|
Status |
Public on Jul 30, 2020 |
Title |
GVC4.BC17 |
Sample type |
SRA |
|
|
Source name |
Ctrl4 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)
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|
|
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
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|
|
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 |
SAMN14906421 |
SRA |
SRX8332917 |