H1 hESC lentiMPRA neural-induction time course
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural InductionA 171-bp lentiMPRA library containing 2,664 candidate, control, and scrambled regulatory elements, with 90 designed 15-bp barcodes per element, was integrated into H1 human embryonic stem cells. Nuclear RNA and genomic DNA barcode counts were collected from three replicate cultures at 0, 3, 6, 12, 24, 48, and 72 hours after neural induction to quantify temporal reporter activity.
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Perturbation & assay details
Dual-SMAD neural induction with 200 ng/mL Noggin and 10 uM SB431542; sampled at 0, 3, 6, 12, 24, 48, and 72 hours post-induction
Array-synthesized 171-bp sequences were cloned upstream of a minimal promoter and EGFP reporter in a lentiviral vector, with 90 distinct 15-bp barcodes per element split across two array halves. The library was packaged into lentivirus, infected at approximately 5-8 integrations per cell, allowed to integrate for 3 days, and assayed by sequencing barcode abundance in nuclear RNA and genomic DNA. The three reported replicates comprise two biological replicates, with one biological replicate split into two technical replicates.
Processed data
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Visible columns (83 of 83)
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 83 definitions
- element_id
- Stable element identifier combining library class, design sequence number, and the FASTA region label
- element_class
- Library class: candidate, control, or scrambled negative control
- design_seq_number
- Sequence number used in the deposited library design
- region
- Region label from the plasmid-library FASTA; ordinary entries are hg19 coordinates and synthetic controls use control labels
- chromosome
- Chromosome or synthetic control label parsed from region
- start
- Start coordinate parsed from region
- end
- End coordinate parsed from region
- length_bp
- Length of the extracted regulatory sequence in base pairs
- sequence_171bp
- 171-bp regulatory sequence extracted from the Array1 oligo design
- array_sequence_discordant
- Whether the Array1 and Array2 FASTA records contain different 171-bp sequences for this element
- designed_barcode_count
- Number of designed barcode records associated with the element
- design_criterion
- Table S2 criterion used to select or classify the sequence
- design_additional_information
- Additional sequence-selection or control information from Table S2
- design_references
- References supplied for the design/control entry in Table S2
- closest_gene
- Closest gene reported for temporal MPRA elements in Table S4
- mpra_temporal_cluster
- MPRA temporal activity cluster from Table S4
- h3k27ac_temporal_cluster
- H3K27ac temporal cluster associated with the element in Table S4
- atac_temporal_cluster
- ATAC-seq temporal cluster associated with the element in Table S4
- rna_temporal_cluster_closest_gene
- RNA-seq temporal cluster of the closest gene from Table S4
- rna_temporal_cluster_correlated_gene
- RNA-seq temporal cluster of the most correlated gene among the four closest genes from Table S4
- published_ratio_0h
- Published Table S2 MPRA RNA/DNA activity ratio at 0 hours
- mean_valid_barcodes_0h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 0 hours
- min_valid_barcodes_0h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 0 hours
- dna_cpm_0h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 0 hours
- rna_cpm_0h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 0 hours
- activity_ratio_0h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 0 hours
- log2_activity_0h
- Base-2 logarithm of activity_ratio_0h
- activity_sd_0h
- Sample standard deviation of the three replicate-level normalized activity ratios at 0 hours
- n_replicates_0h
- Number of replicates contributing to the 0-hour summary
- published_ratio_3h
- Published Table S2 MPRA RNA/DNA activity ratio at 3 hours
- mean_valid_barcodes_3h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 3 hours
- min_valid_barcodes_3h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 3 hours
- dna_cpm_3h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 3 hours
- rna_cpm_3h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 3 hours
- activity_ratio_3h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 3 hours
- log2_activity_3h
- Base-2 logarithm of activity_ratio_3h
- activity_sd_3h
- Sample standard deviation of the three replicate-level normalized activity ratios at 3 hours
- n_replicates_3h
- Number of replicates contributing to the 3-hour summary
- published_ratio_6h
- Published Table S2 MPRA RNA/DNA activity ratio at 6 hours
- mean_valid_barcodes_6h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 6 hours
- min_valid_barcodes_6h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 6 hours
- dna_cpm_6h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 6 hours
- rna_cpm_6h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 6 hours
