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Sample GSM2636230 Query DataSets for GSM2636230
Status Public on Jun 25, 2018
Title MCAS with miR-200 cluster 1 and 2 knockdown
Sample type RNA
Source name Mucinous ovarian cancer cells MCAS with knockdown of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days
Organism Homo sapiens
Characteristics tissue: Ovarian epithelial tumor cell (mucinous subtype)
genotype: Mucinous invasive
Treatment protocol The day for collecion, culture medium were removed and the cysts formed were rinsed with PBS and Trizol solution (Ambion) was added to the culture.
Growth protocol Eight-well glass-chambered slides (BD Biosciences) were coated with growth factor-reduced Matrigel matrix without phenol red (BD Biosciences) . Primary cultures of normal OSE and cancer cells were trypsinized and resuspended as single cells in complete medium with 10% FBS and 2% Matrigel. Fifty thousand single cells were seeded into each Matrigel-coated well. Complete medium with 2% Matrigel was replaced every 4 days. 3D structures would be formed after 4 to 7 days after seeding.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions with subsequent purification by chloroform extraction and isopropanol precipitation
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip WT Terminal Labling User Manual, 2009-2010, Affymetrix).
Hybridization protocol Following fragmentation, 3.5 ug of cRNA were hybridized for 48C on GeneChip Gene 1.1 ST Array in GeneAtlas Hybridization Station. GeneChip was washed and stained according to GeneAtlas TM System User’s Guide (P/N 08-0246)
Scan protocol GeneChips were scanned using the GeneAtlas Instrument.
Description Gene expression data from MCAS with knockdown of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days
Data processing All gene expression data was normalized and summarized with Robust Multi-array Average method RMA algorithm with with Affymetrix Power Tools package using Affymetrix default analysis settings.
Submission date May 23, 2017
Last update date Jun 25, 2018
Contact name pui wah Choi
Phone 6173563166
Organization name Brigham and Women's Hospital
Department OB/GYB
Lab GYN oncology, Alex Ng
Street address 221 longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL11532
Series (1)
GSE99217 Expression data from ovarian cells growing in three dimensional culture (Matrigel) with altered expression of miR-200s

Data table header descriptions

Data table
7896738 3.361472
7896740 2.988385
7896742 7.778767
7896744 3.429276
7896746 8.200192
7896748 8.988396
7896750 8.263436
7896752 9.774021
7896754 5.687948
7896756 3.869719
7896759 4.064357
7896761 5.050203
7896779 5.863198
7896798 5.40791
7896817 5.529231
7896822 9.250004
7896859 4.635346
7896861 3.475971
7896863 4.840942
7896865 5.261246

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.

Supplementary file Size Download File type/resource
GSM2636230_MCAS-KD1KD2.cel.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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