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| Status |
Public on Mar 06, 2020 |
| Title |
Chromatin states and transcriptome of CD8+ T cells over the course of differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The goal of this study is to analyze the contribution of transposable elements (TEs) tocis-regulation in CD8+ T cells. Using a combination of NGS techniques we show that specific subfamilies of TEs are enriched, and distributed in a lineage-specific fashion in core and boundary domains of CD8+T cell enhancers.This study represents the first detailed analysis of the topology and the enhancer domain-associated putative functions of distinct TE types.
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| Overall design |
ATAC-Seq and ChIP-Seq for H3K4me3 (in replicates), and total RNA-seq (in replicates or triplicates) performed in CD8+ T cells, naive (D0) and activated in vitro during one day (D1) and three days (D3).
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| Contributor(s) |
Zueva E, YE M, Goudot C, Amigorena S |
| Citation(s) |
32193341 |
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| Submission date |
Dec 16, 2019 |
| Last update date |
Apr 20, 2020 |
| Contact name |
Mengliang YE |
| E-mail(s) |
mengliang.ye@curie.fr
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| Organization name |
Institut Curie
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| Street address |
26 Rue d'ULM
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| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (23)
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| GSM4221531 |
ATACseq, D1, Replicate 2 |
| GSM4221532 |
ATACseq, D3, Replicate 1 |
| GSM4221533 |
ATACseq, D3, Replicate 2 |
| GSM4221534 |
H3K4me3 ChIPseq, D0, Replicate 1 |
| GSM4221535 |
H3K4me3 ChIPseq, D0, Replicate 2 |
| GSM4221536 |
Input DNA,D0, Replicate 1 |
| GSM4221537 |
Input DNA,D0, Replicate 2 |
| GSM4221538 |
H3K4me3 ChIPseq, D3, Replicate 1 |
| GSM4221539 |
H3K4me3 ChIPseq, D3, Replicate 2 |
| GSM4221540 |
Input DNA,D3, Replicate 1 |
| GSM4221541 |
Input DNA,D3, Replicate 2 |
| GSM4221542 |
RNAseq, D0, Replicate 1 |
| GSM4221543 |
RNAseq, D0, Replicate 2 |
| GSM4221544 |
RNAseq, D0, Replicate 3 |
| GSM4221545 |
RNAseq, D0, Replicate 4 |
| GSM4221546 |
RNAseq, D1, Replicate 1 |
| GSM4221547 |
RNAseq, D1, Replicate 2 |
| GSM4221548 |
RNAseq, D1, Replicate 3 |
| GSM4221549 |
RNAseq, D3, Replicate 1 |
| GSM4221550 |
RNAseq, D3, Replicate 2 |
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| Relations |
| BioProject |
PRJNA595982 |
| SRA |
SRP237808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142151_RAW.tar |
2.5 Gb |
(http)(custom) |
TAR (of BW, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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