Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA-seq data of human hESCs comparing experiments with cDNA library equalization

ABSTRACT: Single cell RNA-seq data of human hESCs comparing experiments with cDNA library equalization

PROVIDER: PRJNA658114 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12477800_1.fastq.gz	Fastqsanger.gz
	SRR12477800_2.fastq.gz	Fastqsanger.gz
	SRR12477900_1.fastq.gz	Fastqsanger.gz
	SRR12477900_2.fastq.gz	Fastqsanger.gz
	SRR12478000_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 576

Similar Datasets

Single cell RNA-seq data of human hESCs comparing experiments with cDNA library equalization

Project description:Considerable effort has been devoted to refining experimental protocols having reduced levels of technical variability and artifacts in single-cell RNA-sequencing data (scRNA-seq). We here present evidence that equalizing the concentration of cDNA libraries prior to pooling, a step not consistently performed in single-cell experiments, improves gene detection rates, enhances biological signals, and reduces technical artifacts in scRNA-seq data. In this submission the original single-cell cDNA is from GSE75748 cells labelled EC2 and TB2 in which the cDNA was not equalized prior to library preparation. We performed a set of experiments with the equalization step and provide three count matrices - 1) EQ (equalized cDNA prior to pooling in equal amounts); 2) EQ Vary (same as EQ but pooled at unequal amounts); 3) EQ-75% (equalized cDNA and pooled equally, sequeced to lower total depth).

2021-11-03 | GSE156494 | GEO

Paralog Specificity in cDNA Microarray Experiments

Project description:cDNA microarrays have become the technology of choice for profiling the expression of thousands of genes simultaneously in a single sample. However, cross-hybridization between targets and probes that do not correspond must be considered carefully during the design, analysis, and interpretation of these experiments. Here, we examined this potentially confounding issue by competitively hybridizing fragments with similar sequence obtained from two paralogous genes to a custom cDNA microarray that contains probes for only one of these two genes. We found that although a large contiguous portion of these two fragments was 84% identical and only one target was represented on the array, there was very little cross-hybridization of the non-represented target to either the paralogous probes or other (non-similar) features. We conclude that cDNA microarrays are indeed very specific and that promiscuous paralog hybridization adds little noise to the data. More generally, the absence of specific probes for any given gene does not increase the chance for cross-hybridization between non-specific probes and targets, even if sequence similarity is relatively high.

2009-07-03 | GSE16939 | GEO

Analysis of a normalised equine cDNA library using deep sequencing

Project description:While a first draft of the equine genome is available and predictions are made regarding resulting genes and proteins, little is known about the actual transcriptome. So far, published expressed sequence tags (ESTs) from different horse tissues were generally rather short (≤600bp) and hardly annotated, reflecting the problem that good cDNA libraries are very difficult to analyse. In this approach, we aimed to establish and analyse a normalised immune cell cDNA library (using freshly isolated and activated lymphocytes, NK cells, monocytes and DC). In particular, we wanted to test next generation sequencing combined with a series of bioinformatic approaches. The resulting cDNA library contained 2x107 clones of which 1056 were used for an initial Sanger sequencing and 4x106 for the deep sequencing analysis. Through the latter we obtained >29k sequences for which more than 5000 matches where found on the equine reference sequences. Additionally we could identify more than 3500 sequences which had matches on both - non-equine RNA sequences as well as the equine genome. In these we find both extensions of existing RefSeq models and novel mRNAs alike. Less than 2% of sequences did not have any match in the mentioned databases.

2012-06-30 | GSE26794 | GEO

Verification of the quality of the retroviral cDNA library composed of 176 proto-oncogenes and HOX genes

Project description:We constructed retroviral cDNA library of 176 proto-oncogenes and HOX genes to screen for the leukemia initiating gene combinations. The present submission is the NGS data of the PCR products of the whole inserts from the library itself and the bone marrow cells infected with retroviral library

2016-11-10 | GSE74806 | GEO

Deep sequencing of small RNAs and degradome cDNA library in soybean

Project description:Deep sequencing of small RNAs and degradome cDNA library in soybean

| PRJNA149105 | ENA

Deep sequencing of the degradome cDNA library in soybean

Project description:We deep sequenced a degradome library constructed from different soybean tissues. As a result, 19,830,257 represented 5,337,590 distinct signatures were obtained. 70.98% of the signatures were assigned to one soybean cDNA sequence and 24.05% matched with two cDNA sequences. 428 potential targets of small RNAs and 25 novel miRNA families were identified in soybean. A total of 211 potential miRNA targets including 150 conserved miRNA targets and 69 soybean-specific miRNA targets were identified. The signatures distribution on soybean primary miRNAs (pri-miRNAs) showed that most of the pri-miRNAs had the characteristic pattern of Dicer processing. The TAS3 small RNAs (siRNAs) biogenesis was conserved in soybean and nine Auxin Response Factors (ARFs) were identified as the TAS3 siRNA targets. The global identification of miRNAs targets would contribute to the functional research of the miRNA in soybean.

2011-11-02 | GSE33379 | GEO

Deep sequencing of the degradome cDNA library in soybean

2011-11-02 | E-GEOD-33379 | biostudies-arrayexpress

Deep sequencing of small RNAs and degradome cDNA library in soybean

Project description:This SuperSeries is composed of the following subset Series: GSE33378: Deep sequencing of small RNAs from different tissues in soybean GSE33379: Deep sequencing of the degradome cDNA library in soybean Refer to individual Series

2011-11-02 | E-GEOD-33380 | biostudies-arrayexpress

Sequence determinants of human gene regulatory elements, STARR-seq motif library experiments

Project description:Sequence determinants of human gene regulatory elements, STARR-seq motif library experiments

| PRJNA746786 | ENA

A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

Project description:A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

| PRJNA688225 | ENA