|
| Status |
Public on Apr 01, 2020 |
| Title |
NOD-ICAM-1 |
| Sample type |
SRA |
| |
|
| Source name |
PNS
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: ICAM-1-1/-NOD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sciatic nerves and the brachial nerve plexus were dissected from intracardial PBS perfused the mice. Nerves were first mechanically dissociated. Cells were then isolated by combining enzymatic digestion (Trypsin, Collagenase II, Hyaluronidase and Pronase) with myelin depletion and flow cytometry-based cell sorting (Calcein-AM, Zombi NIR, DAPI). Rats sciatic nerves were isolated and enzymatically digested in Collagenase/Dispase and DNase I. Cells were centrifuged on a 30%/70% Percoll gradient and the mononuclear interphase was collected. No sorting was performed.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (both from 10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell
ScRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
7
|
| Data processing |
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.0.2)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples without normalization
Genome_build: mm10, Rattus_norvegicus.Rnor_6.0.dna.toplevel
Supplementary_files_format_and_content: Standard cellranger output format
|
| |
|
| Submission date |
Dec 23, 2019 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Michael Heming |
| Organization name |
University Hospital Muenster
|
| Department |
Department of Neurology with Institute of Translational Neurology
|
| Street address |
Albert-Schweitzer-Campus 1, Bldg A1
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE142541 |
Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity |
|
| Relations |
| BioSample |
SAMN13673144 |
| SRA |
SRX7434989 |
