|
| Status |
Public on Jan 21, 2016 |
| Title |
EV+Pio_RNAseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
PCCL3 cell line
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: PCCL3
transfected: empty vector
treatment: 1 μM pioglitazone for 16 hours
growth protocol: EV cells were cultured in 60 mm Petri dishes until 80% confluent
|
| Treatment protocol |
16 hours prior to harvest, pioglitazone was added to achieve 1 uM (from a 1 mM stock in DMSO), or vehicle was added as the control.
|
| Growth protocol |
PCCL3 cells were grown in Coon’s medium/F-12 high zinc supplemented with 5% fetal bovine serum, 0.3 mg/ml glutamine, 1 mU/ml bovine thyrotropin, 10 ug/ml bovine insulin, 5 ug/ml apo-transferrin, 10 nmol/L hydrocortisone, and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using a Qiagen RNeasy kit. Library preparation was with 1 ug of total RNA and the TruSeq RNA prep kit (Illumina Cat #RS-122-2001) according to Illuminas instructions. Adapter ligated products were enriched with 12 cycles of pcr.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Total RNA was prepared using a Qiagen RNeasy kit. Library preparation was with 1 ug of total RNA and the TruSeq RNA prep kit (Illumina Cat #RS-122-2001) according to Illumina’s instructions. Adapter ligated products were enriched with 12 cycles of pcr.
all_sample_raw_count.txt
|
| Data processing |
Basecalls performed using CASAVA-1.8.2
ChIP-seq and input reads were aligned to the rat reference genome (rn4) using BWA (version 0.5.9-r16) with default options. MACS2 (2.0.10.20131216beta) was used to call peaks. Peaks were then filtered by PePr (1.0.5) to remove artifacts.
RNA-Seq reads were aligned to rn4 with tophat2 (v2.0.11) and gene read counts were quantified by HTseq (0.6.1p1) with option “-m intersection-strict” and normalized by edgeR (3.2.4). Differential expression analysis was performed using edgeR with tagwise dispersion.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-Seq peak files were generated by MACS2, RNA-Seq read counts were quantified by HTSeq
|
| |
|
| Submission date |
Jun 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Street address |
9500 Gilman Dr.
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE70354 |
Genomic binding and regulation of gene expression by the thyroid carcinoma-associated PAX8-PPARG fusion protein |
|
| Relations |
| BioSample |
SAMN03799329 |
| SRA |
SRX1074902 |
