Result

Search results for the GEO ID: GSE13493

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM340091

GPL1261

DP thymocytes 1

CD4+CD8+ immature thymocytes

N15TCR+/+Rag2-/- Age: 5-6 weeks old

Gene expression data from N15TCR+/+Rag2-/- DP thymocytes

Sample_geo_accession	GSM340091
Sample_status	Public on Mar 31 2009
Sample_submission_date	Nov 06 2008
Sample_last_update_date	Nov 06 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies
Sample_growth_protocol_ch1	Mice at the specific age were kept in DanaFarber Cancer Institute animal facility
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.
Sample_hyb_protocol	The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h. After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.
Sample_scan_protocol	The chips were scanned in an HIP chip scanner (Affymetrix)
Sample_data_processing	the scanned results were analyzed by dChip
Sample_data_processing	cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline
Sample_platform_id	GPL1261
Sample_contact_name	Young,IL,Choi
Sample_contact_email	young_choi@dfci.harvard.edu
Sample_contact_phone	617-582-8116
Sample_contact_fax	617-632-3351
Sample_contact_laboratory	Immunobiology
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	77 Avenue Louis Pasteur
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM340nnn/GSM340091/suppl/GSM340091.CEL.gz
Sample_series_id	GSE13493
Sample_data_row_count	45101

GSM340092

GPL1261

DP thymocytes 2

CD4+CD8+ immature thymocytes

N15TCR+/+Rag2-/- Age: 5-6 weeks old

Gene expression data from N15TCR+/+Rag2-/- DP thymocytes

Sample_geo_accession	GSM340092
Sample_status	Public on Mar 31 2009
Sample_submission_date	Nov 06 2008
Sample_last_update_date	Nov 06 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies
Sample_growth_protocol_ch1	Mice at the specific age were kept in DanaFarber Cancer Institute animal facility
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.
Sample_hyb_protocol	The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h. After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.
Sample_scan_protocol	The chips were scanned in an HIP chip scanner (Affymetrix)
Sample_data_processing	the scanned results were analyzed by dChip
Sample_data_processing	cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline
Sample_platform_id	GPL1261
Sample_contact_name	Young,IL,Choi
Sample_contact_email	young_choi@dfci.harvard.edu
Sample_contact_phone	617-582-8116
Sample_contact_fax	617-632-3351
Sample_contact_laboratory	Immunobiology
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	77 Avenue Louis Pasteur
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM340nnn/GSM340092/suppl/GSM340092.CEL.gz
Sample_series_id	GSE13493
Sample_data_row_count	45101

GSM340093

GPL1261

CD4intCD8+ thymocytes 1

CD4intCD8+ maturing thymocytes

N15TCR+/+Rag2-/- Age: 5-6 weeks old

Gene expression data from N15TCR+/+Rag2-/- CD4intCD8+ thymocytes

Sample_geo_accession	GSM340093
Sample_status	Public on Mar 31 2009
Sample_submission_date	Nov 06 2008
Sample_last_update_date	Nov 06 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies
Sample_growth_protocol_ch1	Mice at the specific age were kept in DanaFarber Cancer Institute animal facility
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.
Sample_hyb_protocol	The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h. After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.
Sample_scan_protocol	The chips were scanned in an HIP chip scanner (Affymetrix)
Sample_data_processing	the scanned results were analyzed by dChip
Sample_data_processing	cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline
Sample_platform_id	GPL1261
Sample_contact_name	Young,IL,Choi
Sample_contact_email	young_choi@dfci.harvard.edu
Sample_contact_phone	617-582-8116
Sample_contact_fax	617-632-3351
Sample_contact_laboratory	Immunobiology
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	77 Avenue Louis Pasteur
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM340nnn/GSM340093/suppl/GSM340093.CEL.gz
Sample_series_id	GSE13493
Sample_data_row_count	45101

