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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 09, 2013 |
| Title |
WT_HELP rep3 |
| Sample type |
SRA |
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| Source name |
Tailtip fibroblasts
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| Organism |
Mus musculus |
| Characteristics |
cell type: Tailtip fibroblasts
genotype: WT
strain: C57BL/6
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| Growth protocol |
Tailtip fibroblasts and mouse embryonic fibroblasts were cultured in 89% DMEM, 10% FCS and 1% penicillin-streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from fibroblasts using established SDS lysis protocols.
Single ended HELP seq libraries were prepared from fibroblast DNA and sequenced on the Illumina HiSeq instrument using the method of Jing et al., Meth. Mol. Biol. V815, 2012, pp 79-87.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
Processed data files are bed files generated from fastq raw files
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| Data processing |
Raw data was analysed using the WASP online automated piepline (McLellan AS, 2012, Genomics; 100(6); p345-51)
Raw HELP reads were mapped to the mouse genome (mm9) using Bowtie
Alignments were overlapped with repeatmasker annotated murine repetitive DNA elements in Galaxy.
Using custom Perl scripts, reads were counted in respective repeat classes, 2x2 contingency table odds-ratios (OR) were computed using the Text-NSP-1.03 CPAN package.
Finally, signficance was measured between tester and driver lines using Fisher's exact tests and Bonferroni correction for multiple testing.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated by read pileups in Galaxy.
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| Submission date |
Nov 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Donncha S Dunican |
| Organization name |
IGMM / MRC HGU
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| Street address |
Western General Hospital
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| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
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| Platform ID |
GPL15103 |
| Series (2) |
| GSE52476 |
Lsh regulates LTR retrotransposon repression independent of Dnmt3b function (HELP-seq) |
| GSE52479 |
Lsh regulates LTR retrotransposon repression independent of Dnmt3b function |
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| Relations |
| BioSample |
SAMN02404838 |
| SRA |
SRX378819 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1267660_WT_AS10_HELP.bed.gz |
54.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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