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| Status |
Public on Apr 10, 2024 |
| Title |
P21 WT, male, replicate 3, snRNAseq |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
region: Cortex
Sex: Male
age: P21
genotype: WT
strain: MYT1L S710fsX
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For P21 samples, cortices from mice were dissected and flash frozen in liquid nitrogen. The tissue was dissociated by dounce homogenization and a gradient centrifugation step using 25:35 Iodixanol and centrifuged at 10,000 xg for 30 min at 4C was performed to purify the nuclei from cellular debris and myelin generated during tissue dissociation. The nuclei were carefully collected from the interface, filtered through a 40um filter, washed with Nuclei Wash Buffer (DPBS, 1% BSA, and 0.1U/ul RNase Inhibitor), 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. 3 replicates each of male and female MYT1L WT and Het mice were included in this experiment. Libraries were made using the Scale Biosciences Single Cell RNA Kit.
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; instrument model: Illumina NovaSeq X
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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.
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) |
| GSE262366 |
MYT1L deficiency impairs excitatory neuron trajectory during cortical development [P21] |
| GSE262368 |
MYT1L deficiency impairs excitatory neuron trajectory during cortical development |
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| Relations |
| BioSample |
SAMN40600562 |
| SRA |
SRX24041552 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8163949_P21-WT-M-3_barcodes.tsv.gz |
34.0 Kb |
(ftp)(http) |
TSV |
| GSM8163949_P21-WT-M-3_features.tsv.gz |
454.7 Kb |
(ftp)(http) |
TSV |
| GSM8163949_P21-WT-M-3_matrix.mtx.gz |
71.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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