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| Status |
Public on Oct 27, 2021 |
| Title |
GW11C |
| Sample type |
SRA |
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| Source name |
Cells From Spinal Cord
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Spinal Cord
age: 11 weeks after gestation
gender: Male
molecule: Total RNA
region: Cervical
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fetal spinal cords were collected in ice-cold preserve medium containing. The spinal cord was dissected and placed in Hanks Balanced Solution without calcium and magnesium (HBSS, Life Technologies 14185045). The tissue was digested according to the protocol of papain dissociation kit (Worthington Biochemical). In brief spinal cord roughly dissected into small pieces, tissue was then digested in Papain digest medium for 40min at 37°C to dissociate the cells. The cell suspension was pipetted further and filtered twice through 0.35um filters. Centrifuged at 300g 4℃ for 5 min to obtain a cell pellet. After the digestion medium was carefully removed, cell pellet was resuspended in 500 μ HBSS medium and kept on ice. The nuclear islation performed according to the protocol of Nuclei Isolation Kit: Nuclei EZ Prep (NUC101-1KT)
RNA libraries were prepared for sequencing using standard Illumina protocols, the single cells suspension was loaded onto the Chromium single cell controller (10xGenomics). Library preparation was performed using the single cell 3 'Library and Gel Bead Kit V2 (10xGenomics, PN-120235) /V3 (10xGenomics, 1000075) and Chromium Single Cell B Chip Kit (10xGenomics, PN-120236). cDNA amplification involved 11 PCR cycles. Raw sequencing data was processed using Cell Ranger analysis pipeline. Reads were aligned to human genome version GRCh38.
According to the manufacture's introduction, snRNA-seq/scRNA-seq libraries were constructed using Single Cell 3' Library and Gel Bead Kit V3. Finally sequencing was performed on the Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell and 150 bp (PE150) paired-end reads (performed by CapitalBio, Beijing).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Base call files were demultiplexed into FASTQ files by Cellranger 3.1.0
FASTQ files were analysized by "cellranger count" function of Cellranger 3.1.0
"filtered_feature_bc_matrix" was produced and stored in the Market Exchange Format (MEX) for sparse matrices
Genome_build: GRCh38
Supplementary_files_format_and_content: MEX format for sparse matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
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| Submission date |
Sep 16, 2019 |
| Last update date |
Feb 14, 2022 |
| Contact name |
Xianming Wu |
| E-mail(s) |
[email protected]
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| Phone |
+86-15313377580
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| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
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| Street address |
Unit 2, No.1 West Beichen Road
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| City |
Beijing |
| State/province |
Chaoyang District |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE136719 |
Single-cell transcription mapping of neural subtype development in human spinal cord |
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| Relations |
| BioSample |
SAMN12766795 |
| SRA |
SRX6853483 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4080385_GW11C_barcodes.tsv.gz |
69.4 Kb |
(ftp)(http) |
TSV |
| GSM4080385_GW11C_features.tsv.gz |
274.6 Kb |
(ftp)(http) |
TSV |
| GSM4080385_GW11C_matrix.mtx.gz |
102.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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