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| Status |
Public on Jul 22, 2016 |
| Title |
splB_mix_JK5_BL6 |
| Sample type |
SRA |
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| Source name |
splB_mix_JK5_BL6
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild-type
bait locus: JK5
growth protocol: No immunization
age: 4-6 weeks
cell type: Splenic B
primer strategy: Combined with Jk1, Jk2, Jk4 primers in one library preparation
dna amount: 1 ug
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| Treatment protocol |
No immunization, but the food and water are not germ-free
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| Growth protocol |
Mice were bought from Jackson labs and kept in our mouse facility
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were extracted and treated with RBC lysis, resuspended in PBS, and stained for FACS. Bone marrow-derived pro-B (B220+IgM-CD43+) cells were purified from 129SVE or C57BL/6 mice by sorting and after the depletion of erythrocytes. Single cell suspensions were stained with B220-APC, CD43-PE, and IgM-FITC antibodies. Splenic resting B cells were purified using biotin/streptavidin bead methods (B220 positive selection) or EasySep CD43-negative B cell selection. Cells were then processed for genomic DNA extraction.
Libraries were prepared via HTGTS-Rep-seq protocols
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Sample 20
Barcode: CA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait
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| Data processing |
HTGTSrep pipeline was used for generating the processed files with "pass.xls" ends; Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Paire-end sequenced reads were trimmed for barcode and adaptor sequence and joined
The trimmed reads then were searched against VDJ gene databases using igblast1.5 with default parameters and further processed by the HTGTSrep pipeline, or against LAM-HTGTS pipeline with default settings.
For HTGTSrep pipeline, reads can successfully aligned to V, D, J databases are reported and a statistic report including V gene usage and in-frame/non-productive information is created by the pipeline.
Genome_build: mm9, mm9_AJ851868ins (Based on the genome build of mm9, we replaced its chr12 between 114,493,850 and 115,696,909 with the reverse complement sequence of the GeneBank AJ851868.3)
Supplementary_files_format_and_content: tab-delimited text files include aligned V, D, J genes for each read and a V usage report for each sample.
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| Submission date |
Jun 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiazhi Hu |
| E-mail(s) |
heartlead@gmail.com
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| Organization name |
Children's Hospital Boston
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| Department |
PCMM
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| Lab |
Frederick Alt
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| Street address |
300 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE82126 |
A Highly Sensitive and Unbiased Approach for Elucidating Antibody Repertoires |
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| Relations |
| BioSample |
SAMN05194917 |
| SRA |
SRX1814831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2183871_splB_mix_JK5_BL6.pass.xls.gz |
544.7 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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