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| Status |
Public on Apr 10, 2024 |
| Title |
E14 WT, replicate 1, run 1, snRNAseq |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
region: Forebrain
age: E14
genotype: WT
strain: MYT1L S710fsX
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For E14 samples, the forebrains were dissected and flash frozen in liquid nitrogen. The tissue was dissociated by dounce homogenization, filtered through a 40um filter, and washed twice with Nuclei Wash Buffer (DPBS, 1% BSA, and 0.2U/ul RNase Inhibitor). The nuclei were counted and 500k-2.5M nuclei were fixed using the ScaleBio Sample Fixation Kit. The nuclei were stored at -80C until all samples have been collected and fixed.
The libraries were made according to manufacturer's instructions for Scale Biosciences' Single Cell RNA Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Scale Biosciences
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| Data processing |
The demultiplexing, barcode processing, trimming, alignment, and gene counting was done using the ScaleBio ScaleRna Single-cell RNA Nextflow workflow v1.4.0 (https://github.com/ScaleBio/ScaleRna)
Seurat v4.3.0 was used to analyze the feature-barcode matrices, DoubletFinder v2.0.3 was used to remove doublets, DESeq2 v1.38.3 was used for pseudobulk differential gene analysis. Monocle v1.3.1, Python 3.9.18, velocyto v0.17.17, scanpy v1.12.0, scvelo v0.3.1, and cellrank v2.0.2 were used for trajectory analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files
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| Submission date |
Mar 25, 2024 |
| Last update date |
Nov 11, 2024 |
| Contact name |
Joseph D Dougherty |
| E-mail(s) |
jdougherty@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Street address |
4370 Duncan Ave
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE262364 |
MYT1L deficiency impairs excitatory neuron trajectory during cortical development [E14] |
| GSE262368 |
MYT1L deficiency impairs excitatory neuron trajectory during cortical development |
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| Relations |
| BioSample |
SAMN40601635 |
| SRA |
SRX24042801 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8163923_E14-WT-1-1_barcodes.tsv.gz |
22.5 Kb |
(ftp)(http) |
TSV |
| GSM8163923_E14-WT-1-1_features.tsv.gz |
454.7 Kb |
(ftp)(http) |
TSV |
| GSM8163923_E14-WT-1-1_matrix.mtx.gz |
41.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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