|
| Status |
Public on Feb 19, 2024 |
| Title |
ED211111_b |
| Sample type |
SRA |
| |
|
| Source name |
Barcode dataset of ED211111
|
| 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 |
lineage barcode RNA
Illumina NovaSeq 6000/ Illumina NextSeq 500
|
| Data processing |
Barcode dataset TrackerSeq: R2 FASTQ files were pre-processed using BBduk; the sequences to the left and right of the lineage barcodes were trimmed so that only the lineage barcode (BC) remained. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from corresponding Seurat object of the dataset to generate a cell barcode whitelist. The extracted cell barcodes and UMIs were added to the read names of the lineage barcode FASTQ files. The resulting FASTQ files were processed by clonal_annotation.ipynb from LARRY (Klein lab), to output a sparse matrix in csv format, where rows were cells identified by individual cell barcodes and columns were lineage barcode, with 1 indicating its presence and 0 its absence. Only (Cell,UMI,BC) triples supported by at least 10 reads and (Cell,BC) pairs with at least 6 UMI were considered for further analyses. A CloneIDs were assigned to cell barcodes. The distance between the cell barcodes in the matrix could be determined by clustering the matrix using Jaccard similarity and average linkage, as demonstrated by Wagner et al. This could be accomplished by using the R function distance(method = ‘jaccard’) and hclust(method = ‘average’). The resulting dendrogram was cut at a height of 0.999 using cutree(hclust_avg, h = 0.999) to obtain the clonal groupings.
Csv files with columns for "CBC" and "Lineage-Barcode"
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 |
SAMN34718703 |
| SRA |
SRX20742164 |
