Outside ENCODE the resection layer is not one absence but four: 31 BRCA1, 45 CBX3, 22 KDM5A, 14 MRE11 and 8 CtIP ChIP-seq experiments exist in ChIP-Atlas, DNA2 and RAD50 have one each, and only BARD1 and EXO1 have none in any of the three archives

{
  "BRCA1": "measured-not-analysed - 31 distinct ChIP-Atlas SRX in 12 cell types (SH-EP 10, K-562 4, HepG2 3, MCF 10A, TC-32, EWS502, IMR-90, U2OS, GM12878, H1, HeLa, LoVo), 11 ReMap 2022 datasets, 63 GEO GSMs with BRCA1 in the title and ChIP in the record, plus 6 CUT&RUN GSMs (FT190 and one other series). Read at peak level by this beat; NOT read at signal level.",
  "BARD1": "never-measured - ZERO occupancy datasets in ENCODE, ChIP-Atlas and ReMap; 13 GEO GSMs carry BARD1 in the title and every one is RNA-Seq, PAR-CLIP, easyCLIP or 3'READS. ENCODE has a BARD1 TARGET RECORD and two CRISPR RNA-seq experiments, which is a different thing and is the premise Q35 got wrong.",
  "CBX3": "measured-not-analysed - 45 distinct ChIP-Atlas SRX in MCF-7 (23), HCT 116 (8), LNCaP (4), K-562 (3), H1 (2), GM12878 (2), T-47D (2) and LP-1 (1, multiple myeloma, GSE218772/GSE176547, PMID 36894562). Peak-read by this beat.",
  "CBX1": "measured-not-analysed - 8 distinct ChIP-Atlas SRX (HepG2 3, HCT 116 2, HEK293, K-562, HCT116-DKO). Peak-read by this beat; all negative.",
  "CBX5": "measured-not-analysed - 29 distinct ChIP-Atlas SRX in 12 cell types. Q35 listed CBX5's four ENCODE experiments as never read; all 29 archive tracks are now peak-read and all are negative at the breakpoint region.",
  "KDM5A": "measured-not-analysed IN A BLOOD CELL - 22 distinct ChIP-Atlas SRX including NB-4 (APL, GSE152397, PMID 34448811), MM.1S (GSE148046, PMID 34258103) and GM12878 (2). Q32 and Q35 both record KDM5A as never-measured in a blood cell on the strength of ENCODE's A549/H1/HepG2 trio. That is refuted. All 22 are peak-read here and all are negative at the breakpoint region.",
  "EXO1": "never-measured - ZERO in ENCODE (no target record), ZERO in ChIP-Atlas, ZERO in ReMap, and 0 of 55 GEO GSMs carrying EXO1 in the title is an occupancy assay. This is the only protein of the original six for which every class of check comes back empty.",
  "DNA2": "measured-not-analysed - 1 ChIP-Atlas SRX (SRX3520279 = GSM2907060, HCT 116, GSE108619, PMID 29773570) and a second independent series GSE254534/GSE254536 (PMID 39706185) with Ctrl_IP_DNA2 and HU_IP_DNA2 rep1/rep2, deposited as hg38 bigWig plus MACS2 narrowPeak. Q32 and Q35 both class DNA2 never-measured; that is refuted.",
  "RAD50": "measured-not-analysed, thinly - ZERO in ENCODE (target record exists, no experiments), ZERO in ChIP-Atlas, ZERO in ReMap, and exactly one GEO ChIP-Seq pair, GSM5387834/5 (GSE178328, 'Genome-wide maps of chromatin state in DEAF1 overexpression (OE in Multiple Myeloma)', hg38, no PMID). One IP and one input in a DEAF1-overexpressing myeloma line is not a usable occupancy resource, but it is not nothing.",
  "MRE11": "measured-not-analysed - 14 distinct ChIP-Atlas SRX under the RETIRED symbol MRE11A: HEK293 (6, an optogenetic break time-course at 0, 15 and 60 min post-light, GSE218590), HeLa (6) and LNCaP (2). gene-mre11 states 'no ENCODE ChIP-seq experiment for MRE11 exists in any cell type'; the ENCODE half is right and the 'in any cell type' clause is wrong.",
  "NBN": "measured-not-analysed - 4 released ENCODE TF ChIP-seq experiments (ENCSR278SQL GM12878, ENCSR085QEV K562, ENCSR210ZYL HepG2, ENCSR591EBL MCF-7), 8 ChIP-Atlas SRX and 5 ReMap datasets. gene-nbn states 'no ENCODE ChIP-seq experiment exists'; that is a direct factual error, checkable in one call.",
  "RBBP8 (CtIP)": "measured-not-analysed - 8 ChIP-Atlas SRX in U2OS from GSE218590, in a 4-OHT-inducible AsiSI system, i.e. a DAMAGE-STATE resection-factor occupancy dataset. absence-no-resection-factor-localised-at-the-kmt2a-locus records 'RBBP8 - no ENCODE occupancy data either', which is true of ENCODE and false of the archive.",
  "ALL_TWELVE_at_the_KMT2A_breakpoint_region": "negative at peak level in 180 of 180 ChIP-Atlas tracks except the three recorded in the sibling entry. The cheap route is therefore NOT spent - it is open at signal level for 177 tracks and has never been used."
}

