|
| Status |
Public on Apr 17, 2019 |
| Title |
Inhibitory-2 total RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
vGAT-positive brain neurons
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell type: vGAT-positive brain neurons
number of cells: 100 Single cells
|
| Growth protocol |
αCaMKII-Cre and vGAT-IRES-Cre transgenic mouse colonies were maintained by breeding transgenic mice to wild-type C57Bl/6J mice. Mice used for experiments were bred in the Seoul National University (SNU) Specific Pathogen Free center (LML08-404). Male mice (3-5 months) were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fluorescent cells were manually collected by using glass pipette. After washing in HBSS, collected cells were directly lysed with cell lysis buffer containing RNase inhibitor as follow manufacturer’s instruction of SMART-seq v4 (Ultra low input RNA kit, Clontech Laboratories, Inc.).
After generation of cDNA from homogenous cell-type samples, the construction of library was performed by using Nextera XT DNA library prep kit (Illumina, Inc., USA) according to the manufacturer’s instructions. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Sep 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jung-Woong Kim |
| E-mail(s) |
jungkim@cau.ac.kr
|
| Organization name |
Chung-Ang University
|
| Department |
Life Science
|
| Lab |
Genome Dynamics Lab
|
| Street address |
84 Heuksuk-ro Dongjak-ku
|
| City |
Seoul |
| ZIP/Postal code |
06974 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE104089 |
Cell type-specific dysregulation of ERK signaling impairs synaptic plasticity and memory in a mouse model of Noonan syndrome |
|
| Relations |
| BioSample |
SAMN07680549 |
| SRA |
SRX3203503 |
