scAAV miniMPRA of mouse brain enhancer candidates at P7
Parallel functional testing identifies enhancers active in early postnatal mouse brainA 16-element mouse miniMPRA library containing putative enhancer candidates and negative controls was cloned into the 3′ UTR of an Hsp1a minimal-promoter EGFP reporter. The scAAV9(2YF) library was delivered to P0 mouse prefrontal cortex and assayed in P7 brain using four biological replicate RNA/DNA sequencing measurements.
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
Basal / Untreated
The miniMPRA tested 16 long (approximately 900 bp) mouse noncoding sequences selected as putative enhancers or negative controls. Candidate sequences were cloned into the reporter 3′ UTR, packaged in scAAV9(2YF), injected into P0 prefrontal cortex, and collected at P7; previral Maxiprep and four P7 RNA libraries were counted, normalized to library proportions, and summarized as RNA/DNA activity relative to Maxi_prop.
Processed data
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Column dictionary · 28 definitions
- element_id
- Unique miniMPRA tested-sequence label from the authors.
- negative_control
- Package label inferred from an element_id beginning with NEG.
- orthologous_star408_amplicon_number
- Amplicon number of the corresponding human ortholog in the STAR408 library, from the authors' ID field.
- chromosome_mm10
- Mouse chromosome for the tested element.
- start_mm10
- Start coordinate of the tested element on mm10.
- end_mm10
- End coordinate of the tested element on mm10.
- length_bp
- Inclusive coordinate span calculated as end_mm10 - start_mm10 + 1.
- previral_maxiprep_count
- Raw count in the previral Maxiprep library (Maxi).
- replicate_1_rna_count
- Raw RNA-library count for biological replicate S1.
- replicate_2_rna_count
- Raw RNA-library count for biological replicate S2.
- replicate_3_rna_count
- Raw RNA-library count for biological replicate S3.
- replicate_4_rna_count
- Raw RNA-library count for biological replicate S4.
- mean_rna_count
- Mean raw RNA count across S1-S4.
- sd_rna_count
- Standard deviation of raw RNA counts across S1-S4.
- previral_maxiprep_proportion
- Maxi count normalized to the total previral library count.
- replicate_1_rna_proportion
- S1 RNA count normalized to that library's total count.
- replicate_2_rna_proportion
- S2 RNA count normalized to that library's total count.
- replicate_3_rna_proportion
- S3 RNA count normalized to that library's total count.
- replicate_4_rna_proportion
- S4 RNA count normalized to that library's total count.
- mean_rna_proportion
- Mean normalized RNA proportion across S1-S4.
- sd_rna_proportion
- Standard deviation of normalized RNA proportions across S1-S4.
- replicate_1_activity
- RNA/DNA ratiometric activity for S1 relative to Maxi_prop.
- replicate_2_activity
- RNA/DNA ratiometric activity for S2 relative to Maxi_prop.
- replicate_3_activity
- RNA/DNA ratiometric activity for S3 relative to Maxi_prop.
- replicate_4_activity
- RNA/DNA ratiometric activity for S4 relative to Maxi_prop.
- mean_activity
- Mean ratiometric activity across S1-S4.
- sd_activity
- Standard deviation of ratiometric activity across S1-S4.
- qc_pass
- Package QC retention flag; true means all five library/RNA count thresholds passed.
Quality control
Supplementary file 1 provides all 16 tested elements. Package QC retained an element when the previral Maxiprep count and each of the four RNA replicate counts were at least 200; all 16/16 passed (minimum Maxiprep count 709 and minimum RNA replicate count 829).
Curation notes
This is the authors' small-scale in vivo proof-of-principle MPRA, distinct from the 408-element human STAR408 screen. Negative-control status is inferred only from labels beginning with NEG; all other source labels are retained without biological reclassification. Coordinates and the orthologous STAR408 number are taken directly from supplementary file 1.