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| Status |
Public on Jul 11, 2023 |
| Title |
CD45.1+ OT-II viable T cells from dLN, feast diet #2 |
| Sample type |
SRA |
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| Source name |
CD4 T-cells from dLN
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| Organism |
Mus musculus |
| Characteristics |
tissue: CD4 T-cells from dLN
timepoint: 5 days after switch to fest diet
treatment: feast diet
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Peyer’s patches (PPs) were removed from small intestine (SI) and put in TriFastTM (PeqLab, Cat.Nr.: 30-2010). Total RNA was purified using the NucleoSpin RNA II kit (Macherey & Nagel), according to manufacturer’s instructions. RNA sequencing was performed on FACS-sorted CD4+Foxp3- or CD45.1+ OT-II viable T cells isolated from PPs or dLN, respectively.
For library preparation of total PPs and ileum samples, cDNA was used as input to construct 250~300 bp insert cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, USA). Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. For FACS-sorted cells, total RNA was amplified using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, USA) with the double strand cDNA (ds-cDNA) being synthesized. Then ds-cDNA was purified with AMPure XP beads and quantified with Qubit (Life TechnologiesTM). The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, insert size of the library was validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
dLN_CD4_OVA_FD_2
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| Data processing |
Sequencing quality was assessed with FastQC v. 0.11.5, followed by trimming of low quality bases with Trimmomatic v. 0.33 and alignment to the Mus musculus genome draft GRCm38.84 using STAR v. 2.5.0.
Assembly: GRCm38.84
Supplementary files format and content: Raw counts summarized per gene for each sample after alignment with STAR
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| Submission date |
Apr 05, 2023 |
| Last update date |
Jul 11, 2023 |
| Contact name |
Babett Steglich |
| Organization name |
Universitätsklinikum Hamburg-Eppendorf
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| Street address |
Martinistrasse 52
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| City |
Hamburg |
| ZIP/Postal code |
20246 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE229087 |
Synchronized response of CD4+ T cells to short-term dietary changes - CD4+ T cell RNA sequencing |
| GSE229089 |
Synchronized response of CD4+ T cells to short-term dietary changes leads to windows of mucosal and systemic immune depression |
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| Relations |
| BioSample |
SAMN34085994 |
| SRA |
SRX19888298 |
| 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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