Results 81 to 90 of about 10,065,126 (260)

Assessment of Single Cell RNA-Seq Normalization Methods

G3: Genes, Genomes, Genetics, 2017
We have assessed the performance of seven normalization methods for single cell RNA-seq using data generated from dilution of RNA samples. Our analyses showed that methods considering spike-in External RNA Control Consortium (ERCC) RNA molecules ...
Bo Ding, Lina Zheng, Wei Wang
doaj   +1 more source

Engineering IL‐4 resistant proinflammatory human myeloid cells for cancer immunotherapy

Molecular Oncology, EarlyView.
We developed a scalable workflow to generate proinflammatory human myeloid cells. CRISPR/Cas9‐edited CD34+ hematopoietic stem and progenitor cells were expanded and differentiated with M‐CSF. Deletion of STAT6 or STAT6/NFKB1 enhanced macrophage proinflammatory gene expression and cytokine secretion in the presence of IL‐4 while maintaining antibody ...
Theresa Barberi, Alan D. Friedman
wiley   +1 more source

Small RNA pathways in mammalian oocytes

FEBS Open Bio, EarlyView.
Three distinct small RNA pathways operate in mammalian oocytes: RNAi interference (RNAi), the microRNA (miRNA) pathway, and the PIWI‐associated RNA (piRNA) pathway. These pathways use small RNAs to guide sequence‐specific repression and contribute to oocyte biology by targeting genes and mobile elements or appear insignificant since different ...
Petr Svoboda, Josef Pasulka
wiley   +1 more source

A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation

, 2021
© 2020 Elsevier Inc. Empirical optimization of stem cell differentiation protocols is time consuming, is laborintensive, and typically does not comprehensively interrogate all relevant signaling pathways.
Cha, Minsun, Lin, Lin, Sherwood, Richard I, Gifford, David K, Qi, Celine Yueyue, Yeo, Grace Hui Ting, Sherwood, Richard I.   +6 more
core   +1 more source

Identification of SPP1+ macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics

Frontiers in Immunology
IntroductionMacrophages and T cells play crucial roles in liver physiology, but their functional diversity in hepatocellular carcinoma (HCC) remains largely unknown.MethodsTwo bulk RNA-sequencing (RNA-seq) cohorts for HCC were analyzed using gene co ...
Han Jin, Han Jin, Woonghee Kim, Meng Yuan, Xiangyu Li, Hong Yang, Mengzhen Li, Mengnan Shi, Hasan Turkez, Mathias Uhlen, Cheng Zhang, Adil Mardinoglu, Adil Mardinoglu   +12 more
doaj   +1 more source

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

Nature Communications, 2016
Existing single-cell RNA-seq methods provide the transcriptome of a cellular phenotype at a single time point. Here, Kimmerlinget al. present a microfluidic platform that enables off-chip single-cell RNA-seq after multigenerational lineage tracking under
Robert J. Kimmerling, Gregory Lee Szeto, Jennifer W. Li, Alex S. Genshaft, Samuel W. Kazer, Kristofor R. Payer, Jacob de Riba Borrajo, Paul C. Blainey, Darrell J. Irvine, Alex K. Shalek, Scott R. Manalis   +10 more
doaj   +1 more source

Transcripts enriched in codons that trigger P‐site tRNA‐mediated mRNA decay possess stable mRNA

FEBS Open Bio, EarlyView.
PTMD codons were first described by Mendel et al. as mediators of an mRNA decay pathway dependent on the human protein CNOT3, homologous to yeast Not5. Our findings confirm that PTMD codons destabilize transcripts; however, unlike in yeast, the human pathway specifically targets and slightly destabilizes primarily stable mRNAs.
Rodolfo Lopes Carneiro, Fernando Lucas Palhano   +1 more
wiley   +1 more source

Informative sequence-based models for fragment distributions in ChIP-seq, RNA-seq and ChIP-chip data [PDF]

Many high throughput sequencing protocols for RNA and DNA require that the polynucleic acid is fragmented so that the identity of a limited number of nucleic acids of one or both of the ends of the fragments can be determined by sequencing. The nucleic
Dyer, Nigel
core  

Single cell RNA-seq of human epidermis

, 2021
single-cell RNA sequencing (scRNA-seq) on the epidermis derived from healthy donors and psoriasis ...
Wang, Z (via Mendeley Data)
core   +1 more source

Loss of AMBRA1 activates MAPK and angiogenesis signaling pathways in melanoma cells

FEBS Open Bio, EarlyView.
Loss of AMBRA1 in melanoma cells activates multiple oncogenic pathways associated with tumor progression. Transcriptomic and protein network analyses revealed that AMBRA1 depletion enhances MAPK/ERK signaling, angiogenesis, TGF‐β/EMT signaling, and Wnt/axon guidance pathways.
Milad Ibrahim, Marco Corazzari, Iman Osman, Jane Armstrong, Noel Carter   +4 more
wiley   +1 more source