|
| Status |
Public on May 11, 2020 |
| Title |
3C_VH81X_Rad21degron_IAA_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
v-Abl transformed pro-B cell line
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Rad21degron, Emu-Bcl2, RAG2 deficient
treatment: 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days
|
| Growth protocol |
RPMI1640; 15% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.
Linear-amplificate PCR-mediated HTGTS
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
aligned to AJ851868/mm9 hybrid genome
|
| Data processing |
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to inditated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: AJ851868/mm9 hybrid genome
Supplementary_files_format_and_content: bedgraph files
|
| |
|
| Submission date |
Jan 06, 2020 |
| Last update date |
May 12, 2020 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
PCMM
|
| Lab |
Alt
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE142778 |
CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [3C-HTGTS] |
| GSE142781 |
CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning |
|
| Relations |
| BioSample |
SAMN13740687 |
| SRA |
SRX7507502 |
