Ena-DATASET-RIMLS-24-08-2017-14:20:51:416-502 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003581 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNA sequencing data of human small intestinal macrophage subtypes
| EGAD00001002744 | EGA
Project description:To identify potential functional roles of liver-resident NK cells we performed RNA sequencing on FACS sorted NK cell subpopulations from liver perfusates (n=5) and healthy blood controls (n=5). Full-length transcripts were sequenced from low-input samples using a modified version of the SMART-Seq2 protocol. Hepatic CD56brightCD16- and CD56brightCD16+ samples upregulate genes associated with tissue residency.
2022-04-09 | GSE200319 | GEO
Project description:Single cell transcriptome atlas of immune cells in human small intestine and in Celiac disease
| EGAD00001005127 | EGA
Project description:Embryos classified as euploid or aneuploid by PGT-A were re-biopsied and processed for RNA-Seq using a commercial kit (Takara Bio, USA, SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing) following the user manual. The resulting cDNAs were converted to libraries using a Nextera XT kit (Illumina, USA), with a modified protocol according to SMART-Seq v4 user manual. These libraries were pooled and sequenced using a NextSeq 550 instrument (Illumina, USA) with a MidOutput cartridge at 2x75 cycles. The sequencing reads in Fastq files were down-sampled to 6M total reads, aligned to the human genome assembly (hg38), and the number of transcripts per million (TPM) was determined using the CLC Genomics Workbench 12 (Qiagen, USA).
2022-09-07 | E-MTAB-12084 | biostudies-arrayexpress
Project description:Mice deficient in the LDL receptor (LDLR KO mice) fed with high fat diet (HFD) feeding have been widely used as a model to mimic human atherosclerosis. RNA-seq using aortic macrophages to investigate the effects of aortic macrophages on the plaque size progression. LDLR KO mice, 6-8 weeks old, were used, and fed with either an alternative HFD or a regular HFD. After aorta macrophages were isolated, RNeasy Mini Kit (Qiagen) was used to isolate mRNA. Single end (50bp), unstranded, SMART-Seq v4 plus nextera (SMART-Seq v4 Ultra Low Input RNA Kit (Takara) ). The RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara).
2024-07-31 | E-MTAB-12759 | biostudies-arrayexpress
Project description:We used the microarray data to analyze host cells response on mouse macrophage cells infected with HRSV The HRSV infected mouse macrophage cells were harvested at 4 and 24 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to HRSV infection.
2013-08-16 | E-GEOD-31378 | biostudies-arrayexpress
Project description:Here we present a performance evaluation of three different plate-based scRNA-seq protocols. Two commercially available kits; NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T). We evaluated each kit based upon sensitivity, reproducibility, ease of use and price point per cell. This evaluation is specifically relevant for implementation of scRNA-seq in e.g. diagnostics, requiring high sensitivity in regards of gene detection, high reproducibility between samples, minimum hands on time and smooth sample preparation for technicians, as well as keeping a reasonable price point per patient. G&T protocol delivered the highest detection of genes per single cell, at the absolute lowest price point. Takara's kit delivered likewise high gene detection per single cell, and high reproducibility between sample, however at the absolute highest price points. Here we present pros and cons of each protocol, sequencing breast cancer cell line T47D.
2020-08-01 | GSE155506 | GEO
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
Project description:The study profiled the effect of Phf6 deletion on gene expression in hematopoietic stem cells (HSCs), multipotent progenitor cells (MPPs) and hematopoietic progenitor cells (HPC-1). Phf6lox/Y;Tie2-creTg/+ mice were prepared on a C57BL/6 background so that Phf6 deletion could be selectively mediated by Tie2-cre. Cell populations were sorted from bone marrow samples using standard surface markers (Lin–SCA1+cKIT+(LSK) CD150+ CD48– for HSCs, Lin–SCA1+cKIT+(LSK) CD150– CD48– for MPPs and Lin–SCA1+cKIT+(LSK) CD150- CD48+ for HPC-1 cells). Phf6 intact and Phf6-delected cells of all three types were profiled by paired-end RNA-seq using an Illumina NextSeq 500 sequencer. RNA-seq libraries were prepared from the HPC-1 samples used a standard Illumina TruSeq library protocol whereas the libraries for the HSC and MPP samples used a SMART-seq ultra low input kit for cDNA synthesis and amplification. Statistical analysis of the TruSeq and SMART-seq samples was undertaken separately.
2019-02-20 | GSE126316 | GEO
Project description:Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells. Cells of four different origins were profiled using commercial SMARTer and compared to five variants of an improved protocol (Smart-Seq2).
2013-09-01 | E-GEOD-49321 | biostudies-arrayexpress