|
| Status |
Public on Nov 19, 2018 |
| Title |
CTCF-ESC-Inv1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic forelimb
|
| Organism |
Mus musculus |
| Characteristics |
genotype: mutant
developmental stage: E11.5
cell type: G4 ESC
chip antibody: CTCF (Active motif: 613111)
|
| Treatment protocol |
Dissected tissue from embryos was pooled and turned into a single-cell suspension by digestion with Trypsin-EDTA 0.05% (Gibco) for 10 min at 37°C shaking at 900 RPM.The cells were mixed with 10%FCS/PBS and homogenized using a 40 µm cell strainer (Falcon). After centrifugation, cells were fixed in 1% PFA/10%FCS/PBS for 10’ on ice. Cells were then lysed in buffer 1 and 2 and resuspended in buffer 3 for sonication (Lee et al. 2006).
|
| Growth protocol |
Limb bud (stage E11.5) were micro-dissected from mouse embryos
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate chromatin modification ChIP and 30μg for CTCF and RAD21 ChIP. ChIP for H3K9me3 (Abcam: ab8898), CTCF (Active motif: 613111) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006.
Libraries were prepared using the Nextera adaptors and sequenced
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed.
Reads were extended (chromatin modifications: 300bp, CTCF&Rad21: 200bp) and scaled (one million / total of unique reads) to produce coverage tracks. For figure display purposes, replicate ChIP-seq tracks were merged.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Nov 19, 2018 |
| Contact name |
Andreas Magg |
| E-mail(s) |
magg@molgen.mpg.de
|
| Phone |
01703338494
|
| Organization name |
Max-Planck-Institute for Molecular Genetics
|
| Department |
Development and Disease
|
| Lab |
RG Mundlos
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE116790 |
Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations [ChIP-seq] |
| GSE116794 |
Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations |
|
| Relations |
| BioSample |
SAMN09631666 |
| SRA |
SRX4369704 |
