databaseArrayExpressfile_versionsfilesTxt C BolesChristopher A FasanoSally TempleThomas R KiehlJoyce van de LeemputspeciesHomo Sapienssubmitter_keywordsRNA-seq of coding RNAfull_dataset_link Protocol - H9 cells were cultured in HES-medium (all reagents were obtained from Life Technologies): DMEM/F12 (1:1) with 20% (v/v) KSR, 1 mM L-glutamine, 100 µM non-essential amino acids, 55 µM 2-mercaptoethanol, and 10 ng ml-1 FGF-2. Sample Treatment - When cultures were at ~90% confluency the culture medium was changed to KSR-medium (all reagents were obtained from Life Technologies unless indicated otherwise): knockout-DMEM with 15% (v/v) KSR, 2mM L-glutamine, 100 µM non-essential amino acids, 55 µM 2-mercaptoethanol, supplemented with 100 nM LDN193189 (Stemgent) and 10 µM SB431542 (Tocris). Medium was changed daily, on the third day 1µM cyclopamine (Stemgent) was added. Medium was changed every other day, as of day five increasing amounts of N2-medium (25%, 50%, 75%, 100%) was added, cyclopamine concentration was maintained at 1 µM. N2-medium (all reagents were obtained from Life Technologies unless indicated otherwise): DMEM/F12 (1:1) with N-2 supplement and 0.775 g glucose (Sigma). In the Test case, the protocol was started when cells were ~65% confluent. Library Construction - Samples were collected using RNAprotect cell reagent (Qiagen), homogenized with QIAshredder (Qiagen), and total RNA extracted using RNeasy plus mini kit (Qiagen), according to manufacturer’s protocol. Samples were prepared for RNA-seq (including library preparation, bar-coding, etcetera) by Expression Analysis (Durham, NC, USA), or Covance (Seattle, WA, USA)data_protocolData Transformation - Data was mapped to human genome 19 using BFAST Mapped files were analyzed utililzing R in conjunction with multiple packages: GenomicFeatures, rtracklayer, Rsamtools, GenomicRanges, edgeR, Mfuzz, DESeq, DESeq2, goseq, SPIA, ggplot2, igraph, RcolorBrewer, GO.db,, foreach, parallel, multicore, doMC Genome_build: hg19 Supplementary_files_format_and_content: text, counts normalized for library size with DESeqsample_synonymsFgf-2, gluco-hexose, GLUTAMINE, 2-ME, lifespan, C6H12O6, determination, Glucose, 5-diamino-5-oxopentanoic acid, Glukose, 酪氨酸蛋白激酶试剂盒, B-KSR1, ES130, nutrient medium, SCF receptor activity, Levoglutamide, C5H10N2O3, Monohydrate, hES, hes, (DL)-Isomer, (2S)-2-amino-4-carbamoylbutanoic acid, FGFB, L-(+)-glutamine, HBGF-2, Ethanol, Heparin-binding growth factor 2, method, KL receptor activity, BETA2AR, L-glutamine, RNF47, Gsfsco1, L-Glutaminsaeure-5-amid, Loeffler Endocarditis, method used in an experiment, bFGF, Dextrose, SCO5, RRp, HRR-1, L-2-aminoglutaramic acid, 原癌基因c-Kit, SB 431542, SCO1, LDN-193189, Gsfsow3, SCFR, Gsfsco5, Essential Amino Acids, BFGF, SOW3, ji, treatment, LDN193189, Idiopathic Hypereosinophilic Syndrome, Fdc, CANDF6, Basic fibroblast growth factor, entire lifespan, cell, entire life cycle, HAEX, (2S)-2, SB431542, Q, FXII, 2 Mercaptoethanol, nucleic acid library construction, chemical analysis., CLAC, nucleic acid library preparation, W, RSU2, NICR1333, BNIP-H, HAE3, HAF, sample, disease management, Bs, L-Glutamine, ML1, BB077577, Sl, RIP14, Anhydrous, Fgfb, D-MEM, B2AR, proto-oncogene c-Kit, Essential Amino, SB-431542, HRR1, ES|130, (beta-D)-Isomer, total RNA extract, Tr-kit, RNA-seq, L-2-Aminoglutaramic acid, Cell, HES 细胞, PBT, ML-1, KIT ligand receptor activity, ADRBR, Glutamic acid 5-amide, L-Glutamin, KIT, (alpha-D)-Isomer, Loeffler's Endocarditis, HES cell, L Glucose, tyrosine-protein kinase Kit, FXR, D-Glucose, D11Bhm183e, c-KIT, Glutamic acid amide, medium, library construction, growth medium, life, 3322401A10Rik, DMEM, reagent, (S)-2, CD117, study protocol, sample population, Anhydrous Dextrose, L-glutamic acid