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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 04, 2016 |
| Title |
Foxp3Plus_WT_B |
| Sample type |
SRA |
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| Source name |
WT Treg cells, CD4+
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| Organism |
Mus musculus |
| Characteristics |
tissue source: Spleen
cell type: WT Treg cells, CD4+
strain: NOD.FoxP3GFP
t cell receptor: polyclonal
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| Growth protocol |
Cells are isolated from mouse spleen tissues
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nucleospin RNA XS kit (Macherey-Nagel)
mRNA was selected by poly-dT magnetic beads, then RNA was fragmented and reverse-transcribed preserving strand information, and cDNA was end-repaired, adenylated, adapter-ligated and PCR amplified
RNA-Seq (RNA-Seq libraries were sequenced on Illumina HiSeq2500 at single-end 50-bp (base pair), resulting 25-30 million reads per library)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
poly-dT selected mRNA
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| Data processing |
Basecalling softwares version was HiSeq Control Software 2.2.38 and RTA 1.18.61
BCL files to fastq files conversion and demultiplexing were done using CASAVA v1.8.2
Reads were filtered by quality score using FASTQC (v0.10.1)
Reads were trimmed for Illumina adapters using Trimmomatic (v0.33)
Reads are aligned to reference genome using STAR (v2.4.1a)
Gene expression was quantified using aligned reads to exons of RefSeq transcripts using HOMER (v4.7)
differential gene expression was determined with edgeR (bioconductor version: release 3.1)
Genome_build: mus musculus mm9 (NCBI Build 37)
Supplementary_files_format_and_content: tab-delimited text files include transcript per million (tpm) values for each Sample
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| Submission date |
Jun 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Manching Ku |
| Organization name |
Medical Center - University of Freiburg
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| Department |
Hematology and Oncology
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| Street address |
Mathildenstrasse 1
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| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE70156 |
Nuclear Transfer nTreg model reveals fate-determining TCRbeta and peripheral nTreg precursors |
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| Relations |
| BioSample |
SAMN03786815 |
| SRA |
SRX1070002 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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