Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Short Tandem Repeats - Targeted-Sequencing of human cells for Lineage tracing

ABSTRACT: Raw sequencing data used in the paper \"A biological-computational cell lineage discovery platform based on duplex MIPs\" (doi: https://doi.org/10.1101/191296) involving single cells from the YUCLAT melanoma patient and DU145 cell line which cultured in standart condition as recommend. The single cells were prepared by CellCellector for DU145 and FACS for YUCLAT, amplified by RepliG WGA kit . Targeting sequencing library is cronstructed with duplex Molecular Inversion Probes wtih the protocol as described in the paper. Illumina NextSeq is used to sequence these libraries.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Ehud Shapiro

PROVIDER: E-MTAB-6411 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single Stem Cell Lineage Analysis of the Leukemic Clones Responsible for Acute Myeloid Leukemia Relapse Based on the Functional and Genomic Properties at Diagnosis

Project description:Single cell lineage analysis was used to assess clonal genetic heterogeneity and functional aspects of AML HSPCs derived at diagnosis and relapse. To address inherent limitations of single cell analysis, we developed a unique high-resolution technique capable of following single cell-derived subclones of different HSPC subpopulations during the AML course. Each of these subclones was evaluated for chemo-resistance, in-vivo leukemogenic potential in Nod Scid Gamma (NSG) mice, mutational profile, and the subclone cell of origin identified using retrospective cell lineage reconstruction.

2022-08-12 | E-MTAB-11884 | biostudies-arrayexpress

RNA-seq of AtPIN5 overexpressing tobacco BY-2 cells

Project description:This RNA-seq is a part of the paper describing the role of PIN5 in generating auxin sinks. https://www.biorxiv.org/content/10.1101/2024.01.24.576992v1

2024-03-31 | GSE260945 | GEO

Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing

Project description:Advances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the need for a dedicated kit selection depending on the desired single cell assay.

2017-09-24 | E-MTAB-5968 | biostudies-arrayexpress

Transcriptome analysis and microRNAs profile of mesodermal iPSCs derived progenitors

Project description:Mesodermal iPSC derived progenitors (MiPs) obtained from human fetal fibroblasts and skeletal muscle mesoangioblasts show a different myogenic potential in vitro and when injected in vivo in mice model of Muscular Dystrophy. MAB-MiPs hold greater myogenic commitment compared to f-MiPs, showed by increased engraftment and regeneration of the hindlimb muscle. Here we report that RNA sequencing of MiPs and of induced pluripotent stem cells (iPSCs) of origin allows identification of genes differentially regulated between fibroblast and MABs progenies that might be responsible for the different contribution to muscle regeneration. MicroRNA- sequencing of the same cell lines further allowed a selection of a set of miRNAs that can drive the myogenic propensity of MiPs in vivo and identification of promyogenic and antimyogenic miRNA cocktails. Manipulation of the selected miRNAs improved the engraftment and regeneration of MiPs. Additional RNA-sequencing after the treatment with the defined promyogenic and antimyogenic cocktails unraveled additional information on the pathways modulated by the selected factors.

2017-09-14 | GSE102283 | GEO

MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements

Project description:MHC I-peptides (MIPs) play an essential role in normal homeostasis and diverse pathological conditions. MIPs derive mainly from defective ribosomal products (DRiPs), a subset of nascent proteins that fail to achieve a proper conformation and whose physical nature remains elusive. We used high-throughput proteomic and transcriptomic methods to unravel the structure and biogenesis of MIPs presented by HLA-A and -B molecules on human EBV-infected B lymphocytes from four subjects. We found that although HLA-different subjects present different MIPs derived from different proteins, these MIPs originate from proteins that are functionally interconnected and implicated in similar biological pathways. Secondly, the MIP repertoire of human B cells showed no bias toward conserved vs. polymorphic genomic sequences, derived preferentially from abundant transcripts and conveyed to the cell surface a cell type-specific signature. Finally, we discovered that MIPs derive preferentially from transcripts bearing miRNA response elements. Furthermore, while MIPs of HLA-disparate subjects are coded by different sets of transcripts, these transcripts are regulated by mostly similar miRNAs. Our data support an emerging model in which i) the generation of MIPs by a transcript depends on its abundance and DRiP rate, and ii) the DRiP rate is regulated to a large extent by miRNAs. We performed genome-wide miRNA expression profiling of B cells and non-lymphoid cells to confirm that miRNAs predicted to regulate transcripts source of MHC I-associated peptides are expressed in a cell-specific manner.

