20710d4500737f2022bed8e3935ee8428fd88702 kent Wed Sep 4 08:05:28 2019 -0700 Adding test files and script. Test script isn't perfect yet, it's a little tricky working with stuff that modifies a database like this. diff --git src/hg/sqlUpdateRelated/tests/hcat_project.tsv src/hg/sqlUpdateRelated/tests/hcat_project.tsv new file mode 100644 index 0000000..25a6d2a --- /dev/null +++ src/hg/sqlUpdateRelated/tests/hcat_project.tsv @@ -0,0 +1,2 @@ +#short_name @state_reached_id@hcat_projectstate@state@id title stars @@lab@id@hcat_project_labs@project_id@lab_id@hcat_lab@short_name@id @consent_id@hcat_consent@short_name@id @cur_state_id@hcat_projectstate@state@id @effort_id@hcat_efforttype@short_name@id origin_name sheet_from_lab description @@publications@id@hcat_project_publications@project_id@publication_id@hcat_publication@short_name@id @@species@id@hcat_project_species@project_id@species_id@hcat_species@common_name@id @@contributors@id@hcat_project_contributors@project_id@contributor_id@hcat_contributor@name@id @@organ@id@hcat_project_organ@project_id@organ_id@hcat_organ@short_name@id @@organ_part@id@hcat_project_organ_part@project_id@organpart_id@hcat_organpart@short_name@id @@assay_type@id@hcat_project_assay_type@project_id@assaytype_id@hcat_assaytype@short_name@id @@disease@id@hcat_project_disease@project_id@disease_id@hcat_disease@short_name@id +HumanLymphoMyeloidProgenitorCells suitable "Single Cell RNA sequencing analysis of human haemopoietic lympho-myeloid progenitor populations (LMPP, MLP and GMP)" 5 Gottgens University of Cambridge already openly published suitable import GEO GSE100618 /uploads/project/GSE100618.tsv "We performed single cell RNA sequencing of human haemopoietic lympho-myeloid progenitors with the aim to separate functionally and transcriptionally distinct progenitors within the heterogeneous GMP, LMPP and MLP populations. We performed RNA sequencing in a total of 415 single cells. From donors 1 (CB369) and 2 (CB431), 163/166 and 157/249 cells passed quality control.We further analysed the 320 single cells that passed quality control from two different donors (157 and 163 from each donor; 91 LMPP, 110 MLP and 119 GMP). We performed clustering using Seurat package, which identified 3 clusters of cells. We identified genes that were differentially expressed among cells of the different clusters. The majority of the cells in cluster 1 were MLP, the majority of cluster 3 were GMP while cluster comprised of LMPP and GMP cells. Cluster 1 showed high expression of lymphoid-affiliated genes. Conversely, cluster 3 showed increased expression of myeloid genes, while cluster 2 showed a mixed transcriptional signature. PCA analysis revealed a transcriptional continuum of LMPP, MLP and GMP populations." pmid: 29167569 human "Evangelia,,Diamanti","Fiona,,Hamey","Dimitris,,Karamitros","Bilyana,,Stoilova" umbilical cord cord blood RNA levels healthy