Search results for the GEO ID: GSE19176  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM469557 | GPL1261 |
|
Wild type primary cerebellar granule progenitor cells 1
|
Mouse cerebellar granule cells primary culture
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: wild type
|
1_Bmi1plusCGCs.CEL
mz_141205_mz_1_Bmi1++CGCs.CHP
|
| Sample_geo_accession | GSM469557
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 11 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P5–7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 96-, 24- or 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469557/suppl/GSM469557.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469557/suppl/GSM469557.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM469987 | GPL1261 |
|
Wild type primary cerebellar granule progenitor cells 3
|
Cerebellar granule progenitor cells
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: wild type
|
3_Bmi1plusCGCs.CEL
mz_141205_mz_3_Bmi1++CGCs.CHP
|
| Sample_geo_accession | GSM469987
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | Shh (R&D Systems)i f applicable was added for 24 hours to give a at final concentration of 3 mg/ml.
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 96-, 24- or 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469987/suppl/GSM469987.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469987/suppl/GSM469987.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM469988 | GPL1261 |
|
Bmi1 knockout primary cerebellar granule progenitor cells 2
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: Bmi1 knockout
|
2_Bmi1minusCGCs.CEL
mz_141205_mz_2_Bmi1--CGCs.CHP
|
| Sample_geo_accession | GSM469988
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469988/suppl/GSM469988.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469988/suppl/GSM469988.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM470014 | GPL1261 |
|
Bmi1 knockout primary cerebellar granule progenitor cells 4
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: Bmi1 knockout
|
4_Bmi1minusCGCs.CEL
mz_141205_mz_4_Bmi1--CGCs.CHP
|
| Sample_geo_accession | GSM470014
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 Bmi-1 knockout mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470014/suppl/GSM470014.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470014/suppl/GSM470014.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM470015 | GPL1261 |
|
Wild type primary cerebellar granule progenitor cells treated with Shh 7
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: wild type
treatment group: treated with Shh
|
7_Bmi1plusShh.CEL
mz_141205_mz_7_Bmi1++Shh.CHP
|
| Sample_geo_accession | GSM470015
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | Shh (R&D Systems) was added for 24 hours to give a at final concentration of 3 mg/ml.
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470015/suppl/GSM470015.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470015/suppl/GSM470015.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM470016 | GPL1261 |
|
Bmi-1 knockout primary cerebellar granule progenitor cells treated with Shh 8
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: Bmi1 knockout
treatment group: treated with Shh
|
8_Bmi1minusShh.CEL
mz_141205_mz_8_Bmi1--Shh.CHP
|
| Sample_geo_accession | GSM470016
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | Shh (R&D Systems) was added for 24 hours to give a at final concentration of 3 mg/ml.
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 Bmi-1 knockout mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470016/suppl/GSM470016.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470016/suppl/GSM470016.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM470057 | GPL1261 |
|
Wild type primary cerebellar granule progenitor cells 5
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: wild type
|
5_Bmi1plusCGCs.CEL
mz_141205_mz_5_Bmi1++CGCs.CHP
|
| Sample_geo_accession | GSM470057
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470057/suppl/GSM470057.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470057/suppl/GSM470057.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM470058 | GPL1261 |
|
Bmi-1- knockout primary cerebellar granule progenitor cells 6
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: Bmi1 knockout
|
6_Bmi1minusCGCs.CEL
mz_141205_mz_6_Bmi1--CGCs.CHP
|
| Sample_geo_accession | GSM470058
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | O.Shakhova, Institute of Surgical Pathology, University Hospital, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 Bmi-1 knockout mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470058/suppl/GSM470058.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470058/suppl/GSM470058.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
GSM470059 | GPL1261 |
|
Wild type primary cerebellar granule progenitor cells treated with Shh 9
|
Cerebellum
|
cell type: Primary cerebellar granule precursor cells (GCPs)
tissue: cerebellum (brain)
developmental stage: P5-7
genome/variation: wild type
treatment group: treated with Shh
|
9_Bmi1plusShh.CEL
mz_141205_mz_9_Bmi1++Shh.CHP
|
| Sample_geo_accession | GSM470059
| | Sample_status | Public on Jan 20 2010
| | Sample_submission_date | Nov 12 2009
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Shh (R&D Systems) was added for 24 hours to give a at final concentration of 3 mg/ml.
| | Sample_growth_protocol_ch1 | Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100
| | Sample_hyb_protocol | Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
| | Sample_data_processing | Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
| | Sample_data_processing | in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tatiana,,Subkhankulova
| | Sample_contact_email | subkhankul@hotmail.com
| | Sample_contact_phone | 02075941825
| | Sample_contact_laboratory | Silvia Marino
| | Sample_contact_department | Neuroscience
| | Sample_contact_institute | Queen Mary University London
| | Sample_contact_address | 4 Newark Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | E1 2AD
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470059/suppl/GSM470059.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470059/suppl/GSM470059.CHP.gz
| | Sample_series_id | GSE19176
| | Sample_data_row_count | 45101
| | |
|
| |
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