Search results for the GEO ID: GSE12408  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM311313 | GPL570 |
|
Healthy control N1
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 10
Genotype: WT
Chart_Ref.: CDL-047-99S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311313
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311313/suppl/GSM311313.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311314 | GPL570 |
|
Healthy control N2
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 12
Genotype: WT
Chart_Ref.: CDL-043-99S1
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311314
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311314/suppl/GSM311314.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311315 | GPL570 |
|
Healthy control N4
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 8
Genotype: WT
Chart_Ref.: 27572-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311315
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311315/suppl/GSM311315.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311316 | GPL570 |
|
Healthy control N5
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 7
Genotype: WT
Chart_Ref.: 95-3985-S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311316
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311316/suppl/GSM311316.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311317 | GPL570 |
|
Healthy control N6
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 8
Genotype: WT
Chart_Ref.: 95-3999-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311317
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311317/suppl/GSM311317.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311318 | GPL570 |
|
Healthy control N7
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 1.5
Genotype: WT
Chart_Ref.: AGS222-s
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311318
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311318/suppl/GSM311318.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311319 | GPL570 |
|
Healthy control N8
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 5
Genotype: WT
Chart_Ref.: 27573-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311319
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311319/suppl/GSM311319.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311320 | GPL570 |
|
Healthy control N9
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: < 5
Genotype: WT
Chart_Ref.: AGS139-s
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311320
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311320/suppl/GSM311320.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311321 | GPL570 |
|
Healthy control N10
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 6.8
Genotype: WT
Chart_Ref.: GIA-001-S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311321
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311321/suppl/GSM311321.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311322 | GPL570 |
|
Healthy control N11
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 2
Genotype: WT
Chart_Ref.: 95-3988-S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311322
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311322/suppl/GSM311322.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311323 | GPL570 |
|
Healthy control N12
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 3.5
Genotype: WT
Chart_Ref.: 27574-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311323
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311323/suppl/GSM311323.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311324 | GPL570 |
|
Healthy control N13
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: <5
Genotype: WT
Chart_Ref.: AGS248-s
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311324
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311324/suppl/GSM311324.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311325 | GPL570 |
|
Healthy control N14
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 12
Genotype: WT
Chart_Ref.: 95-1680-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311325
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311325/suppl/GSM311325.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311326 | GPL570 |
|
Healthy control N15
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 18.5
Genotype: WT
Chart_Ref.: CDL-145-03S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311326
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311326/suppl/GSM311326.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311327 | GPL570 |
|
Healthy control N16
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 14
Genotype: WT
Chart_Ref.: 95-1681-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311327
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311327/suppl/GSM311327.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311328 | GPL570 |
|
Healthy control N17
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 10
Genotype: WT
Chart_Ref.: 95-3986-S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311328
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311328/suppl/GSM311328.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311329 | GPL570 |
|
Healthy control N18
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 13
Genotype: WT
Chart_Ref.: 95-3991-S
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311329
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311329/suppl/GSM311329.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311330 | GPL570 |
|
CdLS patient PT1
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 6.9
Genotype: c.6407insA / Frameshift
Severe
Yes
Chart_Ref.: CDL-173-04P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311330
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311330/suppl/GSM311330.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311331 | GPL570 |
|
CdLS patient PT2
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 0
Genotype: c.2449_2450insG / Frameshift
Severe
Yes
Chart_Ref.: CDL-285-05P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311331
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311331/suppl/GSM311331.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311332 | GPL570 |
|
CdLS patient PT3
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 0
Genotype: c.1444_1447delAGAG / Frameshift
Severe
No
Chart_Ref.: CDL-198-04P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311332
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311332/suppl/GSM311332.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311333 | GPL570 |
|
CdLS patient PT4
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 19.5
Genotype: c.4606C>T / Nonsense
Severe
Yes
Chart_Ref.: CDL-157-04P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311333
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311333/suppl/GSM311333.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311334 | GPL570 |
|
CdLS patient PT5
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 0
Genotype: c.3048_3051delATTA / Frameshift
Severe
Yes
Chart_Ref.: CDL-227-05P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311334
