Resolve split-GAL4 lines to their AD and DBD hemidriver halves

Source: R/split.R

Split-GAL4 driver lines are built by combining two hemidriver transgenes: an activation-domain (AD) half and a DNA-binding-domain (DBD) half. Each half is itself an enhancer-driven transgene, named for the enhancer fragment (a GMR R* or VT VT* identifier). Knowing the two halves matters for cross-referencing: a split can “share” one half with a published Gen1 line that may itself have independent expression data (e.g. in the KDRC KGutProject).

split_halves() looks up each line in the FlyLight Split-GAL4 image-release metadata on S3 (https://s3.amazonaws.com/janelia-flylight-imagery/). For each SS*, IS*, MB*, OL* or SL* line that is present in any of the published split-GAL4 collections, the FlyLight metadata JSON carries ad and dbd string fields (e.g. "72F01-p65ADZp in attP40") which we parse into canonical enhancer codes (R72F01, VT048352, etc.).

Gen1 lines (plain R* or VT*) are returned as-is with ad and dbd both NA.

split_halves(lines, timeout = 10, quiet = FALSE)

Arguments

lines

character vector of line identifiers.

timeout

seconds for each individual S3 request.

quiet

logical; if FALSE (the default) emit a progress line every 25 inputs.

Value

a data.frame with one row per input line and columns

  • line - the query string.

  • is_split - logical; TRUE if the line looks like a split-GAL4 (prefix SS/IS/MB/OL/SL).

  • ad - resolved AD-half enhancer code (R* or VT*), or NA.

  • ad_full - the raw ad: field from the S3 metadata (includes landing site and balancer info), or NA.

  • dbd - resolved DBD-half enhancer code, or NA.

  • dbd_full - the raw dbd: field, or NA.

  • source_release - the FlyLight image release in which metadata was found (e.g. “Split-GAL4 Omnibus Broad”), or NA.

Details

The S3 release folders checked are (in order, first hit wins):

  • "Split-GAL4 Omnibus Broad" (Meissner et al. 2024 Initial Split IS* lines and the broad-screen SS* lines)

  • "Split-GAL4 Omnibus Rescreen" (2024 rescreen)

  • "Split-GAL4" (legacy Aso 2014 and similar SS*/ MB* releases)

  • "Split GAL4" (alternate folder name used by some releases)

If none of these contain a metadata JSON for a queried line, ad and dbd are returned as NA. As a fallback for unlisted lines, users can paste the line name into https://splitgal4.janelia.org/cgi-bin/view_splitgal4_imagery.cgi or the Bloomington Drosophila Stock Center stock page to find the two components by hand.

Examples

# \donttest{
if (FALSE) { # \dontrun{
split_halves(c("SS36097", "IS34128", "MB543B", "R20A02"))
} # }# }