title: Single-nucleus RNA sequencing of dorsolateral prefrontal cortex from normal, pathological aging, and Alzheimer’s disease human brains

status: Public on Oct 02 2023

first: Edward

last: Lee

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

summary: We performed single-nucleus RNA sequencing of the dorsolateral prefrontal cortex from 15 normal, pathological aging, and Alzheimer’s disease human brains that varied by APOE and TREM2 genotype to analyze cell-type specific transcriptomic changes across the range of Alzheimer’s disease pathology and genetic risk factors.

overall_design: Nuclei were isolated and sequenced from normal (no amyloid or tau pathology), pathological aging (amyloid pathology without tau pathology), and Alzheimer’s disease (amyloid and tau pathology) human brain tissues that varied by Alzheimer’s disease genetic risk factors (APOE, TREM2).

first: David

middle: L

last: Dai

first: Aivi

last: Nguyen

first: Kui

last: Wang

first: Gang

last: Hu

first: Xuran

first: Zhen

last: Miao

first: Joashua

last: Azevedo

first: EunRan

last: Suh

first: Vivianna

last: Van Deerlin

last: Choi

first: Kathryn

last: Roeder

first: Mingyao

last: Li


title: Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy [CRISPR]

status: Public on Sep 11 2023

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

country: USA

institute: NYU Grossman School of Medicine

summary: KRAS G12C inhibitors (G12Ci) alone and in various combinations are being tested in multiple tumors with over-activation of the RAS/ERK pathway. KRAS plays a critical role in normal cell signaling; hence, G12Cis has been reported to create resistance. We found several novel pathways, including Hippo pathways, are enriched from significant dropouts upon MRTX849 treatment. Our results argue for testing KRAS G12C and TEAD inhibitor combinations in NSCLC patients.

overall_design: CRISPR/Cas9 screens in 4 human NSCLC cell lines (H2122, H2030, H23, HCC44) to identify SL hits to G12C inhibitor (MRTX-849) and also G12C+SHP2 (MRTX-849 +TNO155)

first: Suman

last: Mukhopadhyay

first: Alireza

last: Khodadadi-Jamayran

first: Benjamin

middle: G

last: Neel


title: Evolution of neuronal cell classes and types in the vertebrate retina [Rhabdomys]

status: Public on Oct 01 2023

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

type: Expression profiling by high throughput sequencing

summary: The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

overall_design: Single nucleus RNA-seq was performed on nuclei isolated from frozen retina. Fluorescence-activated cell sorting was used to collect DAPI-positive nuclei. For some collections, DAPI+ nculei were further seprated using NEUN/RBFOX3 and/or CHX10/VSX2 expression as an strategy to enrich for RGCs and/or bipolar cells, respectively (PLease note that he enrichment strategy was not effective for some species/samples). Approximately 8000 nuclei were recovered from each sample, and each nucleus was sequenced to a depth of ~40000 reads.

first: Aboozar

last: Monavarfeshani

first: Mu

last: Qiao

first: Allison

last: Kao

first: Yvonne

last: Kölsch

first: Ayush

last: Kumar

first: Ashley

middle: M

last: Rasys

first: Rose

last: Richardson

first: Herwig

last: Baier

first: Robert

middle: J

last: Lucas

first: Wei

first: Markus

last: Meister

middle: T

last: Trachtenberg

first: Wenjun

last: Yan

first: Yi-Rong

last: Peng

middle: R

last: Sanes

first: Karthik

last: Shekhar


title: Visceral adipose tissue contributes to improved insulin resistance after DJB via growth hormone-adiponectin axis

status: Public on Sep 22 2023

city: Jinan

first: Zitian

last: Liu

address: 107 Wenhua west road

department: Department of General Surgery

country: China

institute: Qilu Hospital of Shandong University

summary: To explore the potential mechanism of duodeno-jejunal bypass (DJB) in improving insulin resistance in diabetic rats, we suggest that adipose tissue is involved in the regulation. To investigate genetic changes in adipose tissue after duodeno-jejunal bypass, we performed RNA-seq analysis to establish the relationship between growth hormone, adiponectin, and insulin sensitivity by measuring changes in growth hormone pathways, including downstream JAK2 and MAPK pathways, and investigated non-PPAR signaling pathways. This study deepens our understanding of the complex mechanism by which DJB affects insulin resistance. This meticulous exploration fills an important gap in the literature and may pave the way for more targeted and effective diabetes management interventions.

