNA9252-009

Sample_geo_accession	GSM672187
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672187/suppl/GSM672187.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672188

GPL570

SMA-Fibro-02

Fibroblasts, SMA patient

genotype/variation: SMN1D7;SMN2+/+ cell type: fibroblasts

DNA9252-010

Sample_geo_accession	GSM672188
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672188/suppl/GSM672188.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

GSM672189

GPL570

WT-Fibro-01

Fibroblasts, father

genotype/variation: SMN1D7/+;SMN2+/+ cell type: fibroblasts

DNA9252-012

Sample_geo_accession	GSM672189
Sample_status	Public on Jan 04 2013
Sample_submission_date	Feb 09 2011
Sample_last_update_date	Jan 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.
Sample_hyb_protocol	Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.
Sample_scan_protocol	Affymetrix RUO platform.
Sample_data_processing	RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.
Sample_platform_id	GPL570
Sample_contact_name	Stefania,,Corti
Sample_contact_email	stefania.corti@unimi.it
Sample_contact_phone	+390255033817
Sample_contact_fax	+390250320430
Sample_contact_department	Neurological Sciences
Sample_contact_institute	University of Milan
Sample_contact_address	via F. Sforza 35
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20100
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672189/suppl/GSM672189.CEL.gz
Sample_series_id	GSE27206
Sample_series_id	GSE27207
Sample_data_row_count	54675

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