|
Status |
Public on Jul 26, 2021 |
Title |
Spleen_1_PG_JH1 |
Sample type |
SRA |
|
|
Source name |
RAG1.P326G splenic B220+ cells
|
Organism |
Mus musculus |
Characteristics |
genotype: RAG1.P326G tissue: Spleen cell type: B220+ htgts-rep-seq bait: JH1
|
Extracted molecule |
genomic DNA |
Extraction protocol |
B cells were isolated from mice aged 5-7 weeks. Splenic B cells were isolated using B220 magnetic beads (Miltenyi Biotec) or by FACS sorting. B220+ IgM- cells were purified via FACS sorting from bone marrow. Genomic DNA samples were obtained using phenol-chloroform extraction of whole cell lysates. HTGTS-Rep-seq libraries were prepared as previously described (Hu et al., 2016; Lin et al., 2016). Briefly, genomic DNA was sonicated and subjected to LAM-PCR using biotinylated JH1 or JH3 bait primers (Lin et al., 2016). LAM-PCR products were purified using Dynabeads MyONE C1 streptavidin beads (Life Technologies, 65002) and ligated to bridge adaptors. Adaptor-ligated products were amplified by nested PCR with indexed JH1/JH3 primers (8-bp indexes were unique to each sample) and primer annealed to the adaptor. PCR products were further tagged with Illumina sequencing adaptor sequences and size-selected via gel extraction. Libraries were sequenced by paired-end 300-bp sequencing on an Illumina MiSeq by the Yale Center for Genome Analysis.
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
|
|
Description |
Beilinson_et_al_HTGTS_Rep_seq_Spleen1.xlsx
|
Data processing |
Library strategy: HTGTS-Rep-seq Fastq-multx tool based demultiplexing. Cutadapt was used to trim adaptors. The joined Paired-end sequence reads were then aligned and further processed using HTGTSrep pipeline (VDJ)/LAM-HTGTS pipeline (DJ) with default settings. Genome_build: mm10 (GRCm38) Supplementary_files_format_and_content: *.xlsx: Excel files
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|
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Submission date |
Jul 23, 2021 |
Last update date |
Jul 26, 2021 |
Contact name |
Helen Alexander Beilinson |
E-mail(s) |
beilinsonh@uchicago.edu, helen.beilinson@yale.edu
|
Organization name |
Yale University
|
Department |
Immunobiology
|
Street address |
300 Cedar Street
|
City |
New Haven |
State/province |
CT |
ZIP/Postal code |
06520 |
Country |
USA |
|
|
Platform ID |
GPL16417 |
Series (1) |
GSE180734 |
The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination |
|
Relations |
BioSample |
SAMN20362663 |
SRA |
SRX11534827 |