|
| Status |
Public on May 01, 2017 |
| Title |
0h fear conditioning EGFP |
| Sample type |
SRA |
| |
|
| Source name |
dorsal hippocampus, EGFP-AAV control, before memory retrieval
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
tissue: dorsal hippocampus
shRNA: EGFP
treatment: fear conditioning
timepoint: 0h (before memory retrieval)
|
| Treatment protocol |
CAD cells were infected with lentiviral hairpin constructs (TRC collection) designed against ACL (#TRCN0000055217) or ACSS2 (#TRCN0000076124, #TRCN0000076125) in medium containing 8 mg/mL polybrene and 10% FBS for 24 h. Cells then underwent selection in culture medium supplemented with 0.5 mg/mL puromycin for 5 days to obtain a stably infected population. To induce neuronal differentiation, 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.
|
| 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 extracted using the Dynabeads mRNA Direct kit (Ambion) according to the manufacturer's instructions.
RNA-seq libraries for scrambled control (referred to in text as WT), shACL, and shACSS2 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 (50bp, single-end reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
NextSeq sequencing data was demultiplexed using bcl2fastq2-v02.14.01.07.
Demultiplexed FASTQs were aligned by RNA-STAR 2.3.0.e using the genome index mm10 generated from iGenome UCSC mm10 FASTQ genome sequence.
The aligned reads were mapped to genomic features using cufflinks-2.2.1 (-G parameter to only quantitate known features), and iGenomes mm10 UCSC genomic transcript loci.
Genome_build: GRCm38 (mm10 UCSC)
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Jan 13, 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) |
| GSE76853 |
Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory [RNA-seq] |
| GSE76854 |
Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory |
|
| Relations |
| BioSample |
SAMN04412730 |
| SRA |
SRX1530261 |
