|
| Status |
Public on Jul 26, 2011 |
| Title |
ID3 LCL 2 |
| Sample type |
RNA |
| |
|
| Source name |
LCL
|
| Organism |
Homo sapiens |
| Characteristics |
method: EBV transformed LCL
individual (indiv.id): ID3
visit: 2
ChIP: 7
yield: 6.8221
rin: N/A
tissue: LCL
cell type: Lymphoblastoid cell line LCL
|
| Treatment protocol |
For each individual, five different post venipuncture methods were performed. B Lymphocytes from 10ml of blood were isolated by tubes with sodium citrate. LCLs were generated by EBV-mediated transformation and cells were grown for eight weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the isolation of CD19 and CD20 B-cells, 40ml whole blood from EDTA tubes was collected and PBMCs were isolated by using a Ficoll-Paque™ gradient (Amersham). CD19 and CD20 B-cells were prepared by positive selection from the PBMCs by incubation with magnetic anti-CD19 or CD20 mAb-coated microbeads (MACS, Miltenyi Biotec). For the isolation of PBMCs from whole blood, BD Vacutainer® CPT Mononuclear Cell Preparation Tubes (Becton and Dickinson) were used. Total RNA was isolated from 5 ml of whole blood samples with the PAXGene Blood RNA system (Qiagen) and samples were left at room temperature for 24 hours before processing according to manufacturer’s instructions.Only two people at a time were sampled on any one day for logistical reasons. After blood draw standard protocols were followed for cell isolation, transformation or RNA extraction. With the exception of the PAXgene samples all RNA was isolated using TRI™ reagent (SIGMA) and resuspended in RNase free water.
|
| Label |
biotin
|
| Label protocol |
Manufacturer’s instructions
|
| |
|
| Hybridization protocol |
Arrays were hybridised with labelled cRNA material and scanned according to manufacturer’s instructions.
|
| Scan protocol |
Manufacturer’s instructions
|
| Description |
1718911595_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number
|
| Data processing |
The resultant data was parsed with the software package BeadStudio to produce raw intensity values for all probes. Signal was checked for quality using hybridisation and labelling controls internal to each array and subtracted for background within the statistical scripting environment, R v2.4.1. Signal was transformed and normalised using the variance stabilization algorithm as implemented in the vsn2 Bioconductor package.
|
| |
|
| Submission date |
Jul 25, 2011 |
| Last update date |
Jul 26, 2011 |
| Contact name |
Josine Min |
| E-mail(s) |
jlmin@well.ox.ac.uk
|
| Organization name |
The Wellcome Trust Centre for Human Genetics
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL7350 |
| Series (1) |
| GSE30916 |
Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
|
