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Sample GSM915804 Query DataSets for GSM915804
Status Public on Dec 31, 2021
Title Mouse Lung epithelial cells rep1
Sample type other
 
Source name Mouse Lung epithelial cells rep1
Organism Mus musculus
Characteristics tissue: lung
cell type: epithelial cells
Growth protocol To prepare embryonic lung epithelium, noon of the day when a vaginal plug was detected was considered approximately E0.5. Embryos were collected in cold 1 X phosphate buffered saline (PBS). Lungs were dissected out from embryos at the E13.5 stages. Epithelium and mesenchyme were separated as reported previously86. For adult donor cell preparation, female mice of 10-weeks of age were sacrificed and perfused with PBS. Lungs and mammary glands were harvested, minced and dissociated in buffer [5% fetal bovine serum (FBS), insulin 5 µg/ml, Penicillin-Streptomycin 100 U/ml in DMEM/F12] containing trypsin (2 mg/ml) and collagenase A (2 mg/ml) for 45 minutes and 30 minutes, respectively, at 37ºC. Primary epithelia were purified by differential centrifugation: specifically, lung and mammary epithelia were washed in dissociation buffer without collagenase and collected using a swing-bucket centrifuge at 400 X g. The process was repeated for seven and five times for lung and mammary tissues, respectively. To prepare single cells, primary epithelia from embryonic lung and adult lung and mammary gland were washed in Hank’s (Ca2+ Mg2+ free) buffer and dissociated in 0.05% Trypsin/EDTA buffer. Cells were counted using a Hausser Scientific Hemocytometer and prepared in 50% Matrigel™ (growth factor reduced, BD Biosciences) for transplantation.
Extracted molecule other
Extraction protocol Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Cy3
Label protocol miRNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers’ protocol
 
Hybridization protocol Labeled RNA was hybridized to Agilent custom UCSF miRNA v3.4 multi-species 8x15K Ink-jet arrays (Agilent). Hybridizations were performed for 16 hrs according to the manufacturers protocol (Agilent).
Scan protocol Arrays were scanned using the Agilent microarray scanner (Agilent).
Data processing Raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent)
 
Submission date Apr 16, 2012
Last update date Dec 31, 2021
Contact name Andrew H Sims
E-mail(s) andrew.sims@ed.ac.uk
Organization name University of Edinburgh
Department Institute of Genetics and Molecular Medicine
Lab Applied Bioinformatics of Cancer
Street address Systems Medicine Building
City Carrington Crescent
State/province Edinburgh
ZIP/Postal code EH4 2XR
Country United Kingdom
 
Platform ID GPL13992
Series (2)
GSE37308 In Vivo Organ Regeneration via Stroma-Dependent Adult Lineage Reprogramming (miRNA)
GSE37309 In Vivo Organ Regeneration via Stroma-Dependent Adult Lineage Reprogramming

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
UCSF034_000310 13.69713204
UCSF034_000311 13.60619435
UCSF034_000312 4.890657839
UCSF034_000313 4.832890014
UCSF034_000314 5.090353049
UCSF034_000315 13.80090495
UCSF034_000316 5.445955386
UCSF034_000317 14.39268393
UCSF034_000318 5.112623017
UCSF034_000319 5.074871264
UCSF034_000320 12.84792041
UCSF034_000321 10.95221156
UCSF034_000322 10.04195549
UCSF034_000323 5.724203763
UCSF034_000324 11.29260922
UCSF034_000325 6.193627395
UCSF034_000326 5.789879301
UCSF034_000327 12.00063226
UCSF034_000328 5.249652194
UCSF034_000329 4.91807654

Total number of rows: 2270

Table truncated, full table size 59 Kbytes.




Supplementary file Size Download File type/resource
GSM915804_252372310015_S01_miRNA_105_Dec08_1_1.txt.gz 866.7 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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