Phenotype | Cell Types/Tissues | Cell Types/Tissues additional information | Chip-Seq Source for enhancer annotation | Enhancer annotation (based on Chip-Seq), Main Procedure | RNA-Seq Source | Gene Expression quantification main procedure | HiC – TAD maps Source | TAD maps main procedure | ||
Cardiovascular | Day 5 | Day 5 cardiac mesodermal cells, from 80 days ESC differentiation towards ventricular cardiomyocytes For + info: https://www.nature.com/articles/s41588-019-0479-7 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called after reads mapping with Bowtie2 with Macs2) | FPKMs directly obtained from source | TAD map generated upon processing Day 5 cardiomyocyte differentiation HiC data. TADs were called with the usage of the tool DomainCaller by considering the 50kb contact matrices in the .hic files | |||||
Day 7 | Day 7 cardiac progenitors, from 80 days ESC differentiation towards ventricular cardiomyocytes For + info: https://www.nature.com/articles/s41588-019-0479-7 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called after reads mapping with Bowtie2 with Macs2) | FPKMs directly obtained from source | TAD map generated upon processing Day 7 cardiomyocyte differentiation HiC data. TADs were called with the usage of the tool DomainCaller by considering the 50kb contact matrices in the .hic files | ||||||
Day 15 | Day 15 primitive cardiomyocytes, from 80 days ESC differentiation towards ventricular cardiomyocytes For + info: https://www.nature.com/articles/s41588-019-0479-7 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called after reads mapping with Bowtie2 with Macs2) | FPKMs directly obtained from source | TAD map generated upon processing Day 15 cardiomyocyte differentiation HiC data. TADs were called with the usage of the tool DomainCaller by considering the 50kb contact matrices in the .hic files | ||||||
Day 80 | Day 80 ventricular cardiomiocytes, from 80 days ESC differentiation towards ventricular cardiomyocytes For + info: https://www.nature.com/articles/s41588-019-0479-7 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called after reads mapping with Bowtie2 with Macs2) | FPKMs directly obtained from source | TAD map generated upon processing Day 80 cardiomyocyte differentiation HiC data. TADs were called with the usage of the tool DomainCaller by considering the 50kb contact matrices in the .hic files | ||||||
Head-Neck | Neural Crest Early | Neural Crest Data of hNCC differentiation This NC data corresponds with an early and heterogeneous stage of NC differentiation For +info: https://pubmed.ncbi.nlm.nih.gov/22981823/ | p300 peak, intersecting H3K27ac peak, with distance > 10Kb to protein coding TSS (Peaks were called upon reads mapping with Bowtie2 with Macs2) | FPKMs obtained upon reads mapping with Tophat2 and gene expression quantification with Cufflinks | 3D genome browser: http://3dgenome.fsm.northwestern.edu/ TAD maps: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ESC TAD map directly obtained from: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ||||
Neural Crest Late | Neural Crest Data of hNCC differentiation P4 differentiation stage, it corresponds with a later and more homogeneous stage of NC differentation in comparison with Neural Crest Early For +info: https://pubmed.ncbi.nlm.nih.gov/26365491/ | p300 peak, intersecting H3K27ac peak, with distance > 10Kb to protein coding TSS (Peaks were called upon reads mapping with Bowtie2 with Macs2) | FPKMs obtained upon reads mapping with Tophat2 and gene expression quantification with Cufflinks | 3D genome browser: http://3dgenome.fsm.northwestern.edu/ TAD maps: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ESC TAD map directly obtained from: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | |||||
PalateCS20 | Embryonic Palate Carnagie Stage 20 For +info: https://pubmed.ncbi.nlm.nih.gov/29719267/ | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called with Macs2 using the provided alignment files (tagAlign)) | To obtain the FPKMs, first, the bedfiles containing the reads mapping coordinates (.unique.bed12) for Palate1 sample were converted into bam files with bedToBam tool. Next FPKMs were computed with Cufflinks. | 3D genome browser: http://3dgenome.fsm.northwestern.edu/ TAD maps: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ESC TAD map directly obtained from: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | |||||
