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Sample GSM4500785 Query DataSets for GSM4500785
Status Public on Mar 12, 2023
Title COVID-19 patient1, Sputum
Sample type SRA
 
Source name COVID-19 patient Sputum
Organism Homo sapiens
Characteristics cell type: Sputum
disease: COVID-19
disease state: severe
Extracted molecule polyA RNA
Extraction protocol Cells were collected ad resuspended in DPBS with 0.04% BSA. Then, cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D). Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using STAR
Fastq reads were aligned to the genome using STARsolo with the setting ‘--outSAMattributes NH HI AS nM CR CY UR UY --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1’.
Genome_build: hg38
Supplementary_files_format_and_content: .h5ad
 
Submission date Apr 27, 2020
Last update date Mar 12, 2023
Contact name Jiangping He
E-mail(s) he_jiangping@grmh-gdl.cn
Organization name Guangzhou Institutes of Biomedicine and Health (GIBH), CAS
Street address Kai yuan avenue 190
City GuangZhou
ZIP/Postal code 510530
Country China
 
Platform ID GPL20795
Series (1)
GSE146943 Single-cell sequencing of pleural effusion reveals immune response of COV2019 infection
Relations
BioSample SAMN14737490

Supplementary file Size Download File type/resource
GSM4500785_patient1.clean.h5ad.gz 14.2 Mb (ftp)(http) H5AD
Processed data provided as supplementary file
Raw data not provided for this record

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