Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA656271: Single cell RNA-seq analysis of pMN neural progenitors from zebrafish

来源: NCBI / GSE155988
提交时间: Aug 10 2020
释放时间: Aug 11 2020
最后更新时间: Aug 19 2020

概要: The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so, we sorted fluorescently marked pMN cells obtained from Tg(olig2:EGFP) zebrafish embryos at 24, 36 and 48 hours post fertilization and performed 10X Chromium single cell RNA-seq.

项目整体设计: Three samples obtained from wild-type zebrafish embryos at three developmental timepoints were analyzed.

GEN 数据集:
GEND000146
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方案
生长方案: developmental stage: 24 hours post fertilization; strain: Tg(olig2:EGFP) ZFIN ID: ZDB-ALT-041129-8; developmental stage: 36 hours post fertilization;strain: Tg(olig2:EGFP) ZFIN ID: ZDB-ALT-041129-8; developmental stage: 48 hours post fertilization; strain: Tg(olig2:EGFP) ZFIN ID: ZDB-ALT-041129-8
处理方案: -
提取方案: 24, 36, and 48 hpf Tg(olig2:EGFP) euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre-chilled Ca free Ringers solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES, pH 7.0) on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution (10 mg/ml BI protease, 125 U/ml DNase, 2.5 mM EDTA, 1X PBS) was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution (30% FBS, 0.8 mM CaCl2, 1X PBS) was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice, 1 ml of chilled suspension media (1% FBS, 0.8 mM CaCl2, 50 U/ml Penicillin, 0.05 mg/ml Streptomycin) was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed, and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU-SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS.
建库方案: The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell 3' Reagent Kit part no. PN-1000075.  Libraries were sequenced on the Illumina NovaSEQ6000 Instrument. 
测序信息
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 NovaSeq 6000
链特异性: Specific
样本
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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
文章
Prdm8 regulates pMN progenitor specification for motor neuron and oligodendrocyte fates by modulating the Shh signaling response.
Development (Cambridge, England) . 2020-08-27 [PMID: 32680935]