 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 24, 2023 |
| Title |
mutant mouse brain 1, infratentorial, Smarcb11148del/1148del |
| Sample type |
SRA |
| |
|
| Source name |
brain, infratentorial
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain, infratentorial
genotype: Smarcb11148del/1148del
age: 0 days
Sex: Male
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Isolated brains from two Smarcb11148del/1148del and two Smarcb1+/+ P0 mice were divided into a supratentorial and an infratentorial part and each minced with scalpels on ice. For enzymatic dissociation, 2-3 mL of a solution composed of 1 vial Papain (Worthington), 5 mL pre-equilibrated DMEM:F12 and 34 µL DNAse I diluted in 250 µL DMEM:F12 were added to each sample, followed by incubation at 37 °C in 5 % CO2 for 30 min. Afterwards, the cell solution was transferred onto a 40 µm cell strainer. The reaction was stopped with 2 mL PBS / 10 % BSA before washing with 10 mL PBS. The obtained single-cell suspensions were stained with 7-Aminoactinmycin D (7-AAD) (eBioscience). Non-viable, 7-AAD-positive cells were removed by Fluorescence-activated cell sorting (BD FACS Aria II), followed by manual counting with Trypan Blue staining.
Approximately 25,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2000 (Agilent Technologies). Indexed libraries were sequenced separately by the Illumina NextSeq 500 sequencing platform (v 2.5 chemistry, 75 cycle kit). For all samples, the same library was sequenced a second time to increase sequencing saturation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The samples were demultiplexed and processed with the 10x Genomics CellRanger v3.0.2 program suite.
Raw 10X scRNA-seq data was converted to the standard fastq format with CellRanger's mkfastq function.
The CellRanger count algorithm was subsequently used to align the sample data against the murine reference transcriptome mm10 v3.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Sep 04, 2022 |
| Last update date |
May 24, 2023 |
| Contact name |
Carolin Walter |
| E-mail(s) |
c_walt03@uni-muenster.de
|
| Organization name |
Westfälische Wilhelms-Universität Münster
|
| Department |
Medical Faculty of the WWU Münster
|
| Lab |
Institute of Medical Informatics
|
| Street address |
Domagkstraße 9
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE212672 |
A Carboxy-terminal Smarcb1 Point Mutation Induces Hydrocephalus Formation and Affects AP‑1 and Neuronal Signalling Pathways in Mice |
|
| Relations |
| BioSample |
SAMN30670326 |
| SRA |
SRX17420953 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6543165_unicorn_1i_Homo_barcodes.tsv.gz |
52.1 Kb |
(ftp)(http) |
TSV |
| GSM6543165_unicorn_1i_Homo_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6543165_unicorn_1i_Homo_matrix.mtx.gz |
111.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
