NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3734012 Query DataSets for GSM3734012
Status Public on Aug 19, 2019
Title JH1_DFL16.1replaceDQ52_JH1bait_rep3
Sample type SRA
 
Source name v-Abl transformed pro-B cell line
Organism Mus musculus
Characteristics cell type: v-Abl transformed pro-B cell line
genotype: DH-JH1+/-, DFL16.1-del, DQ52 replaced by DFL16.1, Emu-Bcl2, RAG2 deficient
Treatment protocol RAG2 retrovirally complemented and then 3 uM STI-571 treated for 4 days for RAG2 deficient v-Abl pro-B cells.
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
HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description aligned to modified mm9 genome with DQ52 replaced by DFL16.1
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_DFL16.1-replace-DQ52 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_DFL16.1-replace-DQ52
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 Apr 23, 2019
Last update date Aug 20, 2019
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)
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
Relations
BioSample SAMN11484035
SRA SRX5726929

Supplementary file Size Download File type/resource
GSM3734012_JH1_DFL16.1replaceDQ52_JH1bait_rep3.tlx.txt.gz 4.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap