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| Status |
Public on Jun 09, 2024 |
| Title |
E15_rep_2_scMultiome_RNA |
| Sample type |
SRA |
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| Source name |
prefrontal cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: prefrontal cortex
genotype: WT
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Transfer fresh frozen tissue sample to a pre-chilled 1.5 mL Eppendorf tube, add 500 μL of chilled Nuclei Lysis Buffer, and then transfer to a Douncer. Dounce the tissue with A and B pestle for complete homogenization, filter with a 40 μm strainer, and add 500 μL of chilled Nuclei Lysis Buffer. Mix gently and incubate on ice for 5 min. Centrifuge the nuclei at 500 x g for 5 min at 4°C. Remove supernatant without disturbing the pellet. Isolate pure nuclei using gradient centrifugation, and quantify the nuclei using Trypan blue staining on a hemocytometer.
For single-nucleus multi-omics library construction, the isolated nuclei were resuspended with 500 μL diltuted nuclei buffer (1 x nuclei buffer (10X Genomics, PN-2000207), 1mM DTT, 1U/μL RNase inhibitor, nuclease-free Water). The nuclei were counted using Trypan blue staining on a hemocytometer, and 6,000 nuclei were loaded per lane. All libraries were constructed based on the user guide of Chromium Next GEM Single Cell Multiome ATAC + GEX kit (10X Genomics). Libraries were sequenced on the Illumina NovaSeq 6000 platform.
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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 |
10x Genomics scMultiome transcriptom part
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| Data processing |
The demultiplexing, barcode processing and fragment generation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?). Peak calling and insertion counts were made in ArchR.
Assembly: Mmul_10
Supplementary files format and content: bed format, peak called using scMultiome data from all samples
Supplementary files format and content: Tab-seperated table format, gene counts matrix
Supplementary files format and content: Matrix market format, Tn5 insertion counts matrix
Supplementary files format and content: Tab-seperated table format, meta data for each cell
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| Submission date |
Sep 29, 2023 |
| Last update date |
Jun 09, 2024 |
| Contact name |
Yiming Sun |
| E-mail(s) |
yimingsun@pku.edu.cn
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| Organization name |
Peking University
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| Department |
School of Life Sciences
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| Street address |
NO.5, Yiheyuan Road, Haidian District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE241429 |
Comparative single-cell multiome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis |
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| Relations |
| BioSample |
SAMN37622044 |
| SRA |
SRX21941642 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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