|
| Status |
Public on Oct 10, 2020 |
| Title |
E12.5 R1_1F |
| Sample type |
SRA |
| |
|
| Source name |
Rhombomere 1 cells
|
| Organism |
Mus musculus |
| Characteristics |
Stage: E12.5
tissue: brain
brain region: Rhombomere 1
Sex: Female
genotype: wildtype
|
| Treatment protocol |
Mice, their tissues and cells were untreated
|
| Growth protocol |
The tissues and cells were extracted from freshly dissected mouse embryos. All the animal experiments were approved by the Laboratory Animal Center, University of Helsinki, and the National Animal Experiment Board in Finland.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ventral r1 was dissected in the 5% FBS (fetal bovine serum; Millipore, Cat#ES-009-B) in L-15 (Gibco, Cat#11415-049). The ventral r1 was separated from the brain by using visible landmarks (such as the constriction of midbrain-hindbrain boundary). The pieces were washed 3 times with cold 500ul 1xPBS (Lonza, Cat#BE17-516Q) and dissociated using the Papain Dissociation System (Worthington, Cat#LK003150) according to the manufacturer's protocols.
The dissociated cells were collected on 10x Genomics Chromium Single Cell 3’RNAseq platform. The collection rate was 5000 cells/sample and the cDNA synthesis was done using the Chromium™ Single Cell 3' Reagent version 3 chemistry.
The 10XGenomics E12.5 and E13.5 cDNA libraries were sequenced on Illumina NovaSeq 6000 system using read lengths: 28bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 89bp (Read 2). Read quality was assessed by running FASTQC (version 0.10.1)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
5000 cells/sample
|
| Data processing |
The 10xGenomics data processing, genome alignment and gene expression scoring were performed using recommended 10x Genomics Cell Ranger v3.0.1 pipelines.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Standard CellRanger features table is provided for each sample
|
| |
|
| Submission date |
Sep 15, 2020 |
| Last update date |
Oct 11, 2020 |
| Contact name |
Kaia Achim |
| E-mail(s) |
kaia.achim@helsinki.fi
|
| Organization name |
University of Helsinki
|
| Department |
Faculty of Biological and Environmental Sciences
|
| Street address |
Viikinkaari 9
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE157963 |
Single-cell RNAsequencing of the ventral rhombomere 1 of the developing mouse [10X Genomics] |
| GSE157964 |
RNA sequencing of the ventral rhombomere 1 of the developing mouse |
|
| Relations |
| BioSample |
SAMN16134208 |
| SRA |
SRX9124765 |
