|
Status |
Public on Feb 06, 2019 |
Title |
Q11_24H_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: 24 hours genotype/variation: stable expression human alpha1ACT
|
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 |
SAMN10873234 |
SRA |
SRX5333740 |