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Sample GSM2428145 Query DataSets for GSM2428145
Status Public on Jun 01, 2017
Title DNAN-62.5ppm-1
Sample type RNA
 
Source name Wild type C. elegans var. Bristol strain N2
Organism Caenorhabditis elegans
Characteristics tissue: Pooled somatic tissue of approx. 400 nematodes
gender: hermaphrodite
developmental stage: Late L3 stage grown from synchronized culture
24-hr acute treatment: DNAN
concentration: 62.5ppm
replicate: 1
Treatment protocol After harvesting from agar plates, worms were spun at 1150 x g for 2.5 min and re-suspended in a given volume of K Medium. Twenty µL of worms were deposited on a microscope slide containing a grid sticker and worms were counted. The number of worms/mL was then calculated. Wide-bore pipet tips or transfer pipets were always used to avoid shearing of worms. Worms were exposed in 24-well tissue-culture treated (TC) plates for 24 hours to DNAN, NTO, or NQ. All test solutions were prepared in K medium except that acetone was used to dissolve DNAN, resulting in 5% carrier in the final solution. Each weel in the TC plates contained 400 worms and 1 ml of K medium or test solution. The nominal concentrations were: Vehicle control, 1.9, 15.5, 62 mg DNA/L, Blank control, 187, 750, 3000 mg NTO/L, and Blank control, 83, 666, 2667 mg NQ/L. Each treatment had 5 replicates.
Growth protocol The wild-type C. elegans var. Bristol, strain N2, was maintained at 20°C on NGM agar plates seeded with Escherichia coli OP50 bacteria. The culture was synchronized at the first larval stage (L1) by bleaching with a 5% sodium hypochlorite solution. Worms were harvested by gentle rinsing with K Medium in late L3 stage which were determined by both length and age (Donkin and Williams 1995; Altun and Hall 2005).
Extracted molecule total RNA
Extraction protocol After the 24-hr exposure, all 400 worms per well were collected into a cryogenic vial and spun at 1150 x g for 2.5 min. Supernatant was removed and the vial were flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from each vial using RNeasy mini kits (Qiagen, Valencia, CA) and treated as one biological replicate. Four of the five replicates (total RNA samples) per treatment were chosen for further microarray hybridization.
Label Cy3
Label protocol One hundred ng of total RNA was first reverse-transcribed into cDNA, followed by cDNA labeling using Low Input Quick Amp Labeling Kits (Agilent, Palo Alto, CA) in the presence of cyanine 3-CTP dye.
 
Hybridization protocol The labeled cDNA was hybridized to the C. elegans-specific 44K-olig array (one sample/array) at 65°C for 17 hrs using Agilent’s Gene Expression Hybridization Kits. A total of 48 samples (3 chemicals × 4 treatments per chemical × 4 replicates per treatment) were hybridized to six 8 × 44K-array slides in a randomized fashion to reduce systematic errors.
Scan protocol An Agilent high-resolution DNA Microarray Scanner Model G2565CA was used to scan microarray images (resolution = 3 microns per pixel).
Description Labeled cRNA was hybridized to the genome-wide microarray to profile global gene expression.
Data processing Raw microarray gene expression data were extracted from acquired array images as spot and background signal intensity using Agilent’s Feature Extraction software v10.7. A spot was flagged out if its raw signal intensity was below its background level, or if it was saturated. A gene was flagged out if over 50% of the 48 samples had missing values for this gene. The filtered data was background subtracted and log-transformed. The spike-in RNA mix with known composition and RNA copy numbers was used to construct standard linear regression curves, from which the unknown worm RNA concentrations were derived. The derived RNA concentrations were normalized to the median value per array (sample).
 
Submission date Dec 13, 2016
Last update date Jun 01, 2017
Contact name Ping Gong
E-mail(s) ping.gong@usace.army.mil
Phone (601) 634-3521
Organization name U.S Army Engineer Research and Development Center
Department Environmental Laboratory
Street address 3909 Halls Ferry Road
City Vicksburg
State/province Mississippi
ZIP/Postal code 39180
Country USA
 
Platform ID GPL22795
Series (1)
GSE92365 Comparative toxicogenomic effects of three IMX-101 constituents DNAN, NTO and NQ on C. elegans

Data table header descriptions
ID_REF
VALUE Normalized (to the array median) value of pre-processed (background corrected and log-transformed) signal intensity

Data table
ID_REF VALUE
6
7
8
9 0.622575
10
12
14 5.175888
18
20 2.796001
21 1.210898
22 3.473114
24 10.132791
25 0.221747
27 10.166546
28 0.398218
31 3.103976
33
34 0.892332
35
38

Total number of rows: 42862

Table truncated, full table size 574 Kbytes.




Supplementary file Size Download File type/resource
GSM2428145_US10293825_256483210010_S01_GE1_107_Sep09_1_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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