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311334/suppl/GSM311334.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311335 | GPL570 |
|
CdLS patient PT6
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 11.9
Genotype: c.5167C>T / Nonsense
Severe
No
Chart_Ref.: CDL-013-98-P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311335
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311335/suppl/GSM311335.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311336 | GPL570 |
|
CdLS patient PT7
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 5.3
Genotype: c.4193C>G / Nonsense
Severe
Yes
Chart_Ref.: CDL-035-99P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311336
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311336/suppl/GSM311336.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311337 | GPL570 |
|
CdLS patient PT8
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 14.6
Genotype: c.961delA / Frameshift
Severe
Yes
Chart_Ref.: CDL-038-99P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311337
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311337/suppl/GSM311337.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311338 | GPL570 |
|
CdLS patient PT9
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 7
Genotype: c.742_743delCT / Frameshift
Severe
Yes
Chart_Ref.: CDL-006-98-P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311338
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311338/suppl/GSM311338.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311339 | GPL570 |
|
CdLS patient PT10
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 10.5
Genotype: c.2969delG / Frameshift
Severe
Yes
Chart_Ref.: CDL-015-98-P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311339
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311339/suppl/GSM311339.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311340 | GPL570 |
|
CdLS patient PT11
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 6.7
Genotype: c.1902_1903insA / Frameshift
Severe
Yes
Chart_Ref.: CDL-001-98-P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311340
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311340/suppl/GSM311340.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311341 | GPL570 |
|
CdLS patient PT12
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 0.3
Genotype: c.150delG / Nonsense
Severe
No
Chart_Ref.: CDL-066-99P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311341
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311341/suppl/GSM311341.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311342 | GPL570 |
|
CdLS patient PT13
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 8.3
Genotype: c.2494C>T / nonsense
Severe
Yes
Chart_Ref.: CDL-049-99P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311342
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311342/suppl/GSM311342.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311343 | GPL570 |
|
CdLS patient PT14
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 23.5
Genotype: c.1546_1547insG / Frameshift
Severe
Yes
Chart_Ref.: CDL-108-00P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311343
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311343/suppl/GSM311343.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311344 | GPL570 |
|
CdLS patient PT15
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 0.8
Genotype: c.1934delA / Nonsense
Severe
Yes
Chart_Ref.: CDL-276-05P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311344
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311344/suppl/GSM311344.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311345 | GPL570 |
|
CdLS patient PT16
|
Lymphoblastoid cell line
|
Gender: Female
Age, year: 9
Genotype: c.4606C>T / Nonsense
Severe
No
Chart_Ref.: CDL-132-01P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311345
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311345/suppl/GSM311345.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311346 | GPL570 |
|
Healthy control (test sample)
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 7
Genotype: WT
Chart_Ref.: 94-3854-B
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311346
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311346/suppl/GSM311346.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311347 | GPL570 |
|
CdLS patient (test sample)
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 0
Genotype: c.4002_4005del4
Severe
No
Chart_Ref.: CDL-302-05P
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Egyptian
|
| Sample_geo_accession | GSM311347
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311347/suppl/GSM311347.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311348 | GPL570 |
|
RBS patient RS-Val-1 (test sample)
|
Lymphoblastoid cell line
|
Gender: N/A
Age, year: N/A
Genotype: ESCO2 mutation
N/A
Chart_Ref.: RS-20
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
race unknown
|
| Sample_geo_accession | GSM311348
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311348/suppl/GSM311348.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311349 | GPL570 |
|
RBS patient RS-Val-2 (test sample)
|
Lymphoblastoid cell line
|
Gender: N/A
Age, year: N/A
Genotype: ESCO2 mutation
N/A
Chart_Ref.: RS-44
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
race unknown
|
| Sample_geo_accession | GSM311349
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311349/suppl/GSM311349.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311350 | GPL570 |
|
Alagille syndrome patient ASG-Val-1 (test sample)
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 7
Genotype: JAG1 mutation
N/A
Chart_Ref.: ASG- J.S.
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311350
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311350/suppl/GSM311350.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
GSM311351 | GPL570 |
|
Alagille syndrome patient ASG-Val-2 (test sample)
|
Lymphoblastoid cell line
|
Gender: Male
Age, year: 8
Genotype: JAG1 mutation
disease_severity: N/A
Chart_Ref.: ASG-R.Z.
|
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Sample_geo_accession | GSM311351
| | Sample_status | Public on May 28 2009
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
| | Sample_growth_protocol_ch1 | Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
| | Sample_hyb_protocol | Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
| | Sample_data_processing | CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | IAN,D.,KRANTZ
| | Sample_contact_email | ian2@mail.med.upenn.edu
| | Sample_contact_phone | 215-590-2828
| | Sample_contact_fax | 215-590-3850
| | Sample_contact_laboratory | 1012G, ARC
| | Sample_contact_department | Division of Human and Molecular Genetics
| | Sample_contact_institute | The Children's Hospital of Philadelphia
| | Sample_contact_address | 34th and Civic Blvd.
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311351/suppl/GSM311351.CEL.gz
| | Sample_series_id | GSE12408
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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