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Sample GSM3680734 Query DataSets for GSM3680734
Status Public on May 14, 2019
Title d9_1mM_Input
Sample type SRA
 
Source name d9 1mM_Glucose
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)
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.
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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Description d9 1mM_Glucose
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
 
Submission date Mar 20, 2019
Last update date Feb 17, 2020
Contact name Immunometabolism Department
E-mail(s) jcurti29@jhmi.edu
Organization name Johns Hopkins University
Department Immunometabolism
Street address 1650 Orleans Street
City Baltimore
State/province Maryland
ZIP/Postal code 21287
Country USA
 
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
Relations
BioSample SAMN11177594
SRA SRX5547269

Supplementary file Size Download File type/resource
GSM3680734_d9_1mM_Input.bw 14.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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