|
| Status |
Public on May 05, 2024 |
| Title |
4C_f_brain_homo_rep2 |
| 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
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 |
Briefly, 1 × 105 - 1 × 106 digested cell suspensions from tissues were cross-linked with 2% formaldehyde for 10 min, stopped by 0.2 M glycine. The cell pellet was permeabilized and digested with DpnII overnight followed by proximity ligation. Then DNA was extracted and sonicated below 1000 bp. To enrich ligation events associated with a specific viewpoint, an appropriate amount of sonicated DNA was taken as template to linearly amplify for 100 cycles using a 5’ biotin-labeled probe of the interested viewpoint. The amplified products were incubated at 95°C for 5 min and immediately cooled on ice to obtain amplified ssDNA and then enriched with Dynabeads™ M-280 streptavidin. The ssDNA-on-beads were then ligated with adapters.
QHR-4C libraries were constructed with specific primer pairs (forward primers containing Illumina P5 and sequences near a specific viewpoint, and reverse primers containing Illumina P7 index and sequences matching the adapter) and then sequenced on Illumina NovaSeq platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: 4C-seq
Adaptor sequences in raw paired end reads were removed with Trim Galore, then subjected to cutadapt to trim primer sequence in 5’ end of read 1. Reads that didn’t contain primer sequence were discarded. Reads were mapped to mm10 genome using bowtie2 with the following parameters:--very-sensitive --end-to-end --no-unal -X 2000. Bam files were imported to r3Cseq package to generate normalized bedgraph files, and then transformed into bigwig files using bedGraphToBigWig tool.
Assembly: mm10
Supplementary files format and content: Normalized bigwig 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) |
| GSE214688 |
Dissecting developmental disorders caused by CTCF mutation at R567 [4C] |
| GSE214692 |
Dissecting developmental disorders caused by CTCF mutation at R567 |
|
| Relations |
| BioSample |
SAMN31137685 |
| SRA |
SRX17781321 |
