The 3′UTR library was packaged in AAV9 and injected bilaterally into the striatum of perinatal Slc32a1/Vgat-Cre mice; striatum was dissected at P21 for reporter RNA and viral DNA barcode sequencing. Six animal RNA replicates were used for the reproducible medium-spiny-neuron screen.
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.
Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
UBERON:0002435
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
AAV9 library delivery into perinatal Vgat-Cre mice with bilateral striatal injection
Cre-dependent DiO tdTomato reporter was activated in GABAergic medium spiny neurons in dissected striatum; activity is log2 RNA CPM / viral DNA CPM. The paper notes that more than 90% of striatal neurons are GABAergic, improving library density versus the failed sparse cortical pilot.
Processed data
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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 · 35 definitions
element_id
Identifier for the synthesized 120-bp element, shared across its allele or control constructs.
allele
Construct class: ref, alt, shuf, or dnvctl.
element_class
Normalized construct class: genomic_reference, variant_alternate, GC_matched_shuffle, or synthetic_control.
element_sequence
Sequence tested in the reporter 3′UTR.
sequence_length_bp
Length of the tested element in base pairs.
barcode_count_designed
Number of designed 9-bp barcodes assigned to the construct; the library design used six.
phenotype
Phenotype or cohort label from the supplementary element annotation.
source_variant
Source variant or patient/cohort identifier from the supplementary annotation.
family_id
Family identifier from the supplementary annotation when available.
sample_id
Source sample identifier from the supplementary annotation when available.
mouse_ortholog
Mouse ortholog annotation for the source human element when available.
gene
Associated gene symbol from the supplementary annotation.
transcript_id
Associated transcript identifier from the supplementary annotation.
ensembl_gene_id
Associated Ensembl gene identifier from the supplementary annotation.
hg38_position_tag
Original hg38-style position tag from the supplementary annotation.
chromosome
Chromosome annotation for the source element.
hg19_start
Start coordinate on hg19 when available.
strand
Strand of the source element.
reference_allele
Reference allele reported for the source variant.
alternate_allele
Alternate allele reported for the source variant.
oe_lof_upper
gnomAD observed/expected loss-of-function upper-bound annotation when available.
Number of allele or control classes represented by published activity summaries for this element.
qc_pass
True for rows retained after the published QC and availability of a numeric published activity.
activity_log2_rna_dna
Published striatal reporter activity, log2(normalized RNA / normalized viral DNA).
activity_sem_log2_rna_dna
Standard error of the published striatal RNA/DNA activity.
ref_alt_log2fc_rna_dna
Alt minus Ref difference in published striatal RNA/DNA activity, in log2 units.
ref_shuf_log2fc_rna_dna
Shuf minus Ref difference in published striatal RNA/DNA activity, in log2 units.
ref_shuf_rna_dna_p
Published nominal p-value for the Ref-versus-Shuf striatal RNA/DNA comparison.
ref_shuf_rna_dna_fdr
Published FDR-adjusted p-value for the Ref-versus-Shuf striatal RNA/DNA comparison.
ref_shuf_rna_dna_bonferroni
Published Bonferroni-adjusted p-value for the Ref-versus-Shuf striatal RNA/DNA comparison.
ref_alt_rna_dna_p
Published nominal p-value for the Ref-versus-Alt striatal RNA/DNA comparison.
ref_alt_rna_dna_fdr
Published FDR-adjusted p-value for the Ref-versus-Alt striatal RNA/DNA comparison.
ref_alt_rna_dna_bonferroni
Published Bonferroni-adjusted p-value for the Ref-versus-Alt striatal RNA/DNA comparison.
Quality control
Author QC was retained: edgeR/CPM normalization, fewer-than-10-count barcode filtering in RNA or DNA, removal of absent-DNA elements, and in-vivo allele testing requiring both alleles to have at least five barcodes with at least 10 counts in both RNA and DNA in at least six replicates. Published Source Data 7 rows with numeric activity were retained; known mis-designed alternatives were excluded.
Curation notes
The Vgat striatal screen used six animal RNA replicates and three viral-DNA libraries according to Supplementary Data 2. The earlier sparse cortical Vgat/RBP4 pilot suffered jackpotting and was not treated as a successful experiment; this table is the final reproducible striatal dataset. Pairwise log2FC columns use Alt−Ref or Shuf−Ref and are repeated across the element's allele rows; published differential statistics come from Supplementary Data 4/5. Some Source Data 7 rows have a numeric activity but no reported SEM; those rows were retained and the SEM is left blank.