Search results for the GEO ID: GSE15303  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM387039 | GPL1261 |
|
MRF CKO Oligodendrocyte Replicate 1
|
MRF conditional knockout cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor conditional knockout
|
MRF conditional knockout cultured oligodendrocytes
|
| Sample_geo_accession | GSM387039
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387039/suppl/GSM387039.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387040 | GPL1261 |
|
MRF CKO Oligodendrocyte Replicate 2
|
MRF conditional knockout cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor conditional knockout
|
MRF conditional knockout cultured oligodendrocytes
|
| Sample_geo_accession | GSM387040
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387040/suppl/GSM387040.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387041 | GPL1261 |
|
MRF CKO Oligodendrocyte Replicate 3
|
MRF conditional knockout cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor conditional knockout
|
MRF conditional knockout cultured oligodendrocytes
|
| Sample_geo_accession | GSM387041
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387041/suppl/GSM387041.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387042 | GPL1261 |
|
MRF control Oligodendrocyte Replicate 1
|
MRF control littermate cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor control littermate
|
MRF control littermate cultured oligodendrocytes
|
| Sample_geo_accession | GSM387042
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387042/suppl/GSM387042.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387043 | GPL1261 |
|
MRF control Oligodendrocyte Replicate 2
|
MRF control littermate cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor control littermate
|
MRF control littermate cultured oligodendrocytes
|
| Sample_geo_accession | GSM387043
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387043/suppl/GSM387043.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387044 | GPL1261 |
|
MRF control Oligodendrocyte Replicate 3
|
MRF control littermate cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor control littermate
|
MRF control littermate cultured oligodendrocytes
|
| Sample_geo_accession | GSM387044
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387044/suppl/GSM387044.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387045 | GPL1261 |
|
MRF control Oligodendrocyte Replicate 4
|
MRF control littermate cultured oligodendrocytes
|
cell: Cultured oligodendrocytes
genotype: Myelin-gene Regulatory Factor control littermate
|
MRF control littermate cultured oligodendrocytes
|
| Sample_geo_accession | GSM387045
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387045/suppl/GSM387045.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387046 | GPL1261 |
|
Cultured OPCs Control Replicate 1
|
Purified OPCs cultured in PDGF for 6 days
|
cell: Cultured oligodendrocyte progenitors
|
Purified OPCs cultured in PDGF for 6 days
|
| Sample_geo_accession | GSM387046
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387046/suppl/GSM387046.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387047 | GPL1261 |
|
Cultured OPCs Control Replicate 2
|
Purified OPCs cultured in PDGF for 6 days
|
cell: Cultured oligodendrocyte progenitors
|
Purified OPCs cultured in PDGF for 6 days
|
| Sample_geo_accession | GSM387047
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387047/suppl/GSM387047.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387048 | GPL1261 |
|
Cultured OPCs Control Replicate 3
|
Purified OPCs cultured in PDGF for 6 days
|
cell: Cultured oligodendrocyte progenitors
|
Purified OPCs cultured in PDGF for 6 days
|
| Sample_geo_accession | GSM387048
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387048/suppl/GSM387048.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
|
GSM387049 | GPL1261 |
|
Cultured OPCs Control Replicate 4
|
Purified OPCs cultured in PDGF for 6 days
|
cell: Cultured oligodendrocyte progenitors
|
Purified OPCs cultured in PDGF for 6 days
|
| Sample_geo_accession | GSM387049
| | Sample_status | Public on May 31 2009
| | Sample_submission_date | Mar 27 2009
| | Sample_last_update_date | Mar 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).
| | Sample_hyb_protocol | Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_scan_protocol | Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility
| | Sample_data_processing | Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ben,,Emery
| | Sample_contact_email | bemery@stanford.edu
| | Sample_contact_laboratory | Barres
| | Sample_contact_department | Neurobiology
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 299 Campus Dr. W.
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387049/suppl/GSM387049.CEL.gz
| | Sample_series_id | GSE15303
| | Sample_data_row_count | 45101
| | |
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