|
| Status |
Public on Dec 09, 2013 |
| Title |
Lsh_fib_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Tailtip fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: Lsh-/-
cell type: adult tailtip fibroblasts
|
| Growth protocol |
Tailtip fibroblasts were cultured in 89% DMEM, 10% FCS and 1% penicillin-streptomycin. E13.5 embryos were isolated using standard techniques.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fibroblasts and embryos using TriZol Reagent.
Paired-end strand-specific RNA-Seq libraries were prepared from fibroblast and embryo RNA using the dUTP method and libraries were sequenced using the Illumina HiSeq instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Processed data files are tabular files generated from fastq raw files and input into EdgeR
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were groomed using Fastqgroomer and filtered for read quality.
Reads were mapped using TopHat v1.4.0 using the settings: -p 4 -r 24 -a 8 -m 0 -I 70 -l 500000 -g 20 --library-type fr-firststrand --no-novel-indels --no-coverage-search --no-closure-search --mate-std-dev 27 --initial-read-mismatches 0 --segment-mismatches 0 -segment
Galaxy pipeline was used to filter for unique hits generating interval files which were used to create read pile-ups by the Galaxy inner join package.
Read pile-up files were input into EdgeR to calculate differential expression between libraries and also pile-ups were converted to bed files for this submission.
Genome_build: Mouse mm9
Supplementary_files_format_and_content: abundance
|
| |
|
| Submission date |
Nov 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Donncha S Dunican |
| Organization name |
IGMM / MRC HGU
|
| Street address |
Western General Hospital
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15103 |
| Series (2) |
| GSE52477 |
Lsh regulates LTR retrotransposon repression independent of Dnmt3b function (RNA-Seq) |
| GSE52479 |
Lsh regulates LTR retrotransposon repression independent of Dnmt3b function |
|
| Relations |
| BioSample |
SAMN02404845 |
| SRA |
SRX378826 |
