Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deciphering Runx1 interacted RNAs during definitive hematopoiesis by ultra-low-input RIP-seq

ABSTRACT: Deciphering Runx1 interacted RNAs during definitive hematopoiesis by ultra-low-input RIP-seq

PROVIDER: PRJNA872366 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Deciphering Runx1 interacted RNAs during definitive hematopoiesis by ultra-low-input RIP-seq

Project description:our work established a powerful method for physically studying TF-RNA interaction in very few cells, and provide valuable recourse for decoding more precious regulatory network of Runx1 during embryonic hematopoiesis.

2022-08-26 | GSE211847 | GEO

Haematopoetic RNA-seq from ultra low input

Project description:Haematopoetic RNA-seq from ultra low input

| PRJNA419186 | ENA

Cell-free DNA methylome profiling by MBD-seq with ultra-low input

Project description:Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions of cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data showed that cfMBD-seq performs equally to the standard MBD-seq (>1000 ng input) even when using 1 ng DNA as the input. cfMBD-seq demonstrated equivalent sequencing data quality as well as similar methylation profile when compared to cfMeDIP-seq. We showed that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulfite-free ultra-low input methylation profiling technology has a great potential in non-invasive and cost-effective cancer detection and classification.

2021-01-01 | GSE161331 | GEO

Ultra-low-input native ChIP-seq data of four germ-cell types during mouse spermatogenesis

Project description:We applied ultra-low-input native ChIP-seq and profiled genome-wide H3K9me3 distribution in four germ cell types during spermatogenesis.

2020-07-17 | GSE137742 | GEO

Combined ultra-low input mRNA and whole-genome sequencing from human embryonic stem cells

Project description:Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample material down to single cells. Nevertheless investigating such sample material still limits the analysis to either the genome or transcriptome, hence a combined analysis of both types of nucleic acids from the same sample material is still in demand.We developed a protocol which enables the combined analysis of the genome as well as the transcriptome by Next Generation Sequencing from ultra-low input samples. The protocol was evaluated by sequencing sub-colony structures from human embryonic stem cells containing 150 to 200 cells. The method can be adapted to any available sequencing system (e.g. Illumina, SOLiD, 454, etc.).To our knowledge, this is the first report where sub-colonies of human embryonic stem cells have been analyzed both at the genomic as well as transcriptome level. The method of this proof of concept study may find useful practical applications for cases where only a limited number of cells are available, e.g. for tissues samples from biopsies, circulating tumor cells and cells from early embryonic development. The results we present demonstrate that a combined analysis of genomic DNA and messenger RNA from ultra low input samples is feasible and can readily be applied to other cellular systems with limited material available.

2015-11-17 | GSE69471 | GEO

Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome

Project description:Deeper understanding of T cell biology is crucial for the development of new therapeutics. Human naïve T cells have low RNA content and their numbers can be limiting; therefore we set out to determine the parameters for robust ultra-low input RNA sequencing. We performed transcriptome profiling at different cell inputs and compared three protocols: Switching Mechanism at 5’ End of RNA Template technology (SMART) with two different library preparation methods (Nextera (SMART_Nxt) and Clontech (SMART_CC)), and AmpliSeq technology. As the cell input decreased the number of detected coding genes decreased with SMART, while stayed constant with AmpliSeq. However, SMART enables detection of non-coding genes, which is not feasible for AmpliSeq. The detection is dependent on gene abundance, but not transcript length. The consistency between technical replicates and cell inputs was comparable across methods above 1K but highly variable at 100 cell input. Sensitivity of detection for differentially expressed genes decreased dramatically with decreased cell inputs in all protocols, support that additional approaches, such as pathway enrichment, are important for data interpretation at ultra-low input. Finally, T cell activation signature was detected at 1K cell input and above in all protocols, with AmpliSeq showing better detection at 100 cells.

2019-05-24 | GSE130882 | GEO

Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples

Project description:RNA-seq is the standard method for profiling gene expression in many biological systems. Due to the wide dynamic range and complex nature of the transcriptome, RNA-seq provides an incomplete characterisation, especially of lowly expressed genes and transcripts. Targeted RNA sequencing (RNA CaptureSeq) focuses sequencing on genes of interest, providing exquisite sensitivity for transcript detection and quantification. However, uses of CaptureSeq have focused on bulk samples and its performance on very small populations of cells is unknown. Here we show CaptureSeq greatly enhances transcriptomic profiling of target genes in ultra-low-input samples and provides equivalent performance to that on bulk samples. We validate the performance of CaptureSeq using multiple probe sets on samples of iPSC-derived cortical neurons. We demonstrate up to 275-fold enrichment for target genes, the detection of 10% additional genes and a greater than 5-fold increase in identified gene isoforms. Analysis of spike-in controls demonstrated CaptureSeq improved both detection sensitivity and expression quantification. Comparison to the CORTECON database of cerebral cortex development revealed CaptureSeq enhanced the identification of sample differentiation stage. CaptureSeq provides sensitive, reliable and quantitative expression measurements on hundreds-to-thousands of target genes from ultra-low-input samples and has the potential to greatly enhance transcriptomic profiling when samples are limiting.

2019-11-16 | GSE140442 | GEO

Cell-free DNA methylome profiling by MBD-seq with ultra-low input

Project description:Cell-free DNA methylome profiling by MBD-seq with ultra-low input

| PRJNA677900 | ENA

Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples

Project description:Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples

| PRJNA589751 | ENA

TAF-ChIP: An ultra low input approach for genome wide chromatin immunoprecipitation assay

Project description:TAF-ChIP: An ultra low input approach for genome wide chromatin immunoprecipitation assay

| PRJNA448587 | ENA