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Sample GSM1314441 Query DataSets for GSM1314441
Status Public on Aug 31, 2014
Title 4% 8p4
Sample type RNA
 
Source name human umbilical cord fibroblast
Organism Homo sapiens
Characteristics cell id: CTL #8
passage #: 4
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 135.5312 0.548052
ILMN_2055271 160.1198 0.02207792
ILMN_1736007 154.3304 0.05584415
ILMN_2383229 133.1159 0.6779221
ILMN_1806310 135.5272 0.548052
ILMN_1779670 147.5496 0.1428571
ILMN_1653355 143.7142 0.2311688
ILMN_1717783 128.3605 0.8935065
ILMN_1705025 142.4944 0.2701299
ILMN_1814316 137.1845 0.4649351
ILMN_2359168 131.5928 0.7636364
ILMN_1731507 126.8258 0.9428571
ILMN_1787689 139.4305 0.3649351
ILMN_3241953 595.3177 0
ILMN_1745607 130.7546 0.7987013
ILMN_2136495 126.2023 0.9480519
ILMN_1668111 136.7483 0.4883117
ILMN_2295559 136.4792 0.5103896
ILMN_1735045 438.8354 0
ILMN_1680754 144.1189 0.2194805

Total number of rows: 47323

Table truncated, full table size 1361 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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