Search results for the GEO ID: GSE10746  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM271331 | GPL570 |
|
Mucositis-BRENC1
|
Buccal mucosa biopsy, healthy control subject
|
BRENC1, healthy control
|
Gene expression data from healthy control subjects
|
| Sample_geo_accession | GSM271331
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271331/suppl/GSM271331.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271332 | GPL570 |
|
Mucositis-BRENC2
|
Buccal mucosa biopsy, healthy control subject
|
BRENC2, healthy control
|
Gene expression data from healthy control subjects
|
| Sample_geo_accession | GSM271332
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271332/suppl/GSM271332.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271333 | GPL570 |
|
Mucositis-BRENC3
|
Buccal mucosa biopsy, healthy control subject
|
BRENC3, healthy control
|
Gene expression data from healthy control subjects
|
| Sample_geo_accession | GSM271333
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271333/suppl/GSM271333.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271334 | GPL570 |
|
Mucositis-BREN11
|
Buccal mucosa biopsy, AML patient pre-chemotherapy
|
BREN11, pre-chemotherapy
|
Gene expression data from AML patient the same day before induction chemotherapy
|
| Sample_geo_accession | GSM271334
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271334/suppl/GSM271334.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271335 | GPL570 |
|
Mucositis-BREN21
|
Buccal mucosa biopsy, AML patient pre-chemotherapy
|
BREN21, pre-chemotherapy
|
Gene expression data from AML patient the same day before induction chemotherapy
|
| Sample_geo_accession | GSM271335
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271335/suppl/GSM271335.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271336 | GPL570 |
|
Mucositis-BREN41
|
Buccal mucosa biopsy, AML patient pre-chemotherapy
|
BREN41, pre-chemotherapy
|
Gene expression data from AML patient the same day before induction chemotherapy
|
| Sample_geo_accession | GSM271336
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271336/suppl/GSM271336.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271337 | GPL570 |
|
Mucositis-BREN51
|
Buccal mucosa biopsy, AML patient pre-chemotherapy
|
BREN51, pre-chemotherapy
|
Gene expression data from AML patient the same day before induction chemotherapy
|
| Sample_geo_accession | GSM271337
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271337/suppl/GSM271337.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271338 | GPL570 |
|
Mucositis-BREN22
|
Buccal mucosa biopsy, AML patient two days post-chemotherapy
|
BREN22, two days post-chemotherapy
|
Gene expression data from AML patients two days following induction chemotherapy
|
| Sample_geo_accession | GSM271338
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271338/suppl/GSM271338.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271339 | GPL570 |
|
Mucositis-BREN32
|
Buccal mucosa biopsy, AML patient two days post-chemotherapy
|
BREN32, two days post-chemotherapy
|
Gene expression data from AML patients two days following induction chemotherapy
|
| Sample_geo_accession | GSM271339
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271339/suppl/GSM271339.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271340 | GPL570 |
|
Mucositis-BREN42
|
Buccal mucosa biopsy, AML patient two days post-chemotherapy
|
BREN42, two days post-chemotherapy
|
Gene expression data from AML patients two days following induction chemotherapy
|
| Sample_geo_accession | GSM271340
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271340/suppl/GSM271340.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
|
GSM271341 | GPL570 |
|
Mucositis-BREN52
|
Buccal mucosa biopsy, AML patient two days post-chemotherapy
|
BREN52, two days post-chemotherapy
|
Gene expression data from AML patients two days following induction chemotherapy
|
| Sample_geo_accession | GSM271341
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Mar 06 2008
| | Sample_last_update_date | Mar 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean-Luc,C,Mougeot
| | Sample_contact_email | jean-luc.mougeot@carolinas.org
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Carolinas Medical Center
| | Sample_contact_address | 1542 Garden Terrace
| | Sample_contact_city | Charlotte
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 28232-2861
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM271nnn/GSM271341/suppl/GSM271341.CEL.gz
| | Sample_series_id | GSE10746
| | Sample_data_row_count | 54675
| | |
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