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| Status |
Public on Aug 14, 2024 |
| Title |
E14.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep2 |
| Sample type |
SRA |
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| Source name |
dorsal telencephalon
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| Organism |
Mus musculus |
| Characteristics |
time point: E14.5
tissue: dorsal telencephalon
Sex: male
genotype: Chd8 het
strain: C57BL/6J
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The dorsal telencephalon was dissected from four litter- and sex-matched pairs of wild type and Chd8+/- embryos at four time points: embryonic day (E) 12.5, E14.5, E16.0, and E17.5. The medial dorsal telencephalon was removed to avoid capturing the hippocampal primordium. Freshly dissected tissue was immediately dissociated into single cells, then loaded onto the 10x Genomics Chromium Controller for single cell capture.
Libraries were generated and indexed using the 10x Chromium Next GEM Single-Cell 3' kit with v2 chemistry, then sequenced using standard Illumina protocols on an Illumina HiSeq 2500, with 26 cycles for read 1 and 98 cycles for read 2.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
rm5
10x Genomics, v2 chemistry, single-indexed
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| Data processing |
Reads were mapped to the mm10 reference genome with STAR v2.7.9a, using recommended settings to generate genome indices (cellranger reference 2020-A; parameters: --outSAMtype BAM Unsorted --outSAMattributes NH HI AS nM CR CY UR UY GX GN --outSAMprimaryFlag AllBestScore --outSAMmultNmax 10 --outBAMcompression 10 --sjdbOverhang 99 --genomeSAsparseD 3). Reads mapping to more than 10 loci or with more than one best-scoring alignment were discarded. Droplet filtering and generation of cell-by-gene count matrices was performed using STARsolo (STAR v2.7.9a; parameters: --soloType CB_UMI_Simple --soloCBwhitelist 737K-august-2016.txt --soloBarcodeReadLength 1 --soloCBmatchWLtype 1MM_multi --soloInputSAMattrBarcodeSeq CR UR --soloInputSAMattrBarcodeQual CY UY --soloMultiMappers Unique --soloUMIdedup 1MM_CR --soloUMIfiltering - --soloCellFilter CellRanger2.2 3000 0.99 10).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, which constitute outputs from STARsolo
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| Submission date |
Jul 28, 2024 |
| Last update date |
Aug 14, 2024 |
| Contact name |
James Noonan |
| E-mail(s) |
james.noonan@yale.edu
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| Organization name |
Yale School of Medicine
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| Department |
Genetics
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| Street address |
333 Cedar St
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE273271 |
Cell type-specific dysregulation of gene expression due to Chd8 loss of function during mouse cortical development [scRNA-seq] |
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| Relations |
| BioSample |
SAMN42882207 |
| SRA |
SRX25494395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8425542_rm5_barcodes.tsv.gz |
15.9 Kb |
(ftp)(http) |
TSV |
| GSM8425542_rm5_features.tsv.gz |
245.4 Kb |
(ftp)(http) |
TSV |
| GSM8425542_rm5_matrix.mtx.gz |
36.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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