Result

Search results for the GEO ID: GSE6022

(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

GSM139836

GPL570

Total cDNA from HeLa cell extract from Immunoprecipitation experiment 1 U2AF

HeLa cell cytoplasmic extract

HeLa cell line

Total cDNA from HeLa cell extract from Immunoprecipitation experiment 1

Sample_geo_accession	GSM139836
Sample_status	Public on Oct 14 2006
Sample_submission_date	Oct 12 2006
Sample_last_update_date	Oct 13 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Gama-Carvalho et al, 2006
Sample_growth_protocol_ch1	Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin
Sample_hyb_protocol	hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols
Sample_scan_protocol	Gama-Carvalho et al, 2006
Sample_data_processing	The data were analyzed with dChip using default analysis settings. The model based expression index was calculated using the PM/MM model
Sample_platform_id	GPL570
Sample_contact_name	Margarida,,Gama-Carvalho
Sample_contact_email	m.gamacarvalho@fm.ul.pt
Sample_contact_institute	Institute of Molecular Medicine
Sample_contact_address	Av. Prof. Egas Moniz
Sample_contact_city	Lisboa
Sample_contact_zip/postal_code	1649-028
Sample_contact_country	Portugal
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM139nnn/GSM139836/suppl/GSM139836.CEL.gz
Sample_series_id	GSE6022
Sample_data_row_count	54675

GSM139837

GPL570

Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 1 U2AF

anti-U2AF65 immunoprecipitate from HeLa cell cytoplasmic extract

HeLa cell line

Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 1

Sample_geo_accession	GSM139837
Sample_status	Public on Oct 14 2006
Sample_submission_date	Oct 12 2006
Sample_last_update_date	Oct 13 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Gama-Carvalho et al, 2006
Sample_growth_protocol_ch1	Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin
Sample_hyb_protocol	hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols
Sample_scan_protocol	Gama-Carvalho et al, 2006
Sample_data_processing	The data were analyzed with dChip using default analysis settings. The model based expression index was calculated using the PM/MM model
Sample_platform_id	GPL570
Sample_contact_name	Margarida,,Gama-Carvalho
Sample_contact_email	m.gamacarvalho@fm.ul.pt
Sample_contact_institute	Institute of Molecular Medicine
Sample_contact_address	Av. Prof. Egas Moniz
Sample_contact_city	Lisboa
Sample_contact_zip/postal_code	1649-028
Sample_contact_country	Portugal
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM139nnn/GSM139837/suppl/GSM139837.CEL.gz
Sample_series_id	GSE6022
Sample_data_row_count	54675

GSM139838

GPL570

Total cDNA from HeLa cell extract from Immunoprecipitation experiment 2 U2AF

HeLa cell cytoplasmic extract

HeLa cell line

Total cDNA from HeLa cell extract from Immunoprecipitation experiment 2

Sample_geo_accession	GSM139838
Sample_status	Public on Oct 14 2006
Sample_submission_date	Oct 12 2006
Sample_last_update_date	Oct 13 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Gama-Carvalho et al, 2006
Sample_growth_protocol_ch1	Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin
Sample_hyb_protocol	hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols
Sample_scan_protocol	Gama-Carvalho et al, 2006
Sample_data_processing	The data were analyzed with dChip using default analysis settings. The model based expression index was calculated using the PM/MM model
Sample_platform_id	GPL570
Sample_contact_name	Margarida,,Gama-Carvalho
Sample_contact_email	m.gamacarvalho@fm.ul.pt
Sample_contact_institute	Institute of Molecular Medicine
Sample_contact_address	Av. Prof. Egas Moniz
Sample_contact_city	Lisboa
Sample_contact_zip/postal_code	1649-028
Sample_contact_country	Portugal
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM139nnn/GSM139838/suppl/GSM139838.CEL.gz
Sample_series_id	GSE6022
Sample_data_row_count	54675

GSM139839

GPL570

Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 2 U2AF

anti-U2AF65 immunoprecipitate from HeLa cell cytoplasmic extract

HeLa cell line

Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 2

Sample_geo_accession	GSM139839
Sample_status	Public on Oct 14 2006
Sample_submission_date	Oct 12 2006
Sample_last_update_date	Oct 13 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Gama-Carvalho et al, 2006
Sample_growth_protocol_ch1	Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin
Sample_hyb_protocol	hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols
Sample_scan_protocol	Gama-Carvalho et al, 2006
Sample_data_processing	The data were analyzed with dChip using default analysis settings. The model based expression index was calculated using the PM/MM model
Sample_platform_id	GPL570
Sample_contact_name	Margarida,,Gama-Carvalho
Sample_contact_email	m.gamacarvalho@fm.ul.pt
Sample_contact_institute	Institute of Molecular Medicine
Sample_contact_address	Av. Prof. Egas Moniz
Sample_contact_city	Lisboa
Sample_contact_zip/postal_code	1649-028
Sample_contact_country	Portugal
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM139nnn/GSM139839/suppl/GSM139839.CEL.gz
Sample_series_id	GSE6022
Sample_data_row_count	54675