gamma-amide, plan specification, IL-17F, D11Bhm184e, L-Glucose, C-Kit, concentration, D Glucose, KSR, Ksr, 2-Mercaptoethanol, Ssm, 2-mercapto-, (L)-Isomer, FGF-2, BAR, Acids, assay, HES, Glucose Monohydrate, hb, ADRB2R, AW492498, Glcdescription_synonymsprojections, Arhinencephaly, Ribonucleic, Par1c, Materials, Disorders, single-organism developmental process, determination, "familial alobar holoprosencephaly -RETIRED-" EXACT [SNOMEDCT_2005_07_31:44519006], Kanner's Syndrome, Stem Cells, AW491150, Homo sapiense, Behavioral disorders, temporal, Holoprosencephalies, Readability, cortical plate (areas), Homo sapien, diseases, Associations, Homo sapians, Reil Insula, childhood autism, Arhinencephalies, Mother Cells, Insular, diseases and disorders, Gpi-1, cortex cerebralis, Archipallium, Non Polyadenylated, Paleocortices, HPE, Insular Cortices, RNA Gene Products, 人(human being), Semilobar Holoprosencephalies, Autisms, human disease, Homo sapients, Gene Expressions, Cortex Cerebrus, Nlk, Moods, long, Early Infantile Autism, AA959811, Behavioral problems, present in organism, Psychiatric disturbances, h, Homo sapience, papilla, Human Embryonic Stem, Pathologies, Plate, 人(man), Autism, Homo sapiens disease, Mental Disorders, Home sapiens, Gpi, Lobar Holoprosencephalies, anatomical protrusion, Data Set, neocortex development, ribose nucleic acid, Arts, Paleocortex, lamina, ribonucleic acids, flanges, RNA-seq, Mother., Infantile, Behavioral/psychiatric abnormalities, Plates, cortical plate (CTXpl), Autistic Disorder, mOC-X, Colony-Forming Unit, Stem Cell, Homo sapian, Ribonukleinsaeure, Holoprosencephaly, shelf, Diseases, Genetic Materials, pentosenucleic acids, Ribonucleic acids, NK|GPI, Early, Genetic Material, Psychiatric disorders, Familial Alobar, Mother Cell, Acid, Epistemology, Industrial, ORG, Org, Cortices, Industrial Arts, shelves, Stem, Archipalliums, Cerebri, Gpi1-r, Gpi1-s, Colony Forming Units, Tgif, study protocol, Gpi1-t, projection, Homo sapines, ridge, human, "holoprosencephaly" EXACT [CSP2005:0723-2277], disease, Human Embryonic Stem Cell, spine, Material, Behavioural/Psychiatric abnormality, Cells, MARK, Autistic disorder of childhood onset (disorder), Insular Cortex, Behavioral disturbances, Cistron, pallium of the brain, mKIAA1477, Allocortex, TGIF, cortex cerebri, Bglap-rs1, Gpi1s, Behavioral changes, other disease, human being, AI461847, lamellae, Colony-Forming Units, Par-1c, Progenitor Cell, Gene, Tfig, process of organ, Alobar, protrusion, lamella, Homo spaiens, method, Infantile autism (disorder), method used in an experiment, Infantile Autism, Gene Products, disease or disorder, Mood, Pgi, Early Infantile, “人” EXACT genbank_common_name [], Cerebral, Progenitor, Kanner Syndrome, cortex of cerebral hemisphere, Allocortices, Genetic, Semilobar Holoprosencephaly, Alobar Holoprosencephalies, Gpi-1r, Cortical, Gpi-1s, Phi, Gpi-1t, Mother, ridges, Holoprosencephaly Sequence, man, Expressions, non-neoplastic, Non-Polyadenylated RNA, corticogenesis, Kanner's, Homo sampiens, Lobar Holoprosencephaly, Disorder, Syndrome, disorder, B930025N23Rik, Expression, AI462167, Cortex Cerebri, laminae, incidence, "Holoprosencephaly sequence (disorder)" EXACT [SNOMEDCT_2005_07_31:30915001], Semilobar, data, RNA, Colony Forming Unit, Cerebral Cortices, Affects, anatomical process, Progenitor Cells, Cortical Plates, 人(human), disorders, RNS, medical condition, MF, Cistrons, Amf, Mental illness, Cell, development, Cortex, Cerebrus, yeast nucleic acid, chemical analysis, Kanners Syndrome, Entire cerebral cortex, condition, Infantile psychosis (disorder), Alobar Holoprosencephaly, HPE4, Homo sapeins, flange, organ process, Data Base, NK, Human Embryonic, ribonucleic acid, brain cortex, Non Polyadenylated