|
| Status |
Public on May 05, 2024 |
| Title |
CTCF_ChIP_brain_homo |
| Sample type |
SRA |
| |
|
| Source name |
brain tissue from E18.5 mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain tissue from E18.5 mouse embryo
genotype: Ctcf homozygous mutation
chip antibody: CTCF
strain background: C57BL/6
|
| Treatment protocol |
CTCF-R567W mutation were generated by CRISPR/Cas9-mediated genome editing.
|
| Growth protocol |
Mice were housed in a specific pathogen–free (SPF) facility with a 12 h dark/12 h light cycle and provided with food and water ad libitum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
An appropriate amount of mouse tissues were crushed with homogenizer, cross-linked with 1% formaldehyde for 10 min followed by quenching with 0.125 M glycine. Cross-linked tissues were lysed in ChIP lysis buffer and then sonicated to obtain chromatin fragments of 200-400 bp in size. For normalization, an equal amount of HEK293T chromatin was added to the sample chromatin solution of different groups for subsequent ChIP experiments. ChIPed DNA was eluted using 200 μl freshly prepared elution buffer, reverse-crosslinked and purified using MinElute PCR Purification Kit.
ChIP-seq libraries were constructed using VAHTS Universal V3 DNA Library Prep Kit for Illumina according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed to remove adaptors using Trim Galore, and then mapped to mouse (mm10) and human (hg38) mixed genomes using bowtie2 with the following parameters: --very-sensitive --end-to-end --no-unal --no-mixed --no-discordant. Only unique mapped reads with MAPQ > 30 were retained. Reads mapped to mouse or human genome were separated, then subjected to peak calling using macs2 with default options.
The summit value of averaged CTCF binding strength from HEK293T cells for each sample was extracted to calculate scale factor. Scale factor for wild type samples was considered as 1. For corresponding CTCF mutated samples, scale factor was calculated as summit (wild type)/summit (mutant). Normalized bigwig files were generated with bamCoverage using RPGC normalization and scale factors.
Assembly: mm10
Supplementary files format and content: Normalized bigWig and peak file for each sample.
|
| |
|
| Submission date |
Oct 03, 2022 |
| Last update date |
May 05, 2024 |
| Contact name |
gongcheng Hu |
| Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
|
| Street address |
190 Kai Yuan Avenue, Science Park, Guangzhou, China
|
| City |
guangzhou |
| State/province |
guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE214686 |
Dissecting developmental disorders caused by CTCF mutation at R567 [ChIP-seq] |
| GSE214692 |
Dissecting developmental disorders caused by CTCF mutation at R567 |
|
| Relations |
| BioSample |
SAMN31138048 |
| SRA |
SRX17781589 |
