|
| Status |
Public on Jul 31, 2015 |
| Title |
WT mouse PolyA+ RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
WT mouse
|
| Organism |
Mus musculus |
| Characteristics |
p53 mutation status: WT
treatment: Untreated
antibody: None
|
| Treatment protocol |
As indicated in the SAMPLES section
|
| Growth protocol |
All cells were grown in DMEM with 10% FBS, at 3% oxygen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Covaris S220 sonicator
For RNA-seq, polyA+ RNA was isolated by two rounds of polyA selection using the Life Technologies mRNADirect kit per manufacturer's recommendations.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions. Sequencing libraries for polyA+, stranded-RNA-seq were constructed using the NEBnext Ultra Directional RNAseq kit as per manufacturer's recommended instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PolyA+ RNAseq in primary WT MEFs
|
| Data processing |
Raw fastq files were aligned to mm9 using Bowtie2, allowing for only uniquely aligned reads to be reported.
bowtie2 -N1 -k1 mm9
Uniquely mapped reads were processed into HOMER TagDirectories (makeTagDirectory <file> <TagDir_file>)
Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
Expression values (FPKM) for RNAseq experiments were derived using HOMER (analyzeRepeats.pl mm9 -condenseGene)
genome build:mm9
processed data files format and content: Text file (of FPKM expression values from RNAseq)
processed data files format and content: BedGraph files (from HOMER, for visualization in UCSC)
|
| |
|
| Submission date |
Dec 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Morgan Sammons |
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19129 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE59176 |
Prevalent p53 gain-of-function mutants co-opt epigenetic pathways to drive cancer growth |
|
| Relations |
| BioSample |
SAMN03273078 |
| SRA |
SRX835937 |
