Result

Search results for the GEO ID: GSE11283

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Title

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Description

Characteristics

GSM284885

GPL341

Rat S4_bone marrow derived mesenchymal stromal cells_rep1

Bone marrow derived mesenchymal stromal cells

GFP transgenic Sprague-Dawley rat, 3 months old, female

Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

Sample_geo_accession	GSM284885
Sample_status	Public on Apr 26 2009
Sample_submission_date	Apr 28 2008
Sample_last_update_date	Apr 28 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).
Sample_hyb_protocol	After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.
Sample_scan_protocol	The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.
Sample_platform_id	GPL341
Sample_contact_name	Qiling,,He
Sample_contact_email	qhe@uab.edu
Sample_contact_department	Microbiology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1825 University Blvd, Shelby Building
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284885/suppl/GSM284885.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284885/suppl/GSM284885.EXP.gz
Sample_series_id	GSE11283
Sample_data_row_count	15923

GSM284886

GPL341

Rat S5_bone marrow derived mesenchymal stromal cells_rep2

Bone marrow derived mesenchymal stromal cells

GFP transgenic Sprague-Dawley rat, 3 months old, male

Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

Sample_geo_accession	GSM284886
Sample_status	Public on Apr 26 2009
Sample_submission_date	Apr 28 2008
Sample_last_update_date	Apr 28 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).
Sample_hyb_protocol	After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.
Sample_scan_protocol	The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.
Sample_platform_id	GPL341
Sample_contact_name	Qiling,,He
Sample_contact_email	qhe@uab.edu
Sample_contact_department	Microbiology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1825 University Blvd, Shelby Building
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284886/suppl/GSM284886.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284886/suppl/GSM284886.EXP.gz
Sample_series_id	GSE11283
Sample_data_row_count	15923

GSM284887

GPL341

Rat S6_bone marrow derived mesenchymal stromal cells_rep3

Bone marrow derived mesenchymal stromal cells

GFP transgenic Sprague-Dawley rat, 3 months old, male

Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

Sample_geo_accession	GSM284887
Sample_status	Public on Apr 26 2009
Sample_submission_date	Apr 28 2008
Sample_last_update_date	Apr 28 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).
Sample_hyb_protocol	After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.
Sample_scan_protocol	The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.
Sample_platform_id	GPL341
Sample_contact_name	Qiling,,He
Sample_contact_email	qhe@uab.edu
Sample_contact_department	Microbiology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1825 University Blvd, Shelby Building
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284887/suppl/GSM284887.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284887/suppl/GSM284887.EXP.gz
Sample_series_id	GSE11283
Sample_data_row_count	15923

GSM284888

GPL341

Rat S4_peripheral blood derived mesenchymal stromal cells_rep1

Peripheral blood derived mesenchymal stromal cells

GFP transgenic Sprague-Dawley rat, 3 months old, female

Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

Sample_geo_accession	GSM284888
Sample_status	Public on Apr 26 2009
Sample_submission_date	Apr 28 2008
Sample_last_update_date	Apr 28 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).
Sample_hyb_protocol	After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.
Sample_scan_protocol	The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.
Sample_platform_id	GPL341
Sample_contact_name	Qiling,,He
Sample_contact_email	qhe@uab.edu
Sample_contact_department	Microbiology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1825 University Blvd, Shelby Building
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284888/suppl/GSM284888.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284888/suppl/GSM284888.EXP.gz
Sample_series_id	GSE11283
Sample_data_row_count	15923

GSM284889

GPL341

Rat S5_peripheral blood derived mesenchymal stromal cells_rep2

Peripheral blood derived mesenchymal stromal cells

GFP transgenic Sprague-Dawley rat, 3 months old, male

Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

Sample_geo_accession	GSM284889
Sample_status	Public on Apr 26 2009
Sample_submission_date	Apr 28 2008
Sample_last_update_date	Apr 28 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).
Sample_hyb_protocol	After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.
Sample_scan_protocol	The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.
Sample_platform_id	GPL341
Sample_contact_name	Qiling,,He
Sample_contact_email	qhe@uab.edu
Sample_contact_department	Microbiology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1825 University Blvd, Shelby Building
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284889/suppl/GSM284889.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284889/suppl/GSM284889.EXP.gz
Sample_series_id	GSE11283
Sample_data_row_count	15923

GSM284890

GPL341

Rat S6_peripheral blood derived mesenchymal stromal cells_rep3

Peripheral blood derived mesenchymal stromal cells

GFP transgenic Sprague-Dawley rat, 3 months old, male

Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

Sample_geo_accession	GSM284890
Sample_status	Public on Apr 26 2009
Sample_submission_date	Apr 28 2008
Sample_last_update_date	Apr 28 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).
Sample_hyb_protocol	After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.
Sample_scan_protocol	The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.
Sample_platform_id	GPL341
Sample_contact_name	Qiling,,He
Sample_contact_email	qhe@uab.edu
Sample_contact_department	Microbiology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1825 University Blvd, Shelby Building
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284890/suppl/GSM284890.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284890/suppl/GSM284890.EXP.gz
Sample_series_id	GSE11283
Sample_data_row_count	15923

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