Données
CRISPRi + scRNAseq
LISEZMOI (see README_scCRISPRi_HUDEP_Ilboudo_etal.txt) et la table de comptes (see scCRISPRi_HUDEP_Ilboudo_etal.txt) pour « CRISPRi + scRNAseq for regulators of fetal hemoglobin in HUDEP-2 (Ilboudo et al.) »
Fibrillation auriculaire et rythme sinusal
Tables de comptes RNAseq tissu complet de l’appendice auriculaire gauche de patients atteints de fibrillation auriculaire et de rythme sinusal d’une cohorte majoritairement européenne (CTSN) et d’une cohorte d’Asie de l’Est (Harbin).
| CTSN | |
| counts.ctsn.tsv | meta.ctsn.tsv |
| Harbin | |
| counts.harbin.tsv | meta.harbin.tsv |
| LINC01629_KD | |
| counts.LINC01629_KD.tsv | meta.LINC01629_KD.tsv |
Blood pressure pLoF variants (UKB)
Statistiques sommaires GWAS d’association de variants pLoF avec la pression systolique et diastolique dans UKB rapportées dans l’article suivant:
- Association analyses of predicted loss-of-function variants prioritized 15 genes as blood pressure regulators, Canadian Journal of Cardiology 2023
| Systolic blood pressure | Diastolic blood pressure | |
| WES pLoF 200k discovery UKB cohort (additive and recessive) | file | file |
| WES pLoF 300k replication UKB cohort (additive and recessive) | file | file |
| WES pLoF whole 500k UKB cohort (additive and recessive) | file | file |
| WES pLoF whole 500k UKB cohort (gene-based test) | file | file |
Blood Cell Consortium (BCX)
Sommaire de données d’association (voir readme_BCX2_meta_analyses.txt), résultats de fine-mapping (voir readme_BCX2_CS95_VEP.txt) et résultats d’enrichissement g-chromVar (voir readme_BCX2_gchromVAR_5Sept2019.txt) rapportés dans l’article suivant:
- Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations, Cell 2020
| MR-MEGA | GWAMA | ||||||
| Trans-ethnic | Trans-ethnic | European | East-Asian | African | Hispanics/Latinos | ||
| Red blood cells | red blood cell count (RBC count) | file | file | file | file | file | file |
| hemoglobin concentration (HGB) | file | file | file | file | file | file | |
| hematocrit (HCT) | file | file | file | file | file | file | |
| mean corpuscular hemoglobin (MCH) | file | file | file | file | file | file | |
| mean corpuscular volume (MCV) | file | file | file | file | file | file | |
| mean corpuscular hemoglobin concentration (MCHC) | file | file | file | file | file | file | |
| RBC distribution width (RDW) | file | file | file | N.A. | file | file | |
| White blood cells | total white blood cell count (WBC count) | file | file | file | file | file | file |
| neutrophil count (Neutro) | file | file | file | file | file | file | |
| lymphocyte count (Lympho) | file | file | file | file | file | file | |
| monocyte count (Mono) | file | file | file | file | file | file | |
| basophil count (Baso) | file | file | file | file | file | file | |
| eosinophil count (Eosin) | file | file | file | file | file | file | |
| Platelets | platelet count (PLT count) | file | file | file | file | file | file |
| mean platelet volume (MPV) | file | file | file | file | file | file | |
| Fine-mapping results (95% credible sets) | BCX2_CR95_VEP.zip |
| G-chromVar enrichment results | CS.trans_all.PP01.strong_atac_overlap.tsv |
| CS.trans_subancestry.PP01.strong_atac_overlap.tsv |
Données d’association sur l’ExomeChip rapportées dans l’articles suivant: (pour plus d’information, voir readme2.txt)
- Rare coding variants pinpoint genes that control human hematological traits, PLoS Genet 2017
| Red blood cells | red blood cell count (RBC count) | meta_rare_rbc.txt.gz (3.3MB) |
| hemoglobin concentration (HGB) | meta_rare_hgb.txt.gz (3.4MB) | |
| hematocrit (HCT) | meta_rare_hct.txt.gz (3.4MB) | |
| mean corpuscular hemoglobin (MCH) | meta_rare_mch.txt.gz (3.3MB) | |
| mean corpuscular volume (MCV) | meta_rare_mcv.txt.gz (3.3MB) | |
| mean corpuscular hemoglobin concentration (MCHC) | meta_rare_mchc.txt.gz (3.3MB) | |
| RBC distribution width (RDW) | meta_rare_rdw.txt.gz (3.3MB) | |
| White blood cells | total white blood cell count (WBC count) | meta_rare_wbc.txt.gz (3.4MB) |
| neutrophil count (Neutro) | meta_rare_neutro.txt.gz (3.4MB) | |
| lymphocyte count (Lympho) | meta_rare_lympho.txt.gz (3.3MB) | |
| monocyte count (Mono) | meta_rare_mono.txt.gz (3.3MB) | |
| basophil count (Baso) | meta_rare_bas.txt.gz (3.2MB) | |
| eosinophil count (Eosin) | meta_rare_eos.txt.gz (3.2MB) | |
| Platelets | platelet count (PLT count) | meta_rare_plt.txt.gz (3.4MB) |
| mean platelet volume (MPV) | meta_rare_mpv.txt.gz (3.2MB) |
Données d’association sur l’ExomeChip rapportées dans les articles suivants: (pour plus d’information, voir readme.txt)
- Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits, Am J Hum Genet. 2016
- Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases, Am J Hum Genet. 2016
- Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals, Am J Hum Genet. 2016
| African ancestry | European ancestry | All ancestries | |
| Red blood cell | BCX_RBC_AA.tar.gz (56.1MB) | BCX_RBC_EA.tar.gz (61.1MB) | BCX_RBC_ALL.tar.gz (67.3MB) |
| White blood cell | BCX_WBC_AA.tar.gz (43.4MB) | BCX_WBC_EA.tar.gz (48.3MB) | BCX_WBC_ALL.tar.gz (56.5MB) |
| Platelet | BCX_PLT_AA.tar.gz (15.8MB) | BCX_PLT_EA.tar.gz (17.3MB) | BCX_PLT_ALL.tar.gz (19.1MB) |
Logiciel
CRISPR Off-Target Tool
Ce script vise à trouver les régions hors-cibles dans les expériences CRISPR/Cas9 à partir d’une liste de guides ARN (sgRNAs).
- Version 2.0.5: [Documentation] [R scripts]
- Version 1.02: [Documentation] [R script]
Tableaux supplémentaires pour Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, and Canver MC. Human genetic variation alters CRISPR/Cas9 on- and off-targeting specificity at therapeutically implicated loci [PNAS 2017]
- Supplementary data. List of individual aggregate off-target scores for samples from the 1,000 Genomes Project and their local scores. CFD: cutting frequency determination.
- Supplementary data. List of individual aggregate off-target scores for samples from the French Canadian dataset and their local scores. CFD: cutting frequency determination.
KnockoutQT
Ce script (knockoutQT.rb) vise à trouver des « knock-outs » (KOs) de gènes et à tester leurs associations avec un phénotype quantitative donné.