Result

Search results for the GEO ID: GSE20358

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GSM ID

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Title

Source name

Description

Characteristics

GSM510066

GPL1355

P4_Ovary_Control_biological rep1

P4 Ovary cultured for 48 hours with no treatment

strain: Sprague-Dawley gender: Female tissue: ovary developmental stage: day P4 cultured for 2 more days

Gene expression data from rat P4 Ovary cultured for 48 hours with no treatment

Sample_geo_accession	GSM510066
Sample_status	Public on Feb 16 2010
Sample_submission_date	Feb 16 2010
Sample_last_update_date	Feb 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).
Sample_growth_protocol_ch1	Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Sample_scan_protocol	GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing and global scaling as normalization method. The trimmed mean target intensity of each array was set to 210.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,K,Skinner
Sample_contact_email	skinner@mail.wsu.edu
Sample_contact_department	SBS
Sample_contact_institute	WSU
Sample_contact_address	Abelson 507
Sample_contact_city	Pullman
Sample_contact_state	WA
Sample_contact_zip/postal_code	99163
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510066/suppl/GSM510066.CEL.gz
Sample_series_id	GSE20358
Sample_data_row_count	31099

GSM510067

GPL1355

P4_Ovary_Control_biological rep2

P4 Ovary cultured for 48 hours with no treatment

strain: Sprague-Dawley gender: Female tissue: ovary developmental stage: day P4 cultured for 2 more days

Gene expression data from rat P4 Ovary cultured for 48 hours with no treatment

Sample_geo_accession	GSM510067
Sample_status	Public on Feb 16 2010
Sample_submission_date	Feb 16 2010
Sample_last_update_date	Feb 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).
Sample_growth_protocol_ch1	Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Sample_scan_protocol	GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing and global scaling as normalization method. The trimmed mean target intensity of each array was set to 210.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,K,Skinner
Sample_contact_email	skinner@mail.wsu.edu
Sample_contact_department	SBS
Sample_contact_institute	WSU
Sample_contact_address	Abelson 507
Sample_contact_city	Pullman
Sample_contact_state	WA
Sample_contact_zip/postal_code	99163
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510067/suppl/GSM510067.CEL.gz
Sample_series_id	GSE20358
Sample_data_row_count	31099

GSM510068

GPL1355

P4_Ovary_Control_biological rep3

P4 Ovary cultured for 48 hours with no treatment

strain: Sprague-Dawley gender: Female tissue: ovary developmental stage: day P4 cultured for 2 more days

Gene expression data from rat P4 Ovary cultured for 48 hours with no treatment

Sample_geo_accession	GSM510068
Sample_status	Public on Feb 16 2010
Sample_submission_date	Feb 16 2010
Sample_last_update_date	Feb 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).
Sample_growth_protocol_ch1	Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Sample_scan_protocol	GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing and global scaling as normalization method. The trimmed mean target intensity of each array was set to 210.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,K,Skinner
Sample_contact_email	skinner@mail.wsu.edu
Sample_contact_department	SBS
Sample_contact_institute	WSU
Sample_contact_address	Abelson 507
Sample_contact_city	Pullman
Sample_contact_state	WA
Sample_contact_zip/postal_code	99163
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510068/suppl/GSM510068.CEL.gz
Sample_series_id	GSE20358
Sample_data_row_count	31099

GSM510069

GPL1355

P4_Ovary_NT3_biological rep1

P4 Ovary cultured for 48 hours with NT3

strain: Sprague-Dawley gender: Female tissue: ovary developmental stage: day P4 cultured for 2 more days

Gene expression data from rat P4 Ovary cultured for 48 hours with NT3

Sample_geo_accession	GSM510069
Sample_status	Public on Feb 16 2010
Sample_submission_date	Feb 16 2010
Sample_last_update_date	Feb 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).
Sample_growth_protocol_ch1	Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Sample_scan_protocol	GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing and global scaling as normalization method. The trimmed mean target intensity of each array was set to 210.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,K,Skinner
Sample_contact_email	skinner@mail.wsu.edu
Sample_contact_department	SBS
Sample_contact_institute	WSU
Sample_contact_address	Abelson 507
Sample_contact_city	Pullman
Sample_contact_state	WA
Sample_contact_zip/postal_code	99163
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510069/suppl/GSM510069.CEL.gz
Sample_series_id	GSE20358
Sample_data_row_count	31099

GSM510070

GPL1355

P4_Ovary_NT3_biological rep2

P4 Ovary cultured for 48 hours with NT3

strain: Sprague-Dawley gender: Female tissue: ovary developmental stage: day P4 cultured for 2 more days

Gene expression data from rat P4 Ovary cultured for 48 hours with NT3

Sample_geo_accession	GSM510070
Sample_status	Public on Feb 16 2010
Sample_submission_date	Feb 16 2010
Sample_last_update_date	Feb 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).
Sample_growth_protocol_ch1	Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Sample_scan_protocol	GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing and global scaling as normalization method. The trimmed mean target intensity of each array was set to 210.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,K,Skinner
Sample_contact_email	skinner@mail.wsu.edu
Sample_contact_department	SBS
Sample_contact_institute	WSU
Sample_contact_address	Abelson 507
Sample_contact_city	Pullman
Sample_contact_state	WA
Sample_contact_zip/postal_code	99163
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510070/suppl/GSM510070.CEL.gz
Sample_series_id	GSE20358
Sample_data_row_count	31099

GSM510071

GPL1355

P4_Ovary_NT3_biological rep3

P4 Ovary cultured for 48 hours with NT3

strain: Sprague-Dawley gender: Female tissue: ovary developmental stage: day P4 cultured for 2 more days

Gene expression data from rat P4 Ovary cultured for 48 hours with NT3

Sample_geo_accession	GSM510071
Sample_status	Public on Feb 16 2010
Sample_submission_date	Feb 16 2010
Sample_last_update_date	Feb 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).
Sample_growth_protocol_ch1	Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
Sample_scan_protocol	GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing and global scaling as normalization method. The trimmed mean target intensity of each array was set to 210.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,K,Skinner
Sample_contact_email	skinner@mail.wsu.edu
Sample_contact_department	SBS
Sample_contact_institute	WSU
Sample_contact_address	Abelson 507
Sample_contact_city	Pullman
Sample_contact_state	WA
Sample_contact_zip/postal_code	99163
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510071/suppl/GSM510071.CEL.gz
Sample_series_id	GSE20358
Sample_data_row_count	31099

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