Search results for the GEO ID: GSE11819  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM181425 | GPL96 |
|
CHC357N-U133A
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CHC357N_U133A
|
Sample: CHC357N;
Gender: female;
Age at onset: 28 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM181425
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Jun 20 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80], and the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15], and with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181425/suppl/GSM181425.CEL.gz
| | Sample_series_id | GSE7473
| | Sample_series_id | GSE9536
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM181426 | GPL96 |
|
CHC535N-U133A
|
CHC535N_U133A
|
Sample: CHC535N;
Gender: female;
Age at onset: 30 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM181426
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Jun 20 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80], and the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15], and with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181426/suppl/GSM181426.CEL.gz
| | Sample_series_id | GSE7473
| | Sample_series_id | GSE9536
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM181427 | GPL96 |
|
CHC562N-U133A
|
CHC562N_U133A
|
Sample: CHC562N;
Gender: female;
Age at onset: 33 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM181427
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Jun 20 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80], and the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15], and with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181427/suppl/GSM181427.CEL.gz
| | Sample_series_id | GSE7473
| | Sample_series_id | GSE9536
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM181428 | GPL96 |
|
CHC573N-U133A
|
CHC573N_U133A
|
Sample: CHC573N;
Gender: female;
Age at onset: 28 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM181428
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Jun 20 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80], and the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15], and with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181428/suppl/GSM181428.CEL.gz
| | Sample_series_id | GSE7473
| | Sample_series_id | GSE9536
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM298747 | GPL96 |
|
CHC364T-RMA-U133A
|
CHC364T_U133A
|
Sample: CHC364T;
Gender: female;
Age at onset: 44 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM298747
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 18 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298747/suppl/GSM298747.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM298748 | GPL96 |
|
CHC382T-RMA-U133A
|
CHC382T_U133A
|
Sample: CHC382T;
Gender: female;
Age at onset: 45 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM298748
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 18 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298748/suppl/GSM298748.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM298749 | GPL96 |
|
CHC471T-RMA-U133A
|
CHC471T_U133A
|
Sample: CHC471T;
Gender: female;
Age at onset: 30 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM298749
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 18 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298749/suppl/GSM298749.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM298750 | GPL96 |
|
CHC466T-RMA-U133A
|
CHC466T_U133A
|
Sample: CHC466T;
Gender: female;
Age at onset: 50 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM298750
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 18 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298750/suppl/GSM298750.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299110 | GPL96 |
|
CHC364T-dChip-U133A
|
CHC364T_U133A
|
Sample: CHC364T;
Gender: female;
Age at onset: 44 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM299110
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299110/suppl/GSM299110.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299111 | GPL96 |
|
CHC471T-dChip-U133A
|
CHC471T_U133A
|
Sample: CHC471T;
Gender: female;
Age at onset: 30 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM299111
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299111/suppl/GSM299111.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299112 | GPL96 |
|
CHC466T-dChip-U133A
|
CHC466T_U133A
|
Sample: CHC466T;
Gender: female;
Age at onset: 50 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM299112
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299112/suppl/GSM299112.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299113 | GPL96 |
|
CHC382T-dChip-U133A
|
CHC382T_U133A
|
Sample: CHC382T;
Gender: female;
Age at onset: 45 years;
Disease: Inflammatory hepatocellular adenomas (IHCA);
Tissue: tumor liver.
|
see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]
|
| Sample_geo_accession | GSM299113
| | Sample_status | Public on Dec 24 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Dec 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299113/suppl/GSM299113.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299244 | GPL96 |
|
CHC357N-dChip-U133A
|
CHC357N_U133A
|
Sample: CHC357N;
Gender: female;
Age at onset: 28 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM299244
| | Sample_status | Public on Jun 23 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Jun 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299244/suppl/GSM299244.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299245 | GPL96 |
|
CHC535N-dChip-U133A
|
CHC535N_U133A
|
Sample: CHC535N;
Gender: female;
Age at onset: 30 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM299245
| | Sample_status | Public on Jun 23 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Jun 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299245/suppl/GSM299245.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299246 | GPL96 |
|
CHC562N-dChip-U133A
|
CHC562N_U133A
|
Sample: CHC562N;
Gender: female;
Age at onset: 33 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM299246
| | Sample_status | Public on Jun 23 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Jun 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299246/suppl/GSM299246.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
|
GSM299247 | GPL96 |
|
CHC573N-dChip-U133A
|
CHC573N_U133A
|
Sample: CHC573N;
Gender: female;
Age at onset: 28 years;
Disease: hepatocellular adenoma;
Tissue: non tumoral liver.
|
Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].
|
| Sample_geo_accession | GSM299247
| | Sample_status | Public on Jun 23 2008
| | Sample_submission_date | Jun 20 2008
| | Sample_last_update_date | Jun 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).
| | Sample_data_processing | Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].
| | Sample_platform_id | GPL96
| | Sample_contact_name | Sandrine,,Imbeaud
| | Sample_contact_email | sandrine.imbeaud@inserm.fr
| | Sample_contact_phone | +33 (0)1 53 72 51 98
| | Sample_contact_fax | +33 (0)1 53 72 51 92
| | Sample_contact_department | Génomique Fonctionnelle des tumeurs solides
| | Sample_contact_institute | INSERM, UMR U-674, Université Paris Descartes
| | Sample_contact_address | 27 rue Juliette Dodu
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75010
| | Sample_contact_country | France
| | Sample_contact_web_link | http://www.inserm-u674.net/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299247/suppl/GSM299247.CEL.gz
| | Sample_series_id | GSE11819
| | Sample_data_row_count | 22283
| | |
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