|
| Status |
Public on Feb 19, 2024 |
| Title |
ED211124_t |
| Sample type |
SRA |
| |
|
| Source name |
Transcriptomic dataset of tCROP-seq
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Forebrain
strain: C57bl/6
treatment: FACSorted for GFP
age: E16
|
| Extracted molecule |
total RNA |
| Extraction protocol |
embryonic tissue was collected in ice-cold Leibowitz medium and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custom primers with standard Illumina adapters.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
total RNA
|
| Data processing |
Transcritpomic dataset: Sequencing reads in FASTQ files were aligned to a reference transcriptome (mm10-2.1.0) and collapsed into unique molecular identifier counts using the 10x Genomics Cell Ranger software (version 3.0.2 and 5.0.1).Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome (applied cut-offs see Supplementary Data 1, Bandler et al. 2021).
Filtered count matrix
Assembly: mm10-2.1.0
|
| |
|
| Submission date |
May 05, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Christian Mayer |
| Organization name |
Max Planck Institute of Neurobiology.
|
| Lab |
Mayerlab
|
| Street address |
Am Klopferspitz 18
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE231774 |
Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development |
| GSE231779 |
Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development |
|
| Relations |
| BioSample |
SAMN34718706 |
| SRA |
SRX20742161 |
