|
| Status |
Public on Jun 09, 2021 |
| Title |
posterior Piriform cortex viral injection [sn-seq P] |
| Sample type |
SRA |
| |
|
| Source name |
posterior Piriform cortex viral injection
|
| Organism |
Mus musculus |
| Characteristics |
Stage: adult
strain: WT
treatment: posterior Piriform cortex viral injection
|
| Treatment protocol |
A retrogradely transported Adeno Associated Virus (retroAAV-CAG-H2B-GFP) was injected stereotaxically into multiple sites of posterior piriform cortex (PCx) for the P experiment, on into anterior olfactory nucleus (AON) for the A experiment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5). Fluorescence-activated nuclei sorting of single nuclei was performed using a BD FACSAriaTM III Cell Sorter with a 70 μm nozzle at a sheath pressure of 70 psi.
Libraries were prepared using the 10x Library Construction Kit PN-1000190. The quality and quantity of the final libraries were assessed with TapeStation D5000 Assay (Agilent Technologies) before sequencing with an Illumina NextSeq 500 using the 10X kit version Chromium Single Cell 3 dual index" v 3.1.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Jun 09, 2021 |
| Contact name |
Andreas Schaefer |
| E-mail(s) |
Andreas.Schaefer@crick.ac.uk
|
| Organization name |
The Francis Crick Institute
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE176350 |
Validation of molecularly-defined olfactory bulb projection neurons targeting anterior or posterior brain areas |
|
| Relations |
| BioSample |
SAMN19604707 |
| SRA |
SRX11091678 |
