|
| Status |
Public on Sep 12, 2016 |
| Title |
PACAP GFP Input 2 |
| Sample type |
SRA |
| |
|
| Source name |
Preoptic neurons
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Preoptic neurons PACAP+
strain: C57Bl6/J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Detailed protocol and buffer recipes are described previously(Knight et al., 2012). Briefly, mice were rapidly sacrificed by cervical dislocation and brains were removed, rinsed briefly with cold dissection buffer and place in a cold sectioning matrix. 0.5 mm sections were obtained and the anterior hypothalamus was removed under a dissecting microscope.
Amplified cDNA was prepared using Ovation RNA-Seq System V2, and sequencing library was prepared using the Ovation Ultralow DR Multiplex system and sequenced on an Illumina HiSeq4000 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Total RNA
Antibody for TRAP seq experiments : Anti-EGFP, equal mixture of clones 19C8 and 19F7 from Monoclonal Antibody Core Facility at Memorial Sloan-Kettering cancer center.
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences and index sequences.
Mapping to annotated mRNA and abundance calculations done using ArrayStar software (DNA star)
Genes with read count =0 are excluded.
Genes with both match input and immunoprecipitated RPKM value<1 are excluded
Genome_build: mm9
Supplementary_files_format_and_content: read count and RPKM values
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chan Lek Tan |
| E-mail(s) |
ChanLek.Tan@ucsf.edu
|
| Organization name |
University of California
|
| Department |
Physiology
|
| Lab |
Zachary Knight
|
| Street address |
1550 Fourth St. Room 346
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE80120 |
Cell-specific gene expression profiling of warm-sensitive neurons |
| GSE80224 |
Identification and characterization of warm-sensitive thermoregulatory neurons in the preoptic area |
|
| Relations |
| BioSample |
SAMN04849243 |
| SRA |
SRX1701838 |
