Summary: 10X-based scRNA-seq data human fetal kidneys at 5 different ages
Overall Design: w9, w11, w13, w16 and w18 human fetal kidneys
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Growth Protocol: | - |
Treatment Protocol: | - |
Extract Protocol: | One human embryo of w16 was isolated and the kidney dissected in cold saline solution (0.9% NaCl, Versylene Fresenius, FranceThe obtained kidney was decapsulated and kept on ice in dissociation buffer (DPBS + Penicillin 100U/ml + Streptomycin 0.1 mg/ml) before cutting it into 1 – 2 mm pieces. The pieces were washed 3 times with washing solution (Advanced DMEM F12 supplemented with: ITS commercial solution (Insulin – Transferrin – Selenium), Glutamax, Penicillin 100 U/ml and Streptomycin 0.1 mg/ml) with brief centrifugation (160g) in order to remove as many red blood cells as possible. The washed kidney tissue was then incubated with digestion solution (Trypsin/EDTA solution 0.25% and Collagenase-II 280 U/ml) and incubated overnight at 4°C. The next day, the digestion solution was removed, the kidney was rinsed with washing solution and incubated with washing solution for 30 min at 37°C with agitation. Subsequently, the sample was sequentially passed through sterile cell-strainers of 100, 70 and 40 µm pore size with the help of washing solution. The cells were then centrifuged, counted and viability was measured to be 78% (trypan blue assay) before proceeding with single-cell RNA sequencing library preparation.10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol. Libraries were sequenced on a NextSeq500 in Mid Output mode using a version 2, 150 cycles kit (Illumina).; Human fetal embryos were isolated and the kidney dissected in cold saline solution (0.9% NaCl, Versylene Fresenius, France). The obtained kidneys were decapsulated and kept on ice in dissociation buffer (DPBS + Penicillin 100U/ml + Streptomycin 0.1 mg/ml) before cutting it into 1 – 2 mm pieces. The pieces were washed 3 times with washing solution (Advanced DMEM F12 supplemented with: ITS commercial solution (Insulin – Transferrin – Selenium), Glutamax, Penicillin 100 U/ml and Streptomycin 0.1 mg/ml) with brief centrifugation (160g) in order to remove as many red blood cells as possible. The washed kidney tissues were then incubated with digestion solution (Trypsin/EDTA solution 0.25% and Collagenase-II 280 U/ml) and incubated overnight at 4°C. The next day, the digestion solution was removed, the kidneys were rinsed with washing solution and incubated with washing solution for 30 min at 37°C with agitation. Subsequently, the samples were sequentially passed through sterile cell-strainers of 100, 70 and 40 µm pore size with the help of washing solution. The cells were then centrifuged, counted and viability was measured to be 78% (trypan blue assay) before proceeding with single-cell RNA sequencing library preparation.10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol. Libraries were sequenced on a NextSeq500 in Mid Output mode using a version 2, 150 cycles kit (Illumina). |
Library Construction Protocol: | - |
Molecule Type: | poly(A)+ RNA |
Library Source: | |
Library Layout: | PAIRED |
Library Strand: | Forward |
Platform: | ILLUMINA |
Instrument Model: | Illumina NextSeq 500 |
Strand-Specific: | Specific |
Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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