C1_R2_Non-adherent precursors_mouse2

Sample type: SRA

Source name: bone marrow derived
Organism: Mus musculus
Characteristics strain: C57BL/6
Sex: male
age: 8 to 10 weeks
Growth protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS, non-adherent cells were incubated for a second day in a fresh dish containing 0.6ng/ml CSF1 in alpha+ MEM /15% FCS
Extracted molecule total RNA
Extraction protocol mRNA was harvested using RNeasy kit( QIAGEN) with DNase treatment on column. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols

Library strategy: RNA-Seq
Library source: transcriptomic
Library selection: cDNA
Instrument model: Ion Torrent Proton

Description: C1_R2
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt
Data processing: Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence- returning a fastq file (raw data)
Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p

样本类型：SRA

样本来源：骨髓来源

生物：小家鼠（Mus musculus）

特征：品系为C57BL/6

性别：雄性

周龄：8至10周

细胞培养流程：将细胞置于添加了0.6ng/ml集落刺激因子1（Colony-Stimulating Factor 1, CSF1）的α修饰伊格尔培养基（α-modified Eagle's Medium, α+MEM）/15%胎牛血清（Fetal Calf Serum, FCS）中培养1天后，将非贴壁细胞转移至含相同浓度CSF1的新鲜培养皿中，继续培养1天。

提取的核酸分子：总RNA（total RNA）

提取方案：采用带有柱上脱氧核糖核酸酶（Deoxyribonuclease, DNase）处理的RNeasy试剂盒（QIAGEN品牌）提取mRNA。取1μg总RNA用于构建测序文库。采用标准Ion Torrent建库流程制备测序文库。

文库构建策略：RNA测序（RNA Sequencing, RNA-Seq）

文库来源：转录组

文库筛选方式：cDNA筛选

测序仪器型号：Ion Torrent Proton

样本标识文件：C1_R2、C1_C2_C3_allprobes_reads.txt、C1_C2_C3_allprobes_log2_RPM.txt

数据处理流程：使用Torrent Suite Software 5.10进行碱基识别，对测序reads进行接头序列修剪、低复杂度与低质量序列屏蔽，最终得到fastq格式原始数据文件。使用开源比对软件Hisat2-2.0.5将过滤后的reads比对至GRCm38.p6参考基因组。将Hisat2生成的二进制比对映射（BAM）文件上传至SeqMonk（版本1.42），设置最小比对质量阈值为60。借助集成于SeqMonk中的edgeR分析平台，按照负二项分布分析的要求，从原始测序reads中生成差异基因表达列表，并导出所有基因及差异表达基因的制表符分隔文本文件（以p值<[原文未完整标注]）