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| Status |
Public on Jul 25, 2017 |
| Title |
KMC18 |
| Sample type |
SRA |
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| Source name |
Macrophage with Control siRNA and RANKL for 48h_rep#2
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Macrophage
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy. Illumina TruSeq RNA Sample Prep Kit was use for the construction of sequencing libraries.
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 Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSChg Hg19 using TopHat v0.9.0 using Garaxy (Goecks et al. 2010)
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) was calculated using Cuffdiff program (V2.2.1) using Garaxy
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jun 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Koichi Murata |
| E-mail(s) |
[email protected]
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| Organization name |
Kyoto University
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| Department |
Orthopaedics
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| Street address |
54, Kawahara-cho, Shogoin, Sakyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
6068507 |
| Country |
Japan |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE99987 |
Next Generation Sequencing Facilitates Quantitative Analysis of Normoxia and Hypoxia Macrophage Transcriptomes |
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| Relations |
| BioSample |
SAMN07228214 |
| SRA |
SRX2915438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2667035_KMC18.txt.gz |
179.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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