Result

Search results for the GEO ID: GSE17772

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM443832

GPL570

hTFC_1

Human testis biopsy sample

tissue: testis isolate: biopsy sample was obtained from patient (patient 16)

BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

Sample_geo_accession	GSM443832
Sample_status	Public on Jun 29 2010
Sample_submission_date	Aug 24 2009
Sample_last_update_date	Jun 29 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Department of Urology in University of Muenster, Muenster, Germany, Dr. Sabine Kliesch
Sample_growth_protocol_ch1	hTFCs were derived from human testis biopsy. The cells were cultured for 10 days in basic medium (DMEM high glucose, 15% FCS, 1% non-essential amino acids, 1% L-glutamin and 0.05 mM beta-mercaptoethanol, and 1000 units/ml leukemia inhibitory factor (LIF) on 0.1% gelatin coated dishes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The cluster of cells were mechanically harvested and washed with PBS. The cells were centrifuged at 1000 rpm at 4C fro 5 mins. Total RNAs were isolated using Qiagen RNeasy kit. Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Data postprocessing and graphics were performed using in-house developed functions in Matlab®.
Sample_platform_id	GPL570
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM443nnn/GSM443832/suppl/GSM443832.CEL.gz
Sample_series_id	GSE17772
Sample_data_row_count	54675

GSM443833

GPL570

hTFC_2

Human testis biopsy sample

tissue: testis isolate: biopsy sample was obtained from patient (patient 16)

Sample_geo_accession	GSM443833
Sample_status	Public on Jun 29 2010
Sample_submission_date	Aug 24 2009
Sample_last_update_date	Jun 29 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Department of Urology in University of Muenster, Muenster, Germany, Dr. Sabine Kliesch
Sample_growth_protocol_ch1	hTFCs were derived from human testis biopsy. The cells were cultured for 10 days in basic medium (DMEM high glucose, 15% FCS, 1% non-essential amino acids, 1% L-glutamin and 0.05 mM beta-mercaptoethanol, and 1000 units/ml leukemia inhibitory factor (LIF) on 0.1% gelatin coated dishes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The cluster of cells were mechanically harvested and washed with PBS. The cells were centrifuged at 1000 rpm at 4C fro 5 mins. Total RNAs were isolated using Qiagen RNeasy kit. Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Data postprocessing and graphics were performed using in-house developed functions in Matlab®.
Sample_platform_id	GPL570
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM443nnn/GSM443833/suppl/GSM443833.CEL.gz
Sample_series_id	GSE17772
Sample_data_row_count	54675

GSM443834

GPL570

hTFC_3

Human testis biopsy sample

tissue: testis isolate: biopsy sample was obtained from patient (patient 16)

Sample_geo_accession	GSM443834
Sample_status	Public on Jun 29 2010
Sample_submission_date	Aug 24 2009
Sample_last_update_date	Jun 29 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Department of Urology in University of Muenster, Muenster, Germany, Dr. Sabine Kliesch
Sample_growth_protocol_ch1	hTFCs were derived from human testis biopsy. The cells were cultured for 10 days in basic medium (DMEM high glucose, 15% FCS, 1% non-essential amino acids, 1% L-glutamin and 0.05 mM beta-mercaptoethanol, and 1000 units/ml leukemia inhibitory factor (LIF) on 0.1% gelatin coated dishes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The cluster of cells were mechanically harvested and washed with PBS. The cells were centrifuged at 1000 rpm at 4C fro 5 mins. Total RNAs were isolated using Qiagen RNeasy kit. Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Data postprocessing and graphics were performed using in-house developed functions in Matlab®.
Sample_platform_id	GPL570
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM443nnn/GSM443834/suppl/GSM443834.CEL.gz
Sample_series_id	GSE17772
Sample_data_row_count	54675

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