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| Status |
Public on Jan 15, 2018 |
| Title |
Igll1 PerC B-1a Rep2 |
| Sample type |
SRA |
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| Source name |
Pertionteal B-1a cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Igll1 knockout
tissue: Peritoneal cavity
cell type: peritoneal cavity B-1a cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were sorted from 6-8 week old mice. Genomic DNA was extracted from lysed cells and this gDNA was used as template for PCR prior to library prep/adaptor ligation.
Primers were used to amplify sucessfully rearranged BCR heavy chains and size selected by gel extraction for 120-280bp from an agarose gel. PCR products were end-repaired using a combination of T4 PNK and T4 polymerase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of preannelaed Illumina compatible adapters, NEXTflex DNA barcodes (Bioo Scientific) which have a single 'T' base overhang at the 3’ end. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina HISeq 4000 following the manufacturer's protocols.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Library strategy: VDJ-seq
Reads were trimmed for adaptor sequence and masked for low-complexity of low quality sequence
Reads 1 and reads 2 were overlapped and unique sequences were filtered out
These unique sequences were subject to IMGT/High V-Quest (version 1.5.5) analysis for mapping and assigning gene segment usage, Alamyar, et al. Immunome Res. 2012
IMGT/High V-Quest output was used as input for IMGT/StatClonotype (version 1.0.2) statstical analysis and visualization, Aouinti et. Al., Front. Immunol, 2016. IMGT/StatClonotype is atool that evaluates and visualizes statstical significance of pairwise comparisons of IMGT clonotype diversity per V, D orJ gene segments .
Genome_build: IMGT/GENE-DB for Mus musculus (Giudicelli, V. et al. Nucleic Acids Res. 2005)
Supplementary_files_format_and_content: tab-delimited file that contains information on AA sequence, V, D and J gene segment assignment, percent alignment, etc. This file is used as input for using the IMGT/StatClonotype tool.
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| Submission date |
Sep 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jane Skok |
| E-mail(s) |
[email protected]
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| Organization name |
NYU
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| Street address |
550 First Ave, Smillow 307
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE104111 |
BCR heavy and light chain repertoire sequencing of pertitoneal cavity B-1a cells from wild-type and Igll1 knockout mice |
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| Relations |
| BioSample |
SAMN07682344 |
| SRA |
SRX3203788 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2790123_Igll1_PerC_B-1a_Rep2_stats_JW041_IGH.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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