|
| Status |
Public on Jun 13, 2009 |
| Title |
Erythroid GATA |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
GATA1 Erythroid d10 ChIP input sample
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: erythroid cells
|
| Growth protocol |
Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. GATA1 ChIP study. Sample precessed as ChIP input.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP material generated from 30 million cells using the NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Followed NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
GATA1 Erythroid d10 ChIP test sample
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: erythroid cells
|
| Growth protocol |
Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. GATA1 ChIP study. Sample precessed as ChIP test.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP material generated from 30 million cells using the NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
Followed NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
Followed NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.
|
| Scan protocol |
GenePix scanner at 5 micron resolution.
|
| Description |
Images generated at 635 and 532 nm as per NimbleGen ChIP protocol.
|
| Data processing |
Images processed and data generated using NimbleScan v2 exactly as described in NimbleChip Arrays User's Guide. The Scaled Log2-ratio is the ratio of the input signals for the experimental and test samples co-hybridised to the array. The log2-ratio is computed and scaled to cenre the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.
|
| |
|
| Submission date |
Jun 10, 2009 |
| Last update date |
Jun 12, 2009 |
| Contact name |
Steve Best |
| E-mail(s) |
steve.best@kcl.ac.uk
|
| Organization name |
King's College London
|
| Department |
The James Black Centre
|
| Lab |
Molecular Haematology
|
| Street address |
125 Coldharbour Lane
|
| City |
London |
| ZIP/Postal code |
SE5 9NU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL8694 |
| Series (1) |
| GSE16541 |
Human Erythroid Day 10 ChIP using GATA, PolII, H3 and H4 |
|
