|
| Status |
Public on Feb 27, 2015 |
| Title |
NAc projector, experiment-2: NAc_537 |
| 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 |
|
| Relations |
| BioSample |
SAMN03378770 |
| SRA |
SRX892636 |
