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Sample GSM2039066 Query DataSets for GSM2039066
Status Public on May 01, 2017
Title 0h fear conditioning shACSS2
Sample type SRA
 
Source name dorsal hippocampus, ACSS2-AAV knockdown, before memory retrieval
Organism Mus musculus
Characteristics strain/background: C57BL/6
tissue: dorsal hippocampus
shRNA: ACSS2
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 SAMN04412715
SRA SRX1530262

Supplementary file Size Download File type/resource
GSM2039066_0h-FC-hp-shACSS2_S7.rmdup.bam.bw 12.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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