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Sample GSM4550326 Query DataSets for GSM4550326
Status Public on Jul 30, 2020
Title GVC5.BC5
Sample type SRA
 
Source name Ctrl5 B Cells with LPS+IL4
Organism Mus musculus
Characteristics strain: Lsh+/-
tissue: spleen
cell type: murine B lymphocyte
marker: CD19+ B220+
Treatment protocol B cells were stimulated with LPS(25µg/ml)+IL4(10ng/ml) for 72 hrs.
Growth protocol CTRL (Hells+/-) and KO (Hells-/-) B cells derived from spleen were grown in RPIM1640 (GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, Omega Scientific), 1x GlutaMAXTM (Gibco), 1x Non Essential Amino Acids and 50 U/ml Pen/Strep (Gibco). Each sample represents purified B cells derived from an individual mouse, except sample GVK2.Oct that represents. pooled lymphocytes from seven KO animals. "Hells" is official genome symbol for "Lsh" (Lymphoid-specific helicase).
Extracted molecule genomic DNA
Extraction protocol genomic DNA were extracted according to Frederick Alt's lab protocol (Panchakshari RA, et al., Proc Natl Acad Sci U S A. ( 2018)23;115(4):762-767)
Linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) libraries were generated as described by Frederick Alt's lab protocol (Panchakshari RA, et al., Proc Natl Acad Sci U S A. ( 2018)23;115(4):762-767). Sequencing runs were performed on an Illumina Miseq with 300-base-pair (bp) paired mode using miseq-500V2 kit
Linear Amplification-Mediated High-throughput genome-wide translocation sequencing (LAM-HTGTS)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Data processing library strategy: Linear Amplification-Mediated High-throughput genome-wide translocation sequencing (LAM-HTGTS)
Align with HiSAT (hihsat2, Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015) giving suggested breakpoints of individual samples.
Select the breakpoints with a deletion around 90,000 bp (which indicates the switch recombination process).
The breakpoints were further evaluated using UCSC BLAT program (Genome Research 12(4):656-64 · May 2002).
Genome_build: mm10
Supplementary_files_format_and_content: text containing potential breakpoints
 
Submission date May 12, 2020
Last update date Jul 30, 2020
Contact name Scott Durum
E-mail(s) durums@mail.nih.gov
Phone 3018461545
Organization name National Cancer Institute
Department CCR
Lab Cancer Innovation Labratory
Street address Building 560, Room 31-71
City Frederick
State/province MD
ZIP/Postal code 21702-1201
Country USA
 
Platform ID GPL16417
Series (1)
GSE150423 Lsh/HELLS is required for B lymphocyte development and immunoglobulin class switch recombination
Relations
BioSample SAMN14906419
SRA SRX8332919

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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