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| Status |
Public on Jul 30, 2018 |
| Title |
26_KO.stim |
| Sample type |
SRA |
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| Source name |
spleen, inguinal and axillary lymph node
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: spleen, inguinal and axillary lymph node
genotype: Nur77KO
agent: stimulated
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
CD4 positive T cells were isolated from spleen and lymph nodes and subsequently stimulated with aCD3 and aCD28 for 12h. RNA was isolated using RNeasy Mini Kit (Qiagen) with an integrated DNA digestion on the column using RNase-Free DNase Set (Qiagen) according to manufacturer’s instruction.
quality checked (Bioanalyzer RIN value) total RNA was enriched for Poly(A) RNA (NEBNext Poly(A) Isolation Module, NEB) and used for directional RNA library preparation (NEBNext Ultra RNA II directional, NEB) according to manufacturer´s instructions
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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 |
Trimming: Trimmomatic 0.36 (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
Alignment: hisat 2.1.0 (Parameter: default)
Sorting: samtools sort names (Version: Version: 1.2-25-gf995b71-dirty using htslib 1.2.1-39-g5ffc4a2-dirty)
Counting: htseq-count 0.9.1 (Parameter: --minaqual 0, --stranded reverse)
Differential Expression Analysis inside R: R version 3.4.4 (2018-03-15) plus Bioconductor BiocInstaller_1.28.0 using Platform: x86_64-w64-mingw32/x64 (64-bit) and Running under: Windows 10 x64 (build 9200), used R-packages: DESeq2_1.18.1
Visualization of significant Genes: pathview_1.18.2, gplots version 3.0.1, ggplot2_2.2.1, ggbiplot_0.55
Preparation for Gene Set Enrichment Analysis on DAVID inside R using the following packages: AnnotationDbi_1.40.0, org.Mm.eg.db_3.5.0
Gene Set Enrichment Analysis was performed using DAVID-Online tool Version 6.8 (https://david.ncifcrf.gov/summary.jsp)
Genome_build: mm10
Supplementary_files_format_and_content: The count files (Output of htseq-count) are tab-separated plain-text files: 1. column gene name, 2. column read count
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| Submission date |
May 25, 2018 |
| Last update date |
Jul 30, 2018 |
| Contact name |
Luisa Klotz |
| Organization name |
Universitätsklinikum Münster
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| Street address |
Albert-Schweitzer-Campus 1, A1
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| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE114912 |
RNA-Seq of murine CD4 positive T cells isolated from Nur77-deficient mice and their Nur77-competent counterparts |
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| Relations |
| BioSample |
SAMN09259599 |
| SRA |
SRX4124247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3154422_htseq_mm10_trim_26_180306.cnt.txt.gz |
94.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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