C1_R3_Non-adherent precursors_mouse3

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_R3
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：序列读取存档（Sequence Read Archive, 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
年龄：8~10周龄
培养方案：将细胞置于添加15%胎牛血清（Fetal Calf Serum, FCS）的α-MEM培养基中，加入0.6ng/ml集落刺激因子1（Colony-Stimulating Factor 1, CSF1）培养1天后，将非贴壁细胞转移至含有相同浓度CSF1及相同培养基的新培养皿中继续培养1天。
提取分子：总核糖核酸（total RNA）
提取方案：采用柱上脱氧核糖核酸酶（DNase）处理的RNeasy试剂盒（QIAGEN）提取信使核糖核酸（mRNA），取1μg总RNA用于测序文库构建；采用标准Ion Torrent测序流程制备RNA测序文库。
文库策略：RNA测序（RNA-Seq）
文库来源：转录组学
文库筛选方式：互补脱氧核糖核酸（cDNA）
测序仪器型号：Ion Torrent Proton
描述：C1_R3、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，对测序读段进行接头序列修剪、低复杂度/低质量序列屏蔽，得到FASTQ格式原始数据文件；使用开源比对工具Hisat2-2.0.5将读段比对至GRCm38.p6版本参考基因组；将Hisat2生成的BAM文件上传至SeqMonk（版本1.42），并设置最小比对质量阈值为60；借助SeqMonk内置的edgeR分析平台，从原始读段中生成差异基因表达列表，以满足负二项分布分析的需求；生成所有基因及差异表达基因的制表符分隔文本文件（p值未完整给出）