Experiment / E4YAMJ2WXIntegrated lentiMPRA

Three-stage integrated lentiMPRA time course in human iPSCs and forebrain organoids

Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids

A 270-bp enhancer library was integrated by lentivirus into three independent culture replicates and assayed at the iPSC stage and after terminal differentiation to TD0 and TD30 forebrain organoids. The table retains the authors' QC-passed enhancer and control records and reports MPRAnalyze activity, background p-values, significance calls, linked-gene annotations, predicted TFs, and external ATAC-seq overlaps.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: UNMAPPED:human_iPSC_and_forebrain_organoid_timecourse
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Candidate 270-bp regulatory cores, 122 positive controls, and shuffled negative controls were synthesized with adapters, cloned upstream of a minimal promoter and GFP in a pLS-SceI lentiMPRA vector, and tagged with 15-bp random barcodes. The library was delivered at an average MOI of 4-5; DNA and RNA barcode sequencing was processed with MPRAflow and MPRAnalyze. The nine activity columns represent 11251, ACE1815 technical replicate ACE_a, and ACE1815 technical replicate ACE_b at iPSC, TD0, and TD30.

Processed data

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Visible columns (65 of 65)

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Column dictionary · 65 definitions

element_id: Element identifier from Supplementary Table S1: genomic interval for tested regions or NEGCTRL/POSCTRL identifier.
element_label: Source label distinguishing MPRA-tested enhancers, positive controls, and negative controls.
chromosome: Chromosome parsed from element_id for genomic elements; blank for controls.
start: Start coordinate parsed from element_id; blank for controls.
end: End coordinate parsed from element_id; blank for controls.
tested_length_bp: Length computed as end minus start for genomic elements; 270 bp for each coordinate-tested element and blank for controls.
activity_11251_iPSC: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for culture 11251 at the iPSC stage.
activity_11251_TD0: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for culture 11251 at TD0.
activity_11251_TD30: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for culture 11251 at TD30.
activity_ACE_a_iPSC: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for ACE1815 technical replicate ACE_a at the iPSC stage.
activity_ACE_a_TD0: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for ACE1815 technical replicate ACE_a at TD0.
activity_ACE_a_TD30: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for ACE1815 technical replicate ACE_a at TD30.
activity_ACE_b_iPSC: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for ACE1815 technical replicate ACE_b at the iPSC stage.
activity_ACE_b_TD0: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for ACE1815 technical replicate ACE_b at TD0.
activity_ACE_b_TD30: Authors' MPRAnalyze-normalized RNA/DNA enhancer activity for ACE1815 technical replicate ACE_b at TD30.
pvalue_11251_iPSC: Authors' p-value for activity above the negative-control background for culture 11251 at iPSC.
pvalue_11251_TD0: Authors' p-value for activity above the negative-control background for culture 11251 at TD0.
pvalue_11251_TD30: Authors' p-value for activity above the negative-control background for culture 11251 at TD30.
pvalue_ACE_a_iPSC: Authors' p-value for activity above the negative-control background for ACE_a at iPSC.
pvalue_ACE_a_TD0: Authors' p-value for activity above the negative-control background for ACE_a at TD0.
pvalue_ACE_a_TD30: Authors' p-value for activity above the negative-control background for ACE_a at TD30.
pvalue_ACE_b_iPSC: Authors' p-value for activity above the negative-control background for ACE_b at iPSC.
pvalue_ACE_b_TD0: Authors' p-value for activity above the negative-control background for ACE_b at TD0.
pvalue_ACE_b_TD30: Authors' p-value for activity above the negative-control background for ACE_b at TD30.
active_11251_iPSC: Authors' sig.recal flag for 11251 at iPSC: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_11251_TD0: Authors' sig.recal flag for 11251 at TD0: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_11251_TD30: Authors' sig.recal flag for 11251 at TD30: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_ACE_a_iPSC: Authors' sig.recal flag for ACE_a at iPSC: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_ACE_a_TD0: Authors' sig.recal flag for ACE_a at TD0: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_ACE_a_TD30: Authors' sig.recal flag for ACE_a at TD30: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_ACE_b_iPSC: Authors' sig.recal flag for ACE_b at iPSC: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_ACE_b_TD0: Authors' sig.recal flag for ACE_b at TD0: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_ACE_b_TD30: Authors' sig.recal flag for ACE_b at TD30: 1 indicates significant activity after Bonferroni correction, 0 otherwise.
active_replicate_count_iPSC: Derived count of the three cultures with an author active flag at iPSC.
active_replicate_count_TD0: Derived count of the three cultures with an author active flag at TD0.
active_replicate_count_TD30: Derived count of the three cultures with an author active flag at TD30.
n_active_samples: Authors' number of active sample/time-point measurements out of nine.
active_any: Authors' overall active flag: 1 if active in at least one of the nine sample/time-point measurements, 0 otherwise.
max_activity_iPSC: Maximum activity across the three cultures at iPSC from Supplementary Table S3.
max_activity_TD0: Maximum activity across the three cultures at TD0 from Supplementary Table S3.
max_activity_TD30: Maximum activity across the three cultures at TD30 from Supplementary Table S3.
predicted_tf_binding_factors: Dollar-delimited transcription factors predicted by FIMO/JASPAR to bind the tested sequence.
linked_genes_confident_set1: Gene identifiers in the Amiri et al. confident_set1 enhancer-gene links.
confident_set1_deg_genes: confident_set1 linked genes that were differentially expressed for the indicated transition.
confident_set1_deg_logfc_td0_vs_iPSC: confident_set1 DEG log fold-change for TD0 versus iPSC.
confident_set1_deg_pvalue_td0_vs_iPSC: confident_set1 DEG p-value for TD0 versus iPSC.
confident_set1_deg_logfc_td30_vs_iPSC: confident_set1 DEG log fold-change for TD30 versus iPSC.
confident_set1_deg_pvalue_td30_vs_iPSC: confident_set1 DEG p-value for TD30 versus iPSC.
linked_genes_confident_set2: Gene identifiers in the Amiri et al. confident_set2 enhancer-gene links.
confident_set2_deg_genes: confident_set2 linked genes that were differentially expressed for the indicated transition.
confident_set2_deg_logfc_td0_vs_iPSC: confident_set2 DEG log fold-change for TD0 versus iPSC.
confident_set2_deg_pvalue_td0_vs_iPSC: confident_set2 DEG p-value for TD0 versus iPSC.
confident_set2_deg_logfc_td30_vs_iPSC: confident_set2 DEG log fold-change for TD30 versus iPSC.
confident_set2_deg_pvalue_td30_vs_iPSC: confident_set2 DEG p-value for TD30 versus iPSC.
linked_genes_proximity: Gene identifiers linked to the enhancer by proximity in the source annotation.
proximity_deg_genes: Proximity-linked genes that were differentially expressed for the indicated transition.
proximity_deg_logfc_td0_vs_iPSC: Proximity-linked DEG log fold-change for TD0 versus iPSC.
proximity_deg_pvalue_td0_vs_iPSC: Proximity-linked DEG p-value for TD0 versus iPSC.
proximity_deg_logfc_td30_vs_iPSC: Proximity-linked DEG log fold-change for TD30 versus iPSC.
proximity_deg_pvalue_td30_vs_iPSC: Proximity-linked DEG p-value for TD30 versus iPSC.
overlap_atac_fleck: 1/0 indicator for overlap with the Fleck scATAC-seq dataset.
overlap_atac_trevino_bulk: 1/0 indicator for overlap with Trevino bulk ATAC-seq peaks.
overlap_atac_ziffra_fetal_brain: 1/0 indicator for overlap with Ziffra fetal-brain scATAC-seq peaks.
overlap_atac_ziffra_organoids: 1/0 indicator for overlap with Ziffra organoid scATAC-seq peaks.
qc_pass: TRUE for every row because it was included in the authors' QC-passed Supplementary Table S1 subset; failed elements are omitted.

