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

PRJNA401782: T cell activation in skin explants from patients with psoriasis and controls

来源: NCBI / GSE103489
提交时间: Sep 05 2017
释放时间: Mar 16 2018
最后更新时间: May 15 2019

概要: We have worked on skin explants and activated T cells locally with a CD3 antibody, whole biopsies were activated, then epidermal and dermal RNA was sequenced. Sequencing was performed by BGI (Hong Kong) as well as the group analysis.

项目整体设计: Examination of skin tissue responses to local T cell activation (acd3) compared to isotype at the RNA level. Samples include biopsies from healthy controls and patients with psoriasis treated with Ustekinumab or untreated lesional psoriasis. All biopsy samples were treated either with acd3 or with isotype as indicated.

GEN 数据集:
GEND000084
测序方法:
物种:
组织:
健康状况:
方案
生长方案: -
处理方案: Incubated with CD3 antibody; Incubated with Isotype control; Treated with Ustekinumab incubated with CD3 antibody; Treated with Ustekinumab incubated with Isotype control; Untreated with Ustekinumab incubated with CD3 antibody; Untreated with Ustekinumab incubated with Isotype control
提取方案: Skin is sampled, treated with antibodies. The days after epidermis and dermis are separated with dispase, then flash frozen on dry ice. RNA is extracted with Qiazol (qiagen) and send for sequencing. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary.
建库方案: RNA libraries were prepared for sequencing using standard Illumina protocols
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: Illumina HiSeq 2000
链特异性: Unspecific
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
Resident T Cells in Resolved Psoriasis Steer Tissue Responses that Stratify Clinical Outcome.
The Journal of investigative dermatology . 2018-03-03 [PMID: 29510191]