Restore search queries and accession screening records

README.md

@@ -26,6 +26,8 @@ subtypes, 28 primary tissues and 25 metastatic tissues.
 
 [Single-cell quality control](figures/figure2.png) · [Bulk quality control](figures/figure3.png) · [Figure legends](figures/legends.md)
 
+The [complete search queries](search_queries.md) and [accession-level GEO screening table](screening_en.xlsx), including screening decisions and exclusion counts by reason, are available for download.
+
 ## Data files
 
 Datasets are organized by their original study accession under `scRNA-seq/` and

screening_en.xlsx

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search_queries.md

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+## Search strategies
+
+**Search date:** 18 October 2026  
+**Publication date range:** 1 January 1900 to 12 October 2026
+
+The following Boolean search queries were used to retrieve candidate GEO Series records.
+
+### 1. Single-cell and single-nucleus RNA sequencing
+
+**Search results:** 1,246 GEO Series
+
+```text
+gse[ETYP] AND Homo sapiens[ORGN] AND ("1900/01/01"[PDAT] : "2026/10/12"[PDAT]) AND "Expression profiling by high throughput sequencing"[GTYP] AND (cancer OR tumor OR tumour OR carcinoma OR neoplasm OR neoplastic) AND ("single cell" OR "single-cell" OR "single nucleus" OR "single-nucleus" OR "scRNA-seq" OR scRNAseq OR "snRNA-seq" OR snRNAseq) AND ((metastasis OR metastatic OR metastases OR "lymph node" OR "lymph nodes") OR (("tumor microenvironment" OR "tumour microenvironment") AND (tissue OR tissues OR specimen OR specimens))) AND (patient OR patients OR tissue OR tissues OR specimen OR specimens)
+```
+
+### 2. Bulk RNA sequencing and microarray
+
+**Search results:** 2,041 GEO Series
+
+```text
+gse[ETYP] AND Homo sapiens[ORGN] AND ("1900/01/01"[PDAT] : "2026/10/12"[PDAT]) AND ("Expression profiling by high throughput sequencing"[GTYP] OR "Expression profiling by array"[GTYP]) AND (cancer OR tumor OR tumour OR carcinoma OR neoplasm OR neoplastic) AND (metastasis OR metastatic OR metastases) AND (primary OR normal) AND (patient OR patients OR tissue OR tissues OR specimen OR specimens) AND (bulk OR "RNA-seq" OR RNAseq OR "RNA sequencing" OR transcriptom* OR microarray OR "Expression profiling by array"[GTYP])
+```
+
+### 3. Search results and overlap
+
+| Search category | GEO Series records |
+|---|---:|
+| Single-cell and single-nucleus RNA sequencing | 1,246 |
+| Bulk RNA sequencing and microarray | 2,041 |
+| Overlapping GEO Series between searches | 345 |
+| **Unique GEO Series after deduplication** | **2,942** |
+
+The two searches shared 345 GEO Series accessions, yielding 2,942 unique records after deduplication.
+
+### 4. PubMed
+
+**Verification date:** 19 October 2026  
+**Publication date range:** 1 January 1900 to 12 October 2026  
+**Search results:** 9,831 publication records
+
+```text
+RNA AND primary AND (metastasis OR metastatic) AND (tumor OR tumour OR cancer OR carcinoma OR neoplasm OR neoplastic) AND Humans[MeSH Terms] AND ("1900/01/01"[Date - Publication] : "2026/10/12"[Date - Publication])
+```
+
+PubMed publication records are counted separately from GEO Series records. The same query returned 9,822 records on 12 October 2026 and 9,831 when verified on 19 October 2026.
+
+### 5. GEO metadata screening
+
+The accompanying [screening workbook](screening_en.xlsx) provides one accession per row within each assay branch, screening decisions, primary exclusion reasons, GEO evidence and exclusion counts. Each excluded branch record has one primary reason; percentages use the corresponding branch search total as the denominator. The workbook contains 1,161 single-cell exclusions (93.2% of 1,246 records) and 1,857 bulk exclusions (91.0% of 2,041 records). The branches overlap and must not be added as independent studies. After deduplication, 2,673 unique GEO Series were excluded, 156 retained as candidates and 113 matched the curated collection. Candidate retention does not mean final inclusion.