|
| Status |
Public on Nov 07, 2020 |
| Title |
BM_INV_3C_3CBEbait_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CB7BL/6 mouse BM pro-B cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Igh Inversion,RAG1 deficient
|
| Treatment protocol |
Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)
3 uM STI-571 treated for 4 days
|
| Growth protocol |
Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days
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.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
aligned to mm9 genome
|
| Data processing |
Library strategy: Linear-amplificate PCR-mediated HTGTS
Standard basecalling formats for Nextseq reads
Nextseq 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: mm9 genome
Supplementary_files_format_and_content: bedgraph files
|
| |
|
| Submission date |
Sep 23, 2020 |
| Last update date |
Nov 07, 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) |
| GSE151909 |
Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (3C-HTGTS) |
| GSE151910 |
Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination |
|
| Relations |
| BioSample |
SAMN16249446 |
| SRA |
SRX9180080 |
