Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The circadian transcriptome of mouse CD8+ T cells

ABSTRACT: To address the T cell-intrinsic rhythms underlying circadian variations of their functions, we analyzed gene expression rhythms in mouse CD8+ T cells. To do this, we entrained 8 weeks old male C57BL/6J mice for at least 2 weeks in a light:dark cycle, then put them in constant darkness (DD). Mice were sacrificed every 4 h over 48 h, on the second and third day in DD, and brachial, axillary and inguinal lymph nodes (LNs) were harvested. For each of the 12 time points, LNs from 6 mice were pooled. CD8+ T cells were isolated using EasySepTM mouse CD8a positive selection kit (STEMCELL technologies). The purity of the CD8 T cells was between 95.6 and 98.9% in all samples. Total RNA was extracted and RNA sequencing performed. Subsequent analysis aimed to identify transcript that show significant rhythmicity.

ORGANISM(S): Mus musculus

PROVIDER: GSE128995 | GEO | 2019/09/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of eyes from wild type and Bma knock-out mice after different lengths of time in a 12:12-hr LD cycle or in constant darkness to identify daily rhythms in ocular gene expression

Project description:To explore daily rhythms of ocular gene expression in adult mice we performed the following experiments: i) Mice were entrained to a 12:12-hr light-dark (LD) cycle for 3 weeks. Then mice were transferred to constant darkness (DD) or remained in LD and eyes were collected at four-hour intervals over a three-day period; ii) Bmal1-/- mice and wild-type littermates were entrained to a 12:12-hr LD cycle for 3 weeks and eyes were collected at four-hour intervals over a one-day period in LD.

2007-08-24 | E-TABM-285 | biostudies-arrayexpress

scRNA-seq of mouse thymocyte CD4 CD8 lineage choice and differentiation

Project description:CD4 and CD8 identify helper and cytotoxic T cell lineages, and serve as co-receptors for MHC-restricted TCR recognition. Despite decades of investigation, questions remain about how TCR specificity and co-receptor gene expression are matched during T cell repertoire selection. Here we address the order and logic of CD4/CD8 lineage choice and differentiation by scRNA-seq. Maturation, activation, and lineage specification emerged as principle components, in this order. Co-receptor gene expression uncovered waves of Cd4+Cd8a+, Cd4+Cd8a- and Cd4-Cd8a+ selection intermediates and revealed gene expression programs associated with each pattern, including TCR- and cytokine signaling genes, lineage markers and transcription factors. While in the unperturbed thymus early Cd4+Cd8a+ selection intermediates were followed first by CD4-like Cd4+Cd8a- and later by CD8-like Cd4-Cd8a+ selection intermediates, the order of co-receptor gene expression was not inherently fixed. These data provide a benchmark for models of CD4/CD8 lineage choice, and a rich resource for interrogating T cell differentiation.

2020-10-25 | GSE149207 | GEO

Transcriptional profiling of CD8 cells laser captured from skin biopsies at dermal-epidermal junction and at deeper dermal area near blood vessel during the healed phase of mucocutaneous HSV-2 reactivation

Project description:We aim to get a comprehensive analysis on gene expression of CD8a+ T-cells during the post healed phases of HSV-2 reactivation at different anatomic location (CD8a+ cells at dermal-epidermal junction versus CD8a+ cells in deeper dermal area near blood vessel). Our hypothesis is that JC_CD8 cells may function as a resident effector-like T-cells while BV_CD8 cells may be infiltrating cells from circulation. CD8 cells were immunofluorescently stained and laser captured from genital skin biopsies at dermal-epidermal junction at 2 and 8 weeks post healed (JC_2wks_CD8 and JC_8wks_CD8) and at deeper dermal area near blood vessel (BV_2wks_CD8 and BV_8wks_CD8); total RNA were purified from captured cells and cDNA were amplified from the total RNA using NuGEN pico kits

2013-04-11 | E-GEOD-44975 | biostudies-arrayexpress

Gene expression analysis of thymocyte subsets

Project description:Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells. We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets. Mouse thymocytes were divided into four subsets based on CD4, CD8a, and TCRb expression and purified by flw cytometry. FACS purified DN (CD4-CD8a-TCRb-), DP (CD4+CD8a+), CD4SP (CD4+CD8a-TCRbhi) and CD8SP (CD4-CD8a+TCRbhi) populations were lysed in Trizol, and provided to the Genomics Core Facility of the Memorial Sloan-Kettering Cancer Center (MSKCC) for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturer’s specifications for the Affymetrix MOE430v2 chip.

2011-08-09 | E-GEOD-31082 | biostudies-arrayexpress

Circadian rhythm in clock mutants

Project description:One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ul RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at –80 degrees C until use. This SuperSeries is composed of the SubSeries listed below.

2007-02-07 | GSE3751 | GEO

Circadian liver_wt and Clock mutants

Project description:One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ?l RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at –80?C until use. Keywords: time course

2007-02-08 | GSE3748 | GEO

Circadian liver_wt and Clock mutants

Project description:One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ?l RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at â80?C until use. Keywords: time course duplicates consisted of pools from independent mice

2010-06-11 | E-GEOD-3748 | biostudies-arrayexpress

Analysis of classical and migratory DC from the skin draining LNs of Flt3L treated mice and comparison to LPS treated DC from skin draining LN and peritoneal macrophages

Project description:Analysis of the differential transcriptome of DC derived from tissue vs. LN origin. The overall hypothesis is these data would reveal how migratory DC may be differently programmed from classical DC and might also suggest difference within migratory DC subsets relating to function. RNA obtained from migratory DC subsets and classical CD8a DC isolated by flow cytometry sorting from skin draining LNs of Flt3L treated mice or LPS treated mice

2014-08-01 | E-GEOD-53588 | biostudies-arrayexpress

Circadian rhythm in clock mutants

Project description:One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ul RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at â80 degrees C until use. Keywords: SuperSeries This reference Series links data in the following related Series: GSE3746 Circadian skeletal muscle_wt and Clock mutants GSE3748 Circadian liver_wt and Clock mutants

2010-06-12 | E-GEOD-3751 | biostudies-arrayexpress

Transcription profiling of mouse adrenal gland samples at multiple time points after release into DD to characterise rhythmic gene expression in the adrenal gland

Project description:This study was performed to characterize the rhythmic transcriptome of the murine adrenal gland with a focus on the corticosterone synthesis pathway. Experiment Overall Design: LD entrained male animals were released into DD and from the second day on whole adrenals were prepared from 12 time points at 4 hrs intervals.

2007-12-12 | E-GEOD-4238 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data