Result

Search results for the GEO ID: GSE21382

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM534257

GPL570

Jurkat_pMIGR-EGFP_control

Jurkat cells

vector: pMIGR-EGFP protocol: control

Jurkat_co

Sample_geo_accession	GSM534257
Sample_status	Public on Sep 01 2010
Sample_submission_date	Apr 19 2010
Sample_last_update_date	Aug 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The human T cell leukemia and lymphoma cell line Jurkat was maintained in RPMI-1640 medium supplemented with 10% fetal calf serum (PanBiotech Berlin, Germany), Glutamax (Invitrogen, CA, USA) and Plasmocin (Lonza Scientific, Switzerland). The retrovirus producing cell line GP2-293 (Clontech Laboratories, CA, USA) was maintained in Dulbecco’s modified Eagle’s medium (Invitrogen, CA, USA) supplemented as above. For recombinant retrovirus production, non-confluent GP2-293 cells were co-transfected with 10 μg of purified pVSV-G and empty pMIGR plasmid (mock) or pMIGR encoding BCL11B. The transfection procedure was performed using CalPhos Mammalian Transfection Kit (Clontech Laboratories, CA, USA) according to the manufacturer’s instructions. The retrovirus-containing media were collected 48h after transfection and used immediately or stored at 4˚C and used within 7 days. To transduce the target cells, the retroviral supernatants were supplemented with 8 μg/ml Polybrene (Sigma Chemicals, Germany) and added to exponentially growing Jurkat cells for 8 hours. The procedure was repeated three times. The efficiency of gene transfer was estimated by FACS detection of EGFP reporter gene.
Sample_growth_protocol_ch1	The human T cell leukemia and lymphoma cell line Jurkat was maintained in RPMI-1640 medium supplemented with 10% fetal calf serum (PanBiotech Berlin, Germany), Glutamax (Invitrogen, CA, USA) and Plasmocin (Lonza Scientific, Switzerland). The retrovirus producing cell line GP2-293 (Clontech Laboratories, CA, USA) was maintained in Dulbecco’s modified Eagle’s medium (Invitrogen, CA, USA) supplemented as above.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell were lysed in Trizol Reagent (Invitrogen) and total RNA was extracted according to the manufacturer's instructions. RNA was quantified spectrophotometrically (NanoDrop ND-1000; Thermo Fisher Scientific, Wilmington, DE, USA) and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA) were used for synthesis of labeled material for hybridization. The protocol started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of double stranded DNA, DNA purification, in-vitro transcription for amplification and labeling, and purification of resulting cRNA according to the manufacturer’s protocols. Concentration and quality of cRNA were measured with a NanoDrop ND-1000 photometer and an Agilent 2100 Bioanalyzer, respectively.
Sample_hyb_protocol	For hybridization 20 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, of which 15 µg fragmented cRNA were added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA and 10% DMSO in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Human Gene U133 Plus 2.0 were loaded with 200 µl hybridization cocktail (containing 10 µg of fragmented cRNA) and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 450 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Scanner 3000 (Affymetrix, Santa Clara, CA, USA) under the control of GeneChip Operating Software GCOS (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	Analysis of CEL-files was performed in GeneChip Operating Software GCOS 1.4 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 500.
Sample_platform_id	GPL570
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM534nnn/GSM534257/suppl/GSM534257.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM534nnn/GSM534257/suppl/GSM534257.CHP.gz
Sample_series_id	GSE21382
Sample_data_row_count	54675

GSM534258

GPL570

Jurkat_pMIGR-EGFP-Bcl11b_overexpression

Jurkat cells

vector: pMIGR-Bcl11b-EGFP protocol: BCL11B overexpression

Jurkat_Bcl11b-oe

Sample_geo_accession	GSM534258
Sample_status	Public on Sep 01 2010
Sample_submission_date	Apr 19 2010
Sample_last_update_date	Aug 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The human T cell leukemia and lymphoma cell line Jurkat was maintained in RPMI-1640 medium supplemented with 10% fetal calf serum (PanBiotech Berlin, Germany), Glutamax (Invitrogen, CA, USA) and Plasmocin (Lonza Scientific, Switzerland). The retrovirus producing cell line GP2-293 (Clontech Laboratories, CA, USA) was maintained in Dulbecco’s modified Eagle’s medium (Invitrogen, CA, USA) supplemented as above. For recombinant retrovirus production, non-confluent GP2-293 cells were co-transfected with 10 μg of purified pVSV-G and empty pMIGR plasmid (mock) or pMIGR encoding BCL11B. The transfection procedure was performed using CalPhos Mammalian Transfection Kit (Clontech Laboratories, CA, USA) according to the manufacturer’s instructions. The retrovirus-containing media were collected 48h after transfection and used immediately or stored at 4˚C and used within 7 days. To transduce the target cells, the retroviral supernatants were supplemented with 8 μg/ml Polybrene (Sigma Chemicals, Germany) and added to exponentially growing Jurkat cells for 8 hours. The procedure was repeated three times. The efficiency of gene transfer was estimated by FACS detection of EGFP reporter gene.
Sample_growth_protocol_ch1	The human T cell leukemia and lymphoma cell line Jurkat was maintained in RPMI-1640 medium supplemented with 10% fetal calf serum (PanBiotech Berlin, Germany), Glutamax (Invitrogen, CA, USA) and Plasmocin (Lonza Scientific, Switzerland). The retrovirus producing cell line GP2-293 (Clontech Laboratories, CA, USA) was maintained in Dulbecco’s modified Eagle’s medium (Invitrogen, CA, USA) supplemented as above.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell were lysed in Trizol Reagent (Invitrogen) and total RNA was extracted according to the manufacturer's instructions. RNA was quantified spectrophotometrically (NanoDrop ND-1000; Thermo Fisher Scientific, Wilmington, DE, USA) and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA) were used for synthesis of labeled material for hybridization. The protocol started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of double stranded DNA, DNA purification, in-vitro transcription for amplification and labeling, and purification of resulting cRNA according to the manufacturer’s protocols. Concentration and quality of cRNA were measured with a NanoDrop ND-1000 photometer and an Agilent 2100 Bioanalyzer, respectively.
Sample_hyb_protocol	For hybridization 20 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, of which 15 µg fragmented cRNA were added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA and 10% DMSO in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Human Gene U133 Plus 2.0 were loaded with 200 µl hybridization cocktail (containing 10 µg of fragmented cRNA) and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 450 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Scanner 3000 (Affymetrix, Santa Clara, CA, USA) under the control of GeneChip Operating Software GCOS (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	Analysis of CEL-files was performed in GeneChip Operating Software GCOS 1.4 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 500.
Sample_platform_id	GPL570
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM534nnn/GSM534258/suppl/GSM534258.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM534nnn/GSM534258/suppl/GSM534258.CHP.gz
Sample_series_id	GSE21382
Sample_data_row_count	54675

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