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| Status |
Public on Jun 27, 2019 |
| Title |
QXT15 |
| Sample type |
SRA |
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| Source name |
ear
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| Organism |
Mus musculus |
| Characteristics |
tissue: ear
mouse id: T09694
Sex: M
strain: B6
genotype: Chr4-cl KO/KO (F4)
ancestry: T00460 x T00431/T00432
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from Proteinase K digested lysates using the gDNA Clean & Concentrator kit (Zymo)
Libraries were constructed and enriched using the SureSelectQXT Target Enrichment kit (Agilent) and custom RNA capture probes complementary to ETn LTRs.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Library strategy: gDNA capture-seq
R1 and R2 reads were mapped to the mm9 genome separately, each both in under settings that only allows non-duplicated, uniquely mappable reads (Bowtie -m 1 --best --strata; samtools rmdup -s) and under settings that allows multimapping and duplicated reads (Bowtie --best).
Of the multimapping reads, only reads that overlap (min. 50% of read) with RLTRETN, MMETn-int, ETnERV-int, ETnERV2-int or ETnERV3-int repeats were kept.
Non-duplicated and uniquely mappable reads whose paired read partners were overlapping ETn repeats were then clustered (as bed files) using bedtools (bedtools merge -i -n -d 1000) to receive a list of all potential annotated and non-annotated new ETn insertions.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with clustered ETn-paired reads
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| Submission date |
Jun 04, 2018 |
| Last update date |
Jun 27, 2019 |
| Contact name |
Gernot Wolf |
| Organization name |
NIH
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| Department |
NICHD
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| Lab |
Macfarlan lab
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| Street address |
6 Center Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE115285 |
Identification of novel ETn insertions in KRAB-ZFP cluster depleted mice |
| GSE115291 |
Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice |
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| Relations |
| BioSample |
SAMN09323423 |
| SRA |
SRX4159190 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3173604_QXT15_ETn_merged.bed.gz |
79.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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