overall_design: In order to study the effect of duodenal-jejunal bypass on adipocytes, we took samples from mesentery and groin of T2DM rats and post-DJB rats, representing visceral fat and subcutaneous fat, respectively, and analyzed the difference of gene expression in adipose tissues of different parts by RNA-seq, analyzed the changes of fat function after duodenal-jejunalbypass, and explored the potential mechanism of fat cell function changes.

first: Guangwei

last: Yang

first: Xiang

last: Zhao

first: Yang

last: Jiao

first: Zheng

last: Ge

last: Zhang

first: Zhiqiang

last: Cheng

first: Kexin

last: Wang


title: The cytoplasmic phosphate level has a central regulatory role in the phosphate starvation response of Caulobacter crescentus

status: Public on Oct 20 2023

city: Marburg

first: Martin

last: Thanbichler

address: Karl-von-Frisch-Str. 10

country: Germany

institute: MPI for Terrestrial Microbiology

summary: In bacteria, the availability of environmental inorganic phosphate is typically sensed by the conserved PhoRB two-component signaling pathway, which uses the flux through the Pst phosphate transporter as a readout of the extracellular phosphate level to control a variety of phosphate-responsive genes. While the sensing of environmental phosphate is well-established, the regulatory effects of cytoplasmic phosphate are still unclear. Here, we disentangle the physiological and transcriptional responses of Caulobacter crescentus to changes in the environmental and cytoplasmic phosphate levels. To this end, we are uncoupling phosphate uptake from the activity of the Pst system by producing an additional, heterologous phosphate transporter. This approach reveals a bi-pronged response of C.crescentus to phosphate limitation, in which the PhoRB signaling mostly facilitates the utilization of alternative phosphate sources, whereas the cytoplasmic phosphate level controls the morphological and physiological adaptation of cells to growth in conditions of global phosphate limitation. These findings open the door to a more comprehensive understanding of phosphate signaling in bacteria.

overall_design: Duplicate mRNA profiles of C. crescentus WT and mutant (ΔphoB and ΔpstS) cells expressing or not the heterologous PitA transporter from Escherichia coli, were generated by next-generation sequencing with an Illumina NextSeq 500. We next procceeded to comparative transcript analysis of the phosphate strarved mutants (ΔphoB and ΔpstS) against strains with restored cytoplamsic phosphate levels either due to the presence of the PitA transporter (ΔphoB Pxyl::Pxyl-PitA and ΔpstS Pxyl::Pxyl-PitA) or due to the presence of the native Pst transport system (WT and WT Pxyl::Pxyl-PitA)

first: Maria

last: Billini


title: DNA methylation restricts default deterministic fates towards neural and germline lineages

status: Public on Oct 09 2023

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Improved Super-Resolution Ribosome Profiling Reveals Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

status: Public on Sep 20 2023

city: East Lansing

first: Polly

last: Hsu

state: MI

address: 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of Arabidopsis Col-0 seedling. We generated 6 biological replicates of RNA-seq and Ribo-seq data for Arabidopsis Col-0 seedling. 3 of the replicates were collected after 20 minutes of 0.1% DMSO treatment and the other 3 samples were collected after 60 minutes of DMSO treatmeant. The resulting RNA-seq and Ribo-seq files were used to discover translated up-stream ORFs (uORFs) and analyze the translation efficiency of uORF-containing genes in Arabidopsis.

overall_design:
6 biological replicates of 7-day old Arabidopsis seedling collected and processed for Ribo-seq and RNA-seq sample preparation. The Ribo-seq library was sequenced with illumina single-end 50 sequencing and the RNA-seq library was sequenced with illumina paired-end 100 sequencing.

