|
Status |
Public on Mar 24, 2015 |
Title |
E14.5_liver_Rlf_mutant_RNA-Seq_rep1 |
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: Male
|
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 |
SAMN02837155 |
SRA |
SRX567349 |