|
| Status |
Public on May 01, 2017 |
| Title |
Untreated Replicate #2 |
| Sample type |
SRA |
| |
|
| Source name |
differentiated CAD cells_DMSO
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CAD cells (Cath.-a-differentiated)
treated with: DMSO for 24hrs
treatment: No treatment
|
| Treatment protocol |
Sub-confluent CAD cell cultures (50-60%) were transferred to serum-free media (DMEM:HAMS F12 (1:1) supplemented with 2mM Glutamine) and maintained in 15 cm2 culturing dishes for 5 days. Cells were treated for 24h with ACSS2i (1-(2,3-di(thiophen-2-yl)quinoxalin-6-yl)-3-(2-methoxyethyl)urea) at 20 µM, or DMSO for the no treatment control group.
|
| Growth protocol |
CAD cells (Cath.-a-differentiated; generously donated from the Holzbaur Lab at the University of Pennsylvania) were grown in DMEM:HAMS F12 (1:1), supplemented with 2mM Glutamine, 1% penicillin/streptomycin, and 10% Fetal Bovine Serum (FBS).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
To generate libraries for RNA-seq, polyA+ RNA was was extracted using the Dynabeads mRNA Direct kit (Ambion) according to the manufacturer’s instructions.
RNA-seq libraries were made using a ScriptSeq v2 RNA-seq Library Preparation Kit from Epicentre (now Illumina). The quantity and quality of the libraries were assessed by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems). The multiplexed libraries were pooled and sequenced on a single lane on the Illumina NextSeq 500 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
inh_5
|
| Data processing |
Demultiplexing: done using bcl2fastq (v02.14.01.07) on BaseSpace.
Alignment: data were aligned using STAR (RNA-STAR 2.3.0) on BaseSpace.
Quantitation: aligned reads were mapped to genomic features using Cufflinks (v2.2.1) with the -G parameter to only quantitate known features. FPKMs were calculated using CuffDiff.
Genome_build: mm10
Supplementary_files_format_and_content: Only a single text table with CuffDiff-computed FPKM values for each gene is included.
|
| |
|
| Submission date |
Dec 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shelley L. Berger |
| E-mail(s) |
bergers@mail.med.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Berger
|
| Street address |
3400 CIVIC CENTER BLVD
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE76854 |
Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory |
| GSE90854 |
Acetyl CoA metabolism by ACSS2 regulates neuronal histone acetylation and hippocampal memory [RNA-seq In Vitro] |
|
| Relations |
| BioSample |
SAMN06109302 |
| SRA |
SRX2394877 |