UPDATE: [07-26-2024] The titles of Samples GSM5554178-GSM5554183 were corrected from 'root' to 'seedling'.

middle: Y

first: Hsin-Yen

last: Wu


title: K562 erythroleukemia cells after erythroid differentiation caused by incubation in the presence of hemin

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology


title: Integration of human stem cell-derived in vitro systems and mouse preclinical models identifies complex pathophysiologic mechanisms in retinal dystrophy

status: Public on Sep 15 2023

city: South San Francisco

first: Christine

last: Clarke

state: California

address: 1 DNA Way

department: OMNI Bioinformatics

institute: Genentech

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Integration of human stem cell-derived in vitro systems and mouse preclinical models identifies complex pathophysiologic mechanisms in retinal dystrophy [mouse_choroid_scRNAseq]

summary: We are investigating the AMD-associated gene DRAM2. Our in vitro data showed that DRAM2 loss in human embryonic stem cell derived eye organoids generates a distinct fibroblast-like population secreting proteins related to connective tissue extracellular matrix. We generated Dram2 KO mice and did scRNA-seq on cells from the retina, and did not find any significant difference between DRAM2 KO and WT. However, our data from human organoids indicates that the difference should be in the choroid, and not in the retina of the eye. Indeed, we find that DRAM2 KO cells from mouse choroid have a growth advantage compared with WT. Here we investigate the cell type composition of mouse choroid and identify putative genes responsible for the growth advantage in DRAM2 KO choroid cells.

overall_design: 6 total samples. 3 samples of choroid from Dram2 wt/wt mice (as controls); and 3 samples from choroid of Dram2 KO/KO mice. All samples sequenced for single cell RNAseq


title: Integration of human stem cell-derived in vitro systems and mouse preclinical models identifies complex pathophysiologic mechanisms in retinal dystrophy [human_retinal_organoid]

summary: We have optimized CRISPR/Cas genome editing in human Embryonic Stem Cells (hESCs) and developed a method to generate hESC-derived eye organoids to investigate the cell type composition of these eye organoids using single cell RNA sequencing. We also investigate the consequences of the loss of a new AMD-associated gene, DRAM2, on the cell composition of the eye organoids.

overall_design: 2 samples from eye organoids. 1 organoid sample derived from DRAM2 WT stem cells with three replicates (as controls); 1 organoid sample derived from DRAM2 KO stem cells with four replicates. All samples sequenced for single cell RNAseq


title: Analysis of gene expression changes in K562 erythroleukemia cells after erythroid differentiation caused by incubation in the presence hemin [RNA-Seq]

summary: Expression of the clusters of rDNA genes influences pluripotency, but the underlying mechanisms are not known yet. The clusters shape inter-chromosomal contacts with numerous genes controlling differentiation in human cells. The fact suggests the possible role of these contacts in formation of 3D chromosomal structures and regulation of gene expression in development. We used human leukemia K562 cells induction to erythroid differentiation in order to study the changes in gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells untreated and incubated for 108h with 50 μM concentration of hemin.

middle: A

first: Yuri

middle: V

last: Kravatsky


title: Efficient generation of human cerebral organoids directly from adherent cultures of pluripotent stem cells

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

summary: This is a simple and reproducible protocol in which the hCOs generated are homogeneous and develop properly presenting proliferative ventricular zones (VZs) formed by neural and radial glia (RG) precursors that differentiate to give rise to mature neurons and glia cells. The hCOs at four weeks of maturation present additional cell types such as oligodendrocyte precursors, astrocytes, microglia and endothelial cells as shown by single‐cell RNA sequencing (scRNA‐seq) and immunohistochemistry (IHC).

overall_design: hCOs were generated directly from 2D cultures of pluripotent stem cells (AND2) and analyzed using scRNAseq

first: Isabel

last: Liste

first: Rosa

last: González-Sastre


title: Microglia gravitate toward amyloid plaques surrounded by externalized phosphatidylserine via TREM2

status: Public on Sep 01 2023

city: Seoul

first: Jong-Il

last: Kim

address: Daehakro 103

country: South Korea

institute: Seoul National University

summary: iPSC-derived brain organoids with microglial cells (assembloids) were used for this study. We used single cell RNA sequencing (scRNA-seq) to analyze the difference between APOE3 and APOE4 genotypes

overall_design: Induced pluripotent stem cell (iPSC)-derived brain organoid with microglial cells (assembloids), APOE3 vs APOE4

