|
| Status |
Public on Jul 01, 2019 |
| Title |
PTU_WT_rep2_RNA |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: WT
treatment: PTU
chip antibody: n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 5 mg of liver tissue were homogenized using Ultra-Thorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) in EconoSpin columns (Epoc Life) according to manufacturer’s instructions.
Total RNA (1000 ng) was prepared for sequencing using polyA enrichment followed by fragmentation and random priming for cDNA synthesis according to the manufacturer's (NEB) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
RPKM_RNA_WT_PTU_T3_NCORdeltaID_PTU.txt
This sample has runs from 2 instrument models: Illumina HiSeq 1500 and Illumina NovaSeq 6000.
|
| Data processing |
RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM
|
| |
|
| Submission date |
Mar 19, 2019 |
| Last update date |
Sep 24, 2019 |
| Contact name |
Lars Grøntved |
| E-mail(s) |
larsgr@bmb.sdu.dk
|
| Phone |
+45 24 60 14 06
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE128535 |
Histone 3 K9 and K27 acetylation of enhancers in response to thyroid hormone |
|
| Relations |
| BioSample |
SAMN11166384 |
| SRA |
SRX5543283 |
