Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation.

Abstract:

:Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labeled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as from Drosophila midguts. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.

journal_name

Elife

journal_title

eLife

authors

Amamoto R,Garcia MD,West ER,Choi J,Lapan SW,Lane EA,Perrimon N,Cepko CL

doi

10.7554/eLife.51452

subject

Has Abstract

pub_date

2019-12-09 00:00:00

issn

2050-084X

pii

51452

journal_volume

8

pub_type

杂志文章

相关文献

eLife文献大全
  • Insulin signaling controls neurotransmission via the 4eBP-dependent modification of the exocytotic machinery.

    abstract::Altered insulin signaling has been linked to widespread nervous system dysfunction including cognitive dysfunction, neuropathy and susceptibility to neurodegenerative disease. However, knowledge of the cellular mechanisms underlying the effects of insulin on neuronal function is incomplete. Here, we show that cell aut...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.16807

    authors: Mahoney RE,Azpurua J,Eaton BA

    更新日期:2016-08-15 00:00:00

  • Organic electrochemical transistor arrays for real-time mapping of evoked neurotransmitter release in vivo.

    abstract::Though neurotransmitters are essential elements in neuronal signal transduction, techniques for in vivo analysis are still limited. Here, we describe an organic electrochemical transistor array (OECT-array) technique for monitoring catecholamine neurotransmitters (CA-NTs) in rat brains. The OECT-array is an active sen...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.50345

    authors: Xie K,Wang N,Lin X,Wang Z,Zhao X,Fang P,Yue H,Kim J,Luo J,Cui S,Yan F,Shi P

    更新日期:2020-02-11 00:00:00

  • Transverse sinus injections drive robust whole-brain expression of transgenes.

    abstract::Convenient, efficient and fast whole-brain delivery of transgenes presents a persistent experimental challenge in neuroscience. Recent advances demonstrate whole-brain gene delivery by retro-orbital injection of virus, but slow and sparse expression and the large injection volumes required make this approach cumbersom...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.53639

    authors: Hamodi AS,Martinez Sabino A,Fitzgerald ND,Moschou D,Crair MC

    更新日期:2020-05-18 00:00:00

  • Listening in.

    abstract::Zebra finches communicate with each other in ways that are more complex than previously thought. ...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.11665

    authors: Jarvis ED

    更新日期:2015-10-21 00:00:00

  • Spatial sequestration and detoxification of Huntingtin by the ribosome quality control complex.

    abstract::Huntington disease (HD) is a neurological disorder caused by polyglutamine expansions in mutated Huntingtin (mHtt) proteins, rendering them prone to form inclusion bodies (IB). We report that in yeast, such IB formation is a factor-dependent process subjected to age-related decline. A genome-wide, high-content imaging...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.11792

    authors: Yang J,Hao X,Cao X,Liu B,Nyström T

    更新日期:2016-04-01 00:00:00

  • Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore.

    abstract::Pathological metabolic conditions such as ischemia induce the rupture of the mitochondrial envelope and the release of pro-apoptotic proteins, leading to cell death. At the onset of this process, the inner mitochondrial membrane becomes depolarized and permeable to osmolytes, proposedly due to the opening of a non-sel...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.23781

    authors: Zhou W,Marinelli F,Nief C,Faraldo-Gómez JD

    更新日期:2017-02-10 00:00:00

  • The Sec61 translocon limits IRE1α signaling during the unfolded protein response.

    abstract::IRE1α is an endoplasmic reticulum (ER) localized endonuclease activated by misfolded proteins in the ER. Previously, we demonstrated that IRE1α forms a complex with the Sec61 translocon, to which its substrate XBP1u mRNA is recruited for cleavage during ER stress (Plumb et al., 2015). Here, we probe IRE1α complexes in...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.27187

    authors: Sundaram A,Plumb R,Appathurai S,Mariappan M

    更新日期:2017-05-15 00:00:00

  • Adult axolotls can regenerate original neuronal diversity in response to brain injury.

    abstract::The axolotl can regenerate multiple organs, including the brain. It remains, however, unclear whether neuronal diversity, intricate tissue architecture, and axonal connectivity can be regenerated; yet, this is critical for recovery of function and a central aim of cell replacement strategies in the mammalian central n...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.13998

    authors: Amamoto R,Huerta VG,Takahashi E,Dai G,Grant AK,Fu Z,Arlotta P

    更新日期:2016-05-09 00:00:00

  • Using evolution to generate sustainable malaria control with spatial repellents.

    abstract::Evolution persistently undermines vector control programs through insecticide resistance. Here we propose a novel strategy which instead exploits evolution to generate and sustain new control tools. Effective spatial repellents are needed to keep vectors out of houses. Our approach generates such new repellents by com...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.15416

    authors: Lynch PA,Boots M

    更新日期:2016-10-25 00:00:00

  • Local and global influences on protein turnover in neurons and glia.

