Search results for the GEO ID: GSE22601  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM560775 | GPL96 |
|
CordBlood_1_amplified
|
cord blood, purified using high-speed cell sorting
|
development stage: cord blood
tissue (organ): cord blood
double amplification: yes
cd1a: -
cd3: -
cd4: -
cd8: -
cd34: +
|
CB_1a
|
| Sample_geo_accession | GSM560775
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560775/suppl/GSM560775.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560776 | GPL96 |
|
CordBlood_2_amplified
|
cord blood, purified using high-speed cell sorting
|
development stage: cord blood
tissue (organ): cord blood
double amplification: yes
cd1a: -
cd3: -
cd4: -
cd8: -
cd34: +
|
CB_2a
|
| Sample_geo_accession | GSM560776
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560776/suppl/GSM560776.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560777 | GPL96 |
|
StemCellLike_1_amplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: stem-cell like
tissue (organ): thymus
double amplification: yes
cd1a: -
cd3: -
cd4: -
cd8: -
cd34: +
cd38: -
|
SCL_1a
|
| Sample_geo_accession | GSM560777
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560777/suppl/GSM560777.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560778 | GPL96 |
|
StemCellLike_2_amplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: stem-cell like
tissue (organ): thymus
double amplification: yes
cd1a: -
cd3: -
cd4: -
cd8: -
cd34: +
cd38: -
|
SCL_2a
|
| Sample_geo_accession | GSM560778
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560778/suppl/GSM560778.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560779 | GPL96 |
|
DoubleNegative12_1_amplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double negative 1+2 (pro-T)
tissue (organ): thymus
double amplification: yes
cd1a: +
cd3: -
cd4: -
cd8: -
cd34: +
cd38: +
|
DN12_1a
|
| Sample_geo_accession | GSM560779
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560779/suppl/GSM560779.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560780 | GPL96 |
|
DoubleNegative12_2_amplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double negative 1+2 (pro-T)
tissue (organ): thymus
double amplification: yes
cd1a: +
cd3: -
cd4: -
cd8: -
cd34: +
cd38: +
|
DN12_2a
|
| Sample_geo_accession | GSM560780
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560780/suppl/GSM560780.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560781 | GPL96 |
|
DoubleNegative12_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double negative 1+2 (pro-T)
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: -
cd8: -
cd34: +
cd38: +
|
DN12_1na
|
| Sample_geo_accession | GSM560781
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560781/suppl/GSM560781.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560782 | GPL96 |
|
DoubleNegative12_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double negative 1+2 (pro-T)
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: -
cd8: -
cd34: +
cd38: +
|
DN12_2na
|
| Sample_geo_accession | GSM560782
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560782/suppl/GSM560782.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560783 | GPL96 |
|
DoubleNegative3_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double negative 3 (pre-T)
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: -
cd8: -
cd34: -
cd38: +
|
DN3_1na
|
| Sample_geo_accession | GSM560783
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560783/suppl/GSM560783.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560784 | GPL96 |
|
DoubleNegative3_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double negative 3 (pre-T)
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: -
cd8: -
cd34: -
cd38: +
|
DN3_2na
|
| Sample_geo_accession | GSM560784
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560784/suppl/GSM560784.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560785 | GPL96 |
|
ImmatureSinglePositive_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: immature single positive
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: +
cd8: -
cd34: -
cd38: +
|
ISP_1na
|
| Sample_geo_accession | GSM560785
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560785/suppl/GSM560785.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560786 | GPL96 |
|
ImmatureSinglePositive_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: immature single positive
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: +
cd8: -
cd34: -
cd38: +
|
ISP_2na
|
| Sample_geo_accession | GSM560786
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560786/suppl/GSM560786.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560787 | GPL96 |
|
DoublePositive1_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double positive 1
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: +
cd8: +
cd34: -
cd38: +
|
DP1_1na
|
| Sample_geo_accession | GSM560787
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560787/suppl/GSM560787.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560788 | GPL96 |
