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| Status |
Public on Dec 01, 2023 |
| Title |
DS Muscle_1 |
| Sample type |
SRA |
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| Source name |
DS Muscle
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| Organism |
Homo sapiens |
| Characteristics |
source id: embryo 5
karyotype: trisomy 21
age: 21 weeks
tissue: Muscle
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| Treatment protocol |
Donated tissues were transported on ice, transferred to cold DPBS, and minced into ~1-mm pieces on ice using scissors. The samples were treated with various enzymes for different amounts of time.
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| Growth protocol |
untached tissues
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cold lysis buffer (0.1 M Tris-HCl pH 7.5, 0.5 M LiCl, 1% SDS, 10 mM EDTA, and 5 mM dithiothreitol) was pipetted over the surface of the plate and removed after 12 min of incubation. The beads were then collected. After reverse transcription, exonuclease I treatment and cDNA amplification, the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
HiSeq X Ten |
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| Description |
Microwell-seq analysis
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| Data processing |
Data were aligned to the Homo sapiens GRCh38 genome using STAR 2.5.2a
The DGE data matrices were obtained using the Dropseq Core Computational Protocol with default parameters
Downstream standard procedures for filtering, variable gene selection, dimensionality reduction and clustering were performed using the Seurat 2.4.3 in R3.5.0
Cellphonedb was to used to make ligand-receptor analysis
GRN analysis were performed using the CellRouter in R3.5.0
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
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| Submission date |
Jul 29, 2020 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Yao Chen |
| E-mail(s) |
ciaocy@zju.edu.cn
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| Organization name |
Zhejiang University
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| Department |
School of Medicine
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| Lab |
Key Laboratory of Reproductive Genetics (Ministry of Education)
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| Street address |
866 Yuhangtang Rd
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE155409 |
Single-cell Landscape Analysis Reveals HSA21 Induced Regulatory Network in Mammalian Down Syndrome |
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| Relations |
| BioSample |
SAMN15676234 |
| SRA |
SRX8849064 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4703999_DSMscle_1_dge.txt.gz |
5.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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