    abstract::Regulation of protein turnover allows cells to react to their environment and maintain homeostasis. Proteins can show different turnover rates in different tissue, but little is known about protein turnover in different brain cell types. We used dynamic SILAC to determine half-lives of over 5100 proteins in rat primar...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.34202

    authors: Dörrbaum AR,Kochen L,Langer JD,Schuman EM

    更新日期:2018-06-19 00:00:00

  • Inhibition of protein synthesis in M1 of monkeys disrupts performance of sequential movements guided by memory.

    abstract::The production of action sequences is a fundamental aspect of motor skills. To examine whether primary motor cortex (M1) is involved in maintenance of sequential movements, we trained two monkeys (Cebus apella) to perform two sequential reaching tasks. In one task, sequential movements were instructed by visual cues, ...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.53038

    authors: Ohbayashi M

    更新日期:2020-02-10 00:00:00

  • Laminin signals initiate the reciprocal loop that informs breast-specific gene expression and homeostasis by activating NO, p53 and microRNAs.

    abstract::How mammalian tissues maintain their architecture and tissue-specificity is poorly understood. Previously, we documented both the indispensable role of the extracellular matrix (ECM) protein, laminin-111 (LN1), in the formation of normal breast acini, and the phenotypic reversion of cancer cells to acini-like structur...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.26148

    authors: Furuta S,Ren G,Mao JH,Bissell MJ

    更新日期:2018-03-21 00:00:00

  • HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis.

    abstract::Iron and heme play central roles in the production of red blood cells, but the underlying mechanisms remain incompletely understood. Heme-regulated eIF2α kinase (HRI) controls translation by phosphorylating eIF2α. Here, we investigate the global impact of iron, heme, and HRI on protein translation in vivo in murine pr...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.46976

    authors: Zhang S,Macias-Garcia A,Ulirsch JC,Velazquez J,Butty VL,Levine SS,Sankaran VG,Chen JJ

    更新日期:2019-04-29 00:00:00

  • Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes.

    abstract::Extracellular vesicles (EVs) encompass a variety of vesicles secreted into the extracellular space. EVs have been implicated in promoting tumor metastasis, but the molecular composition of tumor-derived EV sub-types and the mechanisms by which molecules are sorted into EVs remain mostly unknown. We report the separati...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.47544

    authors: Temoche-Diaz MM,Shurtleff MJ,Nottingham RM,Yao J,Fadadu RP,Lambowitz AM,Schekman R

    更新日期:2019-08-22 00:00:00

  • Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation.

    abstract::During cell locomotion and endocytosis, membrane-tethered WASP proteins stimulate actin filament nucleation by the Arp2/3 complex. This process generates highly branched arrays of filaments that grow toward the membrane to which they are tethered, a conflict that seemingly would restrict filament growth. Using three-c...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.01008

    authors: Smith BA,Padrick SB,Doolittle LK,Daugherty-Clarke K,Corrêa IR Jr,Xu MQ,Goode BL,Rosen MK,Gelles J

    更新日期:2013-09-03 00:00:00

  • Building customizable auto-luminescent luciferase-based reporters in plants.

    abstract::Bioluminescence is a powerful biological signal that scientists have repurposed as a reporter for gene expression in plants and animals. However, there are downsides associated with the need to provide a substrate to these reporters, including its high cost and non-uniform tissue penetration. In this work we reconstit...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.52786

    authors: Khakhar A,Starker CG,Chamness JC,Lee N,Stokke S,Wang C,Swanson R,Rizvi F,Imaizumi T,Voytas DF

    更新日期:2020-03-25 00:00:00

  • Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.

    abstract::One of the major unanswered questions in evolutionary biology is when and how the transition between diderm (two membranes) and monoderm (one membrane) cell envelopes occurred in Bacteria. The Negativicutes and the Halanaerobiales belong to the classically monoderm Firmicutes, but possess outer membranes with lipopoly...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.14589

    authors: Antunes LC,Poppleton D,Klingl A,Criscuolo A,Dupuy B,Brochier-Armanet C,Beloin C,Gribaldo S

    更新日期:2016-08-31 00:00:00

  • Mechanistic signs of double-barreled structure in a fluoride ion channel.

    abstract::The Fluc family of F(-) ion channels protects prokaryotes and lower eukaryotes from the toxicity of environmental F(-). In bacteria, these channels are built as dual-topology dimers whereby the two subunits assemble in antiparallel transmembrane orientation. Recent crystal structures suggested that Fluc channels conta...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.18767

    authors: Last NB,Kolmakova-Partensky L,Shane T,Miller C

    更新日期:2016-07-23 00:00:00

  • Voltage-dependent dynamics of the BK channel cytosolic gating ring are coupled to the membrane-embedded voltage sensor.

    abstract::In humans, large conductance voltage- and calcium-dependent potassium (BK) channels are regulated allosterically by transmembrane voltage and intracellular Ca2+. Divalent cation binding sites reside within the gating ring formed by two Regulator of Conductance of Potassium (RCK) domains per subunit. Using patch-clamp ...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.40664

    authors: Miranda P,Holmgren M,Giraldez T

    更新日期:2018-12-11 00:00:00

  • Neuropeptide VF neurons promote sleep via the serotonergic raphe.

