|
Status |
Public on Feb 19, 2024 |
Title |
ED201020_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: P7
|
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 |
SAMN34718711 |
SRA |
SRX20742154 |