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Sample GSM1314436 Query DataSets for GSM1314436
Status Public on Aug 31, 2014
Title 4% 3p2
Sample type RNA
 
Source name human umbilical cord fibroblast
Organism Homo sapiens
Characteristics cell id: CTL #3
passage #: 2
cell type: umbilical cord fibroblast
diagnosis: healthy
Treatment protocol All cells for RNA collection were cultured in low glucose (5.6 mM)-DMEM medium containing 10% FBS, 1% NEAA, 2mM glutamine, 0.1mM beta-mercaptoethanol and 4ng/ml FGF2 under 4% or 20 O2 in 37 ℃ incubator. The human umbilical cord fibroblast cultures were maintained and expanded by media in every two days. When the culture reached 80-90% confluency, cells were detached dissociated with TrypLE and split at ratio of 1:4 into new T-25 flasks coated with 0.1% gelatin.
Growth protocol Human umbilical cord (UC) tissues were washed at least twice with phosphate buffered saline (PBS) to remove blood cells and cut into two pieces. One was placed in high glucose (HG, 25 mM), the other in low glucose (LG, 5.6 mM) DMEM medium, respectively. Tissues were minced into 1–2 mm3 fragments with scissors and placed into a 48-well plate (one small piece per well, 12 wells for HG and 12 wells LG medium, respectively) that had been coated with 0.1% gelatin in HG/LG medium containing 10% FBS, 1% NEAA, 2mM glutamine, 0.1mM 2-mercaptoethanol and 4ng/ml FGF2, and cultured at 37C in an atmosphere of either 4 % O2/5 % CO2/91 % N2 or 5 % CO2/air (20 % O2) respectively to generate outgrowths of adherent cells.
Extracted molecule total RNA
Extraction protocol RNA was isolated from early passages (< p5) of UC fibroblast lines (15 PE and 9 CTL lines, grown in T25 flasks) when they reached ~90% confluency in 4 % O2 conditions. In order to collect RNA from cells under 20 % O2, cell lines at either p 4, 5, or 6 were switched from 4 % O2 conditions to 20 % O2 conditions when they were approximately 20 % confluent. When they reached ~90% confluency (generally 2 days in 4 % O2 and 3-4 days in 20 % O2 conditions), medium was removed and RNA STAT60 (I ml; Tel-Test, Friendswood, TX) was immediately added to each T25 flask and RNA extracted by following the manufacturer?s instructions. The samples of RNA were submitted to University Texas Southwestern Medical Center Microarray Core Facility (https://microarray.swmed.edu/) and microarray analysis performed with Illumina HumanHT-12 v4 expression BeadChips. Raw intensity data were background subtracted by using BeadStudio software and analyzed further by GeneSpring 12.6 software (Agilent Technologies Inc., Santa Clara CA), according to the advanced workflow protocol: percentile shift and filter by flags (detected).
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 1
Data processing The data were normalised using quantile normalisation
 
Submission date Jan 24, 2014
Last update date Aug 31, 2014
Contact name Toshihiko Ezashi
E-mail(s) ezashit@missouri.edu
Phone 573 884-9601
Organization name University of Missouri-Columbia
Department Animal Sciences
Lab R.M. Roberts
Street address 240a CS Bond Life Sciences Center
City Columbia
State/province MO
ZIP/Postal code 65211
Country USA
 
Platform ID GPL10558
Series (1)
GSE54400 Transcriptome analysis of human umbilical cord fibroblasts from babies whose mother experienced preeclampsia

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 147.3941 0.1571429
ILMN_2055271 169.9314 0.007792208
ILMN_1736007 146.4017 0.1818182
ILMN_2383229 137.3651 0.5103896
ILMN_1806310 138.4034 0.4753247
ILMN_1779670 145.9579 0.1922078
ILMN_1653355 141.9693 0.3090909
ILMN_1717783 131.0304 0.8051948
ILMN_1705025 140.9178 0.361039
ILMN_1814316 137.1885 0.5181818
ILMN_2359168 134.3511 0.6623377
ILMN_1731507 130.2468 0.8233766
ILMN_1787689 138.9146 0.4545455
ILMN_3241953 295.7391 0
ILMN_1745607 125.0451 0.9610389
ILMN_2136495 125.5371 0.9558442
ILMN_1668111 139.2777 0.438961
ILMN_2295559 135.1971 0.6194805
ILMN_1735045 275.1768 0
ILMN_1680754 145.6718 0.2012987

Total number of rows: 47323

Table truncated, full table size 1357 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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