|
| Status |
Public on Jan 11, 2012 |
| Title |
Patient 4-severe |
| Sample type |
RNA |
| |
|
| Source name |
Patient 4-severe
|
| Organism |
Homo sapiens |
| Characteristics |
patient: Patient 4
tissue: blood
age: 23 months
malaria status: severe
|
| Treatment protocol |
The children were enrolled in a longitudinal study of severe malaria in Blantyre Malawi. Human subjects approval was obtained prior to protocol initiation; consent was obtained for all samples.
|
| Growth protocol |
3mL of blood obtained from venipuncture was added to Tri_reagent BD (Molecular Researc Center). The samples were immediately frozen at minus 80, and shipped in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA sample was thawed at room temperature and extracted following manufacturers protocol. RIN were evaluated prior to sample hybridization and analysis.
|
| Label |
biotin
|
| Label protocol |
Biotinylated sscDNA were prepared according to the standard Ambion and Affymetrix protocols from 5.5 ug total sscDNA (The Ambion WT Expression Kit For Affymetrix GeneChip Whole Transcript (WT) Expression Manuals, 2009, Ambion and Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.5 ug of sscDNA were hybridized for 17 hrs at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G7
|
| Description |
JPD-HuGene-1_0-ST-8810.CEL
|
| Data processing |
CEL files were analyzed using softward GenePattern; Robust Multi-array Average (RMA) procedure was used, and the data was quantile normalized with 28,132 gene-level probe sets. This gene list was thresholded to a minimum of 20 expression units (EU) and a maximum of 20000 EU. A filtered gene list of 3110 genes (linked as supplementary file on Series record) was generated by removing genes that varied less than 3 fold or 100 EU across the data set. Differentially abundant transcripts between the severe and mild clinical states for each paired sample were identified using a paired Student t-test of log2 transformed data.
|
| |
|
| Submission date |
Nov 18, 2011 |
| Last update date |
Jan 11, 2012 |
| Contact name |
Johanna Patricia Daily |
| E-mail(s) |
jdaily@einstein.yu.edu
|
| Phone |
718-678-1176
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Medicine (Infectious Disease)
|
| Lab |
Daily Lab
|
| Street address |
1301 Morris Park Avenue, Price Center
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE33811 |
Paired whole blood human transcription profiles from children with severe malaria and mild malaria |
|
