|
| Status |
Public on Apr 08, 2024 |
| Title |
v-Abl_SisCBE2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
v-Abl transformed pro-B cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: v-Abl transformed pro-B cell line
strain: 129SV
genotype: Rag2-/-, Emu-Bcl2
treatment: G1-arrest
|
| Treatment protocol |
Pre-B cells were isolated from mouse bone marrow by FACS sorting for B220+ CD43low IgM- cells
G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days
|
| Growth protocol |
v-Abl cell lines were cultured in RPMI1640 media with 15% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 2% formaldehyde, quenched with glycine, lysed in a lysis buffer containing: 150mM NaCl, 0.5% NP-40, 1% Triton X-100, 50mM Tris-HCl pH7.5, 5mM EDTA pH8.0. Nuclei were digested with NlaIII, ligated with T4 DNA Ligase, treated with Proteinase K and RNase A prior to DNA precipitation.
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated high-throughput genome-wide translocation sequencing protocol with indicated bait primers
|
| |
|
| 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
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 the indicated 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 reads 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
Assembly: AJ851868/mm9 hybrid genome
Supplementary files format and content: Tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paired end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)
Library strategy: 3C-HTGTS
|
| |
|
| Submission date |
Apr 03, 2024 |
| Last update date |
Apr 08, 2024 |
| Contact name |
Frederick Alt |
| Organization name |
Boston Children's Hospital / Harvard Medical School
|
| Department |
Program in Cellular and Molecular Medicine
|
| Lab |
Frederick Alt
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE263123 |
Molecular Basis for Differential Igk Versus Igh V(D)J Joining Mechanisms [3C-HTGTS data] |
| GSE263124 |
Molecular Basis for Differential Igk Versus Igh V(D)J Joining Mechanisms |
|
| Relations |
| BioSample |
SAMN40738501 |
| SRA |
SRX24139810 |
