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| Status |
Public on Aug 01, 2021 |
| Title |
Smek1-/- |
| Sample type |
SRA |
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| Source name |
cortices and hippocampus
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| Organism |
Mus musculus |
| Characteristics |
age: 2-month old
strain: C57BL/6
tissue: cortices and hippocampus
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were processed by using the Adult Brain Dissociation Kit (Miltenyi Biotec).
Library preparation was performed according to the instructions of the 10X Chromium single-cell kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
We first processed 10X genomics raw data by the Cell Ranger Single-Cell Software Suite, including using cellranger mkfastq to demultiplexes raw base call files into FASTQ files and then using cellranger count to preform alignment, filtering, barcode counting, and UMI counting.
The reads were aligned to the hg19 reference genome using a pre-built annotation package download from the 10X Genomics website.
Then we mapped UMIs to genes, followed by removing low-quality cells.
Data was first normalized by ‘‘NormalizeData’’ function with setting normalization method as ‘‘LogNormalize’’.
We then restricted the corrected expression matrix to the subsets of highly variable genes (HVGs), and then centered and scaled values before performing dimension reduction and clustering on them.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix, barcodes and genes table for every gene and every cells
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| Submission date |
Apr 13, 2021 |
| Last update date |
Aug 01, 2021 |
| Contact name |
Ruonan Duan |
| E-mail(s) |
[email protected]
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| Phone |
+8618366110727
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| Organization name |
Shandong University
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| Street address |
44# Wen Hua Xi Road
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| City |
Jinan |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE171986 |
Single-cell RNA sequencing of Smek1-/- cortices and hippocampus |
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| Relations |
| BioSample |
SAMN18723501 |
| SRA |
SRX10592620 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5239406_KOexpression.txt.gz |
18.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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