Result

Search results for the GEO ID: GSE11723

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM297554

GPL1261

LSK_OP9-GFP_Rep1

Hematopoietic LSK cells plated on OP9-GFP stroma for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-GFP stroma for 3 days

Sample_geo_accession	GSM297554
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297554/suppl/GSM297554.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297555

GPL1261

LSK_OP9-GFP_Rep2

Hematopoietic LSK cells plated on OP9-GFP stroma for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-GFP stroma for 3 days

Sample_geo_accession	GSM297555
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297555/suppl/GSM297555.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297556

GPL1261

LSK_OP9-GFP_Rep3

Hematopoietic LSK cells plated on OP9-GFP stroma for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-GFP stroma for 3 days

Sample_geo_accession	GSM297556
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297556/suppl/GSM297556.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297557

GPL1261

LSK_OP9-DL1_Rep1

Hematopoietic LSK cells plated on OP9-DL1 stroma for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-DL1 stroma for 3 days

Sample_geo_accession	GSM297557
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297557/suppl/GSM297557.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297558

GPL1261

LSK_OP9-DL1_Rep2

Hematopoietic LSK cells plated on OP9-DL1 stroma for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-DL1 stroma for 3 days

Sample_geo_accession	GSM297558
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297558/suppl/GSM297558.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297559

GPL1261

LSK_OP9-DL1_Rep3

Hematopoietic LSK cells plated on OP9-DL1 stroma for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-DL1 stroma for 3 days

Sample_geo_accession	GSM297559
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297559/suppl/GSM297559.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297560

GPL1261

LSK_OP9-DL1+CompoundE_Rep1

Hematopoietic LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

Sample_geo_accession	GSM297560
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297560/suppl/GSM297560.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297561

GPL1261

LSK_OP9-DL1+CompoundE_Rep2

Hematopoietic LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

Sample_geo_accession	GSM297561
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297561/suppl/GSM297561.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

GSM297562

GPL1261

LSK_OP9-DL1+CompoundE_Rep3

Hematopoietic LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

C57/Bl6

Gene expression data from LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

Sample_geo_accession	GSM297562
Sample_status	Public on Jun 02 2009
Sample_submission_date	Jun 09 2008
Sample_last_update_date	Jun 02 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After 3 days of co-cultures, non-adherent cells were collected
Sample_growth_protocol_ch1	Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,,Mercher
Sample_contact_email	tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Sample_contact_laboratory	Dr. Gary Gilliland
Sample_contact_department	Hematology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	1 blackfan circle
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297562/suppl/GSM297562.CEL.gz
Sample_series_id	GSE11723
Sample_data_row_count	45101

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