Search results for the GEO ID: GSE17840  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM445683 | GPL1261 |
|
Ihh treated mesenchyme, biological rep 1
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: Ihh ligand
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours
|
| Sample_geo_accession | GSM445683
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445683/suppl/GSM445683.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445684 | GPL1261 |
|
Ihh treated mesenchyme, biological rep 2
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: Ihh ligand
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours
|
| Sample_geo_accession | GSM445684
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445684/suppl/GSM445684.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445685 | GPL1261 |
|
Ihh treated mesenchyme, biological rep 3
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: Ihh ligand
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours
|
| Sample_geo_accession | GSM445685
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445685/suppl/GSM445685.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445686 | GPL1261 |
|
Shh treated mesenchyme, biological rep 1
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: Shh ligand
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours
|
| Sample_geo_accession | GSM445686
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445686/suppl/GSM445686.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445687 | GPL1261 |
|
Shh treated mesenchyme, biological rep 2
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: Shh ligand
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours
|
| Sample_geo_accession | GSM445687
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445687/suppl/GSM445687.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445688 | GPL1261 |
|
Shh treated mesenchyme, biological rep 3
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: Shh ligand
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours
|
| Sample_geo_accession | GSM445688
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445688/suppl/GSM445688.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445689 | GPL1261 |
|
Vehicle treated mesenchyme, biological rep 1
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: control
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours
|
| Sample_geo_accession | GSM445689
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445689/suppl/GSM445689.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445690 | GPL1261 |
|
Vehicle treated mesenchyme, biological rep 2
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: control
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours
|
| Sample_geo_accession | GSM445690
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445690/suppl/GSM445690.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
|
GSM445691 | GPL1261 |
|
Vehicle treated mesenchyme, biological rep 3
|
Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours
|
tissue: small intestinal mesenchyme
genotype: C57Bl/6J mice
age: E18.5 mouse embryo
agent: control
|
Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours
|
| Sample_geo_accession | GSM445691
| | Sample_status | Public on Oct 31 2009
| | Sample_submission_date | Aug 27 2009
| | Sample_last_update_date | Aug 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.
| | Sample_growth_protocol_ch1 | Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | William,,Zacharias
| | Sample_contact_department | Department of Cell and Developmental Biology
| | Sample_contact_institute | University of Michigan Medical School
| | Sample_contact_address | 109 Zina Pitcher Place
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109-2200
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM445nnn/GSM445691/suppl/GSM445691.CEL.gz
| | Sample_series_id | GSE17840
| | Sample_data_row_count | 45101
| | |
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