|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 23, 2018 |
Title |
BMDM IFN-γ-LPS-12h-3 |
Sample type |
SRA |
|
|
Source name |
treated with IFN-γ (100 U/ml) and LPS (100 ng/ml) for 12 hrs
|
Organism |
Mus musculus |
Characteristics |
cell type: Bone marrow derived macrophage (BMDM) strain: C57BL/6
|
Growth protocol |
Growth protocol for BMDMs: BMDMs were isolated from C57BL/6 mice. To initiate differentiation, the medium was supplemented with 25 ng/ml recombinant macrophage colony-stimulating factor (M-CSF) (R&D Systems 416-ML) for 4 days. BMDMs were grown in Dulbecco’s Modified Eagle’s Medium (DMEM; Life Technologies, Carlsbad, CA) that was supplemented with 10% foetal bovine serum (FBS) and 4 mM glutamine (Life Technologies, Carlsbad, CA). The cells were maintained in a humidified incubator with a 95% air, 5% CO2 atmosphere at 37°C.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA). Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane) RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Illumina CASAVA v1.8.2 software was used for base calling. To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33) Quality controlled FASTQ files were alignment to Mus musculus UCSC mm10 reference genome sequence using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used. The number of reads mapped to gene ID features were counted using STAR. Genome_build: Mus musculus UCSC mm10 Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample
|
|
|
Submission date |
Sep 18, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Young Gyu Chai |
E-mail(s) |
ygchai@hanyang.ac.kr
|
Phone |
+82-31-400-5513
|
Organization name |
Hanyang Univ.
|
Department |
Molecualr & Life Science
|
Street address |
55 Hanyangdaehak-ro
|
City |
Ansan |
State/province |
Gyeonggi-do |
ZIP/Postal code |
15588 |
Country |
South Korea |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE103958 |
Transcript dynamics in classically and alternatively activated macrophages |
|
Relations |
BioSample |
SAMN07663044 |
SRA |
SRX3195611 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2786914_IFN-LPS-12-BM-3.ReadsPerGene.out.tab.gz |
137.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|