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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 09, 2019 |
| Title |
Control 3 |
| Sample type |
SRA |
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| Source name |
LN-CD4
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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)
TruSeqStranded mRNA Sample Preparation Kit
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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 |
The quality of the sequenced reads was determined using the FastQC tool, and contaminated adaptor sequences were trimmed using the Cutadapt tool.
The trimmed sequence reads were aligned to the mouse reference genome mm9 using Bowtie2.
The abundance of transcripts was estimated using the Tuxedo protocol (Tophat and Cufflinks). Fragments per kilobase of transcript per million mapped reads (FPKM), which is normalized expression level, was generated with Cuffnorm and differentially expressed genes (DEGs) were identified using Cuffdiff.
DEGs were defined as the genes that were differentially expressed, showing less than a false discovery rate (FDR)-adjusted p-value cutoff of 0.05.
We further discarded genes showing less than 1.5-fold changes of up- or down-regulated genes between conditions.
Genome_build: mm9
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| Submission date |
Nov 21, 2018 |
| Last update date |
May 09, 2019 |
| Contact name |
Sin-Hyeog Im |
| E-mail(s) |
iimsh@postech.ac.kr
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| Phone |
+82-54-279-2356
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| Organization name |
Institute for Basic Science
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| Department |
Academy of Immunology and Microbiology
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| Street address |
POSTECH Biotech Center Rm. 428-431, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Republic of Korea
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| City |
Pohang |
| State/province |
Gyeongsangbuk-do |
| ZIP/Postal code |
37673 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE122795 |
Ets1 suppresses atopic dermatitis by suppressing pathogenic T cell responses |
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| Relations |
| BioSample |
SAMN10458774 |
| SRA |
SRX5043633 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3485522_Cont-AD-15.txt.gz |
251.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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