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Sample GSM1620050 Query DataSets for GSM1620050
Status Public on Feb 27, 2015
Title NAc projector, experiment-2: NAc_541
Sample type SRA
Source name Brain tissue (BLA), NAc-projector, Experiment-2
Organism Mus musculus
Characteristics Sex: male
developmental stage: P56-P70
tag: C57BL/6NCrl
tissue: basolateral amygdala complex neurons
Treatment protocol In order to label the BLA neurons projecting to the NAc or CeM, red retrobeads (Lumafluor Inc.) were injected into the NAc and CeM of the adult mice brains. Two weeks after retrobeads injection, the retrobeads are traveled to the BLA, and the brain was quickly removed for acute 330 μm coronal brain slices for subsequent dissociation and isolation of retrobeads labeled BLA neurons. After dissociation of the retrobeads labeled BLA neurons, 30-60 retrobeads-positive neurons were isolated under a fluorescent dissecting microscope for subsequent RNA extraction.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Arcturus PicoPure RNA isolation kit (Life Technologies).
Double stranded cDNA was generated from total RNA using a DNA-RNA chimeric primer mix and reverse transcriptase, and cDNA was amplified by the SPIA amplification process developed by NuGEN (Ovation RNA-Seq System V2 kit (Neugen)).
The amplified double stranded cDNA was fragmented to an average size of 200 bases using Covaris S-S series sonication system. The fragmented cDNA was end-repaired, and adaptors and barcodes were ligated before PCR-based library preparation using Ovation Ultralow DRMultiplex Systems (Nugen).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Experiment-2, NAc
Data processing Sequencing reads were aligned using Tophat version 2.0.10 against the Mus musculus UCSC version mm10 genome and the mm10 RefSeq transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
Submission date Feb 26, 2015
Last update date May 15, 2019
Contact name Suzuko Yorozu
Organization name Harvard Medical School
Department Genetics
Lab Jesse Gray's lab
Street address 77 Avenue Louis Pasteur
City Boston
State/province Massachusettes
ZIP/Postal code 02115
Country USA
Platform ID GPL19057
Series (1)
GSE66345 A Circult Mechanism for Differentiating Positive and Negative Associations
BioSample SAMN03378763
SRA SRX892634

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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