Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling (RNA-seq) experiment where CRISPRi guides were designed to target the human rs2650492 variant, the promoter of GAPDH, and a non-coding region near TUFM in HEK293t cells

ABSTRACT: CRISPRi guides were designed to target genomic regions of interest in HEK293t cells. Four guides were designed per region (see processed file). These regions were an enhancer located in the 3’UTR of SBK1 which harbors the obesity GWAS variant rs2650492, the promoter of GAPDH as a positive control, and a non-coding region near TUFM as a negative control. We also provide transcriptomes for Cas9 transfected cells only. Genes proximal to rs2650492 were assessed for differential expression. This experiment was performed with technical replicates where each replicate is a unique transfection and library preparation.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Noboru Sakabe

PROVIDER: E-MTAB-10460 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling (RNA-seq) of human iPSCs, iPSC-derived ventralized cells, neurons, and hypothalamic neurons where regions of the genome have been deleted that contain the single nucleotide polymorphisms rs9972768 or rs2650492

Project description:Three iPSC lines were differentiated into hypothalamic neuron precursors. Line 1 had an enhancer containing rs9972768 deleted, line 2 had an enhancer containing rs2650492 deleted, and the third line was wild-type. Cells were collected for RNA-seq at 4 time points, 1) iPSCs 2) Ventralized cells 3) Neurons of any type and finally 4) Hypothalamic Neurons. There are either 3 or 4 biological clones represented for each line.

2021-05-22 | E-MTAB-10464 | biostudies-arrayexpress

STRT RNAseq of human foreskin fibroblasts undergoing CRISPRa reprogramming

Project description:Comparison of human foreskin fibroblasts with different guide RNA compositions undergoing CRISPRa-mediated reprogramming. Cell samples have been collected at days 4, 8 and 12 of pluripotency induction. Each time point has three conditions with either (1) pluripotent reprogramming factor promoter targeting guides (OMKSL), (2) EEA-motif targeting guides (36bp), or reprorgamming factor promoter and EEA-motif targeting guides (OMKSL+36bp). Control samples have been collected from non-treated foreskin fibroblasts.

2018-06-07 | E-MTAB-6186 | biostudies-arrayexpress

An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia

Project description:As part of our effort to elucidate the role of IL7RA aberrations, we transduced normal cord blood cells with lentivirus expressing IL7RA with activated mutation. Additionally in part of the experiments cells were transduced with lentivirus expressing CAS9 and guides targeting the CDKN2A gene. Here we deposit Single Nucleotide Polymorphism (SNP) array data of the leukemic samples that were developed after transplantation of the transduced cells in immunodeficient mice.

2021-12-05 | E-MTAB-11258 | biostudies-arrayexpress

RNA-seq of RS4:11 cell line populations that are unedited (SPI1 +/+), mono (SPI1 +/-) and biallelicaly edited (SPI1 -/-)

Project description:The goal of the experiment was to identify which genes are differentially expressed between the unedited and SPI1-edited populations. The RS4:11 cell line was edited both mono and biallelicaly via electroporation with guides and Cas9. Following editing, RNA from unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were extracted through the Direct-zol RNA Microprep kit. cDNA libraries for sequencing were then prepared using the TruSeq Stranded mRNA Library Prep Kit and the IDT for Illumina-TruSeq RNA UD Indexes (Illumina). Samples were then sequenced on the Illumina NovaSeq platform.

2021-03-24 | E-MTAB-8677 | biostudies-arrayexpress

mRNA-Seq from control cells and two clones of Flp-In-T-REx-293 cells modified via CRISPR-Cas9 to knockout SMG7 in combination to knockdowns of control, SMG5, and SMG6

Project description:Mature mRNAs undergo quality control during translation that may lead to RNA degradation by triggering the nonsense mediated decay (NMD) pathway. Aberrant translation due to features such as the presence of a premature stop codon downstream on an exon-exon junction or an intron in the 3'UTR activates NMD. However, many of the features that lead to the activation of this pathway are unclear. UPF1, an RNA helicase, is the core NMD factor. UPF1 forms a multi-protein complex by recruiting a series of factors and other protein complexes in a process that depends on the UPF1 phosphorylation-dephosphorylation cycle. Among the factors recruited by UPF1, SMG5-SMG7 and SMG6 have critical importance in executing NMD. The SMG5-SMG7 heterodimer induces the exonucleolytic degradation of the mRNA, which depends on the recruitment of deadenylation factors. SMG6 has endonucleolytic activity and cleaves the targeted transcript close to the stop codon. The redundancy between the exonucleolytic and endonucleolytic paths to achieve degradation during NMD has been previously reported in the literature. To investigate the apparent redundancy between SMG5-SMG7 and SMG6 activity and to further understand the features that lead to the activation of NMD, we have generated two clones of SMG7 knockout human cells using CRISPR-Cas9. We generated mRNA-Sequencing data for control and both SMG7 KO clones with additional siRNA-mediated knockdown of Luciferase (Luc) as control, SMG5 or SMG6.

