Oncofusion

start / graph / ana-q120-the-murine-mll1-chip-uses-the-same-bethyl-a300-086a-as-the-human-mll1n-track

Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q120-h3k79me2-second-line-and-the-mll1-epitope

The murine MLL1 ChIP that sits beside a FLAG-tagged fusion in GSE260742 uses Bethyl A300-086A - the identical antibody to the human MLL1n track in GSE127507 - which no GEO record in either series would tell you, and which is what makes a masking calibration against a tag possible at all

also called the same antibody in both series · BETHA300-086A-M

The mouse experiment that has a clean tag on the cancer protein also ran the same antibody the human experiments use. That was not written in the public database record for either dataset; it took opening a supplementary spreadsheet attached to the paper.

The same thing, for a scientist

**None of GSE260742's 158 sample records names any antibody.** The string `antibod` appears **zero** times in the 419,824-character SOFT dump. The paper's Methods say only *'All antibodies used in this study are commercially available polyclonal antibodies that have been validated per manufacturer's websites.'* The reagent is in a supplementary key-resources spreadsheet [E1]: > `Rabbit anti-MLL1 Antibody | Bio-Strategy | BETHA300-086A-M` **`BETHA300-086A-M` is a distributor catalogue string for Bethyl A300-086A**, which is exactly the reagent GSE127507 deposits for all six of its `MLL1n` samples as `anti-MLL1n (Bethyl #A300-086A lots: 5 or 6)`. The FLAG reagent in the same sheet is `DYKDDDDK Tag (D6W5B) Rabbit mAb, New England Biolabs 14793S`. **Why this changes what the mouse experiment is.** The question the whole masking argument needs is *how much of an MLL1-N ChIP signal is the fusion*. An arbitrary anti-MLL1 run against a FLAG tag answers it for that antibody. **The same antibody run against a FLAG tag answers it for the antibody the human data actually used**, which is a strictly stronger result and was not knowable from either GEO record. **And it demolishes the paper's own label for that track.** The paper describes the experiment as profiling *'MLLAF9, endogenous MLL1 and active chromatin marks'*. An MLL1 N-terminal epitope is **retained** in MLL-AF9 - the same paper's introduction says MLL-FPs 'retain Menin-mediated chromatin recruitment but lack the C-terminal MLL1 SET domain' - so the track labelled *endogenous MLL1* necessarily contains the fusion as well. The label is not licensed by the epitope, and this beat measures how much difference that makes.

Go deeper
The route, recorded because it is reusable

Four steps, all this session:

  1. acc.cgi?acc=GSE260742&targ=gsm&form=text&view=brief - 158 records, 0 antibody mentions.
  2. acc.cgi?acc=GSE260742&targ=self - two !Series_pubmed_id values.
  3. Europe PMC PMC12904788/fullTextXML, 268,228 bytes, <body> present - Methods name no catalogue numbers.
  4. Europe PMC PMC12904788/supplementaryFiles, a 42,866,859-byte zip of 41 files. MOESM6_ESM.xlsx has eight sheets - Antibody, Chemicals, Peptides, Proteins, Commercial Assays, Deposited Data, Cell Lines, Mouse Strain, Oligos, Software - and the first is a 27-row key-resources table.

The general form. A GEO record that omits the antibody is not a dead end, and the paper's Methods often are one: modern journals push reagents into a key-resources supplementary table, which the full text does not quote and no indexing service searches. Two of the three PDFs in that archive were unreadable for this purpose - the supplementary figures PDF is image-only, 7 pages, zero extractable characters and zero form fields - and the answer was in a spreadsheet.

