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| Status |
Public on Dec 16, 2017 |
| Title |
5ug |
| Sample type |
SRA |
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| Source name |
Splenic B cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 12 weeks
cell type: Enriched B cells by MACS depletion
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
B cells from spleen isolated by depletin of unwated cells using 4 biotin antibodies and Miltenyi Biotec MACS LS columns. DNA was extracted with Qiagen DNeasy Blood & Tissue Kit (69504).
Libraried were constructed using the VDJ-seq protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Sequences were adaptor and quality trimmed using Trim Galore (v0.4.4)
Read were assembled with Pear v0.9.10, germline reads were removed using Bowtie2 v2.3.2 alignment to mm10, part of BabrahamLinkON v0.1 preclean step
Mispriming correction, UMI extraction was done with BabrahamLinkON v 0.1 preclean step
Deduplication and error correction was done with BabrahamLinkON v0.1 deduplicate step
Sequences were annotated with IgBlast v1.7.0 with IMGT reference and parsed with ChangO 0.3.7. Clonotype information was additionally added. All steps are part of BabrahamLinkON v0.1 assemble_clones step
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing annotated V(D)J sequences from IgBlast with IMGT reference
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| Submission date |
Nov 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE106458 |
Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq |
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| Relations |
| BioSample |
SAMN07967437 |
| SRA |
SRX3353526 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2837809_5ug_dedup_assembled_clones.tsv.gz |
19.9 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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