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| Status |
Public on Aug 19, 2019 |
| Title |
JHdel_DQ52RSSUPbait_rep3 |
| Sample type |
SRA |
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| Source name |
v-Abl transformed pro-B cell line
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| Organism |
Mus musculus |
| Characteristics |
cell type: v-Abl transformed pro-B cell line
genotype: JH-del, Emu-Bcl2, RAG2 deficient
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| Treatment protocol |
RAG2 retrovirally complemented and then 3 uM STI-571 treated for 4 days for RAG2 deficient v-Abl pro-B cells.
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| Growth protocol |
RPMI1640+15% FBS
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| 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
HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
aligned to mm9 genome
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| 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 the mm9 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.
Genome_build: mm9
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 paried 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)
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| Submission date |
Apr 23, 2019 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
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| Organization name |
Boston Children's Hospital
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| Department |
PCMM
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| Lab |
Alt
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE130216 |
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [HTGTS V(D)J-seq] |
| GSE130224 |
The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination |
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| Relations |
| BioSample |
SAMN11484029 |
| SRA |
SRX5726935 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3734018_JHdel_DQ52RSSUbait_rep3.tlx.txt.gz |
118.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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