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

PRJNA605214: Cell and molecular transitions during efficient dedifferentiation: single cell RNAseq

来源: NCBI / GSE144890
提交时间: Feb 06 2020
释放时间: Apr 07 2020
最后更新时间: May 07 2020

概要: Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum by single cell RNAseq

项目整体设计: scRNAseq of cells during the first 6 h of dedifferentiation in liquid growth media. Dedifferentiation cultures with staggered start times were harvested simultaneously at 0, 1, 2, 3, 4, 5 and 6 h of dedifferentiation and pooled together for sequencing using the 10x Chromium platform. Cells from different timepoints were pooled before barcoding. Two biological replicates were collected. In each biological replicate, the input cells were split between two Chromium 10x chip inlets (technical replicates) with data from each technical replicate pooled after mapping for downstream analysis. In biological replicate 1, 967 libraries passed UMI filtering by CellRanger v2.2.0 with median of around 25000 total molecular counts. In biological replicate 2, 2961 libraries passed filtering,with a median of around 18000 total molecular counts.

GEN 数据集:
GEND000327
测序方法:
物种:
健康状况:
细胞系:
发育阶段:
方案
生长方案: Before development, cells were grown in HL5 (Formedium, UK).
处理方案: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA then dedifferentiated in HL5 growth medium as a shaken suspension. Start times of development and dedifferentiation were staggered to allow simultaneous collection of samples into ice-cold KK2 at 0, 1, 2, 3, 4, 5 and 6 h of dedifferentiation.
提取方案: Cell suspensions from different timepoints were pooled before loading onto the 10X Chromium Single Cell A Chip using the Chromium 3' Library and Gel Bead Kit v2. Samples were split between two chip inlets and treated as technical replicates
建库方案: The purified GEM-RT product was subjected to 14 cycles of cDNA amplification. 35 microlitres of cDNA was used to prepare the 10X 3' RNA library, with 12/11 cycles used for sample index PCR. Final libraries were run on a NextSeq500 mid-output 150-cycle kit with a 26[8]98 cycle configuration to generate 130 million read pairs in total.
测序信息
分子类型: poly(A)+ RNA
库的片段类型: PAIRED
库的链类型: -
测序平台: ILLUMINA
测序仪型号: NextSeq 500
链特异性: -
样本
基本信息:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
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
Cell and molecular transitions during efficient dedifferentiation.
eLife . 2020-04-07 [PMID: 32255425]