first: Woochan

last: Lee

first: Jong-Chan

last: Park

first: Inhee

last: Mook-Jung


title: Obox4 secures zygotic genome activation upon loss of Dux

status: Public on Aug 29 2023

city: Shinjuku

first: Haruhiko

last: Siomi

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

summary: We report that the multicopy mouse homeobox gene Obox4 encodes a transcription factor that redundantly drives ZGA. OBOX4 is highly expressed in mouse 2-cell embryos. Obox4 or Dux single knockdown is tolerated by embryogenesis, whereas Obox4/Dux double knockdown completely compromises embryonic development. Genome-wide epigenetic profiling reveals that OBOX4 binds MERVL LTRs and murine endogenous retrovirus with lysine tRNA primer (MERVK) LTRs and mediates deposition of active histone modifications.

overall_design: Following data are included in this accession: 1) RNA-seq of Obox4 over-expressed and non-over-expressed mESCs. 2) RNA-seq of scramble knockdown, Obox4 single knockdown, Dux single knockdown, Obox4/Dux double knockdown, and Obox4/Dux double knockdown with Obox4 mRNA rescued mouse 2C-embryos. 3) RNA-seq of scramble knockdown and Obox4/Dux double knockdown mouse morulae. 4) RNA-seq of 2C blastomeres of Dux KO with Obox4 WT/Het/KO genotypes. 5) RNA-seq of PlaB treated WT, Obox4 single knockout, Dux single knockout, and Obox4/Dux double knockout mESCs. 6) CUT&RUN of Obox4 in Obox4 over-expressed mESC, CUT&RUN of Dux in Dux over-expressed mESC. 7) CUT&RUN of H3K4me3, H3K27ac, and H3K27me3 in WT mESCs and Obox4 KO mESCs. 8) CUT&RUN of H3K4me3, H3K27ac, and H3K27me3 in PlaB treated WT mESCs and Obox4 KO mESCs.

first: Youjia

last: Guo

first: Tomohiro

last: Kitano


title: Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [ATAC-Seq]

status: Public on Sep 14 2023

city: CHAPEL HILL

first: SONIA

last: LAURIE

state: NC

address: 125 Mason Farm Road

institute: UNC CHAPEL HILL

summary:
Although allogeneic hematopoietic stem cell transplantation (alloHSCT) is the preferred treatment for a variety of hematologic malignancies, its use is limited by the development of acute graft-versus-host disease (aGvHD).  Type II innate lymphoid cells (ILC2s) are immune cells that play an important role in maintaining homeostasis in mucosal tissues.  Previous work has shown that ILC2 cells fail to reconstitute after chemotherapy or stem cell transplantation, though the mechanism for this finding is unclear, making delineation of the mechanisms involved in their turnover and reconstitution could have a significant impact on transplant outcomes.

We evaluated the hypothesis that the loss of ILC2 cells post-transplant induced epigenetic changes that convert ILC2 cells to ILC1-like cells.  Strikingly, single-cell, multiomic analysis of donor-derived ILC2s after transplantation revealed a previously unreported population of ILC1-like cells that differentiate from ILC2s in the small intestine lamina propria (exILC2s). To recapitulate this transdifferentiation, we modeled skewing of ILC2s in vitro with IL-12, IL-1b, and IL-18 (termed proinflammatory cytokine conditioned ILC2s, pcILC2s) and observed a reduction in Type 2 lineage-defining regulatory factors and the acquisition of proinflammatory Type 1 characteristics consistent with the phenotype and function of the exILC2s recovered post-transplant. Excitingly, our approach confirms the skewed cell population expresses ILC1 associated Tbx21 and reveals Nr4a2, Foxo1, and Fli1 as additional putative drivers of the emergent ILC1-like exILC2s after alloHSCT.

To test whether ex vivo generated pcILC2s contribute to aGVHD-mediated mortality, we infused transdifferentiated donor WT or pcILC2s and measured the clinical score and survival of recipient mice after alloHSCT in a mismatched murine model. Unlike their unmanipulated WT ILC2 counterparts, our pcILC2s accelerated morbidity and mortality. Finally, peripheral blood cells from human patients with aGvHD have an altered chromatin landscape at ILC2-associated regions of accessibility compared to transplanted controls.

