Result

Search results for the GEO ID: GSE24506

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM603984

GPL96

Patient 379 DCIS (mRNA)

ductal carcinoma in situ epithelium

sample type: laser capture microdissected human breast tissue: ductal carcinoma in situ epithelium gender: female age: 43 y

Gene expression data from case 379 ductal carcinoma in situ

Sample_geo_accession	GSM603984
Sample_status	Public on Feb 17 2011
Sample_submission_date	Oct 04 2010
Sample_last_update_date	Feb 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Primary patient breast tissue was snap-frozen in liquid nitrogen, embedded in optimal cutting temperature compound and stored at -80C
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	On average, ~50 10 um-thick cryostat sections were prepared for the extraction of total RNA by laser-capture microdissection from normal or DCIS epithelial regions, which were identified by a surgical pathologist (AdlM) using every 7th section stained by Hematoxylin and Eosin. Total RNA was extracted from the captured epithelium using the Picopure RNA Isolation Kit (Arcturus Engineering) according to manufacturer's protocol with additional DNAse treatment step.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	To convert the RNA to cDNA, the purified total RNA was linearly amplified for two rounds using the MessageAMP aRNA Kit (Ambion, Austin, TX), in which the first round is based on an oligo-dT primer and T7 RNA polymerase. For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
Sample_scan_protocol	The stained arrays were scanned using a G2500 Scanner (Agilent)
Sample_data_processing	Images from the scanned chips were quantified and scaled using Affymetrix Microarray Suite 5.0 (Affymetrix), and the unnormalized data were then rescaled to a target of 100 to remove bias.
Sample_platform_id	GPL96
Sample_contact_name	Bethany,,Hannafon
Sample_contact_email	hannafon@bu.edu, bethanyn_hannafon@dfci.harvard.edu
Sample_contact_laboratory	Carol Rosenberg, M.D.
Sample_contact_department	Medicine/Section of Hematology and Oncology
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	650 Albany Street
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM603nnn/GSM603984/suppl/GSM603984_CR379.CEL.gz
Sample_series_id	GSE24506
Sample_series_id	GSE24509
Sample_data_row_count	22283

GSM603985

GPL96

Patient 446B DCIS (mRNA)

ductal carcinoma in situ epithelium

sample type: laser capture microdissected human breast tissue: ductal carcinoma in situ epithelium gender: female age: 54 y

Gene expression data from case 446B ductal carcinoma in situ

Sample_geo_accession	GSM603985
Sample_status	Public on Feb 17 2011
Sample_submission_date	Oct 04 2010
Sample_last_update_date	Feb 18 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Primary patient breast tissue was snap-frozen in liquid nitrogen, embedded in optimal cutting temperature compound and stored at -80C
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	On average, ~50 10 um-thick cryostat sections were prepared for the extraction of total RNA by laser-capture microdissection from normal or DCIS epithelial regions, which were identified by a surgical pathologist (AdlM) using every 7th section stained by Hematoxylin and Eosin. Total RNA was extracted from the captured epithelium using the Picopure RNA Isolation Kit (Arcturus Engineering) according to manufacturer's protocol with additional DNAse treatment step.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	To convert the RNA to cDNA, the purified total RNA was linearly amplified for two rounds using the MessageAMP aRNA Kit (Ambion, Austin, TX), in which the first round is based on an oligo-dT primer and T7 RNA polymerase. For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
Sample_scan_protocol	The stained arrays were scanned using a G2500 Scanner (Agilent)
Sample_data_processing	Images from the scanned chips were quantified and scaled using Affymetrix Microarray Suite 5.0 (Affymetrix), and the unnormalized data were then rescaled to a target of 100 to remove bias.
Sample_platform_id	GPL96
Sample_contact_name	Bethany,,Hannafon
Sample_contact_email	hannafon@bu.edu, bethanyn_hannafon@dfci.harvard.edu
Sample_contact_laboratory	Carol Rosenberg, M.D.
Sample_contact_department	Medicine/Section of Hematology and Oncology
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	650 Albany Street
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM603nnn/GSM603985/suppl/GSM603985_CR446B-1.CEL.gz
Sample_series_id	GSE24506
Sample_series_id	GSE24509
Sample_data_row_count	22283

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