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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 07, 2022 |
| Title |
E12.5 embryo, KO3-4 |
| Sample type |
SRA |
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| Source name |
KO3
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| Organism |
Mus musculus |
| Characteristics |
age: E12.5 embryo
genotype: knock out
strain: C57BL/6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
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| Data processing |
Unmapped paired bam
Base-calls were performed with MGI software
Sequenced reads were trimmed for adaptor sequence. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. For experiments sequenced with MGISEQ-2000, we used the 150bp paired-end sequencing mode for the read1 (R1) and the read2 (R2). The cell barcode consists of three sequences, which are located at positions 1-6, 22-27, 43-48bp of R1. The UMI barcode is at position 49-54bp of R1. For experiments sequenced with MGI DNBSEQ-T7, we took a dark reaction for R1, where R1 measured 24bp and R2 measured 150bp. The cell barcode is at position 1-18 of R1, and the UMI barcode is at position 19-24 of R1.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: *.csv: Comma-separated text files of digital expression matrix (dge) based on raw UMI counts, columns are cells, and rows are genes.
Supplementary_files_format_and_content: Cell_info.csv: Comma-separated text file provides information for every cell used.
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| Submission date |
Jun 15, 2021 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Lijiang Fei |
| E-mail(s) |
15053291863@zju.edu.cn
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| Organization name |
Zhejiang University
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| Street address |
866 Yuhangtang Rd
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL30215 |
| Series (1) |
| GSE178217 |
Systematic identification of cell fate regulatory programs using a single-cell atlas of mouse development |
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| Relations |
| BioSample |
SAMN19713055 |
| SRA |
SRX11148698 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5384573_KO3-4_dge.csv.gz |
3.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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