Search results for the GEO ID: GSE10820  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM272982 | GPL570 |
|
ALL_BCell_Leu_12
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 12
|
Gender: Male
Age: 8 months
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
|
ALL_BCell_Leu_12
|
| Sample_geo_accession | GSM272982
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272982/suppl/GSM272982.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272982/suppl/GSM272982.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM272983 | GPL570 |
|
ALL_BCell_Leu_22
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 22
|
Gender: Female
Age: 37 years
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Favorable
|
ALL_BCell_Leu_22
|
| Sample_geo_accession | GSM272983
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272983/suppl/GSM272983.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272983/suppl/GSM272983.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273085 | GPL570 |
|
ALL_BCell_Leu_07
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 07
|
Gender: Female
Age: 12 years
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Favorable
|
ALL_BCell_Leu_07
|
| Sample_geo_accession | GSM273085
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273085/suppl/GSM273085.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273085/suppl/GSM273085.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273086 | GPL570 |
|
ALL_BCell_Leu_12_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 12_R
|
Gender: Male
Age: 8 months
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
Note: Technical Replicate of ALL_BCell_Leu_12
|
ALL_BCell_Leu_12_R
|
| Sample_geo_accession | GSM273086
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273086/suppl/GSM273086.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273086/suppl/GSM273086.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273199 | GPL570 |
|
ALL_TCell_Leu_14
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 14
|
Gender: Female
Age: 14 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Poor
|
ALL_TCell_Leu_14
|
| Sample_geo_accession | GSM273199
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273199/suppl/GSM273199.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273199/suppl/GSM273199.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273200 | GPL570 |
|
ALL_TCell_Leu_19
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 19
|
Gender: Male
Age: 3 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
|
ALL_TCell_Leu_19
|
| Sample_geo_accession | GSM273200
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273200/suppl/GSM273200.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273200/suppl/GSM273200.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273201 | GPL570 |
|
ALL_BCell_Leu_24
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 24
|
Gender: Male
Age: 43 Years
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
|
ALL_BCell_Leu_24
|
| Sample_geo_accession | GSM273201
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273201/suppl/GSM273201.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273201/suppl/GSM273201.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273202 | GPL570 |
|
ALL_BCell_Leu_24_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 24_R
|
Gender: Male
Age: 43 Years
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
Note: Technical Replicate of ALL_BCell_Leu_24
|
ALL_BCell_Leu_24_R
|
| Sample_geo_accession | GSM273202
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273202/suppl/GSM273202.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273202/suppl/GSM273202.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273203 | GPL570 |
|
ALL_TCell_Leu_28
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 28
|
Gender: Male
Age: 16 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
|
ALL_TCell_Leu_28
|
| Sample_geo_accession | GSM273203
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273203/suppl/GSM273203.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273203/suppl/GSM273203.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273204 | GPL570 |
|
ALL_TCell_Leu_28_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 28_R
|
Gender: Male
Age: 16 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
Note: Technical Replicate of ALL_TCell_Leu_28
|
ALL_TCell_Leu_28_R
|
| Sample_geo_accession | GSM273204
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273204/suppl/GSM273204.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273204/suppl/GSM273204.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273205 | GPL570 |
|
ALL_TCell_Leu_29
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 29
|
Gender: Male
Age: 18 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
|
ALL_TCell_Leu_29
|
| Sample_geo_accession | GSM273205
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273205/suppl/GSM273205.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273205/suppl/GSM273205.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273206 | GPL570 |
|
ALL_TCell_Leu_29_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 29_R
|
Gender: Male
Age: 18 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
Note: Technical Replicate of ALL_TCell_Leu_29
|
ALL_TCell_Leu_29_R
|
| Sample_geo_accession | GSM273206
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273206/suppl/GSM273206.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273206/suppl/GSM273206.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273207 | GPL570 |
|
ALL_TCell_Leu_30
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 30
|
Gender: Male
Age: 21 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
|
ALL_TCell_Leu_30
|
| Sample_geo_accession | GSM273207
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273207/suppl/GSM273207.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273207/suppl/GSM273207.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273208 | GPL570 |
|
ALL_TCell_Leu_30_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage T, 30_R
|
Gender: Male
Age: 21 Years
Acute Lymphoblastic Leukemia Lineage: T
Sample: Lymphocytes T from Periferical Blood
Prognosis: Favorable
Note: Technical Replicate of ALL_TCell_Leu_30
|
ALL_TCell_Leu_30_R
|
| Sample_geo_accession | GSM273208
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273208/suppl/GSM273208.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273208/suppl/GSM273208.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273209 | GPL570 |
|
ALL_BCell_Leu_33
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 33
|
Gender: Female
Age: 9 Months
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
|
ALL_BCell_Leu_33
|
| Sample_geo_accession | GSM273209
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273209/suppl/GSM273209.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273209/suppl/GSM273209.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273210 | GPL570 |
|
ALL_BCell_Leu_33_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 33_R
|
Gender: Female
Age: 9 Months
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
Note: Technical Replicate of ALL_BCell_Leu_33
|
ALL_BCell_Leu_33_R
|
| Sample_geo_accession | GSM273210
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273210/suppl/GSM273210.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273210/suppl/GSM273210.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273211 | GPL570 |
|
ALL_BCell_Leu_41
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 41
|
Gender: Male
Age: 12 Years
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
|
ALL_BCell_Leu_41
|
| Sample_geo_accession | GSM273211
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273211/suppl/GSM273211.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273211/suppl/GSM273211.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
|
GSM273212 | GPL570 |
|
ALL_BCell_Leu_41_R
|
Periferical blood, Acute Lymphoblastic Leukemia lineage B, 41_R
|
Gender: Male
Age: 12 Years
Acute Lymphoblastic Leukemia Lineage: B
Sample: Lymphocytes B from Periferical Blood
Prognosis: Poor
|
ALL_BCell_Leu_41_R
|
| Sample_geo_accession | GSM273212
| | Sample_status | Public on Mar 15 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | Mar 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All Periferical Blood Samples were collected at the Hematology Service of the University Hospital of the Universidad Autónoma de Nuevo León, following institutional ethics committee guidelines, from February-2005 to August-2007.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water. The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN). The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Angel,,Lugo-Trampe
| | Sample_contact_email | lugoweb_2@hotmail.com
| | Sample_contact_phone | +52(81)83294174
| | Sample_contact_fax | +52(81)83337747
| | Sample_contact_laboratory | Genética Molecular
| | Sample_contact_department | Bioquímica
| | Sample_contact_institute | Universidad Autónoma de Nuevo León
| | Sample_contact_address | Av. Madero y Dr. Eduardo Aguirre Pequeño
| | Sample_contact_city | Monterrey
| | Sample_contact_state | Nuevo León
| | Sample_contact_zip/postal_code | 64460
| | Sample_contact_country | Mexico
| | Sample_contact_web_link | http://www.medicina.uanl.mx/bioquimica/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273212/suppl/GSM273212.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM273nnn/GSM273212/suppl/GSM273212.CHP.gz
| | Sample_series_id | GSE10820
| | Sample_data_row_count | 54675
| | |
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