|
| Status |
Public on Mar 24, 2015 |
| Title |
E14.5_liver_Rlf_mutant_RNA-Seq_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
E14.5 liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
tissue: liver
developmental stage: E14.5
genotype/variation: Rlf mutant
gender: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized in Buffer RLT Plus (Qiagen) and RNA extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
Libraries were prepared and sequenced by the Australian Genome Research Facility (AGRF) using the Illumina TruSeq protocol from polyA-selected RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
reads were mapped to the mouse genome with Tophat using the parametres -I 100000 --no-coverage-search --read-mismatches 2 --library-type fr-unstranded
Transcript read counts (obtained from Ensembl, version 67) were extracted with the script htseq-count using the options -s no -m intersection-strict
Differentially expressed genes were identified using DeSeq
Genome_build: mm9
Supplementary_files_format_and_content: Transcript read counts
|
| |
|
| Submission date |
Jun 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Harald Oey |
| Organization name |
La Trobe University
|
| Department |
Genetics
|
| Street address |
Kingsbury Drive
|
| City |
Bundoora |
| State/province |
Vic |
| ZIP/Postal code |
3086 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE58108 |
Rlf, a widely-spaced zinc finger protein, is involved in maintaining epigenetic marks at CpG island shores and enhancer elements across the genome |
|
| Relations |
| BioSample |
SAMN02837150 |
| SRA |
SRX567351 |
