|
| Status |
Public on Feb 19, 2023 |
| Title |
RNAseq G1297 GFP EWS/ATF1 ON 1 |
| Sample type |
SRA |
| |
|
| Source name |
G1297 clear cell sarcoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
treatment 1: GFP induced
treatment 2: Dox (EWS/ATF1) ON
|
| Growth protocol |
HCC827 cells were grown in DMEM (Nacalai Tesque) supplemented with 10% of FBS (Biosera) and penicillin-streptomycin (PS) (Nacalai Tesque). G1297 cells were cultured in ESC media supplemented with human recombinant LIF (Wako), 2-Mercaptoethanol (Invitrogen) and 50 µg/ml L-ascorbic acid (Sigma) after the transduction of the reprogramming factors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using the NucleoSpin RNA Plus (Takara Bio).
RNA was quantified on a NanoDrop 2000c and Qubit. RNA (200 ng) was prepared for library construction. High-quality RNA (RNA Integrity Number value ≥8, as determined by Bioanalyzer) was used for library preparation. RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The number of PCR cycles was minimized to avoid skewing the representation of the libraries. RNA-seq libraries were sequenced on a NextSeq500 (Illumina) as 86 bp single reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt-1.18 (Martin, 2011). The trimmed reads were mapped to the mouse reference genome (mm10) using STAR v2.6.0c with GENCODE vM25 (Frankish et al., 2019). The uniquely mapped reads were summarized at the gene level using HTSeq-count v0.11.2 (Anders et al., 2015)
Genome_build: mm10
|
| |
|
| Submission date |
Mar 12, 2021 |
| Last update date |
Feb 19, 2023 |
| Contact name |
Yasuhiro Yamada |
| E-mail(s) |
yyamada@m.u-tokyo.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Department of Molecular Pathology
|
| Street address |
7-3-1 Hongo, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE168815 |
The oncogene-dependent resistance to reprogramming unveils cancer therapeutic targets |
|
| Relations |
| BioSample |
SAMN18287629 |
| SRA |
SRX10332191 |
