Gene Expression
Nebulas
Gene Expression Nebulas概要: Time series of single cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships, and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.
项目整体设计: 136,966 single cell transcriptomes were profiled from whole Xenopus tropicalis embryos at ten timepoints during the first 24 hours of its embryonic development. The data includes 75 total single cell RNA sequencing libraries, collected in 2 replicate timeseries. 4 of the 75 libraries focussed on dissected neural plate border tissue. The counts data for all pass filter cells are available in a single matrix (see "Corrected_combined.annotated_counts.tsv.gz" and "Raw_combined.annotated_counts.tsv.gz"). Alternatively, raw FASTQ or unfiltered counts files are also available for each individual library.
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| 处理方案: | - |
| 提取方案: | 5-15 healthy embryos at each desired developmental stage were collected, devitellinized using Pronase (1mg/mL in 1X MMR), dissociated to single cells (as described in Briggs et al., 2018), washed using a density gradient media replacement approach (on ice), and finally resuspended in cold PBS-/- with 0.5mg/mL BSA for scRNA-seq analysis by InDrops. Embryos were processed rapidly to minimize potential artifactual transcriptional changes in response to dissociation. Cells were generally ready for InDrops encapsulation within 1hr of starting Pronase treatment, and kept on ice from the washing steps onwards. |
| 建库方案: | Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with primer modifications for v3 libraries as summarized in supplement of the associated manuscript (Briggs et al., 2018)). |
| 分子类型: | poly(A)+ RNA |
| 库的片段类型: | PAIRED |
| 库的链类型: | Forward |
| 测序平台: | ILLUMINA |
| 测序仪型号: | Illumina NextSeq 500 |
| 链特异性: | Specific |
| 数据来源 | GEN样本编号 | GEN数据集编号 | 系列编号 | 项目编号 | 样本编号 | 样本名称 | 生物样本编号 | 样本访问号 | 实验访问号 | 释放时间 | 提交时间 | 最后更新时间 | 物种 | 种族 | 族裔 | 年龄 | 年龄单位 | 性别 | 来源名称 | 组织 | 细胞类型 | 细胞亚型 | 细胞系 | 疾病 | 疾病状态 | 发育阶段 | 突变/变异 | 表型 | Condition Detail | 生长方案 | 处理方案 | 提取方案 | 建库方案 | 分子类型 | 库的片段类型 | 链特异性 | 库的链类型 | 加标（Spike-In） | 测序方法 | 测序平台 | 测序仪型号 | 细胞数 | 测序片段数 | 碱基数 | 平均测序片段长度_1 | 平均测序片段长度_2 | 唯一比对率 | 多重比对率 | 覆盖度 |
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