C3_R3_Mature macrophage_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 two days in a fresh dish containing 12ng/ml CSF1 in alpha+ MEM /10% FCS and then for 7 days in 120ng/ml CSF1 in alpha+ MEM /10% 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: C3_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：SRA
样本来源：骨髓衍生
生物：小家鼠（Mus musculus）
特征：
品系：C57BL/6
性别：雄性
年龄：8至10周龄
培养方案：将细胞在含0.6ng/ml集落刺激因子1（CSF1）的alpha+ MEM/15%胎牛血清（FCS）培养基中培养1天，随后将非贴壁细胞转移至含12ng/ml集落刺激因子1（CSF1）的alpha+ MEM/10%胎牛血清（FCS）新鲜培养皿中继续培养2天，最后转移至含120ng/ml集落刺激因子1（CSF1）的alpha+ MEM/10%胎牛血清（FCS）培养基中培养7天。
提取分子：总RNA
提取流程：采用RNeasy试剂盒（QIAGEN）结合柱上DNase处理提取mRNA，取1μg总RNA用于构建测序文库。
采用标准Ion Torrent流程制备RNA测序文库。
文库构建策略：RNA测序（RNA-Seq）
文库来源：转录组
文库筛选方式：cDNA
测序仪器型号：Ion Torrent Proton
描述：C3_R3
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt
数据处理：使用Torrent Suite Software 5.10进行碱基识别，对测序reads进行接头序列修剪及低复杂度/低质量序列屏蔽，得到FASTQ格式原始数据文件。随后使用开源比对工具Hisat2-2.0.5将reads比对至GRCm38.p6小鼠参考基因组。将Hisat2生成的BAM格式文件上传至SeqMonk（版本1.42），并将最低比对质量阈值设为60。使用SeqMonk内置的edgeR分析平台，基于原始reads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（标注p值部分原文未完整给出）