|
| Status |
Public on Dec 03, 2012 |
| Title |
Limitations and possibilities of low cell number ChIP-seq |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique.
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| |
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| Overall design |
Two-part ChIPseq study using native chromatin (non-crosslinked) generated with MNase from human CD4+ cells. Part 1: Previously published protocol (Barski et al, 2007, Cell 129:823, hereafter called "Benchmark") used with 2x10e7 cells / ChIP with H3K4me3 antibody, compared to modified method ("new") with decreasing input cell numbers spanning 1000-fold range from 2x10e7 cells / IP to 2x10e4 cells/ IP. Part 2: reproducibility of new method studied using triplicate samples at lowest two cell numbers tested: 1x10e5 and 2x10e4 / ChIP, using H3K4me3 and H3K27me3 antisera.
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| |
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| Contributor(s) |
Gilfillan GD, Lyle R |
| Citation(s) |
23171294 |
| Submission date |
Nov 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregor Duncan Gilfillan |
| E-mail(s) |
gregor.gilfillan@medisin.uio.no
|
| Phone |
+47 23016419
|
| Organization name |
Oslo Universitetssykehus
|
| Department |
Medical Genetics
|
| Lab |
Norwegian Sequencing Centre
|
| Street address |
Medisinsk Genetikk
|
| City |
Oslo |
| ZIP/Postal code |
0407 |
| Country |
Norway |
| |
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| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA179207 |
| SRA |
SRP017125 |
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