    abstract::Although several sleep-regulating neuronal populations have been identified, little is known about how they interact with each other to control sleep/wake states. We previously identified neuropeptide VF (NPVF) and the hypothalamic neurons that produce it as a sleep-promoting system (Lee et al., 2017). Here we show us...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.54491

    authors: Lee DA,Oikonomou G,Cammidge T,Andreev A,Hong Y,Hurley H,Prober DA

    更新日期:2020-12-18 00:00:00

  • Learning lessons from a toddler.

    abstract::Struggling to get her research project up and running in a new country, a mother gets inspiration from her young daughter. ...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.59587

    authors: Sadanandappa MK

    更新日期:2020-06-10 00:00:00

  • Evolutionary dynamics of incubation periods.

    abstract::The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dy...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.30212

    authors: Ottino-Loffler B,Scott JG,Strogatz SH

    更新日期:2017-12-21 00:00:00

  • Endoplasmic reticulum-associated SKN-1A/Nrf1 mediates a cytoplasmic unfolded protein response and promotes longevity.

    abstract::Unfolded protein responses (UPRs) safeguard cellular function during proteotoxic stress and aging. In a previous paper (Lehrbach and Ruvkun, 2016) we showed that the ER-associated SKN-1A/Nrf1 transcription factor activates proteasome subunit expression in response to proteasome dysfunction, but it was not established ...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.44425

    authors: Lehrbach NJ,Ruvkun G

    更新日期:2019-04-11 00:00:00

  • Recalibrating timing behavior via expected covariance between temporal cues.

    abstract::Individuals must predict future events to proactively guide their behavior. Predicting when events will occur is a critical component of these expectations. Temporal expectations are often generated based on individual cue-duration relationships. However, the durations associated with different environmental cues will...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.38790

    authors: De Corte BJ,Della Valle RR,Matell MS

    更新日期:2018-11-02 00:00:00

  • ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas.

    abstract::Tumor-initiating stem cells (SCs) exhibit distinct patterns of transcription factors and gene expression compared to healthy counterparts. Here, we show that dramatic shifts in large open-chromatin domain (super-enhancer) landscapes underlie these differences and reflect tumor microenvironment. By in vivo super-enhanc...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.10870

    authors: Yang H,Schramek D,Adam RC,Keyes BE,Wang P,Zheng D,Fuchs E

    更新日期:2015-11-21 00:00:00

  • LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii.

    abstract::During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mo...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.39625

    authors: Plackett AR,Conway SJ,Hewett Hazelton KD,Rabbinowitsch EH,Langdale JA,Di Stilio VS

    更新日期:2018-10-24 00:00:00

  • Diminished responses to bodily threat and blunted interoception in suicide attempters.

    abstract::Psychological theories of suicide suggest that certain traits may reduce aversion to physical threat and increase the probability of transitioning from suicidal ideation to action. Here, we investigated whether blunted sensitivity to bodily signals is associated with suicidal action by comparing individuals with a his...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.51593

    authors: DeVille DC,Kuplicki R,Stewart JL,Tulsa 1000 Investigators.,Paulus MP,Khalsa SS

    更新日期:2020-04-07 00:00:00

  • Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex.

    abstract::Complexin regulates spontaneous and activates Ca(2+)-triggered neurotransmitter release, yet the molecular mechanisms are still unclear. Here we performed single molecule fluorescence resonance energy transfer experiments and uncovered two conformations of complexin-1 bound to the ternary SNARE complex. In the cis con...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.16886

    authors: Choi UB,Zhao M,Zhang Y,Lai Y,Brunger AT

    更新日期:2016-06-02 00:00:00

  • Meru couples planar cell polarity with apical-basal polarity during asymmetric cell division.

    abstract::Polarity is a shared feature of most cells. In epithelia, apical-basal polarity often coexists, and sometimes intersects with planar cell polarity (PCP), which orients cells in the epithelial plane. From a limited set of core building blocks (e.g. the Par complexes for apical-basal polarity and the Frizzled/Dishevelle...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.25014

    authors: Banerjee JJ,Aerne BL,Holder MV,Hauri S,Gstaiger M,Tapon N

    更新日期:2017-06-30 00:00:00

  • Expanded genetic screening in Caenorhabditis elegans identifies new regulators and an inhibitory role for NAD+ in axon regeneration.

    abstract::The mechanisms underlying axon regeneration in mature neurons are relevant to the understanding of normal nervous system maintenance and for developing therapeutic strategies for injury. Here, we report novel pathways in axon regeneration, identified by extending our previous function-based screen using the C. elegans...

    journal_title:eLife

    pub_type: 杂志文章

    doi:10.7554/eLife.39756

    authors: Kim KW,Tang NH,Piggott CA,Andrusiak MG,Park S,Zhu M,Kurup N,Cherra SJ 3rd,Wu Z,Chisholm AD,Jin Y

    更新日期:2018-11-21 00:00:00