 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 06, 2020 |
| Title |
4CBS_PLAC-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F123 ESC
strain: F1 hybrid (castaneus x S129/SvJae)
chip antibody: Millipore, 04-745
genotype: 4CBS-insertion
|
| Growth protocol |
Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
PLAC-seq experiments were performed in biological replicates using MboI, following the protocol described by Fang, R., Yu, M., et al., Cell research 2016(PMID: 27886167). Hi-C experiments were performed in biological replicates using MboI, following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: PLAC-seq
For PLAC-seq, paired-end reads were first mapped to mm10 reference genome. We modified the original WAPS mapping procedure by replacing the bowtie2 alignment tool with bwa-mem and integrated MAPS feather post-filtering pipeline to resolve the chimeric reads
Hi-C reads were aligned to mm10 using bwa-mem for each read separately and then paired. For chimeric reads, only 5′ end-mapped locations were kept. Duplicated read pairs mapped to the same location were removed to leave only one unique read pair. The output bam files were transformed into juicer file format for visualization in Juicebox. Contact matrices were normalized using the Knight–Ruiz matrix balancing method
Genome_build: mm10
Supplementary_files_format_and_content: juicer hic files that can be visualized in Juicebox and cis-contacts of chr3 of the PLAC-seq data.
|
| |
|
| Submission date |
Jun 27, 2020 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
|
| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE153402 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [Hi-C and PLAC-seq] |
| GSE153403 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains |
|
| Relations |
| BioSample |
SAMN15393351 |
| SRA |
SRX8626604 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4643805_4CBS_PLAC-seq_rep1.chr3.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
