NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4154189 Query DataSets for GSM4154189
Status Public on Jun 29, 2020
Title Sample_2.WT2_GCB
Sample type SRA
 
Source name Germinal Center B-cells
Organism Mus musculus
Characteristics tissue: spleen
genotype: TET2 Knock-Out
strain: C57BL/6
Treatment protocol Not applicable
Growth protocol GC B-cells (B220+Fas+GL7+) were isolated from mouse spleen
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)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
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
 
Submission date Nov 07, 2019
Last update date Jun 29, 2020
Contact name Sheng Li
Organization name The Jackson Laboratory
Lab Li Lab
Street address 10 Discovery Drive
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
 
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
Relations
BioSample SAMN13231575
SRA SRX7115056

Supplementary file Size Download File type/resource
GSM4154189_Sample_2.WT2_GCB.lofreq_vars.vcf.gz 15.4 Kb (ftp)(http) VCF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap