|
| Status |
Public on Jul 26, 2021 |
| Title |
BoneMarrow_1_KR_JH3 |
| Sample type |
SRA |
| |
|
| Source name |
RAG1.K233R bone marrow B220+IgM- cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: RAG1.K233R
tissue: Bone marrow
cell type: B220+IgM-
htgts-rep-seq bait: JH3
|
| 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.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Beilinson_et_al_HTGTS_Rep_seq_BM1.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
|
| |
|
| 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 |
SAMN20362631 |
| SRA |
SRX11534855 |
