{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Qianhui Yu"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15107"],"description":["We utilized FLASH-seq, a full-length bulk RNA sequencing method, to sequence single spheroids in a 96-well format by manually sorting human and chimpanzee spheroids budding at day 3 to day 6 of midgut/hindgut patterning. We would like to use this data to assess the early stages of differentiation and to compare the intestine maturity differences between human and chimpanzee."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Reverse transcription and PCR amplification were carried out using SuperScript IV Reverse Transcriptase ( Thermo Fisher, 18090200) and KAPA HiFi HotStart ReadyMix (Roche, 07958935001). cDNA was purified using SeraMag SpeedBeads (Cytiva, 65152105050250) (0.8:1 bead-to-cDNA ratio) and quantified using the Quant-iT PicoGreen dsDNA assay (Thermo Fisher, P7589). Size distribution was assessed via an Agilent 2100 Bioanalyzer. Samples were normalized to 200 pg/µl for downstream library preparation.","Library Construction - Tagmentation was performed using homemade Tn5 transposase followed by heat inactivation with SDS. Enrichment PCR was conducted with KAPA HiFi DNA Polymerase (Roche, KK2502) and index adapters.","Sample Collection - Human and chimpanzee spheroids budding at day 3 to day 6 of midgut/hindgut patterning were sorted manually into a 96-well format. Spheroids were lysed in a lysis buffer according to the original protocol of FLASH-seq.","Sequencing - Libraries were pooled, cleaned up with SeraMag SpeedBeads, and sequenced on a NextSeq 550 using a high-output kit v2.5 (150 cycles) in a 75-8-8-75 read mode."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - We quantified gene expression using RSEM with default settings and GENCODE v.35 gene annotation as transcriptome reference. We loaded the transcript per million (TPM) output from RSEM as read counts to Seurat and performed downstream analysis. We only kept genes detected in at least two samples and samples with more then five thousand genes. We remove mitochondrial, ribosomal and sex chromosomal genes. We then performed log-normalization on the filtered count matrix with scale factor = 1e6.","Sequence Alignment - We performed read alignment for FLASH-seq data using STAR with hg38-panTro6-rheMac10 consensus genome as reference genome. Construction of consensus genome follows the same procedure as previously described (Kanton, Boyle, He et al., 2019, Nature)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Qianhui Yu","Umut Kilik","J. Gray Camp"],"additional_accession":[]},"is_claimable":false,"name":"FLASH-seq of human and chimpanzee single spheroid budding at different time points","description":"We utilized FLASH-seq, a full-length bulk RNA sequencing method, to sequence single spheroids in a 96-well format by manually sorting human and chimpanzee spheroids budding at day 3 to day 6 of midgut/hindgut patterning. We would like to use this data to assess the early stages of differentiation and to compare the intestine maturity differences between human and chimpanzee.","dates":{"release":"2025-08-08T00:00:00Z","modification":"2025-08-08T09:17:40.513Z","creation":"2025-05-02T11:31:23.508Z"},"accession":"E-MTAB-15107","cross_references":{"ENA":["ERP172205"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}