|
DoublePositive1_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double positive 1
tissue (organ): thymus
double amplification: no
cd1a: +
cd3: -
cd4: +
cd8: +
cd34: -
cd38: +
|
DP1_2na
|
| Sample_geo_accession | GSM560788
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560788/suppl/GSM560788.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560789 | GPL96 |
|
DoublePositive2_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double positive 2
tissue (organ): thymus
double amplification: no
cd1a: +/-
cd3: +
cd4: +
cd8: +
cd34: -
cd38: +
|
DP2_1na
|
| Sample_geo_accession | GSM560789
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560789/suppl/GSM560789.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560790 | GPL96 |
|
DoublePositive2_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: double positive 2
tissue (organ): thymus
double amplification: no
cd1a: +/-
cd3: +
cd4: +
cd8: +
cd34: -
cd38: +
|
DP2_2na
|
| Sample_geo_accession | GSM560790
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560790/suppl/GSM560790.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560791 | GPL96 |
|
SinglePositive4+_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: single positive 4+
tissue (organ): thymus
double amplification: no
cd1a: +/-
cd3: +
cd4: +
cd8: +
cd34: -
cd38: +
|
SP4+_1na
|
| Sample_geo_accession | GSM560791
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560791/suppl/GSM560791.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560792 | GPL96 |
|
SinglePositive4+_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: single positive 4+
tissue (organ): thymus
double amplification: no
cd1a: +/-
cd3: +
cd4: +
cd8: +
cd34: -
cd38: +
|
SP4+_2na
|
| Sample_geo_accession | GSM560792
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560792/suppl/GSM560792.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560793 | GPL96 |
|
SinglePositive8+_1_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: single positive 8+
tissue (organ): thymus
double amplification: no
cd1a: +/-
cd3: +
cd4: +
cd8: +
cd34: -
cd38: +
|
SP8+_1na
|
| Sample_geo_accession | GSM560793
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560793/suppl/GSM560793.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
| | |
|
GSM560794 | GPL96 |
|
SinglePositive8+_2_nonamplified
|
thymic cells, purified using high-speed cell sorting
|
development stage: single positive 8+
tissue (organ): thymus
double amplification: no
cd1a: +/-
cd3: +
cd4: +
cd8: +
cd34: -
cd38: +
|
SP8+_2na
|
| Sample_geo_accession | GSM560794
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Jun 28 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNAesy plus shredder
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | ENZO kit followed by Qiagen RNeasy “clean-up” spin columns
| | Sample_hyb_protocol | Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640
| | Sample_scan_protocol | GeneChip® Scanner 3000 ; GCOSv1
| | Sample_data_processing | Probe intensity background was removed using robust multichip analysis (RMA). The intensity levels were quantile normalized. Array groups (two biologically independent arrays per group) corresponding to the development stages were compared based on the perfect match (PM) probe intensity levels only, by performing a perprobe set two-way analysis of variance (with factors “probe” and “stage”). This results in average expression levels over the two biological repeats for each probe set in each stage, as well as a p-value for the significance of the difference between the stages. As data resulting from the standard protocol (“non-amplified”) are not directly comparable to those from the small sample protocol (“amplified”), the expression levels measured for probe sets under the small sample protocol were scaled, according to the results in the DN1+2 (CD34+CD38+CD1a-) population, which was analyzed by both protocols. For each individual probe set, the scaling factor used was the ratio between the average expression level measured for that probe set in the DN1+2 population, under the standard protocol and the small sample protocol.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Dick,,de Ridder
| | Sample_contact_email | d.deridder@tudelft.nl
| | Sample_contact_phone | +31 15 2785114
| | Sample_contact_fax | +31 15 2781843
| | Sample_contact_laboratory | Delft Bioinformatics Lab
| | Sample_contact_department | Electrical Engineering, Mathematics and Computer Science
| | Sample_contact_institute | Delft University of Technology
| | Sample_contact_address | Mekelweg 4
| | Sample_contact_city | Delft
| | Sample_contact_zip/postal_code | 2628 CD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://ict.ewi.tudelft.nl/~dick
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560794/suppl/GSM560794.CEL.gz
| | Sample_series_id | GSE22601
| | Sample_data_row_count | 22283
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