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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 25, 2018 |
| Title |
mLN_SPF_FSC_7 |
| Sample type |
SRA |
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| Source name |
mLN_SPF
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| Organism |
Mus musculus |
| Characteristics |
ln: gut-draining
transplanted: no
strain: BALB/c
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| Treatment protocol |
For RNA‑seq analysis, CD45 cells depleted with autoMACS were stained using fluorescence‑coupled antibodies and sorted FSCs by FACS (Aria II, 100 μm nozzle; purity).
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| Growth protocol |
ex vivo
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from FACS‑sorted FSC using the RNeasy Plus Micro Kit (Qiagen).
cDNA was synthesized and amplified using template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina). The Agilent Technologies 2100 Bioanalyzer was used to control quality and integrity of nucleic acids after each step.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
DESeq2_genes_diffexp_by_fc_mLN_SPF_vs_pLN_SPF.csv
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| Data processing |
Libraries were aligned versus the mouse reference genome (assembly: GRCm38) using the splice junction mapper Tophat2 v1.2.0 with default parameterization.
Reads aligned to annotated genes were quantified with the htseq-count program [Anders, Pyl, Huber, 2015, Bioinformatics 31, 166-169].
Determined read counts served as input to DESeq2 [Love, Huber, Anders, 2014, Genome Biology 15, 550] for pairwise detection and quantification of differential gene expression.
RPKM (reads per kilobase maximal transcript length per million mapped reads) values were computed for each library from the raw gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: .csv files include RPKM values, q-value and log2(FC) for each pair-wise comparison
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| Submission date |
Nov 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joern Pezoldt |
| E-mail(s) |
jorn.pezoldt@epfl.ch
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| Phone |
0041766040171
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| Organization name |
EPFL
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| Department |
SV
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| Lab |
Laboratory Systems Biology and Genetics
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| Street address |
Station 19, SV 3818.A
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE106636 |
Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [Tx FSC] |
| GSE116633 |
Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells |
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| Relations |
| BioSample |
SAMN07988893 |
| SRA |
SRX3372285 |
| 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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