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Sample GSM5076806 Query DataSets for GSM5076806
Status Public on Jun 02, 2021
Title Day1_050_BLD_R1_Nova
Sample type SRA
 
Source name blood
Organism Homo sapiens
Characteristics donor: PT
hours: 50
bulk or scrna-seq: scRNA-seq
seq_platform: Novaseq
replicate_array: 1
use for merged analysis: 0
Extracted molecule polyA RNA
Extraction protocol Hematoma effluent and blood samples were collected and scRNA-seq was performed using the Seq-Well protocol (Gierahn et al., 2017). Briefly, cells were loaded onto arrays with polyA capture beads (ChemGenes), sealed with a membrane, and subject to cell lysis. RNA was captured, beads were collected, and reverse transcription with Maxima H Minus (ThermoFisher) was performed. Whole transcriptome amplification product was purified and used as input for library construction. Bulk RNAseq for CD4 sorted cells was performed as described in GSE163256.
Sequencing libraries were prepared using Nextera XT (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Raw sequencing data was demultiplexed and aligned to the Hg19 genome using publicly available scripts on Terra (scCloud/dropseq_workflow, version 11, https://app.terra.bio/)
UMI-collapsed digital gene expression matrices were used as input to Seurat (v3) for further analyses in R (v3.6.2)
Bulk CD4 sequencing data were processed as described in GSE163256.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain digital gene expression (dge) matrices for each scRNA-seq sample and a single txt file containing FPKM values for bulk RNA-seq samples.
 
Submission date Feb 11, 2021
Last update date May 19, 2023
Contact name Dunaduan Ma
E-mail(s) maduanduan8@gmail.com
Organization name MIT
Department Koch Institute
Lab Bioinformatics Core
Street address 77 Massachusetts Ave
City Cambridge
State/province Ma
ZIP/Postal code 02139
Country USA
 
Platform ID GPL24676
Series (1)
GSE166638 Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
Relations
BioSample SAMN17882508
SRA SRX10081251

Supplementary file Size Download File type/resource
GSM5076806_Day1_050_BLD_R1_Nova_dge.txt.gz 3.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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