Limbs | EmbryonicLimb1 | Embryonic Lower Limb data of entire limb buds, Carnegie Stages 14-19 For +info: https://www.nature.com/articles/s41467-020-17305-2 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called after reads mapping with Bowtie2 with Macs2) | https://elifesciences.org/articles/15657
| To obtain the FPKMs, first, the bedfiles containing the reads mapping coordinates (.unique.bed12) for Lower Limb samples were converted into bam files with bedToBam tool. Next FPKMs were computed with Cufflinks. | 3D genome browser: http://3dgenome.fsm.northwestern.edu/ TAD maps: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ESC TAD map directly obtained from: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | |||
EmbryonicLimb2 | Embryonic Upper Limb data of entire limb buds, Carnegie Stages 14-19 For +info: https://www.nature.com/articles/s41467-020-17305-2 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were called after reads mapping with Bowtie2 with Macs2) | https://elifesciences.org/articles/15657
| To obtain the FPKMs, first, the bedfiles containing the reads mapping coordinates (.unique.bed12) for Upper Limb samples were converted into bam files with bedToBam tool. Next FPKMs were computed with Cufflinks. | 3D genome browser: http://3dgenome.fsm.northwestern.edu/ TAD maps: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ESC TAD map directly obtained from: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip | ||||
Neurodevelopmental | PfcGw15 | Brain prefrontal cortex Gestation Week 15 For +info: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149268 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149268 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were directly obtained from source) | From database: https://www.brainspan.org/static/home
| Expression values obtained from file: summarized to genes file Given that gestational age is 2 weeks longer than conceptional age, post conception week 13 (pcw13) samples information was considered to match with chip-seq gestation week 15 data Expression value computed as the average of the pcw13 samples: VFC (ventrolateral prefrontal cortex), MFC[anterior (rostral) cingulate (medial prefrontal) cortex] and DFC(dorsolateral prefrontal cortex)
| Brain Prefrontal Cortex TAD map, generated from CO (prefrontal cortex) boundary map provided in the referenced source. The Excelfile containing the boundary maps can be found here: | |||
PfcGw18 | Brain prefrontal cortex Gestation Week 18 For +info: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149268 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149268 | H3K27ac peak with distance > 10Kb to protein coding TSS (Peaks were directly obtained from source) | From database: https://www.brainspan.org/static/home
| Expression values obtained from file: summarized to genes file Given that gestational age is 2 weeks longer than conceptional age, post conception week 16 (pcw16) samples information was considered to match with chip-seq gestation week 18 data Expression value computed as the average of the pcw16 samples: VFC (ventrolateral prefrontal cortex), MFC[anterior (rostral) cingulate (medial prefrontal) cortex] and DFC(dorsolateral prefrontal cortex)
| Brain Prefrontal Cortex TAD map, generated from CO (prefrontal cortex) boundary map provided in the referenced source. The Excelfile containing the boundary maps can be found here: | ||||
Vision-Eye | Retina | Retina (from Adults) For +info: https://pubmed.ncbi.nlm.nih.gov/32265282/ | Liftover of enhancer coordinates from hg38 to hg19, as provided by source (derived of ATAC peaks overlapping H3K27ac peaks) . In addition enhancers < 2.5kb from any protein coding TSS were discarded. | FPKMs obtained upon reads mapping with Hisat2 and gene expression quantification with Cufflinks | Retina TAD map obtained from source after liftovering coordinates from hg38 to hg19. Since no TADs for chrX were provided in the source, those from ESCs were considered as reference for chrX. | |||||
RPE | Retina Pigment Epithelium (from Adults) For +info: https://pubmed.ncbi.nlm.nih.gov/32265282/ | Liftover of enhancer coordinates from hg38 to hg19, as provided by source (derived of Dnase-seq peaks overlapping H3K27ac peaks) . In addition enhancers < 2.5kb from any protein coding TSS were discarded. | FPKMs obtained upon reads mapping with Hisat2 and gene expression quantification with Cufflinks | Retina TAD map obtained from source after liftovering coordinates from hg38 to hg19. Since no TADs for chrX were provided in the source, those from ESCs were considered as reference for chrX. | ||||||