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| Status |
Public on Nov 17, 2022 |
| Title |
EndoMT3 |
| Sample type |
SRA |
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| Source name |
endothelial cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: TC
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| Treatment protocol |
The cells were seeded at a density of 120,000 cells/well onto the 4kPa hydrogels or tissue culture plates (TC). The day after cell seeding, the media was switched to a control medium comprising of endothelial basal medium (EBM, Lonza) supplemented with 5% fetal bovine serum (FBS, Lonza) with or without supplemented TGF-β (20 ng/ml, Peprotech).
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| Growth protocol |
Human coronary artery endothelial cells (ECs, passage 3-8, Lonza) were expanded in endothelial growth media (EGM-2MV, Lonza).
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| Extracted molecule |
total RNA |
| Extraction protocol |
At day 14, cells cultures on 4 kPa hydrogel and TC with and without TGF-β stimulation were dissociated and resuspended in DMEM supplemented with 10% FBS. Single cell libraries were prepared using a 10X Chromium v3 microfluidic chip, targeting for 8000 cells per sample.
The barcoded libraries from individual samples were then pooled and multiplexed, followed by sequencing on an Illumina NovaSeq 6000 platform using a NovaSeq-S1 (2x100bp) flow cell.
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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 |
The FASTQ files for each in vitro sample were generated from the raw bcl data by bcl2fastq. The FASTQ files were subsequently processed using Cell Ranger 3.0 with default parameters. In brief, the alignment was performed by STAR with the human reference genome GRCh38 to generate the bam file. The BAM files were then subjected to the Velocyto pipeline to estimate the unspliced and the spliced read counts. We removed the low-quality cells that expressed less than 200 genes, or the expression of mitochondria genes exceeded 25% of total counts. Any genes that expressed less than 3 cells were excluded.
Genome_build: GRh38
Supplementary_files_format_and_content: TSV, MTX
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| Submission date |
Nov 19, 2021 |
| Last update date |
Nov 19, 2022 |
| Contact name |
Patrick Cahan |
| E-mail(s) |
patrick.cahan@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Lab |
MRB 660
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| Street address |
733 N. Broadway
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| City |
Baltimore |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE189179 |
Single-Cell RNA Sequencing reveals matrix stiffness induction of endothelial phenotypic modulation and its association with atherosclerosis |
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| Relations |
| BioSample |
SAMN23298568 |
| SRA |
SRX13172004 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5695770_EndoMT3_barcodes.tsv.gz |
30.4 Kb |
(ftp)(http) |
TSV |
| GSM5695770_EndoMT3_features.tsv.gz |
264.3 Kb |
(ftp)(http) |
TSV |
| GSM5695770_EndoMT3_matrix.mtx.gz |
79.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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