Result

Search results for the GEO ID: GSE41883

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Title

Source name

Description

Characteristics

GSM1026926

GPL1352

Disc Cells in 3D_Control (95)

Disc Tissue

tissue: Disc Tissue tissue grade: IV cell type: annulus cells agent: control

Sample_geo_accession	GSM1026926
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026926/suppl/GSM1026926_E09-95C.CEL.gz
Sample_relation	Reanalysis of: GSM679415
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026927

GPL1352

Disc Cells in 3D_TNF-a (95)

Disc Tissue

tissue: Disc Tissue tissue grade: IV cell type: annulus cells agent: TNF-a

Sample_geo_accession	GSM1026927
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026927/suppl/GSM1026927_E09-95TNF-a.CEL.gz
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026928

GPL1352

Disc Cells in 3D_Control (126)

Disc Tissue

tissue: Disc Tissue tissue grade: III cell type: annulus cells agent: control

Sample_geo_accession	GSM1026928
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026928/suppl/GSM1026928_E09-126C.CEL.gz
Sample_relation	Reanalysis of: GSM679419
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026929

GPL1352

Disc Cells in 3D_TNF-a (126)

Disc Tissue

tissue: Disc Tissue tissue grade: III cell type: annulus cells agent: TNF-a

Sample_geo_accession	GSM1026929
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026929/suppl/GSM1026929_E09-126TNF-a.CEL.gz
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026930

GPL1352

Disc Cells in 3D_Control (154)

Disc Tissue

tissue: Disc Tissue tissue grade: IV cell type: annulus cells agent: control

Sample_geo_accession	GSM1026930
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026930/suppl/GSM1026930_E09-154C.CEL.gz
Sample_relation	Reanalysis of: GSM679421
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026931

GPL1352

Disc Cells in 3D_TNF-a (154)

Disc Tissue

tissue: Disc Tissue tissue grade: IV cell type: annulus cells agent: TNF-a

Sample_geo_accession	GSM1026931
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026931/suppl/GSM1026931_E09-154TNF-a.CEL.gz
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026932

GPL1352

Disc Cells in 3D_Control (222)

Disc Tissue

tissue: Disc Tissue tissue grade: II cell type: annulus cells agent: control

Sample_geo_accession	GSM1026932
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026932/suppl/GSM1026932_E09-222C.CEL.gz
Sample_series_id	GSE41883
Sample_data_row_count	61359

GSM1026933

GPL1352

Disc Cells in 3D_TNF-a (222)

Disc Tissue

tissue: Disc Tissue tissue grade: II cell type: annulus cells agent: TNF-a

Sample_geo_accession	GSM1026933
Sample_status	Public on Oct 31 2012
Sample_submission_date	Oct 28 2012
Sample_last_update_date	Oct 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_growth_protocol_ch1	Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.
Sample_hyb_protocol	Fragmented cRNA was hybridized to the X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.
Sample_scan_protocol	GeneChips were scanned once via the Affymetrix 3000G scanner.
Sample_data_processing	The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).
Sample_platform_id	GPL1352
Sample_contact_name	Helen,,Gruber
Sample_contact_email	Helen.Gruber@carolinashealthcare.org
Sample_contact_laboratory	Orthopaedic Research
Sample_contact_department	Orthopaedic Surgery
Sample_contact_institute	Carolinas HealthCare System
Sample_contact_address	1542 Graden Terrace
Sample_contact_city	Charlotte
Sample_contact_state	NC
Sample_contact_zip/postal_code	28203
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026933/suppl/GSM1026933_E09-222TNF-a.CEL.gz
Sample_series_id	GSE41883
Sample_data_row_count	61359

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