- activity_ratio_6h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 6 hours
- log2_activity_6h
- Base-2 logarithm of activity_ratio_6h
- activity_sd_6h
- Sample standard deviation of the three replicate-level normalized activity ratios at 6 hours
- n_replicates_6h
- Number of replicates contributing to the 6-hour summary
- published_ratio_12h
- Published Table S2 MPRA RNA/DNA activity ratio at 12 hours
- mean_valid_barcodes_12h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 12 hours
- min_valid_barcodes_12h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 12 hours
- dna_cpm_12h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 12 hours
- rna_cpm_12h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 12 hours
- activity_ratio_12h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 12 hours
- log2_activity_12h
- Base-2 logarithm of activity_ratio_12h
- activity_sd_12h
- Sample standard deviation of the three replicate-level normalized activity ratios at 12 hours
- n_replicates_12h
- Number of replicates contributing to the 12-hour summary
- published_ratio_24h
- Published Table S2 MPRA RNA/DNA activity ratio at 24 hours
- mean_valid_barcodes_24h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 24 hours
- min_valid_barcodes_24h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 24 hours
- dna_cpm_24h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 24 hours
- rna_cpm_24h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 24 hours
- activity_ratio_24h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 24 hours
- log2_activity_24h
- Base-2 logarithm of activity_ratio_24h
- activity_sd_24h
- Sample standard deviation of the three replicate-level normalized activity ratios at 24 hours
- n_replicates_24h
- Number of replicates contributing to the 24-hour summary
- published_ratio_48h
- Published Table S2 MPRA RNA/DNA activity ratio at 48 hours
- mean_valid_barcodes_48h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 48 hours
- min_valid_barcodes_48h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 48 hours
- dna_cpm_48h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 48 hours
- rna_cpm_48h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 48 hours
- activity_ratio_48h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 48 hours
- log2_activity_48h
- Base-2 logarithm of activity_ratio_48h
- activity_sd_48h
- Sample standard deviation of the three replicate-level normalized activity ratios at 48 hours
- n_replicates_48h
- Number of replicates contributing to the 48-hour summary
- published_ratio_72h
- Published Table S2 MPRA RNA/DNA activity ratio at 72 hours
- mean_valid_barcodes_72h
- Mean number of shared, correctly designed RNA/DNA barcodes across the three replicates at 72 hours
- min_valid_barcodes_72h
- Minimum number of shared, correctly designed RNA/DNA barcodes across the three replicates at 72 hours
- dna_cpm_72h
- Mean element-level DNA barcode count normalized to counts per million across replicates at 72 hours
- rna_cpm_72h
- Mean element-level RNA barcode count normalized to counts per million across replicates at 72 hours
- activity_ratio_72h
- Mean replicate-level median-normalized RNA/DNA activity ratio recomputed from the deposited counts at 72 hours
- log2_activity_72h
- Base-2 logarithm of activity_ratio_72h
- activity_sd_72h
- Sample standard deviation of the three replicate-level normalized activity ratios at 72 hours
- n_replicates_72h
- Number of replicates contributing to the 72-hour summary
Quality control
The paper retained correctly sized 15-bp barcodes matched to the designed library and observed at least once in both RNA and DNA from the same sample. For this package, barcode counts were intersected within each of the 21 time-point/replicate pairs, aggregated by element, scaled to counts per million, stabilized with a pseudocount of 1, converted to RNA/DNA ratios, median-normalized within each sample, and averaged over the three replicates. An additional package-level filter required at least 5 shared, correctly designed barcodes for every element in every replicate and time point; all 2,664 elements passed and none were removed.
Curation notes
The paper's data availability statement names the broader GEO superseries GSE115046, while the dedicated MPRA submission is GSE115042. Ordinary Table S2 coordinates use a BED-like 0-based start and were joined to the FASTA labels after adding one to the start; the table retains the exact FASTA region label. One construct has discordant 171-bp Array1 and Array2 sequences; sequence_171bp stores Array1 and array_sequence_discordant marks it. Scrambled controls were assigned to Table S2 scram_seq_1 through scram_seq_200 in deposited FASTA order because their Table S2 labels do not contain genomic coordinates. The downloaded Table S4 contains 1,431 rows with temporal MPRA annotations, whereas the manuscript text also reports 1,547 temporal CRSs; temporal annotation fields are left blank when no Table S4 row is available.