|
| Status |
Public on Jun 30, 2007 |
| Title |
HSPH_MIPS_murlungs_430_Particles16 |
| Sample type |
RNA |
| |
|
| Source name |
Total lung RNA of normal mouse exposed to PBS insufflation
|
| Organism |
Mus musculus |
| Characteristics |
Strain: BALB/c
Gender: female
Gestation: non-pregnant
Exposure: PBS insufflation control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy with on-column DNAse digestion and dual elution.
|
| Label |
biotin
|
| Label protocol |
For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
|
| |
|
| Hybridization protocol |
Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
|
| Scan protocol |
Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility. All systems are CFR21-11 and HIPPA compliant
|
| Description |
Sample # Group OD 260/280 RNA, ug/ul Actb Ct Chip
1 PregPBS 2.0 0.63 13.8 a
2 PregPBS 2.0 0.647 13.3 j
3 PregPBS 2.1 0.612 13.4 l
4 PregPBS 2.0 0.575 13.8 m
6 PregTiO 2.1 0.585 14.3 n
8 PregTiO 2.1 0.458 13.8 o
9 NormPBS 2.0 0.627 13.3 p
11 NormPBS 2.0 0.714 13.4 b
12 NormPBS 2.1 0.462 13.8 c
13 NormTiO 2.0 0.572 15.6 d
14 NormTiO 2.1 0.598 13.1 e
15 NormTiO 2.1 0.682 13.6 f
16 NormTiO 2.1 0.654 13.6 g
17 PregTiO 2.1 0.586 13.7 h
18 PregTiO 2.0 0.833 12.8 i
20 NormPBS 2.0 0.804 12.5 k
|
| Data processing |
GCOS/MAS5 and RMA-SAM-ANOVA
|
| |
|
| Submission date |
Apr 06, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Alexey Fedulov |
| E-mail(s) |
afedulov@rics.bwh.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Brigham and Women's Hospital
|
| Lab |
Fedulov lab
|
| Street address |
75 Francis St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7475 |
Inflammatory response to titanium dioxide particles exposure is enhanced during pregnancy |
|
| Relations |
| Reanalyzed by |
GSE119085 |
