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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 27, 2017 |
| Title |
BMDMs_ABX464_+LPS_678 |
| Sample type |
SRA |
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| Source name |
BMDMs_ABX464_+LPS
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| Organism |
Mus musculus |
| Characteristics |
tissue: Intestinal epitelium
cell type: BMDMs; Intestinal macrophage
treated with: ABX464
stimulated with: LPS
time point: 48h
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| Extracted molecule |
total RNA |
| Extraction protocol |
BMDMs cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA 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 |
BGISEQ-500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm9 whole genome using bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 and HISAT2 with parameters -p 8 --phred64 --sensitive -I 1 -X 1000
Genes expression level is quantified by a software package called RSEM. RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample
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| Submission date |
Mar 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Laurent MANCHON |
| E-mail(s) |
[email protected]
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| Organization name |
CNRS
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| Lab |
RNA metabolism
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| Street address |
1919 Route de Mende
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| City |
Montpellier |
| ZIP/Postal code |
34090 |
| Country |
France |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE97062 |
Next Generation Sequencing Facilitates The Study of the Effect of ABX464 in Intestinal Inflammation |
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| Relations |
| BioSample |
SAMN06645135 |
| SRA |
SRX2674544 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2550706_678.gene.FPKM.txt.gz |
251.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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