{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE336nnn/GSE336417/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Homo sapiens"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE336417"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"ZFP36L2 orchestrates stress-adaptive plasticity in intestinal regeneration and colorectal cancer metastasis (SLAMseq)","description":"Thiol-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) was used to measure genome-wide mRNA half-lives in patient-derived colorectal cancer (CRC) liver metastasis organoids (MSK107Li). Organoids expressing a doxycycline-inducible short hairpin RNA targeting ZFP36L2 (shZFP36L2) or a non-targeting control (shCtrl) were metabolically labeled with 500 μM 4-thiouridine (4sU) for 6 hours, followed by a uridine chase. Total RNA was harvested in triplicate at t=0, 2, 5, and 12 hours post-chase, along with matched unlabeled control samples for background T>C correction. RNA was subjected to iodoacetamide alkylation and libraries were prepared using the QuantSeq 3′ mRNA-seq V2 Library Prep Kit FWD (Lexogen). T>C conversion rates were used to quantify labeled RNA fractions and fit single-exponential decay models to estimate per-gene mRNA half-lives. ZFP36L2 knockdown significantly stabilized transcripts associated with stress-response gene programs, consistent with ZFP36L2 promoting post-transcriptional decay of AU-rich stress-associated mRNAs.","dates":{"publication":"2026/07/20"},"accession":"GSE336417","cross_references":{"GSM":["GSM9834872","GSM9834873","GSM9834870","GSM9834871","GSM9834876","GSM9834877","GSM9834874","GSM9834875","GSM9834878","GSM9834879","GSM9834880","GSM9834883","GSM9834861","GSM9834884","GSM9834862","GSM9834881","GSM9834882","GSM9834860","GSM9834887","GSM9834865","GSM9834866","GSM9834885","GSM9834863","GSM9834864","GSM9834886","GSM9834869","GSM9834867","GSM9834868"],"GPL":["34281"],"GSE":["336417"],"taxon":["Homo sapiens"]}}