Data · dataset · 2022
Transcriptomic analysis in SHP-1 insufficiency mice after renal ischemia-reperfusion injury
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In kidney transplantation, the donor kidney inevitably undergoes ischemia-reperfusion injury.
Description
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.
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The following formula was used to calculate the FPKM value: FPKM = (number of mapped fragments) × 10 3 × 10 6 / [(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 <0.05, after applying Benjamini-Hochberg correction, was chosen for determining significant difference changes in expression.
Links
Where it is published
- Repository landing page figshare.com/articles/dataset/Transcriptomic_analysis_in_SHP-1_insufficienc… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.19525579 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.19525579 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.19525579 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Basic medicine
- Inferred from text
- Immunology 69% · RNA sequencing 75% · Sequencing 75%
Related
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.19525579 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].anzsrc:group:3204 | enrichment · DataCite | taxonomy-embedding@1.1.0 | title+keywords+description (69%) |
| concepts[field].fos:basic-medicine | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |