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| Status |
Public on Jun 29, 2020 |
| Title |
Sample_4.KO1_GCB |
| Sample type |
SRA |
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| Source name |
Germinal Center B-cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
genotype: TET2 Wild-Type
strain: C57BL/6
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| Treatment protocol |
Not applicable
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| Growth protocol |
GC B-cells (B220+Fas+GL7+) were isolated from mouse spleen
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic regions, JH4 (chr12:113,427,959-113,428,543) and Sμ (chr12:113,425,655-113,426,278), were PCR amplified, pooled and cleaned up using the MinElute PCR Purification Kit (Qiagen).
Illumina TruSeq DNA Sample Preparation Kit v2 (Illumina)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Library strategy: DNA-Seq
Raw reads were trimmed using TrimGalore (version 0.4.0) (89), using settings: --stringency 3 -q 20
Trimmed reads were mapped to the GRCm38.p3 reference genome using BWA-Mem (version 0.7.9a) with the default parameters.
Variants were called with LoFreq program (version 2.1.3.1).
Then, using bcftools (version 1.8), called variants were additionally filtered, excluding all known single-nucleotide polymorphisms (European Variation Archive accession GCA_000001635.6).
Separately, previously filtered reads for the analysis with the Immcantation pipeline. More specifically, the AssemblePairs.py, FilterSeq.py, CollapseSeq.py, and SplitSeq.py tools were used to construct clones of the JH4 and Sμ regions represented by at least two pairs of paired-end reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.lofreq_vars.vcf.gz files contain the output calls from LoFreq program
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| Submission date |
Nov 07, 2019 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Sheng Li |
| Organization name |
The Jackson Laboratory
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| Lab |
Li Lab
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| Street address |
10 Discovery Drive
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE140085 |
Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [DNA-Seq] |
| GSE140086 |
Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells |
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| Relations |
| BioSample |
SAMN13231573 |
| SRA |
SRX7115058 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4154191_Sample_4.KO1_GCB.lofreq_vars.vcf.gz |
15.7 Kb |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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