{
  "method": "https://www.encodeproject.org/search/?type=Experiment&status=released&target.label=<SYMBOL>&format=json&limit=all, with NO assay filter, and a separate https://www.encodeproject.org/targets/?label=<SYMBOL> call to separate 'no experiments' from 'no target record'",
  "BRCA1": {
    "experiments": 8,
    "assays": [
      "TF ChIP-seq",
      "siRNA RNA-seq"
    ],
    "target_record": true
  },
  "BARD1": {
    "experiments": 2,
    "assays": [
      "CRISPR RNA-seq"
    ],
    "target_record": true,
    "accessions": [
      "ENCSR104RTM",
      "ENCSR427KVG"
    ]
  },
  "CBX3": {
    "experiments": 4,
    "assays": [
      "TF ChIP-seq"
    ],
    "target_record": true
  },
  "CBX1": {
    "experiments": 2,
    "assays": [
      "TF ChIP-seq"
    ],
    "target_record": true
  },
  "CBX5": {
    "experiments": 4,
    "assays": [
      "TF ChIP-seq"
    ],
    "target_record": true
  },
  "KDM5A": {
    "experiments": 3,
    "assays": [
      "TF ChIP-seq"
    ],
    "target_record": true
  },
  "NBN": {
    "experiments": 4,
    "assays": [
      "TF ChIP-seq"
    ],
    "target_record": true,
    "accessions": [
      "ENCSR278SQL",
      "ENCSR085QEV",
      "ENCSR210ZYL",
      "ENCSR591EBL"
    ]
  },
  "RAD50": {
    "experiments": 0,
    "target_record": true,
    "note": "target record HTTP 200, experiment search HTTP 404 - the pair that proves a 404 is about the query, not the target"
  },
  "EXO1": {
    "experiments": 0,
    "target_record": false
  },
  "DNA2": {
    "experiments": 0,
    "target_record": false
  },
  "MRE11": {
    "experiments": 0,
    "target_record": false,
    "also_tried": "MRE11A - also 404"
  },
  "RBBP8": {
    "experiments": 0,
    "target_record": false,
    "also_tried": "CTIP - 404"
  },
  "CTCF_control_in_the_same_batch": {
    "experiments": 579,
    "note": "the instrument was alive for every 404 above"
  }
}

{
  "instrument": "NCBI E-utilities esearch db=gds, retmode=json, with the pubmed_safe false-zero signature enforced: every zero required a NON-EMPTY querytranslation, and every translation was read back. Script: analyses/q37-archive-sweep-at-the-kmt2a-locus/q37_geo.py",
  "query_form": "<SYMBOL>[Title] AND \"Homo sapiens\"[Organism] AND gsm[ETYP] AND ChIP[All Fields]",
  "counts_gsm_title_and_chip": {
    "BRCA1": 63,
    "BARD1": 0,
    "CBX3": 7,
    "CBX1": 4,
    "CBX5": 7,
    "EXO1": 0,
    "DNA2": 7,
    "RAD50": 2,
    "MRE11": 44,
    "NBN": 0,
    "NBS1": 19,
    "RBBP8": 0,
    "CtIP": 16,
    "KDM5A": 71,
    "CTCF_control": 2300
  },
  "the_retired_symbol_and_protein_name_bound": "NBN returns 0 and NBS1 returns 19; RBBP8 returns 0 and CtIP returns 16; MRE11 returns 44 and MRE11A returns 0. Three of the twelve proteins are invisible under their current HGNC symbol in GEO sample titles. Any GEO census keyed to current symbols alone under-counts this layer badly.",
  "BARD1_all_13_title_GSMs_checked_by_hand": "SKOV3ip1 siRNA x3, OVCAR8ip1 overexpression x3 (RNA-Seq, GSE182677-class), A673 BARD1 rep1-3 (library_strategy RNA-Seq, GSE182677), BARD1 PAR-Clip, easyCLIP BARD1 x2, BARD1 (1_013) (3'READS, TREND-seq). Not one is a chromatin occupancy assay.",
  "EXO1_collision": "of 55 GEO GSMs with EXO1 in the title, the large majority use 'exo1' to mean EXOSOME PREPARATION 1 (hUCMSC-EXOs exo1, MSC_Exo1, plasma S-EVs REC_exo1, Cavin-1PC3_Exo1, HUVEC+HeLa exo_exo1). The rest are EXO1-knockout editing-outcome libraries. Zero are occupancy assays."
}

{
  "endpoint": "https://remap.univ-amu.fr/api/v1/info/byTarget/target=<SYMBOL>&taxid=9606",
  "counts": {
    "BRCA1": 11,
    "CBX3": 4,
    "CBX1": 4,
    "CBX5": 4,
    "NBN": 5,
    "KDM5A": 6,
    "CTCF_control": 628,
    "BARD1": 0,
    "EXO1": 0,
    "DNA2": 0,
    "RAD50": 0,
    "MRE11": 0,
    "RBBP8": 0
  },
  "HOW_REMAP_SPELLS_ZERO": "HTTP 401 with body {\"error\":\"Sorry. There is no experiment for target BARD1 and tax_id 9606 on remap2022\"}. Not 404, not an empty 200. A retry loop reading 401 as an auth failure will retry forever or record the wrong absence class. This is the ReMap sibling of the ENCODE-404 registry row and it was found the same way, with a live CTCF control returning 628 in the same batch.",
  "and_ReMap_holds_an_ENCODE_experiment_ENCODE_no_longer_serves": "ReMap lists ENCSR857KDI.BRCA1.A-549, which does not appear in the live ENCODE released-experiment search. An ENCODE 'released' census is not a superset of what has been processed from ENCODE."
}

[
  "ChIP-Atlas experimentList.tab, 353,024,258 bytes, Last-Modified 2026-09-09, streamed and filtered live 2026-09-22",
  "ENCODE Portal /search/ and /targets/ endpoints",
  "ReMap 2022 REST /api/v1/info/byTarget",
  "NCBI E-utilities esearch/esummary db=gds and db=sra"
]