These data demonstrate that following transplantation ILC2s convert to a pro-pathogenic population ILC1-like cell state. These findings provide novel insights into the contribution of ILC plasticity to mucosal dysregulation and aGvHD pathogenesis after alloHSCT in a murine model and may inform new approaches for modulating innate lymphocytes in human disease.

overall_design: MOUSE: Following 4 days of in vivo administration of 0.4 ug IL-25, C57BL/6 mice were sacrificed and lineage (CD8α [clone 53-6.7], CD4 [RM 4.4], CD3ε [145-2C11], γδTCR [UC7-13DS], TER119 [TER-119], B220 [RA3-6B2], CD11b [M1/70], NK1.1 [PK136], CD11c [N418], CD19 [MB19-1], Ly6G [1A8], and CD49b [DX5]) negative, ST2+ cells from the peritoneum and mesenteric lymph nodes were isolated and expanded in culture for 6 days in the presence of recombinant IL-7 and IL-33 (ILC2). HUMAN: Human ILC2s were isolated from a TrimaAccel LRS Chamber containing peripheral blood of health donors with the RosetteSep Human ILC2 Enrichment Kit (Stem Cell). ILC2s and pro-inflammatory conditioned ILC2s (pcILC2s) were cultured at 2.25 x 105 cells/mL in aMEM medium supplemented with 20% FBS and 1% Pen-Strep along with 50 ng/ml rIL-7, IL-2, IL-25, IL-4 and rIL-33 for the ILC2s and 50 ng/ml rIL-7, 50 ng/ml rIL-12, IL-2, rIL-1b, and 25 ng/ml rIL-18.

first: Sonia

last: Laurie

first: Joseph

middle: P

last: Foster II

first: Danny

middle: W

last: Bruce

first: Hemamalini

last: Bommiasamy

first: Oleg

last: Kolupaev

first: Mostafa

last: Yazdimamaghani

first: Samantha

last: Pattenden

first: Nelson

last: Chao

first: Stefanie

last: Sarantopoulos

first: Joel

middle: S

last: Parker

first: Ian

last: Davis

first: Jonathan

last: Serody


title: Integration of human stem cell-derived in vitro systems and mouse preclinical models identifies complex pathophysiologic mechanisms in retinal dystrophy [mouse_retina_scRNAseq]

first: Christine

last: Clarke

summary: We investigated the cell type composition of mouse retinas and identified which cell type(s) express genes we identified as being AMD-associated in human patients. We generated Dram2 KO mice to investigate how DRAM2 loss affects the mouse retina. Our in vitro data showed that DRAM2 loss affects human stem cell-derived eye organoids, we investigate if it is the case in mice.

overall_design: 2 total samples. 3 replicates of Dram2 KO/KO mouse choroid, and 3 replicates of Dram2 WT/WT mouse choroid (as controls). All samples sequenced for single cell RNAseq


title: Long- and short-read RNA sequencing from five reproductive organs of boar.

status: Public on Aug 24 2023

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: PacBio SMRTseq long reads and Illumina short reads of pig testis, epididymis, vesicular gland, prostate gland, and bulbourethral gland

overall_design: Use PacBio IsoSeq to sequence pig testis, epididymis, vesicular gland, prostate gland, and bulbourethral gland RNAs

first: Jinlong

last: Huo

first: Yu

middle: H

last: Sun

first: Zhipeng

last: Liu

first: Xia

last: Zhang


title: Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy [scRNA-seq]

first: Ziyan

last: Lin

summary: KRAS G12C inhibitors (G12Ci) alone and in various combinations are being tested in multiple tumors with over-activation of the RAS/ERK pathway. KRAS plays a critical role in normal cell signaling; hence, G12Cis could influence the signaling pathways. We found that several novel pathways including Hippo pathways are upregulated upon MRTX849 treatment. Our results argue for testing KRAS G12C and TEAD inhibitor combinations in NSCLC patients.

