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| Status |
Public on Nov 21, 2020 |
| Title |
Day8_accutase |
| Sample type |
SRA |
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| Source name |
Day 10 of in vitro microglial differentiation
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| Organism |
Homo sapiens |
| Characteristics |
cell line source: Human ES cell line (H1)
cell type: primitive hematopoietic cells and hemogenic endothelium
protocol: Later primitive hematopoietic cells (Day 10) were cultured in the presence of SCF, IL6, TPO, and IL3 for 4 days.
dissociation: accutase
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| Growth protocol |
Cells were cultured in hematopoietic cytokines (VEGF, FGF2, SCF, IL6, IL3, TPO) during the in vitro differentiation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Dissociated cells were strained through a 40uM filter and resuspended at 1000 cells/uL in FACS buffer.
Libraries were prepared according to the 10x genomics Chromium Single Cell 3' Library & Gel bead Kit V2 according to manufacturer's protocol.
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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 |
SEQC pipeline was used for: count matrix generation from Illumina fastq files (intermediate steps: cell barcode and UMI extraction, merging of forward and reverse fastq, alignment with STAR, barcode correction, resolving of multi-aligning reads, alignment error correction, count matrix generation, filtering out of 1) empty droplets based on library size distribution; 2) dying cells based on abundance of mitochodrial RNA; 3) low complexity cells based on ratio of number of genes detected over library size, see methods of paper)
only for pre-processed files: count matrix normalization and log transformation as described in paper (normalization of counts to 10,000 RNA molecules per cell, followed by log transformation of counts using natural log and pseudo-count 1)
only for pre-processed files: second cell filtering round as described in paper (removal of putative empty droplets, dying cells and cells differentiating into types not of interest)
Genome_build: hg38
Supplementary_files_format_and_content: csv containing normalized counts
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| Submission date |
Oct 29, 2019 |
| Last update date |
Nov 23, 2020 |
| Contact name |
Sudha Guttikonda |
| Organization name |
MSKCC
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| Department |
Developmental Biology
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| Lab |
Studer Lab
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| Street address |
430 E 67th St
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE139550 |
Fully defined human PSC-derived microglia and tri-culture system reveals cell type specific potentiation of complement C3 production in a model of Alzheimer’s disease [scRNA-seq] |
| GSE139552 |
Fully defined human PSC-derived microglia and tri-culture system reveals cell type specific potentiation of complement C3 production in a model of Alzheimer’s disease |
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| Relations |
| BioSample |
SAMN13153213 |
| SRA |
SRX7069401 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4143593_Day8_accutase_counts.csv.gz |
17.7 Mb |
(ftp)(http) |
CSV |
| GSM4143593_Day8_accutase_preprocessed.csv.gz |
5.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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