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| Status |
Public on Aug 13, 2009 |
| Title |
Expression data from Chd1-deficient mouse ES cells (E14 cell lines) and genome-wide binding of Chd1 in parental ES cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
We used microarrays to study the effect of Chd1 loss of function in mouse ES cells.
We used ChIP-chip to analyze genome-wide binding of Chd1 in normal ES cells.
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| Overall design |
Mouse Embryonic Stem (ES) cells were infected with a lentiviral vector (pSicoR-mCherry) for expression of a shRNA against Chd1 and GFP (as a control). mCherry-sorted ES cells were plated and individual clones were selected and grown under normal ES cell conditions. 6 ES cell clonal lines were isolated and analyzed along with the parental E14 cell line. The final analysis consisted in 3 control cell lines (E14, E1 and G8) and 4 Chd1-deficient cells (3 different clones using a shRNA sequence #1- C1i5, C1i6 and C1i9; 1 clone using a different shRNA (#4) sequence targeting Chd1- C4i2). RNA samples were isolated from these Chd1-deficient ES cells and control ES cells, and hybridized on Affymetrix chip.
For ChIP-chip, parental E14 ES cell line was used.
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| Contributor(s) |
Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason M, Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, Ramalho-Santos M |
| Citation(s) |
19587682 |
| Submission date |
Jun 05, 2009 |
| Last update date |
Mar 04, 2019 |
| Contact name |
Miguel Ramalho-Santos |
| E-mail(s) |
mrsantos@diabetes.ucsf.edu
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| Organization name |
UCSF
|
| Department |
Eli and Edythe Broad Center of Regeneration Medicine
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| Lab |
Santos lab
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| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (2) |
| GPL6246 |
[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] |
| GPL7793 |
Agilent Mouse Promoter ChIP-on-Chip Set 244K Combined Arrays (Slide 1 & 2) mm8 build |
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| Samples (8)
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| GSM409770 |
Chd1 IP from mouse ES cells |
| GSM413497 |
E14 mouse ES cells (parental cells) |
| GSM413498 |
E14 clone with pSicoR-mCherry empty vector E1 |
| GSM413499 |
E14 clone with pSicoR-mCherry GFP shRNAi G8 |
| GSM413500 |
E14 clone with pSicoR-mCherry Chd1 shRNAi1 C1i5 |
| GSM413806 |
E14 clone with pSicoR-mCherry Chd1 shRNAi1 C1i6 |
| GSM413807 |
E14 clone with pSicoR-mCherry Chd1 shRNAi1 C1i9 |
| GSM413809 |
E14 clone with pSicoR-mCherry Chd1 shRNAi4 C4i2 |
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| Relations |
| BioProject |
PRJNA116039 |
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