GSM139840

GPL570

Total cDNA from HeLa cell extract from Immunoprecipitation experiment 3 U2AF

HeLa cell cytoplasmic extract

HeLa cell line

Total cDNA from HeLa cell extract from Immunoprecipitation experiment 3

Sample_geo_accession	GSM139840
Sample_status	Public on Oct 14 2006
Sample_submission_date	Oct 12 2006
Sample_last_update_date	Oct 13 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Gama-Carvalho et al, 2006
Sample_growth_protocol_ch1	Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin
Sample_hyb_protocol	hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols
Sample_scan_protocol	Gama-Carvalho et al, 2006
Sample_data_processing	The data were analyzed with dChip using default analysis settings. The model based expression index was calculated using the PM/MM model
Sample_platform_id	GPL570
Sample_contact_name	Margarida,,Gama-Carvalho
Sample_contact_email	m.gamacarvalho@fm.ul.pt
Sample_contact_institute	Institute of Molecular Medicine
Sample_contact_address	Av. Prof. Egas Moniz
Sample_contact_city	Lisboa
Sample_contact_zip/postal_code	1649-028
Sample_contact_country	Portugal
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM139nnn/GSM139840/suppl/GSM139840.CEL.gz
Sample_series_id	GSE6022
Sample_data_row_count	54675

GSM139841

GPL570

Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 3 U2AF

anti-U2AF65 immunoprecipitate from HeLa cell cytoplasmic extract

HeLa cell line

Immunoprecipitated cDNA HeLa cell extract from Immunoprecipitation experiment 3

Sample_geo_accession	GSM139841
Sample_status	Public on Oct 14 2006
Sample_submission_date	Oct 12 2006
Sample_last_update_date	Oct 13 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Gama-Carvalho et al, 2006
Sample_growth_protocol_ch1	Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting.
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	mRNAs were isolated by immunoprecipitation from 200ul of precleared HeLa cell extract, using the anti-U2AF65 MC3 mAb (Gama-Carvalho, Krauss et al. 1997) or the Bb7 anti-PTB mAb (ATCC) for 2h at 4C. Immune complexes were precipitated with a slurry with 50% of protein A/protein G agarose beads (Amersham), blocked with 100ug/ul of tRNA and RNAse free BSA (Ambion), by rotating for 1h at 4C and washed with lysis buffer. Complexes bound to the beads were eluted with TES buffer (10mM Tris, 0.5M EDTA, 0.5% SDS, pH 8.0) by heating at 65C for 10 minutes and Trizol extracted. Polyadenilated RNA in the cell extract (input) and in the immunoprecipitation sample was reverse transcribed, end-tagged and PCR amplified using the Super SMART PCR cDNA synthesis kit from Clontech, following manufacturer instructions. 1ug of input or precipitated RNA was used per RT-PCR reaction to produce samples for microarray hybridization. For each set of samples (input and immunoprecipitated) a 100ul test PCR reaction was performed according to manufacturer instructions and analyzed by agarose gel electrophoresis to select ideal conditions for amplification in the linear range. PCR reactions were pooled to obtain enough material for microarray hybridization.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	15ug of PCR amplified cDNA from input and immunoprecipitated samples were fragmented, end labeled with biotin
Sample_hyb_protocol	hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays as described (Brodsky, Meyer et al. 2005), following standard Affymetrix hybridization protocols
Sample_scan_protocol	Gama-Carvalho et al, 2006
Sample_data_processing	The data were analyzed with dChip using default analysis settings. The model based expression index was calculated using the PM/MM model
Sample_platform_id	GPL570
Sample_contact_name	Margarida,,Gama-Carvalho
Sample_contact_email	m.gamacarvalho@fm.ul.pt
Sample_contact_institute	Institute of Molecular Medicine
Sample_contact_address	Av. Prof. Egas Moniz
Sample_contact_city	Lisboa
Sample_contact_zip/postal_code	1649-028
Sample_contact_country	Portugal
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM139nnn/GSM139841/suppl/GSM139841.CEL.gz
Sample_series_id	GSE6022
Sample_data_row_count	54675

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