|
| Status |
Public on Jan 19, 2018 |
| Title |
H1299.175R.1 |
| Sample type |
SRA |
| |
|
| Source name |
R variant, p53 mutant R175H, batch b1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1299
p72rpolymorphism: R
hotspot: R175H
batch: b1
|
| Treatment protocol |
Cells were transfected with the constructs of interest (5ugs of DNA) with Fugene and selected in Neomycin 800ugs/ml for 14 days to make stable isogenic cell lines
|
| Growth protocol |
H1299 cell lines were obtained from the ATCC and used at early passage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with Lexogen QuantSeq 3’mRNA-Seq library prep kit at the Wistar Institute Genomics Facility and subjected to a 75 bp single-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H1299 cell line, P72R variant R, p53 mutant R175H, batch b1
|
| Data processing |
RNA-Seq data was aligned using bowtie2 against hg38 version of genome and rsem (ver. 1.2.12) with Ensemble v84 transcriptome information used for gene count
DESeq2 was used for differentail expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene
|
| |
|
| Submission date |
Jan 18, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE109373 |
Mutant p53 controls tumor metabolism and metastasis by regulating PGC-1α |
|
| Relations |
| BioSample |
SAMN08376864 |
| SRA |
SRX3586257 |
