Result

Search results for the GEO ID: GSE11829

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM298941

GPL1355

control 1

rat brain

Cerebral cortices from 19-day-old fetal SD rats (E19)

Primary cortical cells were transfected with control or math2 vector

Sample_geo_accession	GSM298941
Sample_status	Public on Jul 27 2008
Sample_submission_date	Jun 19 2008
Sample_last_update_date	Jul 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Clea Japan, Tokyo, Japan
Sample_treatment_protocol_ch1	Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit according to the manufacturer's protocol.
Sample_growth_protocol_ch1	The culture medium used was Eagle MEM supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.
Sample_scan_protocol	Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000
Sample_data_processing	Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.
Sample_platform_id	GPL1355
Sample_contact_name	Kou,,Takahashi
Sample_contact_email	kou@ncnp.go.jp
Sample_contact_institute	NCNP
Sample_contact_address	4-1-1 Ogawahigashimachi, Kodaira
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	187-8553
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298941/suppl/GSM298941.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298941/suppl/GSM298941.CHP.gz
Sample_series_id	GSE11829
Sample_data_row_count	31099

GSM298942

GPL1355

control 2

rat brain

Cerebral cortices from 19-day-old fetal SD rats (E19)

Primary cortical cells were transfected with control or math2 vector

Sample_geo_accession	GSM298942
Sample_status	Public on Jul 27 2008
Sample_submission_date	Jun 19 2008
Sample_last_update_date	Jul 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Clea Japan, Tokyo, Japan
Sample_treatment_protocol_ch1	Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit according to the manufacturer's protocol.
Sample_growth_protocol_ch1	The culture medium used was Eagle MEM supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.
Sample_scan_protocol	Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000
Sample_data_processing	Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.
Sample_platform_id	GPL1355
Sample_contact_name	Kou,,Takahashi
Sample_contact_email	kou@ncnp.go.jp
Sample_contact_institute	NCNP
Sample_contact_address	4-1-1 Ogawahigashimachi, Kodaira
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	187-8553
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298942/suppl/GSM298942.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298942/suppl/GSM298942.CHP.gz
Sample_series_id	GSE11829
Sample_data_row_count	31099

GSM298943

GPL1355

control 3

rat brain

Cerebral cortices from 19-day-old fetal SD rats (E19)

Primary cortical cells were transfected with control or math2 vector

Sample_geo_accession	GSM298943
Sample_status	Public on Jul 27 2008
Sample_submission_date	Jun 19 2008
Sample_last_update_date	Jul 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Clea Japan, Tokyo, Japan
Sample_treatment_protocol_ch1	Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit according to the manufacturer's protocol.
Sample_growth_protocol_ch1	The culture medium used was Eagle MEM supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.
Sample_scan_protocol	Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000
Sample_data_processing	Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.
Sample_platform_id	GPL1355
Sample_contact_name	Kou,,Takahashi
Sample_contact_email	kou@ncnp.go.jp
Sample_contact_institute	NCNP
Sample_contact_address	4-1-1 Ogawahigashimachi, Kodaira
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	187-8553
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298943/suppl/GSM298943.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298943/suppl/GSM298943.CHP.gz
Sample_series_id	GSE11829
Sample_data_row_count	31099

GSM298944

GPL1355

Math2 1

Rat brain

Cerebral cortices from 19-day-old fetal SD rats (E19)

Primary cortical cells were transfected with control or math2 vector

Sample_geo_accession	GSM298944
Sample_status	Public on Jul 27 2008
Sample_submission_date	Jun 19 2008
Sample_last_update_date	Jul 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Clea Japan, Tokyo, Japan
Sample_treatment_protocol_ch1	Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit according to the manufacturer's protocol.
Sample_growth_protocol_ch1	The culture medium used was Eagle MEM supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.
Sample_scan_protocol	Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000
Sample_data_processing	Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.
Sample_platform_id	GPL1355
Sample_contact_name	Kou,,Takahashi
Sample_contact_email	kou@ncnp.go.jp
Sample_contact_institute	NCNP
Sample_contact_address	4-1-1 Ogawahigashimachi, Kodaira
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	187-8553
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298944/suppl/GSM298944.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298944/suppl/GSM298944.CHP.gz
Sample_series_id	GSE11829
Sample_data_row_count	31099

GSM298945

GPL1355

Math2 2

Rat brain

Cerebral cortices from 19-day-old fetal SD rats (E19)

Primary cortical cells were transfected with control or math2 vector

Sample_geo_accession	GSM298945
Sample_status	Public on Jul 27 2008
Sample_submission_date	Jun 19 2008
Sample_last_update_date	Jul 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Clea Japan, Tokyo, Japan
Sample_treatment_protocol_ch1	Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit according to the manufacturer's protocol.
Sample_growth_protocol_ch1	The culture medium used was Eagle MEM supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.
Sample_scan_protocol	Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000
Sample_data_processing	Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.
Sample_platform_id	GPL1355
Sample_contact_name	Kou,,Takahashi
Sample_contact_email	kou@ncnp.go.jp
Sample_contact_institute	NCNP
Sample_contact_address	4-1-1 Ogawahigashimachi, Kodaira
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	187-8553
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298945/suppl/GSM298945.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298945/suppl/GSM298945.CHP.gz
Sample_series_id	GSE11829
Sample_data_row_count	31099

GSM298946

GPL1355

Math2 3

Rat brain

Cerebral cortices from 19-day-old fetal SD rats (E19)

Primary cortical cells were transfected with control or math2 vector

Sample_geo_accession	GSM298946
Sample_status	Public on Jul 27 2008
Sample_submission_date	Jun 19 2008
Sample_last_update_date	Jul 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Clea Japan, Tokyo, Japan
Sample_treatment_protocol_ch1	Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit according to the manufacturer's protocol.
Sample_growth_protocol_ch1	The culture medium used was Eagle MEM supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.
Sample_scan_protocol	Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000
Sample_data_processing	Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.
Sample_platform_id	GPL1355
Sample_contact_name	Kou,,Takahashi
Sample_contact_email	kou@ncnp.go.jp
Sample_contact_institute	NCNP
Sample_contact_address	4-1-1 Ogawahigashimachi, Kodaira
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	187-8553
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298946/suppl/GSM298946.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM298nnn/GSM298946/suppl/GSM298946.CHP.gz
Sample_series_id	GSE11829
Sample_data_row_count	31099

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes