AAV-mediated capture-and-clone CRE-seq in mouse cerebral cortex
Massively parallel cis-regulatory analysis in the mammalian central nervous systemThe capture-and-clone CRE-seq library was packaged in AAV9(2YF) and injected bilaterally into the primary motor cortex of 4–6-week-old CD-1 mice. Three biological replicates, each from one mouse and harvested 4–5 weeks later, were quantified by barcode RNA/DNA sequencing of microdissected GFP-positive cortical tissue.
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 capture-and-clone library was made from C57BL/6J genomic DNA sheared to approximately 400–500 bp, captured across the central 300 bp of 4,000 mm9 DHS targets, and cloned upstream of a TATA-box minimal promoter-eGFP reporter carrying nominally 15-mer barcodes in the GFP 3-prime UTR. The final plasmid library was packaged in AAV9(2YF), delivered by bilateral stereotactic injection into adult primary motor cortex, and read out from microdissected GFP-positive cortex as normalized RNA/DNA barcode abundance; log2 activity was calculated as log2(0.001 + normalized RNA / normalized DNA).
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 · 31 definitions
- barcode
- Unique reporter barcode associated with the tested construct; the library was nominally 15-mer.
- barcode_length
- Barcode length reported by the MiSeq construct-mapping file; deposited values are 14–16 bp.
- target_id
- Deposited DHS target identifier assigned to the construct.
- target_class
- Target tissue class inferred from the deposited target prefix: retina, brain, heart, or liver.
- chromosome
- mm9 chromosome containing the mapped CRE fragment.
- fragment_start
- Deposited genomic start coordinate of the captured fragment.
- fragment_end
- Deposited genomic end coordinate of the captured fragment.
- strand
- Mapped strand of the captured fragment.
- overlap_bases
- Number of fragment bases overlapping the assigned 300-bp DHS target.
- fragment_length
- Captured fragment length reported by the construct-mapping file.
- construct_mapping_read_count
- Read_top count for the barcode's top mapped fragment species in the MiSeq library assignment.
- dna_count_rep1
- Raw DNA/plasmid barcode count in cortex biological replicate 1.
- dna_count_rep2
- Raw DNA/plasmid barcode count in cortex biological replicate 2.
- dna_count_rep3
- Raw DNA/plasmid barcode count in cortex biological replicate 3.
- rna_count_rep1
- Raw RNA/cDNA barcode count in cortex biological replicate 1.
- rna_count_rep2
- Raw RNA/cDNA barcode count in cortex biological replicate 2.
- rna_count_rep3
- Raw RNA/cDNA barcode count in cortex biological replicate 3.
- qc_min_dna_count
- Minimum of the three raw DNA counts; all output rows are at least 10.
- dna_normalized_rep1
- DNA count normalized to total DNA reads in cortex replicate 1.
- dna_normalized_rep2
- DNA count normalized to total DNA reads in cortex replicate 2.
- dna_normalized_rep3
- DNA count normalized to total DNA reads in cortex replicate 3.
- rna_normalized_rep1
- RNA count normalized to total RNA reads in cortex replicate 1.
- rna_normalized_rep2
- RNA count normalized to total RNA reads in cortex replicate 2.
- rna_normalized_rep3
- RNA count normalized to total RNA reads in cortex replicate 3.
- rna_dna_ratio_rep1
- Normalized RNA divided by normalized DNA for cortex replicate 1.
- rna_dna_ratio_rep2
- Normalized RNA divided by normalized DNA for cortex replicate 2.
- rna_dna_ratio_rep3
- Normalized RNA divided by normalized DNA for cortex replicate 3.
- log2_activity_rep1
- Deposited log2(0.001 + normalized RNA/DNA) activity score for cortex replicate 1.
- log2_activity_rep2
- Deposited log2(0.001 + normalized RNA/DNA) activity score for cortex replicate 2.
- log2_activity_rep3
- Deposited log2(0.001 + normalized RNA/DNA) activity score for cortex replicate 3.
- mean_log2_activity
- Mean of the three cortex replicate log2 activity scores.
Quality control
Applied the authors' GEO/paper QC: retained only barcodes with at least 10 raw DNA counts in each of the three cortex DNA replicates. GEO's expression table is already post-filtered; the output retains 38,826 constructs and all rows passed additional barcode, coordinate, and raw-count consistency checks. The authors also reported FastQC, exact index/flanking-sequence checks, and concordant paired-end mapping for barcode–CRE assignment.
Curation notes
This is a barcode/fragment-level table rather than a target-level average so that the library's tiling and truncation information is retained. The C57BL/6J genomic-DNA source used to construct the library differs from the CD-1 mouse cortex recipients; the study does not make a deliberate allele-versus-reference variant contrast. The library was nominally designed with 15-mer barcodes, while GEO's accepted barcode mappings include 14–16 bp lengths. Target classes R/B/H/L are inferred from the deposited GEO target identifiers and represent the retina, brain, heart, and liver DHS input groups, respectively. Coordinates and fragment lengths are retained exactly as deposited by GEO.