|
| Status |
Public on Jul 26, 2012 |
| Title |
Negative_LPS_1 |
| Sample type |
RNA |
| |
|
| Source name |
Rat_Brain_Negative_LPS_Exposure_4hrs
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: gestation (embryonic) day 15
tissue: fetal brain
class: Negative_LPS
|
| Treatment protocol |
LPS (0.25mg/kg) or saline vehicle was administered to pregnant dams on gestation day 15. 4 h post injection pregnant dams were anesthetized and a midline incision was made into the peritoneal cavity to expose the embryos. Embryos were removed and placed in cold PBS. Fetal brains were removed and placed in Eppendorf tubes filled with 1ml TRIzol reagent (Invitrogen, USA) and stored at -80 until processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Briefly, 200ul chloroform was added to homogenized tissue and centrifuged for 15 min. Aqueous solution was transfered to a new Eppendorf tube and 100ul ETOH was added. Solution was transfered to a Qiagen Column and underwent two centrifuge cycles. Liquid was discarded and 750ul RW1 buffer was added to the column and centrifuged for 10 min. Liquid was discarded and 500 ul RPE buffer was added and centrifuged for 10 min. The step was repeated twice. Column was transfered to a fresh tube and centrifuged at max speed for 1 min. to remove excess liquid. 30ul DEPC-treated water was added and centrifuged 5 min. RNA was quantitated on a spectrophotometer (NanoDrop, Thermo Scientific, USA).
|
| Label |
Biotin
|
| Label protocol |
Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Rat Gene 1.0 ST Array (Affymetrix, Inc). 300 ng of total RNA was used per samples and the arrays stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
|
| |
|
| Hybridization protocol |
Labeled cRNA were hybridized to Affymetrix Rat Gene 1.0 ST Array (Affymetrix, Inc) in blinded interleaved fashion. Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate probe-level measurements for each hybridized cRNA.
|
| Scan protocol |
Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
|
| Description |
SAMPLE_1.CEL
|
| Data processing |
The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 29,215 RMA normalized gene fragment expression values for each hybridized cRNA.
|
| |
|
| Submission date |
Nov 30, 2011 |
| Last update date |
Jul 26, 2012 |
| Contact name |
Kory R Johnson |
| E-mail(s) |
[email protected]
|
| Phone |
301-402-1956
|
| Organization name |
NINDS/NIH
|
| Department |
DIR IT & Bioinformatics
|
| Lab |
Bioinformatics Section
|
| Street address |
10/3B01, 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE34058 |
Maternal immune activation by LPS selectively alters specific gene expression profiles of interneuron migration and oxidative stress in the fetus without triggering a fetal immune response. |
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