|
| Status |
Public on Jan 05, 2018 |
| Title |
06_cit500-3-liq |
| Sample type |
RNA |
| |
|
| Source name |
C.elegans L4_C-SPIONs3
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: stage L4 hermaphrodite
|
| Treatment protocol |
L4 stage animals were exposed 24 hours at 20 ºC in 50% M9 buffer (unexposed) or in 50% M9 supplemented with 500 µg/ml C-SPIONs (exposed).
|
| Growth protocol |
Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L4 stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
200 ng of total RNA was subjected to cDNA conversion and amplification using NuGEN Ovation Pico WTA V2 kit, to produce biotin-labelled cDNA.
|
| |
|
| Hybridization protocol |
5 μg of Biotin labeled cDNA was fragmented and hybridized to the Affymetrix C. elegans Gene 1.0 ST arrays as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.
|
| Scan protocol |
Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.
|
| Description |
Raised on NGM for 48 hours (L1 to L4 stage), then exposed 24 hours in 50% M9 supplemented with 500 µg/ml C-SPIONs
|
| Data processing |
To summarize the probe level data in the Affymetrix GeneChip® arrays, CEL files of C.elegans pOPC7 control condition was imported into the Affymetrix Expression ConsoleTM software for the quality control, data normalization and fold change algorithm. RMA normalization was carried out in Expression COnsole. Exported excel file with all genes and their exposure/control fold changes are listed.
|
| |
|
| Submission date |
Jan 05, 2017 |
| Last update date |
Jan 05, 2018 |
| Contact name |
Stephen Sturzenbaum |
| E-mail(s) |
stephen.sturzenbaum@kcl.ac.uk
|
| Organization name |
King's College London
|
| Department |
Analytical, Environmental and Forensic Sciences
|
| Street address |
150 Stamford Street
|
| City |
London |
| ZIP/Postal code |
SE1 9NH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19230 |
| Series (2) |
| GSE93187 |
Transcriptomic fingerprints of C. elegans exposed to citrate coated superparamagnetic iron oxide nanoparticles (C-SPIONs) |
| GSE93188 |
Transcriptomic fingerprints of C. elegans exposed to citrate coated superparamagnetic iron oxide nanoparticles (C-SPIONs) and to superparamagnetic iron oxide nanoparticles coated with a monolayer of bovine serum albumin (BSA-SPIONs) |
|
