{"data":{"id":"10.6084/m9.figshare.19525579.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.19525579.v1","prefix":"10.6084","suffix":"m9.figshare.19525579.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Yan, Sijia","givenName":"Sijia","familyName":"Yan","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Transcriptomic analysis in SHP-1 insufficiency mice after renal ischemia-reperfusion injury"}],"publisher":"figshare","container":{},"publicationYear":2022,"subjects":[{"subject":"Molecular Biology"},{"subject":"30405 Molecular Medicine","schemeUri":"http://www.abs.gov.au/ausstats/abs@.nsf/0/6BB427AB9696C225CA2574180004463E","subjectScheme":"FOR"},{"subject":"FOS: Basic medicine","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"}],"contributors":[],"dates":[{"date":"2022-04-06","dateType":"Created"},{"date":"2022-04-06","dateType":"Updated"},{"date":"2022","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.19525579","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["28786968 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"In kidney transplantation, the donor kidney inevitably undergoes ischemia-reperfusion injury. It is of great importance to study the pathogenesis of ischemia-reperfusion injury and find effective measures to attenuate acute injury of renal tubules after ischemia-reperfusion. We systematically analyzed differences in the expression profiles of three SHP-1 (encoded by Ptpn6)-insufficient mice and three wild-type mice by RNA-seq. We achieved the expression data of 21367 genes. TopHat v2.1.0 was used with the default parameters to generate acceptable alignments for Cufflinks, which was used to align the RNA sequencing paired-end reads against the reference genome, Ensembl release 90 GRCm38.p5. The expression of the annotated genes in the RNA-seq data was evaluated in fragments per kilobase million (FPKM) using Cufflinks. The following formula was used to calculate the FPKM value: FPKM = (number of mapped fragments) × 10\u003csup\u003e3\u003c/sup\u003e × 10\u003csup\u003e6\u003c/sup\u003e/ [(length of transcript) × (total number of fragments)]. Log transformation and zero-mean normalization were used to normalize the expression data for comparisons. The false discovery rate (FDR) of \u0026lt;0.05, after applying Benjamini-Hochberg correction, was chosen for determining significant difference changes in expression.\u003cbr\u003e","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Transcriptomic_analysis_in_SHP-1_insufficiency_mice_after_renal_ischemia-reperfusion_injury/19525579/1","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":2,"viewsOverTime":[{"yearMonth":"2025-08","total":1},{"yearMonth":"2025-10","total":1}],"downloadCount":0,"downloadsOverTime":[{"yearMonth":"2025-08","total":0},{"yearMonth":"2025-10","total":0}],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2022-04-06T14:42:00.000Z","registered":"2022-04-06T14:42:01.000Z","published":"2022","updated":"2022-04-06T14:42:02.000Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}},"provider":{"data":{"id":"otjm","type":"providers"}},"media":{"data":{"id":"10.6084/m9.figshare.19525579.v1","type":"media"}},"references":{"data":[]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}}}