GSM340094

GPL1261

CD4intCD8+ thymocytes 2

CD4intCD8+ maturing thymocytes

N15TCR+/+Rag2-/- Age: 5-6 weeks old

Gene expression data from N15TCR+/+Rag2-/- CD4intCD8+ thymocytes

Sample_geo_accession	GSM340094
Sample_status	Public on Mar 31 2009
Sample_submission_date	Nov 06 2008
Sample_last_update_date	Nov 06 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies
Sample_growth_protocol_ch1	Mice at the specific age were kept in DanaFarber Cancer Institute animal facility
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.
Sample_hyb_protocol	The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h. After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.
Sample_scan_protocol	The chips were scanned in an HIP chip scanner (Affymetrix)
Sample_data_processing	the scanned results were analyzed by dChip
Sample_data_processing	cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline
Sample_platform_id	GPL1261
Sample_contact_name	Young,IL,Choi
Sample_contact_email	young_choi@dfci.harvard.edu
Sample_contact_phone	617-582-8116
Sample_contact_fax	617-632-3351
Sample_contact_laboratory	Immunobiology
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	77 Avenue Louis Pasteur
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM340nnn/GSM340094/suppl/GSM340094.CEL.gz
Sample_series_id	GSE13493
Sample_data_row_count	45101

GSM340095

GPL1261

CD8SP thymocytes 1

CD4-CD8+ mature thymocytes

N15TCR+/+Rag2-/- Age: 5-6 weeks old

Gene expression data from N15TCR+/+Rag2-/- CD8SP thymocytes

Sample_geo_accession	GSM340095
Sample_status	Public on Mar 31 2009
Sample_submission_date	Nov 06 2008
Sample_last_update_date	Nov 06 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies
Sample_growth_protocol_ch1	Mice at the specific age were kept in DanaFarber Cancer Institute animal facility
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.
Sample_hyb_protocol	The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h. After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.
Sample_scan_protocol	The chips were scanned in an HIP chip scanner (Affymetrix)
Sample_data_processing	the scanned results were analyzed by dChip
Sample_data_processing	cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline
Sample_platform_id	GPL1261
Sample_contact_name	Young,IL,Choi
Sample_contact_email	young_choi@dfci.harvard.edu
Sample_contact_phone	617-582-8116
Sample_contact_fax	617-632-3351
Sample_contact_laboratory	Immunobiology
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	77 Avenue Louis Pasteur
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM340nnn/GSM340095/suppl/GSM340095.CEL.gz
Sample_series_id	GSE13493
Sample_data_row_count	45101

GSM340096

GPL1261

CD8SP thymocytes 2

CD4-CD8+ mature thymocytes

N15TCR+/+Rag2-/- Age: 5-6 weeks old

Gene expression data from N15TCR+/+Rag2-/- CD8SP thymocytes

Sample_geo_accession	GSM340096
Sample_status	Public on Mar 31 2009
Sample_submission_date	Nov 06 2008
Sample_last_update_date	Nov 06 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies
Sample_growth_protocol_ch1	Mice at the specific age were kept in DanaFarber Cancer Institute animal facility
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.
Sample_hyb_protocol	The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h. After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.
Sample_scan_protocol	The chips were scanned in an HIP chip scanner (Affymetrix)
Sample_data_processing	the scanned results were analyzed by dChip
Sample_data_processing	cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline
Sample_platform_id	GPL1261
Sample_contact_name	Young,IL,Choi
Sample_contact_email	young_choi@dfci.harvard.edu
Sample_contact_phone	617-582-8116
Sample_contact_fax	617-632-3351
Sample_contact_laboratory	Immunobiology
Sample_contact_department	Medical Oncology
Sample_contact_institute	Dana-Farber Cancer Institute
Sample_contact_address	77 Avenue Louis Pasteur
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM340nnn/GSM340096/suppl/GSM340096.CEL.gz
Sample_series_id	GSE13493
Sample_data_row_count	45101

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