Search results for the GEO ID: GSE42765 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1049598 | GPL570 |
|
sample 1_PAD_00117
|
White blood human cells
|
disease: pediatric acute leukemia
groups: MLLT10
mrd: Standard Risk
data analysis protocol: MILE1
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049598
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049598/suppl/GSM1049598_PAD_00117.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049599 | GPL570 |
|
sample 2_PAD_00257
|
White blood human cells
|
disease: pediatric acute leukemia
groups: MLLT10
mrd: High Risk
data analysis protocol: MILE1
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049599
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049599/suppl/GSM1049599_PAD_00257.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049600 | GPL570 |
|
sample 3_PAD_00115
|
White blood human cells
|
disease: pediatric acute leukemia
groups: MLLT10
mrd: High Risk
data analysis protocol: MILE1
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049600
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049600/suppl/GSM1049600_PAD_00115.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049601 | GPL570 |
|
sample 4_PAD_00387
|
White blood human cells
|
disease: pediatric acute leukemia
groups: MLLT10
mrd: High Risk
data analysis protocol: MILE2
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049601
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049601/suppl/GSM1049601_PAD_00387_U133.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049602 | GPL570 |
|
sample 5_PAD_00402
|
White blood human cells
|
disease: pediatric acute leukemia
groups: otherHOXA
mrd: Standard Risk
data analysis protocol: MILE2
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049602
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049602/suppl/GSM1049602_PAD_00402_U133.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049603 | GPL570 |
|
sample 6_PAD_00427
|
White blood human cells
|
disease: pediatric acute leukemia
groups: otherHOXA
mrd: Standard Risk
data analysis protocol: MILE2
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049603
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049603/suppl/GSM1049603_PAD_00427_U133.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049604 | GPL570 |
|
sample 7_ES_00132
|
White blood human cells
|
disease: pediatric acute leukemia
groups: otherHOXA
mrd: High Risk
data analysis protocol: ES
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049604
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049604/suppl/GSM1049604_ES_00132_HG-U133_Plus_2_.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049605 | GPL570 |
|
sample 8_ES_00115
|
White blood human cells
|
disease: pediatric acute leukemia
groups: otherHOXA
mrd: High Risk
data analysis protocol: ES
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049605
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049605/suppl/GSM1049605_ES_00115_HG-U133_Plus_2_.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049606 | GPL570 |
|
sample 9_ES_00119
|
White blood human cells
|
disease: pediatric acute leukemia
groups: otherHOXA
mrd: High Risk
data analysis protocol: ES
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049606
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049606/suppl/GSM1049606_ES_00119_HG-U133_Plus_2_2.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
|
GSM1049607 | GPL570 |
|
sample 10_PAD_00102
|
White blood human cells
|
disease: pediatric acute leukemia
groups: patient 1 (patient with new MLLT10 fusion)
mrd: Standard Risk
data analysis protocol: MILE1
|
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049607
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049607/suppl/GSM1049607_PAD_00102.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
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GSM1049608 | GPL570 |
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sample 11_ES_00143
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White blood human cells
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disease: pediatric acute leukemia
groups: patient 2 (patient with new MLLT10 fusion)
mrd: High Risk
data analysis protocol: ES
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MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
Sample_geo_accession | GSM1049608
| Sample_status | Public on Jul 03 2013
| Sample_submission_date | Dec 06 2012
| Sample_last_update_date | Jul 03 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
| Sample_scan_protocol | GeneChips were scanned using the Scan GCS3000Dx.
| Sample_data_processing | Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
| Sample_data_processing | Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
| Sample_platform_id | GPL570
| Sample_contact_name | Andrea,,Zangrando
| Sample_contact_email | andrea.zangrando@unipd.it
| Sample_contact_phone | +390498211457
| Sample_contact_fax | +390498211465
| Sample_contact_laboratory | Hemato-Oncology
| Sample_contact_department | Pediatrics
| Sample_contact_institute | University of Padova
| Sample_contact_address | Via Giustiniani, 3
| Sample_contact_city | Padova
| Sample_contact_zip/postal_code | 35138
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.pediatria.unipd.it
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1049nnn/GSM1049608/suppl/GSM1049608_ES_00143_HG-U133_Plus_2_.CEL.gz
| Sample_series_id | GSE42765
| Sample_data_row_count | 54675
| |
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