What else the same sheet settles
targetreagent, from the key-resources sheet
FLAGDYKDDDDK Tag (D6W5B) Rabbit mAb, New England Biolabs 14793S
MLL1Rabbit anti-MLL1, Bio-Strategy BETHA300-086A-M (= Bethyl A300-086A)
H3K79me2Abcam ab3594
H3K4me3Merck 07-473
H2AK119ubNEB 8240S (D27C4)
RING1BNEB 5694S (D22F2)
KDM2B / JHDM1BMerck ChIPAb+ 17-10264
BCORUnited BioResearch 12107-1-AP
VTP50469MedChemExpress HY-114162
SGC0946Sigma-Aldrich SML1107

One cross-series mismatch worth carrying: GSE260742's H3K79me2 is Abcam ab3594 and GSE127507's is Cell Signaling #5427. Any comparison of H3K79me2 between the two series is a comparison between two different polyclonal reagents, which the ARM 1 half of this beat avoids entirely by staying inside GSE127507.

Facts and figures
statusrun
result summaryThe murine MLL1 ChIP reagent in GSE260742 is Bethyl A300-086A, identical to the human MLL1n reagent in GSE127507; no GEO record in either series would reveal it for the mouse series and the paper's Methods do not either.
seriesGSE260742
paper pmid41634341
antibodyBethyl A300-086A (Bio-Strategy BETHA300-086A-M), MLL1 N-terminus, retained in MLL-AF9
shown for fusionMLL-AF9 / KMT2A::MLLT3 in a murine FLAG-tagged model; the reagent identity is what licenses transferring the measurement to the human KMT2A::AFF1 and KMT2A::MLLT3 MLL1n tracks
absence classmeasured-not-curated
absence class noteThe antibody IS published - in a supplementary key-resources spreadsheet - and is absent from the database this project joins against, GEO, which carries a per-sample antibody field that 158 of 158 records leave empty. Structurally invisible to any GEO-based reagent audit. Closes by reading the supplement, which is what this entry did.
absence class assigned2026-09-23 (Q120)
How this could bite us back
  • If a reagent identity that decides the interpretation of a whole dataset lives only in a supplementary spreadsheet, then automated re-analysis of public ChIP data is systematically blind to the one fact that determines what the tracks mean.
Still open
  1. What is A300-086A's immunogen range? Every masking argument in this project turns on the epitope being N-terminal and retained, and the residue range is not retrievable from the vendor routes tried. It would take one email or one datasheet PDF.
  2. How many other GEO series in this project's evidence base have an empty antibody field with the reagent sitting in a key-resources supplement? The project has a per-sample-metadata habit and no habit of opening the key-resources sheet.
Every source behind this entry (1)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset

    GSE260742 contains no antibody information in any of its 158 sample records (0 occurrences of 'antibod' in 419,824 characters) and PMID 41634341's Methods name no catalogue numbers; the supplementary key-resources table 41556_2025_1859_MOESM6_ESM.xlsx, sheet 'Antibody', lists the MLL1 ChIP reagent as 'Rabbit anti-MLL1 Antibody | Bio-Strategy | BETHA300-086A-M' and the FLAG reagent as 'DYKDDDDK Tag (D6W5B) Rabbit mAb | New England Biolabs | 14793S'. GSE127507 deposits 'anti-MLL1n (Bethyl #A300-086A lots: 5 or 6)' on all six of its MLL1n samples.

    DOI
    What this evidence cannot show

    `BETHA300-086A-M` is read as Bethyl A300-086A on the catalogue string; the distributor Bio-Strategy prefixes the manufacturer's code, and no vendor page confirming the mapping could be retrieved this session - three routes returned HTTP 404 (fortislife.com in two URL forms, bethyl.com/product/A300-086A). Bethyl A300-086A, deposited as 'anti-MLL1n', an MLL1 N-TERMINUS epitope. The N-terminus is retained in every KMT2A fusion, so this track is the sum of the fusion and wild-type MLL1 in unknown proportion and CANNOT distinguish them. The immunogen residue range was not verified: three vendor routes were tried this session (fortislife.com two URL forms, bethyl.com/product/A300-086A) and all returned HTTP 404, so 'N-terminus' rests on the depositors' own target label and on the standard fact that MLL-FPs lack the C-terminal SET domain. The Nature Reporting Summary, which would carry the manufacturer's validation statement, is not present as an extractable file in the Europe PMC supplementary archive.

    Evidence that argues against this (1)
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