#### Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/)
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**Publication:**<b><spanstyle="color:#1f8be0">TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation</span></b>
**Why is interesting?**
- Chip-seq: 2 acetylation marks (H3K9ac, H3K27), other franscription factor (TFIIIC, BDP1, POL3) in different cells
- Hi-C: multiple replicates
- mRNA: in different time points
- ATAC-seq
- Serum starvation/basal conditions en cells
- In Homo-sapiens
- Problem: low number of histone marks, not hESC cells
**Publication:**<b><spanstyle="color:#1f8be0">Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries</span></b>
**Why is interesting?**
- transgenic H9 hESC line expressing a H2B-GFP fusion protein (if only is transgenic for GFP mabye it is possible repeat our results with H9 chip-seqs in Encode repository instead of H1)
- HiC, ATAC-seq, RNA-seq, and ChIP-seq for H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K9me3 and CTCF for every time point, each with two biological replicates.
- six critical time points during differentiation: human embryonic stem cells (hESC) (Day 0), hESC mesodermal cells (Day 2), hESC-cardiac mesodermal cells (Day 5), hESC-cardiac progenitor cell (Day 7), hESC-primitive cardiomyocytes (Day 15) and hESC-ventricular cardiomyocytes (Day 80)
- In Homo-sapiens
- Problem: no nutrient state, low number of histone marks
**Publication:**<b><spanstyle="color:#1f8be0">Transcriptional and epigenetic profiling of nutrient-deprived cells to identify novel regulators of autophagy</span></b>
**Why is interesting?**
- 3 epigenetic marks (H3K4me3, H3K27ac, and H3K56ac)
- Nutrient (amino acid and serum) starvation/normal condition
- Related with macroautophagy: lysosomal degradation pathway critical for maintaining cellular homeostasis and viability, and is predominantly regarded as a rapid and dynamic cytoplasmic process
- Comparation of starving state between
- In Homo-sapiens
- Problem: no nutrient state, no time points, transcription data, not hESC cells
**Publication:**<b><spanstyle="color:#1f8be0">Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation</span></b>
**Why is interesting?**
- 3 epigenetic marks (H3K4me1, H3K27ac, and H3K4me3) and a transcription factor (CTCF) in two cell lines (U2OS, RPE1) in different phases of cell cycle.
- RNA-seq and Hi-C in different time points.
- In Homo-sapiens.
- Problem: no nutrient state, low number of histone marks, not hESC cells
**Publication:**<b><spanstyle="color:#1f8be0">Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency</span></b>
**Why is interesting?**
- 2 epigenetic marks (H3K4me1, H3K27ac) and CTCF transcription factor
- Mapped epigenetic differences in undifferentiated ES cell (hESC) and differentiated ES cell (denoted as DFC) genomes
- ChIP for promoter and enhancer histone modifications were conducted relative to input DNA in hESCs and hESCs treated with BMP4 (bone morphogenetic protein)
- In Homo-sapiens.
- Problem: no nutrient state, Hi-C, transcription data
