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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 20, 2015 |
| Title |
DC_04 |
| Sample type |
SRA |
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| Source name |
human regulatory T cells obtained from peripheral blood mononuclear cells using flowcytometry-based cell-sorting
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| Organism |
Homo sapiens |
| Characteristics |
cell type: regulatory T cells
group: B: Allogeneic mature moDC-expanded nTreg
cell-culture-batch: b2
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| Growth protocol |
Highly pure cell-sorted human regulatory T cells of one donor were either not or expanded for 11 days in the presence of exogenous recombinant human IL-15 (10 ng/mL; Peprotech Rocky Hill, NJ). Expansion was performed in a polyclonal manner using anti-CD3/anti-CD28 coated beads (aCD3/aCD28 T-cell expander dynabeads, Invitrogen Dynal Oslo, Norway) at a 1:1 ratio or expanded in an antigen-specific manner using human leukocyte antigen (HLA)-mismatched mature monocyte-derived dendritic cells at a 1:1 ratio. The beads used were all from one batch and the mature monocyte derived dendritic cells were generated from different donors. Expansion was performed in 96-wells U-bottom plates; 104 or 2.5x104 regulatory T cells were added per well for polyclonal and antigen-specific expansion, respectively. Every 2-3 days, the medium was refreshed or cell-cultures were split and fresh medium (containing double the concentration of IL-15) was added. The samples were obtained in 4 different experiments (batches).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNA Easy kit (Qiagen, Valencia, CA, USA)
Illumina Truseq RNA v2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
supplementary file name: toptags_BA_edgeRwithBatchEffect.txt
supplementary file name: toptags_CB_edgeRwithBatchEffect.txt
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| Data processing |
Basecalling: Illumina RTA 1.17.21.3
Demultiplexing: Illumina CASAVA 1.8.4
Alignment: Tophat 1.3.1 with Bowtie 0.12.7
ReadCounting: custom R script, based on IRanges package
Differential expression analysis: R and edgeR package, with model including terms for group and culture batch
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text file, with toptags listing as produced by R/edgeR. 5 columns: logFC, logCPM, LR, Pvalue, FDR. Data lines have geneID as rowIDs. Header line has one column less than data lines, as is customary for R write.table()
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| Submission date |
Feb 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolle Litjens |
| Organization name |
Erasmus MC
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| Department |
Internal Medicine
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| Lab |
Division of Nephrology and Transplantation
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| Street address |
Wytemaweg 80
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| City |
Rotterdam |
| ZIP/Postal code |
3015 CN |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE66385 |
Allogeneic mature human dendritic cells generate superior alloreactive regulatory T cells in the presence of IL-15 |
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| Relations |
| BioSample |
SAMN03379922 |
| SRA |
SRX893713 |
| 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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