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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 21, 2021 |
| Title |
mock_2 |
| Sample type |
SRA |
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| Source name |
COL-DC
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
QC/adapter sequence trimming for raw FASTQ sequences Raw read quality evaluation by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with default options. Adapter sequence trimming by CutAdapt (https://pypi.python.org/pypi/cutadapt)
Mapping on mouse reference genome By TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
Expression and DEG analysis Expression analysis by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options[4]. DEG analysis by CuffDiff (http://cufflinks.cbcb.umd.edu) with significance thresholds as FDR<0.05, p<0.001, and p<0.01. Scatter plot and volcano plot by in-house R scripts. Unsupervised clustering by in-house R scripts
Genome_build: mm10
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| Submission date |
Feb 22, 2019 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Gi-Cheon careful Kim |
| E-mail(s) |
kimgicheon@gmail.com
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| Phone |
542790646
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| Organization name |
IBS
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| Street address |
POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang
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| City |
Pohang |
| State/province |
Hyoja-dong Namgu |
| ZIP/Postal code |
37673 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE126937 |
Commensal yeast derived b-1,6-glucan induces regulatory T cells |
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| Relations |
| BioSample |
SAMN10987594 |
| SRA |
SRX5408257 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3618423_mock_2.txt.gz |
111.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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