2012-03-25 | GSE35319 | GEO

Expression data from prostate cancer cell lines LNCap (androgen dependent) and DU145 (androgen independent), transfected with Pin1 or control siRNA

Project description:Pin1 inhibiton exerts anti-oncogenic effects on LNCaP and DU145 cells despite the gene regulation patterns by Pin1 were different in both cells. We investigated how Pin1 modulates the gene expressions in the androgen-dependent as well as the androgen-independent prostate cancer cell lines For the knockdown of human Pin1, the siRNAs against Pin1 (Pin1 shRNA-1: 5’-CGGCAACAGCAGCAGUGGUGGCAAA-3’ and Pin1 shRNA-2: 5’-GCCCUGGAGCUGAUCAACGGCUACA-3’) and control siRNA were purchased from Invitrogen (Stealth/siRNA duplex oligoribonucleotides)

2015-04-01 | E-GEOD-67457 | biostudies-arrayexpress

Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides

Project description:We developed a novel approach combining next generation sequencing, bioinformatics and mass spectrometry to assess the impact of non-MHC polymorphisms on the repertoire of MHC I-associated peptides (MIPs). We compared the genomic landscape of MIPs eluted from B lymphoblasts of two MHC-identical siblings and determined that MIPs mirror the genomic frequency of non-synonymous polymorphisms but they behave as recessive traits at the surface level. Moreover, we showed that 11.7% of the MIP coding exome is polymorphic at the population level. Our method provides fundamental insights into the relation between the genomic self and the immune self and accelerates the discovery of polymorphic MIPs (also known as minor histocompatibility antigens), which play a major role in allo-immune responses.

2013-12-08 | GSE48918 | GEO

Expression profiling of prostate cell lines by miRNA array

Project description:Prostate cancer (PCa) is the most common malignant carcinoma that develops in men in Western countries. Up to 30% of patients continue to suffer from disease progression following radical prostatectomy. Therefore, better prognostic markers and molecular targets for cancer treatment are needed. MicroRNA (miRNA) has the potential to be used as biomarkers and as a therapeutic target for the treatment of various cancers, including PCa. Here, to determine how miRNA is involved in PCa progression, we investigated the miRNA expression profiles of 3 PCa cell lines, namely PC3, DU145, and LNCaP, and 2 normal prostate cell lines, namely RWPE-1 and PrSc, using miRNA microarrays. We investigated miRNA genes that were significantly upregulated in PCa cell lines (PC3, DU145, LNCaP) compared with normal cell lines (RWPE-1, PrSc).

2013-09-01 | E-GEOD-40026 | biostudies-arrayexpress

Single-cell RNAseq of differentiating human iPSCs during endothelial-to-hematopoietic transition with targeted CRISPR activation

Project description:This dataset contains single cell RNAseq of human iPSCs undergoing cytokine-mediated differentiation alongside targeted CRISPR-mediated endogenous gene activation. For this experiment we sequenced single cells at day 10 of the differentiation protocol, when the cells undergo the endothelial-to-hematopoietic transition described in the paper Petazzi et al, BiorXiv DOI 10.1101/2022.10.04.510611 The dataset contains four libraries: (1) iSAM line infected with non-targeting guide RNA, (2) iSAM line infected with non-targeting guide RNA treated with Dox, (3) iSAM line infected with targeting guide RNAs library, (4) iSAM line infected with targeting guide RNAs library treated with Dox

2024-03-21 | E-MTAB-12748 | biostudies-arrayexpress

Transcripts coding MHC I-associated peptides are enriched in microRNA-binding sites

2012-03-25 | E-GEOD-35319 | biostudies-arrayexpress