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| Status |
Public on May 14, 2019 |
| Title |
d9_Acetate_Input |
| Sample type |
SRA |
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| Source name |
d9 1mM_Glucose + 5mM Acetate
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleens and peripheral lymph nodes
cell type: CD8 T cells
days of glucose restriction: 5
genotype: OT-I
chip antibody: none (input)
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| Treatment protocol |
After 3 days, cells were switched to 1 mM glucose for 1 or 5 days (referred to as d5 and d9 respectively). 1 day before analysis, cells maintained in 1 mM glucose were treated with or without 5 mM sodium acetate (Sigma). Starting from day 2, and every day, cultured cells were harvested, washed, counted and plated at a concentration of 10^6 cells/ml in fresh medium with rhIL-2.
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| Growth protocol |
OVA peptide-specific T cells were isolated from spleens and peripheral lymph nodes of OT-I transgenic mice and activated with the ovalbumin peptide SIINFEKL (OVA257-264, 100 ng/ml, New England Peptide). T cells were cultured in RPMI 1640, added with 10% heat-inactivated fetal bovine serum (Gibco, lot n. 1640960), glutamine (4 mM), penicillin/streptomycin (1%), β-mercaptoethanol (55 μM) and glucose (concentrations indicated in the text). Cells were grown at 37° C, in 5% CO2, atmospheric O2, in a humidified incubator. Briefly, cells were activated on day 0 with OVA257-264, with rhIL-2 (100 U/ml, Peprotech) in medium containing 25 mM glucose.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed cell pellets (1% paraformaldehyde, 10 minutes, RT) were processed for multiplex RELACS (Arrigoni et al., 2018) and sequenced by the staff at the Deep-sequencing Facility at the Max-Planck-Institute for Immunobiology and Epigenetics.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
d9 1mM_Glucose + 5mM Acetate
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| Data processing |
Sequenced samples were trimmed with Trimmomatic (Bolger et al., 2014)
Mapped using Bowtie2 (Langmead and Salzberg, 2012)
Replicate mapped files merged with SAM tools (Li et al., 2009).
Heatmaps and coverage files were generated with deepTools (Ramírez et al., 2016).
Genome_build: GRCm38
Supplementary_files_format_and_content: Coverage files in bigwig format
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| Submission date |
Mar 20, 2019 |
| Last update date |
Feb 17, 2020 |
| Contact name |
Immunometabolism Department |
| E-mail(s) |
jcurti29@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Department |
Immunometabolism
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| Street address |
1650 Orleans Street
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE128593 |
Acetate promotes T cell effector function during glucose restriction [ChIP-seq] |
| GSE128594 |
Acetate promotes T cell effector function during glucose restriction |
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| Relations |
| BioSample |
SAMN11177593 |
| SRA |
SRX5547270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3680735_d9_acetate_Input.bw |
15.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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