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| Status |
Public on Jun 02, 2021 |
| Title |
Day3_089_HEF_R1_Next |
| Sample type |
SRA |
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| Source name |
hematoma effluent
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| Organism |
Homo sapiens |
| Characteristics |
donor: PT
hours: 89
bulk or scrna-seq: scRNA-seq
seq_platform: Nextseq
replicate_array: 1
use for merged analysis: 1
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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.
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| Submission date |
Feb 11, 2021 |
| Last update date |
May 19, 2023 |
| Contact name |
Dunaduan Ma |
| E-mail(s) |
maduanduan8@gmail.com
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| Organization name |
MIT
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| Department |
Koch Institute
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| Lab |
Bioinformatics Core
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| Street address |
77 Massachusetts Ave
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| City |
Cambridge |
| State/province |
Ma |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE166638 |
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu |
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| Relations |
| BioSample |
SAMN17882479 |
| SRA |
SRX10081262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5076817_Day3_089_HEF_R1_Next_dge.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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