|
| Status |
Public on Feb 06, 2019 |
| Title |
P_10D_1 |
| Sample type |
SRA |
| |
|
| Source name |
PC12
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: PC12
passages: 18-20
cell type: neural crest origin pheochromocytoma
time point: 10 days
genotype/variation: stable expression pCDNA3 vector
|
| Treatment protocol |
N/A
|
| Growth protocol |
PC12 cells (rat pheochromocytoma) stable expressing pCDNA3 or alpha1ACT were cultured in F-12K medium (ATCC, Manassas) supplemented with 10% horse serum and 2.5% FBS in a 37 ºC, 5% CO2 incubator. The medium were changed every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA from PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT(α1ACT) was isolated by RNeasy mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s instructions at expected time points.
PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT at 4 different time points (6h, 24h, 3d, 10d) were analyzed by Agilent Bio-analyzer and submitted to university of Chicago Functional genomic facility for library preparation (TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold, RS-122-2301) and sequencing on Illumina HiSeq2500 platform, with 3 biological replicates for each condition.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
paired-end 100bp sequenced in 3 lanes
|
| Data processing |
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: Tophat v2.0.10
Post alignement QC assessment: RSeQC and Picard tools v1.117
Gene transcripts assembly: htseq-count 0.5.4p5
Differentially expressed genes analysis: edgeR
Genome_build: NCBI rn5
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by htseq-count for each Sample.
|
| |
|
| Submission date |
Feb 05, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Yan Li |
| E-mail(s) |
yli22@bsd.uchicago.edu
|
| Phone |
7738344316
|
| Organization name |
The University of Chicago
|
| Department |
Center for Research Informatics
|
| Street address |
900 East 57th St.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE126087 |
α1ACT is essential for survival and early cerebellar programming in a critical neonatal window [RNA-Seq] |
| GSE126089 |
α1ACT is essential for survival and early cerebellar programming in a critical neonatal window |
|
| Relations |
| BioSample |
SAMN10873221 |
| SRA |
SRX5333749 |
