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Sample GSM4240100 Query DataSets for GSM4240100
Status Public on May 11, 2020
Title JH4_Rad21degron_IAA_b_rep1
Sample type SRA
 
Source name v- Abl transformed pro-B cell line
Organism Mus musculus
Characteristics tissue: v- Abl transformed pro-B cell line
genotype: Rad21degron, Emu-Bcl2, RAG2 deficient
treatment protocol: RAG2 nucleofected, 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days
growth protocol: RPMI1640; 15% FBS
Treatment protocol 3 uM STI-571 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
LAM-HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.
Linear-amplification PCR-mediated HTGTS
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
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 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 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: 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)
 
Submission date Dec 31, 2019
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 GPL16417
Series (2)
GSE142777 CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [LAM-HTGTS]
GSE142781 CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning
Relations
BioSample SAMN13702930
SRA SRX7481975

Supplementary file Size Download File type/resource
GSM4240100_JH4_Rad21degron_IAA_b_rep1.tlx.txt.gz 62.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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