overall_design:
Expression profiling by high throughput sequencing. To compare gene expression of  tumor cells, and associated signaling pathways changes upon  KRAS G12Ci and KRAS G12C+SHP2i drug resistance in patients sample.
KRASG12C inhibitor, AMG510
KRASG12C inhibitor, MRTX849
SHP2 inhibitor, TNO155

first: Suman

last: Mukhopadhyay

first: Alireza

last: Khodadadi-Jamayran

first: Benjamin

last: Neel


title: Sciatic nerve injury-responsive differential mRNA profile and ribosome association efficiency of injury-induced mRNA

status: Public on Aug 18 2023

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

institute: DGIST

summary: After nerve injury in the pheripheral nervous system, axon regeneration occurs through transcriptomic changes in neuronal cell bodies. To investigate which protein-coding transcripts are up-regulated and directed to ribosomes or not, we used RiboTag+/+;Advillin-Cre+ mice, expressing HA-tagged RPL22 specifically in sensory neurons, to profile their ribosome binding RNAs in nerve injured or uninjured dorsal root ganglion(DRG) tissues using HA-IP sequencing. We analyzed the results together with total RNA transcriptomics conducted under the same conditions. Through this analysis, we found mRNA of Gpr151 gene, one of the transcript that highly responds to injury but does not direct to the ribosomes, promoting axon regeneration by a non-coding RNA function.

overall_design: Wild type or RiboTag+/+;Advillin-Cre+ mice were subjected to sciatic nerve injury using forceps in order to profile the injury-responsive changes in total RNA or ribosomal binding RNA transcriptomics within neuronal cell bodies at DRGs. The DRG tissues were collected 72 hours after the injury, and RNAs were extracted from either the whole lysates or the anti-HA immunoprecipitated lysates.

first: Yeonsoo

last: Oh

first: Hoyong

last: Jin

first: Bohm

last: Lee

first: Jinyoung

first: Yewon

last: Jeon

first: Hyemin

last: Kim

first: Minjae

last: Kwon

first: Jung-Eun

last: Shin

first: Yongcheol

last: Cho


title: Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy [RNA-seq-human]

summary: Transcriptomic analysis of NSCLC cells  either under MRTX849 treatment or Ctrl (DMSO) to identify key pathways causing resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MRTX-849 Treated NSCLC cells- H2030 and H2122


title: Comparative ATAC-seq of cultured mouse Acta2-R179C aortic SMCs versus healthy controls

status: Public on Aug 17 2023

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

summary: Explanted aortic SMCs from transgenic,Acta2-R179C/+ mice and littermate controls were cultured and subjected to assay for transposase accessible chromatin by sequencing (ATAC-seq) to determine how the R179C variant influences chromatin accessibility.

overall_design: Explanted mouse aortic SMCs from WT and Acta2SMC-R179C/+ mice were plated at a density of 100,000 cells per 6 well plate, allowed to attach overnight, then serum starved for 24 hours. Two independently prepared wells from separate frozen vials of cells were used as replicates for the experiment. Cells were harvested, counted, then frozen and processed for ATAC sequencing (cell lysis, nuclear permeabilization, transposase reaction, indexed library amplification and sequencing using a commercially available kit (Active Motif, Carlsbad, CA).

first: Callie

last: Kwartler

first: Dianna

last: Milewicz


title: Microglia-derived TGF-β1 ligand maintains microglia homeostasis via autocrine mechanism and is critical for normal cognitive function in adult mouse brain

status: Public on Aug 08 2023

city: Cincinnati

first: Yu

last: Luo

state: Ohio

address: 231 Albert Sabin Way

institute: University of Cincinnati

summary: While TGF-β signaling is essential for microglial function, the cellular source of TGF-β ligand and its spatial regulation remains unclear in adult CNS. Our data supports that microglia but not astrocytes or neurons are the primary producers of TGF-β1 ligands needed for microglial homeostasis. Microglia-Tgfb1 KO leads to activation of microglia featuring a dyshomeostatic transcriptomic profile that resembles disease-associated microglia (DAMs), injury-associated microglia, and aged microglia, suggesting that microglial self-produced TGF-β1 ligands are important in the adult CNS. Interestingly, astrocytes in the MG-tgfb1 iKO mice show a transcriptome profile that is closely aligned with A1-like astrocytes.  Additionally, using sparse mosaic single cell microglia KO of TGF-β1 ligand we established an autocrine mechanism for TGF-β signaling. Importantly MG-Tgfb1 inducible KO mice show cognitive deficits, supporting that precise spatial regulation of TGF-β1 ligand derived from microglia is critical for the maintenance of brain homeostasis and normal cognitive function in the adult brain.