2021-05-07 | E-MTAB-9330 | biostudies-arrayexpress

Amplicon-seq of an enhancer region targeted by CRISPR to assess the mutations introduced by different sgRNA guides

Project description:Following a CRISPR enhancer scan covering the GATA2 super-enhancer region, the top sgRNAs were selected for further inspection. MUTZ3 cells were thus treated with the selected sgRNAs and the region of interested was subjected to amplicons sequencing (amplicon-seq). To that end, we used the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The same experiment was conducted in K562 cells, which do not harbor an inv(3)/t(3;3), to investigate the role of MYB in this enhancer in other leukemia settings

2021-07-26 | E-MTAB-9945 | biostudies-arrayexpress

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair

Project description:Based on the hypothesis that, enhancing the local concentration of donor oligos could increase the correction rates, we generated and tested novel CRISPR-Cas9 systems, in which the DNA repair template is covalently conjugated to Cas9 (RNPD system). To validate our results from the HEK293T reporter cells, we here tested our approach at different endogenous genomic loci and in different cell types. We first targeted the human beta globin (HBB) locus in the K562 cell line, and analyzed correction- and editing frequencies using next generation sequencing (NGS). Next we targeted the Rosa26 and proprotein convertase subtilisin/kexin type 9 (Pcsk9) locus in mouse embryonic stem cells (mESCs). Here, RNPD system was always compared to Cas9 SNAP-tag fusion proteins with uncoupled donor oligos. To also directly compare the engineered RNPD system to the classical CRISPR-Cas9 system, we performed experiments where we used wild-type Cas9 with the uncoupled donor oligos as a control. We therefore targeted the fluorescent reporter locus as well as the endogenous loci HBB, empty spiracles homeobox 1 (EMX1), and C-X-C chemokine receptor type 4 (CXCR4) in HEK293T cells. Finally, we performed the analysis of three computationally predicted off-target sites of the reporter locus.

2018-06-04 | E-MTAB-6808 | biostudies-arrayexpress

Targeted nanopore resequencing and methylation analysis of LINE-1 retrotransposons

Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).

2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress

RNA-sequencing of LEUTX-inducible H9 human embryonic stem cells

Project description:We generated an inducible DDdCas9VP192 activator cell line in H9 human embryonic stem cells using the Sleeping beauty transposition system. The guides targeting a LEUTX promoter and enhancers were introduced by PiggyBac transposition. Three sample types were generated: Promoter only, Promoter+Enhancer1, Promoter+Enhancer2. Cells were collected before and at 24 h, 48 h, and 72 h after doxycycline treatment, and subjected to STRT RNA-sequencing.

2023-02-12 | E-MTAB-10539 | biostudies-arrayexpress

Phosphoproteomic analysis of the Folliculin (FLCN) tumor suppressor reveals FLCN-dependent kinase signaling and TFEB regulation

Project description:In Birt-Hogg-Dubé (BHD) syndrome, germline mutations in the Folliculin (FLCN) gene lead to an increased risk of renal cancer. To address if FLCN is involved regulating cellular signaling pathways via protein and receptor phosphorylation we determined comprehensive complete phosphoproteomic profiles of FLCNPOS and FLCNNEG human renal tubular epithelial cells (RPTEC/TERT1). In total, 15744 phosphorylated peptides were identified, residing on 4329 phosphorylated proteins. Kinase activity inference analysis revealed that FLCN loss elevates phosphorylation of numerous kinases, including tyrosine kinases EPHA2 and MET, as well as activation of downstream MAPK1/3/6 and 8. Three non-canonical phosphorylation sites on EGFR (Tyr1125, Tyr1138 and Tyr1172) were higher phosphorylated upon FLCN loss together with enhanced phosphorylated EGFR substrates ABI, EPS8, ERRFL1, STAT1, PTK2 and CTNND1. In concordance, phosphosite specific signature analyses revealed an enrichment for EGFR signaling in FLCNNEG cells. Interestingly, we detected FLCN dependent phosphorylation of PIK3CD but no canonical downstream Akt/mTOR activation. In agreement with the induction of the E-box transcriptional gene expression signature upon FLCN loss, here we identified that phosphorylation of TFEB on Ser109, Ser114 and Ser122 is dependent on FLCN and absence of this phosphorylation results in constitutive nuclear localization of this transcription factor in FLCNNEG cells. Together, our study reveals enhanced phosphorylation of specific kinases and substrates in FLCNNEG renal epithelial cells, providing important insights in BHD-associated renal tumorigenesis and offering novel handles for the design of targeted therapies.

2022-07-11 | PXD025798 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data