MYBPC2-promoter integrated MPRA in differentiated LHCN-M2 myotubes
Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regionsThis table summarizes the processed LHCN-M2 barcode/count data deposited under GSE247455 for the muscle-context arm of the study. Because the deposited barcode dictionary exposes only the MYBPC2 promoter and six element-group names rather than variant-level oligo identities, the table honestly reports six group-level activity summaries across four RNA and four gDNA replicates.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
No exogenous treatment; lentiviral infection followed by in vitro differentiation to myotubes
The MPRA block was ported to a lentiviral transfer vector and delivered to LHCN-M2 human skeletal myoblasts at approximately MOI 10, followed by one week of passaging and one week of differentiation. The deposited GSE247455 dictionary uses 20-bp barcodes and the count table contains four RNA and four gDNA replicates for a MYBPC2-promoter library. Counts were normalized to TPM and summarized as log2(RNA/DNA) activity.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (29 of 29)
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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 · 29 definitions
- fragment_id
- Stable package identifier combining the deposited promoter and element-group label.
- element_group
- Element-group label exactly as supplied by the GSE247455 barcode dictionary.
- element_class
- Package classification: negative_control or curated_library_group.
- promoter
- Promoter label supplied by the GSE247455 barcode dictionary; all deposited records are MYBPC2.
- n_retained_barcodes
- Number of exact-match barcodes passing the total RNA and total gDNA count thresholds for this group.
- rna_count_rep1
- Aggregated retained-barcode RNA count for replicate 1.
- rna_count_rep2
- Aggregated retained-barcode RNA count for replicate 2.
- rna_count_rep3
- Aggregated retained-barcode RNA count for replicate 3.
- rna_count_rep4
- Aggregated retained-barcode RNA count for replicate 4.
- dna_count_rep1
- Aggregated retained-barcode gDNA/input count for replicate 1.
- dna_count_rep2
- Aggregated retained-barcode gDNA/input count for replicate 2.
- dna_count_rep3
- Aggregated retained-barcode gDNA/input count for replicate 3.
- dna_count_rep4
- Aggregated retained-barcode gDNA/input count for replicate 4.
- rna_tpm_rep1
- RNA count for replicate 1 normalized to transcripts per million across retained matched counts.
- rna_tpm_rep2
- RNA count for replicate 2 normalized to transcripts per million across retained matched counts.
- rna_tpm_rep3
- RNA count for replicate 3 normalized to transcripts per million across retained matched counts.
- rna_tpm_rep4
- RNA count for replicate 4 normalized to transcripts per million across retained matched counts.
- dna_tpm_rep1
- gDNA/input count for replicate 1 normalized to transcripts-per-million-style library units.
- dna_tpm_rep2
- gDNA/input count for replicate 2 normalized to transcripts-per-million-style library units.
- dna_tpm_rep3
- gDNA/input count for replicate 3 normalized to transcripts-per-million-style library units.
- dna_tpm_rep4
- gDNA/input count for replicate 4 normalized to transcripts-per-million-style library units.
- log2_rna_dna_rep1
- Log2 RNA TPM divided by DNA TPM for replicate 1.
- log2_rna_dna_rep2
- Log2 RNA TPM divided by DNA TPM for replicate 2.
- log2_rna_dna_rep3
- Log2 RNA TPM divided by DNA TPM for replicate 3.
- log2_rna_dna_rep4
- Log2 RNA TPM divided by DNA TPM for replicate 4.
- activity_log2_mean
- Mean finite log2 RNA/DNA activity across the four replicates.
- activity_log2_sd
- Sample standard deviation of finite log2 RNA/DNA activity across the four replicates.
- n_valid_replicates
- Number of finite log2 RNA/DNA replicate values used in the summary.
- quality_control_pass
- Whether the deposited group passed barcode matching, count-threshold, and finite-activity QC.
Quality control
GEO describes retaining barcodes with at least five RNA and five gDNA counts; this package applies that rule to totals across the four RNA and four gDNA replicates, requires an exact dictionary/count barcode match, aggregates retained barcodes by the deposited element-group and promoter labels, and emits only groups with at least one finite replicate activity value. 1,240 barcodes passed among 1,579 matched count rows, producing six of six QC-passing groups. TPM denominators are computed across retained matched barcodes for each sample.
Curation notes
GSE247455 is explicitly cited by the paper as the LHCN-M2 data accession, but its current deposited supplemental files contain only a MYBPC2-promoter library with six group labels (curated_set_014, curated_set_164, and four negative-control groups) and four biological replicates. They do not expose variant-level identities or separate SCP1/INS count files. The table therefore should be used as a deposited muscle-context group summary, not as a complete three-promoter reconstruction of Figure 4G.