Result

Search results for the GEO ID: GSE16524

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GPL ID

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Title

Source name

Description

Characteristics

GSM415037

GPL570

Normal Puerto Rican control 1

skin fibroblasts, passage #3

gender: female genotype: Wild type for TWIST2 ethnicity: Puerto Rican

unaffected sister of Setleis patient in Samples Setleis_05 and _06.

Sample_geo_accession	GSM415037
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415037/suppl/GSM415037.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415037/suppl/GSM415037.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415038

GPL570

Normal Puerto Rican control 2

skin fibroblasts, passage #1

gender: female genotype: Wild type for TWIST2 ethnicity: Puerto Rican

unaffected sister of Setleis patient in Samples Setleis_05 and _06.

Sample_geo_accession	GSM415038
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415038/suppl/GSM415038.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415038/suppl/GSM415038.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415039

GPL570

Normal Puerto Rican control 3

skin fibroblasts, passages #2 and 4

gender: female genotype: Wild type for TWIST2 ethnicity: Puerto Rican

1:1 Pool of two control cell lines, one is GM00037, the other is from a normal donor

Sample_geo_accession	GSM415039
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 22 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM00037
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415039/suppl/GSM415039.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415039/suppl/GSM415039.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415040

GPL570

Normal Caucasian control 4

skin fibroblasts, passages #14 and 15

gender: female genotype: Wild type for TWIST2 ethnicity: Caucasian

Pool of RNAs from cells in passages 14 and 15 of Coriell cell line GM03377

Sample_geo_accession	GSM415040
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415040/suppl/GSM415040.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415040/suppl/GSM415040.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415041

GPL570

Setleis Syndrome patient 1

skin fibroblasts, passage #4

gender: female genotype: Homozygous for the Q119X mutation in the TWIST2 gene ethnicity: Puerto Rican

Sister of Setleis_01 and _02

Sample_geo_accession	GSM415041
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415041/suppl/GSM415041.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415041/suppl/GSM415041.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415042

GPL570

Setleis Syndrome patient 2

skin fibroblasts, passage #3

gender: female genotype: Homozygous for the Q119X mutation in the TWIST2 gene ethnicity: Puerto Rican

Sister of Setleis_01 and _02

Sample_geo_accession	GSM415042
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415042/suppl/GSM415042.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415042/suppl/GSM415042.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415043

GPL570

Setleis Syndrome patient 3

skin fibroblasts, passages #3 and 5

gender: mixed genotype: Homozygous for the Q119X mutation in the TWIST2 gene ethnicity: Puerto Rican

1:1 Pool of RNAs from two siblings, female and male, affected with Setleis Syndrome

Sample_geo_accession	GSM415043
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415043/suppl/GSM415043.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415043/suppl/GSM415043.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

GSM415044

GPL570

Setleis Syndrome patient 4

skin fibroblasts, passage #3

gender: female genotype: Homozygous for the Q65X mutation in the TWIST2 gene

Setleis Syndrome Patient described in Al-Gazali and Al-Talabani (1996) Clin Dysmorphol 5(3):249-53.

Sample_geo_accession	GSM415044
Sample_status	Public on Jun 11 2009
Sample_submission_date	Jun 09 2009
Sample_last_update_date	Jun 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.
Sample_hyb_protocol	Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility
Sample_scan_protocol	GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.
Sample_data_processing	A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.
Sample_platform_id	GPL570
Sample_contact_name	Carmen,Lydia,Cadilla
Sample_contact_email	carmen.cadilla@upr.edu
Sample_contact_phone	7877544366
Sample_contact_fax	7872748724
Sample_contact_laboratory	A640
Sample_contact_department	Biochemistry
Sample_contact_institute	University of Puerto Rico School of Medicine
Sample_contact_address	University of Puerto Rico Medical Sciences Campus, Area of Medical Center
Sample_contact_city	San Juan
Sample_contact_state	PR
Sample_contact_zip/postal_code	00936
Sample_contact_country	Puerto Rico
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415044/suppl/GSM415044.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM415nnn/GSM415044/suppl/GSM415044.CHP.gz
Sample_series_id	GSE16524
Sample_data_row_count	54675

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