Result

Search results for the GEO ID: GSE10796

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Title

Source name

Description

Characteristics

GSM272667

GPL1261

Neuroepithelial cell from telencephalons of embryonic day 11.5 mouse cultured for one day E11-1

Neuroepithelial cell from telencephalons of embryonic day 11.5 mouse cultured for one day

Strain: ICR

None

Sample_geo_accession	GSM272667
Sample_status	Public on Jul 31 2008
Sample_submission_date	Mar 12 2008
Sample_last_update_date	Jun 20 2008
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	The total RNA was purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) according to the manufacturer's instruction.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.
Sample_hyb_protocol	For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.
Sample_scan_protocol	Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.
Sample_data_processing	Data transformation algorithm and normalization was done by Affymetrix GCOS.
Sample_data_processing	Scaling:All Probe Sets, Target Signal=500
Sample_data_processing	Normalization value:1
Sample_data_processing	Parameters: defalut settings
Sample_platform_id	GPL1261
Sample_contact_name	Tsukasa,,Sanosaka
Sample_contact_email	t-sanosa@bs.naist.jp
Sample_contact_laboratory	molecular neuroscience
Sample_contact_department	bioscience
Sample_contact_institute	NAIST
Sample_contact_address	8916-5
Sample_contact_city	Ikoma
Sample_contact_state	Nara
Sample_contact_zip/postal_code	630-0101
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272667/suppl/GSM272667.CEL.gz
Sample_series_id	GSE10796
Sample_data_row_count	45101

GSM272668

GPL1261

Neuroepithelial cell from telencephalons of embryonic day 11.5 mouse cultured for one day E11-2

Neuroepithelial cell from telencephalons of embryonic day 11.5 mouse cultured for one day

Strain: ICR

None

Sample_geo_accession	GSM272668
Sample_status	Public on Jul 31 2008
Sample_submission_date	Mar 12 2008
Sample_last_update_date	Jun 20 2008
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	The total RNA was purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) according to the manufacturer's instruction.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.
Sample_hyb_protocol	For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.
Sample_scan_protocol	Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.
Sample_data_processing	Data transformation algorithm and normalization was done by Affymetrix GCOS.
Sample_data_processing	Scaling:All Probe Sets, Target Signal=500
Sample_data_processing	Normalization value:1
Sample_data_processing	Parameters: defalut settings
Sample_platform_id	GPL1261
Sample_contact_name	Tsukasa,,Sanosaka
Sample_contact_email	t-sanosa@bs.naist.jp
Sample_contact_laboratory	molecular neuroscience
Sample_contact_department	bioscience
Sample_contact_institute	NAIST
Sample_contact_address	8916-5
Sample_contact_city	Ikoma
Sample_contact_state	Nara
Sample_contact_zip/postal_code	630-0101
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272668/suppl/GSM272668.CEL.gz
Sample_series_id	GSE10796
Sample_data_row_count	45101

GSM272669

GPL1261

Neuroepithelial cell from telencephalons of embryonic day 14.5 mouse cultured for four days E14-1

Neuroepithelial cell from telencephalons of embryonic day 14.5 mouse cultured for four days

Strain: ICR

None

Sample_geo_accession	GSM272669
Sample_status	Public on Jul 31 2008
Sample_submission_date	Mar 12 2008
Sample_last_update_date	Jun 20 2008
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	The total RNA was purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) according to the manufacturer's instruction.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.
Sample_hyb_protocol	For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.
Sample_scan_protocol	Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.
Sample_data_processing	Data transformation algorithm and normalization was done by Affymetrix GCOS.
Sample_data_processing	Scaling:All Probe Sets, Target Signal=500
Sample_data_processing	Normalization value:1
Sample_data_processing	Parameters: defalut settings
Sample_platform_id	GPL1261
Sample_contact_name	Tsukasa,,Sanosaka
Sample_contact_email	t-sanosa@bs.naist.jp
Sample_contact_laboratory	molecular neuroscience
Sample_contact_department	bioscience
Sample_contact_institute	NAIST
Sample_contact_address	8916-5
Sample_contact_city	Ikoma
Sample_contact_state	Nara
Sample_contact_zip/postal_code	630-0101
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272669/suppl/GSM272669.CEL.gz
Sample_series_id	GSE10796
Sample_data_row_count	45101

GSM272670

GPL1261

Neuroepithelial cell from telencephalons of embryonic day 14.5 mouse cultured for four days E14-2

Neuroepithelial cell from telencephalons of embryonic day 14.5 mouse cultured for four days

Strain: ICR

None

Sample_geo_accession	GSM272670
Sample_status	Public on Jul 31 2008
Sample_submission_date	Mar 12 2008
Sample_last_update_date	Jun 20 2008
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	The total RNA was purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) according to the manufacturer's instruction.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.
Sample_hyb_protocol	For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.
Sample_scan_protocol	Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.
Sample_data_processing	Data transformation algorithm and normalization was done by Affymetrix GCOS.
Sample_data_processing	Scaling:All Probe Sets, Target Signal=500
Sample_data_processing	Normalization value:1
Sample_data_processing	Parameters: defalut settings
Sample_platform_id	GPL1261
Sample_contact_name	Tsukasa,,Sanosaka
Sample_contact_email	t-sanosa@bs.naist.jp
Sample_contact_laboratory	molecular neuroscience
Sample_contact_department	bioscience
Sample_contact_institute	NAIST
Sample_contact_address	8916-5
Sample_contact_city	Ikoma
Sample_contact_state	Nara
Sample_contact_zip/postal_code	630-0101
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272670/suppl/GSM272670.CEL.gz
Sample_series_id	GSE10796
Sample_data_row_count	45101

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