overall_design: enzymatically dissociated FACS microglia and astrocytes from Cx3cr1CreERT2 controls and Cx3cr1CreERT2-Tgfb1fl/fl

first: Alicia

last: Bedolla

first: Aditi

last: Paranjpe


title: Single cell RNAseq of brian cells in the basolateral amygdala with fear conditioning

status: Public on Oct 26 2023

first: Wenfei

last: Sun

address: 318 Campus Dr.

summary: Memory encodes past experiences, thereby enabling future plans. The basolateral amygdala (BLA) is a center of salience networks that underlie emotional experiences and thus plays a key role in long-term fear memory formation. Here we used single-cell transcriptomics to illuminate the cellular and molecular architecture of the role of the basolateral amygdala in long-term memory. We identified transcriptional signatures in subpopulations of neurons and astrocytes that were memory-specific and persisted for weeks. These transcriptional signatures implicate neuropeptide and brain-derived neurotrophic factor (BDNF) signaling, mitogen-activated protein kinase (MAPK) and cAMP response element-binding protein (CREB) activation, ubiquitination pathways, and synaptic connectivity as key components of long-term memory. Strikingly, upon long-term memory formation a neuronal sub-population defined by increased Penk and decreased Tac expression constituted the most prominent component of the BLA’s memory engram.

overall_design: To study the molecular and cellular basis of memory consolidation, we applied fear conditioning paradigm on FosERcre - tdTomato reporter mice and performed single cell RNAseq for the basolateral amygdala.

first: Zhihui

last: Liu

first: Michelle

last: Chen

first: Xian

last: Jiang

first: Hua

last: Dong

first: Thomas

last: Südhof

first: Stephen

last: Quake


title: Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [10X Multiome]

first: SONIA

last: LAURIE

overall_design: Following 4 days of in vivo administration of 0.4 ug IL-25, GFP+ C57BL/6 mice were sacrificed and lineage (CD8α [clone 53-6.7], CD4 [RM 4.4], CD3ε [145-2C11], γδTCR [UC7-13DS], TER119 [TER-119], B220 [RA3-6B2], CD11b [M1/70], NK1.1 [PK136], CD11c [N418], CD19 [MB19-1], Ly6G [1A8], and CD49b [DX5]) negative, ST2+ cells from the peritoneum and mesenteric lymph nodes were isolated and expanded in culture for 6 days in the presence of recombinant IL-7 and IL-33 (ILC2). To probe the plastic nature of these cells, some were cultured in IL-7 and IL-33 for 2 days prior to the addition of IL-12, IL-1b, and IL-18 (pcILC2). In some experiments, following 6 days of expansion GFP+ ILC2s were adoptively transplanted into lethally irradiated B6D2 mice along with T cell depleted bone marrow (TCD BM) plus total splenic T cells. ILCs and T cells were given at a 1:1 ratio and mice were allowed to reconstitute for 20 days after which time animals were sacrificed and GFP+ cells were recovered from the small intestine by FACS sorting for further genomic analysis.

first: Sonia

last: Laurie

first: Joseph

last: Foster II

first: Danny

last: Bruce

first: Hemamalini

last: Bommiasamy

first: Oleg

last: Kolupaev

first: Mostafa

last: Yazdimamaghani

first: Samantha

last: Pattenden

first: Nelson

last: Chao

first: Stefanie

last: Sarantopoulos

first: Joel

last: Parker

first: Ian

last: Davis

first: Jonathan

last: Serody


title: Reconstruction of 3-dimensional tissue organization at the single-cell resolution [scRNA-seq]

city: Chicago

first: Rui

last: Yi

address: 303 E. Chicago Avenue

institute: Northwestern University

summary: We designed a neural network-based computational method that learns transcriptome-to-space mapping and reconstructs 3D tissue organization by learning from scRNA-seq and spatial transcriptomic data.

overall_design: Neonatal human foreskin samples were dissociated and analyzed using scRNA-seq.

first: Yi

last: Rui


title: Reconstruction of 3-dimensional tissue organization at the single-cell resolution

