|
| Status |
Public on Jul 29, 2012 |
| Title |
HapMap YRI sample GM19116 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
lymphoblastoid cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: lymphoblastoid cell line GM19116
|
| Biomaterial provider |
Coriell
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM19116
|
| Growth protocol |
All LCLs were maintained in RPMI 1640 with 1% L-glutamine and 15% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNA was isolated from LCLs that had a viability greater than 85% at the time of pelleting using miRNeasy Plus mini kit (Qiagen).
|
| Label |
Hy3
|
| Label protocol |
miRNA samples were labeled using the miRCURY Hy3/Hy5 power labeling kit.
|
| |
|
| Channel 2 |
| Source name |
pooled all lymphoblastoid cell lines evaluated
|
| Organism |
Homo sapiens |
| Characteristics |
reference: pooled all lymphoblastoid cell lines evaluated
|
| Growth protocol |
All LCLs were maintained in RPMI 1640 with 1% L-glutamine and 15% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNA was isolated from LCLs that had a viability greater than 85% at the time of pelleting using miRNeasy Plus mini kit (Qiagen).
|
| Label |
Hy5
|
| Label protocol |
miRNA samples were labeled using the miRCURY Hy3/Hy5 power labeling kit.
|
| |
|
| |
| Hybridization protocol |
Exiqon standard protocol for miRNAs
|
| Scan protocol |
Agilent G2505B Microarray Scanner system was used. The sensitivity was adjusted to 100% PMT. All microarrays were scanned in an ozone-free environment (less than 2ppb ozone).
|
| Data processing |
Measured signals were background corrected using Normexp with offset value 10 based on the convolution model and normalized using the global Lowess regression algorithm. (Convolution model described by Ritchie ME, Bioinformatics (2007), Vol. 23 no. 20 2007, pages 2700–2707).
|
| |
|
| Submission date |
Dec 13, 2011 |
| Last update date |
Jul 29, 2012 |
| Contact name |
R. Stephanie Huang |
| E-mail(s) |
rhuang@medicine.bsd.uchicago.edu
|
| Organization name |
University of Chicago
|
| Street address |
900 E 57th street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL14999 |
| Series (1) |
| GSE34406 |
Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples |
|
