|
| Status |
Public on Dec 10, 2010 |
| Title |
human.placenta.657 |
| Sample type |
RNA |
| |
|
| Source name |
human placenta
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta
gender: F
classification: Control
gestational age: 39
induction of labor: spontaneous
batch: A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from term human placenta using the Totally RNA kit (Ambion) following the manufacturer’s instructions with slight modifications. Briefly, homogenized tissue chilled in liquid nitrogen was lysed in 10 volumes of denaturation solution (200 mg tissue, 2 ml denaturation solution). The lysed sample was pre-cleared of bulk genomic DNA and cellular debris by spinning at 4,000 x g for 5 minutes. The supernatant was sequentially extracted with equal volumes phenol:chloroform, and acid phenol:chloroform (pH 4.5) using phase divider gels (Sigma), then precipitated with an equal volume of 100% isopropanol. The pellet was washed twice with 70% ethanol and resuspended in elution buffer (1 mM Tris-Cl). Total RNA was treated with Turbo DNA-free to remove traces of genomic DNA contamination (Ambion). RNA integrity was assessed using a Bioanalyzer (Agilent Biotechnologies) and only samples with a RIN > 7 were used.
|
| Label |
biotin
|
| Label protocol |
Labeling for Illumina Human6-v2 BeadArrays was performed according to manufacturer’s instructions. Briefly, the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Foster City, CA) was used for a first and second strand reverse transcription step from 500 ng of total RNA. This was followed by an overnight in vitro transcription reaction that incorporates biotin-labeled nucleotides. 1.5 ug of biotin-labeled cRNA was mixed with an Illumina-supplied hybridization buffer containing several control oligonucleotides.
|
| |
|
| Hybridization protocol |
Hybridization for Illumina Human6-v2 BeadArrays was performed according to manufacturer’s instructions. Labeled cRNA was hybridized to BeadArrays at 58°C for 18 hr. Washing, blocking, and streptavadin-Cy3 staining was performed out following manufacturer’s protocol.
|
| Scan protocol |
BeadChips were scanned on the BeadArray Reader and scanned images were analyzed using BeadStudio software.
|
| Data processing |
Transcript data was log2 transformed, and quantile normalized.
|
| |
|
| Submission date |
Dec 07, 2010 |
| Last update date |
Nov 13, 2015 |
| Contact name |
Shengdar Tsai |
| Organization name |
North Carolina State University
|
| Street address |
4700 Hillsborough St.
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27604 |
| Country |
USA |
| |
|
| Platform ID |
GPL6102 |
| Series (1) |
| GSE25906 |
Transcriptional Profiling of Human Placentas from Pregnancies Complicated by Preeclampsia Reveals Disregulation of Sialic Acid Acetylesterase and Immune Signaling Pathways |
|
| Relations |
| Reanalyzed by |
GSE75010 |
