|
| Status |
Public on Aug 11, 2022 |
| Title |
Prox1pos.NeuNpos.100nuc.monkey.techrep2 |
| Sample type |
SRA |
| |
|
| Source name |
Monkey Visual Cortex
|
| Organism |
Macaca fascicularis |
| Characteristics |
strain: --
tissue: cortex
genotype: Vip-Cre::INTACT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly dissected visual cortices were snap frozen in liquid nitrogen and stored at -80C. Nuclei were then extracted, stained with antibodies and Dapi and FACS-sorted into 0.2ml low-bind tubes containing 2.03 µl lysis buffer.
Libraries were prepared based on the Smart-Seq2 protocol with small modifications. Briefly, 100 nuclei were collected directly into 2.03 microliter lysis buffer (0.2% Triton X-100 in ddW) supplemented with dNTPs (2mM each), SMART-dT30VN primers (1mM), ERCC (1:1.25x107), and RNAse inhibitor. Reverse transcription was performed directly on isolated nuclei, followed by PCR-amplification (17 cycles). After cleanup with Agencourt Ampure XP beads (Beckman Coulter), the amplified cDNA underwent library generation using Nextera XT (Illumina). Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Prox1+ NeuN+ 100 nuclei monkey technical replicate 2
|
| Data processing |
Basecall and quality scoring was performed by the RTA software, version 2.11.3.0
Mouse samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the mm10 genome using STAR version 2.5.3a.
Monkey samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the Macaca fascicularis 6.0 genome using STAR version 2.5.3a.
Genome_build: mm10, Macaca fascicularis 6.0
Supplementary_files_format_and_content: .csv files include raw read values for every gene in the sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Oct 03, 2021 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Daniella Apelblat |
| E-mail(s) |
daniella.apelblat2@gmail.com
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Neuroscience
|
| Lab |
Spiegel
|
| Street address |
Hertzl
|
| City |
Rehovot |
| ZIP/Postal code |
6451311 |
| Country |
Israel |
| |
|
| Platform ID |
GPL22523 |
| Series (1) |
| GSE185221 |
Meso-Seq for in-depth transcriptomics in ultra-low amounts of FACS-purified neuronal nuclei |
|
| Relations |
| BioSample |
SAMN22021561 |
| SRA |
SRX12458449 |
