Search results for the GEO ID: GSE29281 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM723804 | GPL1261 |
|
VSEL_Sample1
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty VSELs
|
tissue: Bone Marrow
cell type: VSEL
strain: C57BL/6
age: 4 weeks after birth
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723804
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723804/suppl/GSM723804.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723805 | GPL1261 |
|
VSEL_Sample2
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty VSELs
|
tissue: Bone Marrow
cell type: VSEL
strain: C57BL/6
age: 4 weeks after birth
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723805
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723805/suppl/GSM723805.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723806 | GPL1261 |
|
VSEL_Sample3
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty VSELs
|
tissue: Bone Marrow
cell type: VSEL
strain: C57BL/6
age: 4 weeks after birth
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723806
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723806/suppl/GSM723806.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723807 | GPL1261 |
|
HSC_Sample1
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty HSCs
|
tissue: Bone Marrow
cell type: HSC
strain: C57BL/6
age: 4 weeks after birth
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723807
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723807/suppl/GSM723807.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723808 | GPL1261 |
|
HSC_Sample2
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty HSCs
|
tissue: Bone Marrow
cell type: HSC
strain: C57BL/6
age: 4 weeks after birth
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723808
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723808/suppl/GSM723808.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723809 | GPL1261 |
|
HSC_Sample3
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty HSCs
|
tissue: Bone Marrow
cell type: HSC
strain: C57BL/6
age: 4 weeks after birth
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723809
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723809/suppl/GSM723809.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723810 | GPL1261 |
|
ESC_Sample1
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty ESC-D3
|
cell line: ESC-D3
strain: 129S2/SvPas
age: embryo before implantation
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723810
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723810/suppl/GSM723810.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
| |
|
GSM723811 | GPL1261 |
|
ESC_Sample2
|
T7-primed cDNA libraries was synthesized using FACS sorted twenty ESC-D3
|
cell line: ESC-D3
strain: 129S2/SvPas
age: embryo before implantation
|
Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
|
Sample_geo_accession | GSM723811
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723811/suppl/GSM723811.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
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GSM723812 | GPL1261 |
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ESC_Sample3
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T7-primed cDNA libraries was synthesized using FACS sorted twenty ESC-D3
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cell line: ESC-D3
strain: 129S2/SvPas
age: embryo before implantation
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Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells
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Sample_geo_accession | GSM723812
| Sample_status | Public on Dec 21 2011
| Sample_submission_date | May 13 2011
| Sample_last_update_date | Dec 21 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter
| Sample_growth_protocol_ch1 | Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
| Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
| Sample_data_processing | The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.
| Sample_platform_id | GPL1261
| Sample_contact_name | DONG-MYUNG,,SHIN
| Sample_contact_email | d0shin03@louisville.edu
| Sample_contact_phone | 502-852-3205
| Sample_contact_fax | 502-852-3032
| Sample_contact_department | Stem Cell Institute at James Graham Brown Cancer Center
| Sample_contact_institute | University of Louisville
| Sample_contact_address | 500 South, Floyd Street
| Sample_contact_city | Louisville
| Sample_contact_state | KY
| Sample_contact_zip/postal_code | 40202
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723812/suppl/GSM723812.CEL.gz
| Sample_series_id | GSE29281
| Sample_data_row_count | 45101
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