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Search results for the GEO ID: GSE39458

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(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

GSM969556

GPL1261

KSL cells_B6xG7_sorted

Mouse bone marrow KSL cells

strain: C57BL/6 genotype/variation: B6xG7 (F1 of C57BL/6 mice crossed with G7 mice) disease state: control gender: male + female age: 6-7 weeks old cell type: KSL cells

B6xG7 KSL

Sample_geo_accession	GSM969556
Sample_status	Public on Dec 31 2012
Sample_submission_date	Jul 18 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.
Sample_growth_protocol_ch1	KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
Sample_data_processing	The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	Kwadwo,,Oduro Jnr
Sample_contact_email	odurolab@yahoo.com
Sample_contact_laboratory	Kyunghee Choi
Sample_contact_department	Pathology and Immunology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	4940 Parkview Place, Room 1024
Sample_contact_city	Saint Louis
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM969nnn/GSM969556/suppl/GSM969556_B6xG7_KSL.CEL.gz
Sample_series_id	GSE39458
Sample_data_row_count	45037

GSM969557

GPL1261

KSL cells_KRN_sorted

Mouse bone marrow KSL cells

strain: C57BL/6 genotype/variation: KRN (KRN TCR transgenic mice on a C57BL/6 background) disease state: control gender: male + female age: 6-7 weeks old cell type: KSL cells

KRN KSL

Sample_geo_accession	GSM969557
Sample_status	Public on Dec 31 2012
Sample_submission_date	Jul 18 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.
Sample_growth_protocol_ch1	KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
Sample_data_processing	The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	Kwadwo,,Oduro Jnr
Sample_contact_email	odurolab@yahoo.com
Sample_contact_laboratory	Kyunghee Choi
Sample_contact_department	Pathology and Immunology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	4940 Parkview Place, Room 1024
Sample_contact_city	Saint Louis
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM969nnn/GSM969557/suppl/GSM969557_KRN_KSL.CEL.gz
Sample_series_id	GSE39458
Sample_data_row_count	45037

GSM969558

GPL1261

KSL cells_KRNxG7_sorted

Mouse bone marrow KSL cells

strain: C57BL/6 genotype/variation: KRNxG7 (KRN mice crossed with G7 mice) disease state: arthritic gender: male + female age: 6-7 weeks old cell type: KSL cells

KRNxG7 KSL

Sample_geo_accession	GSM969558
Sample_status	Public on Dec 31 2012
Sample_submission_date	Jul 18 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.
Sample_growth_protocol_ch1	KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
Sample_data_processing	The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	Kwadwo,,Oduro Jnr
Sample_contact_email	odurolab@yahoo.com
Sample_contact_laboratory	Kyunghee Choi
Sample_contact_department	Pathology and Immunology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	4940 Parkview Place, Room 1024
Sample_contact_city	Saint Louis
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM969nnn/GSM969558/suppl/GSM969558_KRNxG7_KSL.CEL.gz
Sample_series_id	GSE39458
Sample_data_row_count	45037

GSM969559

GPL1261

Lin+_B6xG7_sorted

Mouse bone marrow Lin+ cells

strain: C57BL/6 genotype/variation: B6xG7 (F1 of C57BL/6 mice crossed with G7 mice) disease state: control gender: male + female age: 6-7 weeks old cell type: Lin+ cells

B6xG7 Mature cells

Sample_geo_accession	GSM969559
Sample_status	Public on Dec 31 2012
Sample_submission_date	Jul 18 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.
Sample_growth_protocol_ch1	KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
Sample_data_processing	The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	Kwadwo,,Oduro Jnr
Sample_contact_email	odurolab@yahoo.com
Sample_contact_laboratory	Kyunghee Choi
Sample_contact_department	Pathology and Immunology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	4940 Parkview Place, Room 1024
Sample_contact_city	Saint Louis
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM969nnn/GSM969559/suppl/GSM969559_B6xG7_Mature.CEL.gz
Sample_series_id	GSE39458
Sample_data_row_count	45037

GSM969560

GPL1261

Lin+_KRN_sorted

Mouse bone marrow Lin+ cells

strain: C57BL/6 genotype/variation: KRN (KRN TCR transgenic mice on a C57BL/6 background) disease state: control gender: male + female age: 6-7 weeks old cell type: Lin+ cells

KRN Mature cells

Sample_geo_accession	GSM969560
Sample_status	Public on Dec 31 2012
Sample_submission_date	Jul 18 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.
Sample_growth_protocol_ch1	KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
Sample_data_processing	The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	Kwadwo,,Oduro Jnr
Sample_contact_email	odurolab@yahoo.com
Sample_contact_laboratory	Kyunghee Choi
Sample_contact_department	Pathology and Immunology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	4940 Parkview Place, Room 1024
Sample_contact_city	Saint Louis
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM969nnn/GSM969560/suppl/GSM969560_KRN_Mature.CEL.gz
Sample_series_id	GSE39458
Sample_data_row_count	45037

GSM969561

GPL1261

Lin+_KRNxG7_sorted

Mouse bone marrow Lin+ cells

strain: C57BL/6 genotype/variation: KRNxG7 (KRN mice crossed with G7 mice) disease state: arthritic gender: male + female age: 6-7 weeks old cell type: Lin+ cells

KRNxG7 Mature cells

Sample_geo_accession	GSM969561
Sample_status	Public on Dec 31 2012
Sample_submission_date	Jul 18 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	No ex-vivo treatment of sorted cells prior to RNA extraction. Sorted cells were stored at -80 deg celsius.
Sample_growth_protocol_ch1	KSL cells or Lin+ cells were primary cells sorted from 6-7 week old arthritic (KRNxG7) or control (KRN) or control (B6xG7) mice. No ex-vivo growth of cells.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted and purified using Arcturus Picopure RNA kit (Applied Biosystems) according to manufacturing instructions followed by linear amplification.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45degC on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
Sample_data_processing	The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL1261
Sample_contact_name	Kwadwo,,Oduro Jnr
Sample_contact_email	odurolab@yahoo.com
Sample_contact_laboratory	Kyunghee Choi
Sample_contact_department	Pathology and Immunology
Sample_contact_institute	Washington University School of Medicine
Sample_contact_address	4940 Parkview Place, Room 1024
Sample_contact_city	Saint Louis
Sample_contact_zip/postal_code	63110
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM969nnn/GSM969561/suppl/GSM969561_KRNxG7_Mature.CEL.gz
Sample_series_id	GSE39458
Sample_data_row_count	45037

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