RNA, Emk3, Autistic, Non-Polyadenylated, Humo sapiens, Ribonucleic Acid, Understanding, mPar-1c, plan specification, Insula of Reil, process, processes, Homo spiens, "human" EXACT genbank_common_name [], Periallocortex, Periallocortices, processus, 数据, Lobar, assay, hESCs, Cortical Platedata_synonymsGpi, data, ORG, Org, Library., Genomes, AI461847, Gpi-1r, Nlk, Gpi-1s, content, Phi, Gpi-1t, Gpi1-r, Gpi1-s, composition, whole genome, MF, compositionality, Gpi1-t, Amf, composed of, text, Human, data analysis, data processing, Human Genomes, mOC-X, Human Genome, structure, 数据, Pgi, NK|GPI, Gpi-1, Bglap-rs1, NK, Gpi1sname_synonymsTranscriptome, human being, determination, Transcriptome Profile, neocortex development, Expression Profiles, Stem Cells, 人(human), Gene Expression Profile, Gene, Profiles, Homo sapiense, temporal, whole transcriptome, Gene Expression, hESCs., Homo spaiens, Homo sapien, Homo sapian, Expression Signatures, Homo sapians, Gene Expression Signatures, chemical analysis, Gene Expression Signature, Homo sapeins, “人” EXACT genbank_common_name [], Expression Profile, Human Embryonic, Transcriptome Profiles, 人(human being), Homo sapients, Profile, Humo sapiens, man, Homo sapines, Signatures, human, corticogenesis, Homo spiens, "human" EXACT genbank_common_name [], h, Homo sapience, Human Embryonic Stem Cell, Expression Signature, Gene Expression Profiles, Homo sampiens, Human Embryonic Stem, Cells, Transcriptomes, 人(man), assay, Signature, Home sapiens, incidenceview_count8isClaimabletruecitation_count0search_count48search_domainspatentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0biomodels_parameters~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0ipd-mhc~0genome_assembly~0taxonomy~1ebiweb_people~0enzymeportal_enzymes~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0gpcrdb~0hgnc~0intact~0rhea~0imgt-hla~0patentnucleotides~0ensemblroot~0non-coding~0europepmc~0identifiers_registry~0pdbechem~0biosamples~0interpro~0biotools~0mesh~0coding~0efo~0project~0human_diseases~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0ebiweb_corporate~0sra~47omim~0sbo~0lrg~0ipd-kir~0rnacentral~0orcid_data_claims~0metagenomics~0pfam~0citation_count_scaled0.0reanalysis_count_scaled0.0view_count_scaled0.052986512524084775download_count_scaled2.2609770435464178E-5download_count3normalized_connections0.294117647058824additional_accessionGSE56796SRP041179is_claimabletruenameCORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development From Human Embryonic Stem CellsdescriptionMany neurological and psychiatric disorders affect the cerebral cortex, and a clearer understanding of the molecular processes underlying human corticogenesis will provide greater insight into such pathologies. To date, knowledge of gene expression changes accompanying corticogenesis is largely based on murine data. Here we present a searchable, comprehensive, temporal gene expression dataset encompassing cerebral cortical development from human embryonic stem cells (hESCs). Using a modified differentiation protocol and RNA-Seq technology with computational analysis, we identified sets of genes and long non-coding RNAs that significantly change during corticogenesis, and those enriched for disease-associations. Numerous alternatively-spliced genes with varying temporal patterns of expression are revealed, including TGIF1, involved in holoprosencephaly and MARK1, involved in autism. We have created a database ( that provides online, query-based access to changes in RNA expression and alternatively spliced transcripts during human cortical development. Nine timepoints (days 0,7,12,19,26,33,49,63,77) covering human corticogenesis from embyronic stem cells.datespublication2014-07-01updated2014-09-06accessionE-GEOD-56796cross_referencesTAXONOMY9606