|
| Status |
Public on Jul 08, 2018 |
| Title |
WT129_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
ES Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: WT ES cells
passages: < 20
strain: 129S1/SvImJ
|
| Growth protocol |
Mouse ESCs were cultured in Dulbecco's modified Eagle's medium supplemented with 15% heat-inactivated foetal calf serum, 10e3 units/ml leukemia inhibitory factor and 0.1 mM β-mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 5 million cells with TRI Reagent (Sigma, 93289) according to manufacturer’s instructions.
Sample quality was assessed using a Bioanalyzer and quantified by Qubit. All samples were processed starting with 500 ng of total RNA according to the Illumina Stranded Total RNA protocol (15031048 Rev C, Sept 2012) except that 12 cycles of amplification was used to minimise amplification artefacts. Libraries were quantitated by Qubit and qPCR, and an equimolar pool were made based upon qPCR results. Following denaturation, 200 pM of the library pool was clustered in one lane of a HiSeq 3000 (Illumina Protocol 15006165 v02 Jan 2016) and 50 bp SR sequencing was carried out (Illumina Protocol 15066493 Rev A, February 2015).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Stranded 50 bp single-end RNA-seq reads were aligned to mouse (mm9) with STAR (v.2.4.2a) using default parameters.
Primary alignments were imported into Seqmonk as single-ended RNA-seq. The RNA-Seq quantitation pipeline was used to estimate RPKM read counts with the following parameters: mRNA as transcript feature, strand-specific, merge transcript isoforms, apply transcript length correction and exclude probes with no counts. A total of 26127 mRNA probes were quantitated.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated with Wig/BedGraph-to-bigWig (v1.1.0) in Galaxy with default parameters. Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments.
Supplementary_files_format_and_content: Tab delimited text files contain RPKM values of UCSC annotated genes.
|
| |
|
| Submission date |
Oct 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hsiao Phin Joanna Voon |
| E-mail(s) |
Joanna.Voon@monash.edu
|
| Organization name |
Monash University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Epigenetics and Chromatin
|
| Street address |
Monash University, Wellington Road
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE106204 |
RNA-seq in WT and H3.3 G34R mouse ES cells |
| GSE106205 |
The H3.3 G34R glioma-associated mutation alters H3K9me3 and H3K36me3 chromatin modifications |
|
| Relations |
| BioSample |
SAMN07837510 |
| SRA |
SRX3329719 |
