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| Status |
Public on Jan 23, 2018 |
| Title |
RAW264.7-LPS-4h-1 |
| Sample type |
SRA |
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| Source name |
treated with LPS (100 ng/ml) for 4 hrs
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| Organism |
Mus musculus |
| Characteristics |
cell type: RAW264.7 macrophage cell line
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| Growth protocol |
Growth protocol for RAW 264.7 macrophage cell line: RAW 264.7 macrophage cell line were grown in RPMI medium supplemented with FBS, 100 IU/ml penicillin, and 10 µg/ml of streptomycin (Invitrogen, USA). The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. RAW264.7 macrophage cell line were incubated with LPS (100 ng/ml) for the specified times under normal culture conditions. The medium, containing the appropriate agents, was replaced every other day. LPS (L6529; strain 055:B5) were purchased from Sigma-Aldrich, St. Louis, MO.
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Sep 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Young Gyu Chai |
| E-mail(s) |
ygchai@hanyang.ac.kr
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| Phone |
+82-31-400-5513
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| Organization name |
Hanyang Univ.
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| Department |
Molecualr & Life Science
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| Street address |
55 Hanyangdaehak-ro
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| City |
Ansan |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
15588 |
| Country |
South Korea |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE103958 |
Transcript dynamics in classically and alternatively activated macrophages |
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| Relations |
| BioSample |
SAMN07663048 |
| SRA |
SRX3195623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2786926_Raw-LPS-4hr-1.ReadsPerGene.out.tab.gz |
138.3 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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