|
| Status |
Public on Jan 31, 2024 |
| Title |
non-syn-18 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Danio rerio |
| Characteristics |
tissue: brain
strain: Tg(HuC:H2B-GCaMP6f)
cell type: neurons in dorsal pallium
treatment: non-synchronized in response to CAS
|
| Treatment protocol |
Tg(HuC:H2B-GCaMP6f) fish of 4-5 weeks old were fixed in a recording chamber containing extracellular fluid, and neurons with synchronized or non-synchronized calcium activity after CAS treatment were identified by two-photon imaging and collected separately with glass pipette.
|
| Growth protocol |
Tg(HuC:H2B-GCaMP6f) fish of 4-5 weeks old were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were transferred to the lysis buffer solution. Total RNA was extracted using TRIzol (Invitrogen) and then purified on RNeasy columns (Qiagen).
Total RNA quality was assessed on a bioanalyzer (Thermofisher). RNA-Seq libraries (N=10) for each group were prepared using the Illumina TruSeq Strand mRNA Prep Kit according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
RNA-Seq reads untrimmed. Differential expression analysis was performed using the CPM (counts per million) function in the Bioconductor package edgeR (v 3.14.0). Low expression genes were excluded to make a simple correction for gene counts. Genes with P-value (instead of adjusted P-value) < 0.05 were assigned as differentially expressed.
Assembly: danRer11
Supplementary files format and content: Excel file include readcounts values for each Sample.
|
| |
|
| Submission date |
Jan 11, 2024 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Chun-Xiao Huang |
| Phone |
13419650633
|
| Organization name |
42508444-9
|
| Department |
School of Medcine, Tongji University
|
| Lab |
Neuroscience
|
| Street address |
65 Chifeng Road, Yangpu District
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE253039 |
Patch-Seq of synchronized and non-synchronized neurons in zebrafish dorsal pallium in response to CAS treatment |
|
| Relations |
| BioSample |
SAMN39412009 |
| SRA |
SRX23170204 |