Quality control

Used the authors' Supplementary Table S1 sheet fittedneg.all.withalpha.withsig, which contains 6,892 of the 7,261 original library sequences after the reported stringent QC (94.9%); DNA sequencing recovered 6,907 of 7,261 sequences. Every retained S1 row has at least one nonempty activity measurement, so no additional element-level rows were removed. Sample-specific missing measurements remain blank. The active flags are the authors' significance calls based on activity above the negative-control Gaussian background with p < 0.05 after Bonferroni correction.

Curation notes

This is one time-course lentiMPRA experiment with nine reported culture/stage measurements, not nine independent libraries. Supplementary Table S1 contains 6,892 retained records: 6,635 MPRA-tested enhancers, 122 positive controls, and 135 negative controls; the original library contained 7,261 sequences and the paper reports 6,907 recovered by DNA sequencing and 94.9% passing stringent QC. The processed table retains all S1 rows with at least one activity value, joins the two S3 developmental gene-expression sheets on element_id, and joins S2 external ATAC overlap annotations for the 6,757 coordinate elements; control elements therefore have blank genomic and external-overlap fields. ACE_a and ACE_b are technical replicates of the ACE1815 iPSC line, while 11251 is a second donor line. The experiment mixes iPSC and forebrain-organoid stages, so the biosample is recorded as an unmapped composite term. GRCh38 is assigned from the paper's GRCh38 processing context and the GENCODE V25/Amiri coordinate source; the exact assembly is not repeated in the S1 workbook. The public PsychENCODE source folder syn51296303 was found, but its file downloads require access requirement 5612415; no raw sequencing reads were included, consistent with the package instructions.

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