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants

status: Public on Aug 07 2023

city: Chapel Hill

first: Hyejung

last: Won

address: 116 Manning Drive, CB# 7250

institute: University of North Carolina at Chapel Hill

summary: Genome-wide association studies (GWAS) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium (LD) makes it challenging to discern causal variants. Computational finemapping prioritized thousands of credible variants, ~98% of which lie within poorly characterized non-coding regions. To functionally validate their regulatory effects, we performed a massively parallel reporter assay (MPRA) on 5,173 finemapped schizophrenia GWAS variants in primary human neural progenitors (HNPs). We identified 440 variants with allelic regulatory effects (MPRA-positive variants), with 72% of GWAS loci containing at least one MPRA-positive variant. Transcription factor binding had modest predictive power for predicting the allelic activity of MPRA-positive variants, while GWAS association, finemap posterior probability, enhancer overlap, and evolutionary conservation failed to predict MPRA-positive variants. Furthermore, 64% of MPRA-positive variants did not exhibit eQTL signature, suggesting that MPRA could identify yet unexplored variants with regulatory potentials. MPRA-positive variants differed from eQTLs, as they were more frequently located in distal neuronal enhancers. Therefore, we leveraged neuronal 3D chromatin architecture to identify 273 genes that physically interact with MPRA-positive variants. These genes annotated by chromatin interactome displayed higher mutational constraints and regulatory complexity than genes annotated by eQTLs, recapitulating a recent finding that eQTL- and GWAS-detected variants map to genes with different properties. Finally, we propose a model in which allelic activity of multiple variants within a GWAS locus can be aggregated to predict gene expression by taking chromatin contact frequency and accessibility into account. In conclusion, we demonstrate that MPRA can effectively identify functional regulatory variants and delineate previously unknown regulatory principles of schizophrenia.

sample_organism:
Homo sapiens
Adeno-associated virus

platform_organism:
Homo sapiens
Adeno-associated virus

overall_design: Massively parallel reporter assay (MPRA) on finemapped schizophrenia risk variants in human neural progenitors (HNP) and human embryonic kidney (HEK) cells

first: Jessica

last: McAfee

first: Sool

last: Lee


title: A subpopulation of human bone marrow erythroid cells displays a myeloid gene expression signature similar to that of classic monocytes

status: Public on Aug 01 2023

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: In this work, we study the expression profiles of immunity-related genes in adult bone marrow Erythroid cells.

overall_design: We profiled total RNA from the CD235a+ erythroid cells from bone marrow on NanoString Sprint Platform using Immunology V2 panel.


title: Nuclear RNA-seq in Drosophila mushroom body to determine Kdm4B target genes

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary:
Purpose: In Drosophila, we tried to determine the neural activity-dependent transcription controlled by Kdm4B. We conducted nuclear RNA-seq analysis in mushroom body in Drosophila, either in naive state or after optogenetic activation.
Methods: The nuclei of mushroom body were collected by immunoprecipitation-based method (Hirano Y., et al, 2016, Nature Communications, also see extraction protocol below). mRNA was purified from the mushroom body nuclei with oligo dT magnetic beads, and used to prepare library. After deep sequencing in triplicate using illumine Hiseq X, the adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR. The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated. The filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2
Results: Using an optimized data analysis workflow, we mapped about 9-18 million reads for ChIP-seq, and 30-40 million reads for nuclear RNA-seq to Drosophila reference genome, dm6  In ChIP-seq, binding of all proteins was enriched nearby the transcriptional start site (TSS). The binding sites determined were 1,237 for CoRest-C, 2,717 for Rpd3, and 6,684 for CBP. Importantly, among CoRest-C binding sites, overlapping sites of CoRest-C and CBP were 1,038/1,237 (83.9%), those of CoRest-C and Rpd3 were 789/1,237 (63.8%), and those of CoRest-C, Rpd3, and CBP were 704/1,237 (56.9%), suggesting that these three proteins colocalize on the specific genomic regions In nuclear RNA-seq, we found that upregulation of gene expression is robust at 10-min after 5-min optogenetic activation. The genes showing significant difference were 2,702 at this time point, in which 1,582 genes showed increase, and the rest showed decrease in the expression. Among the 1,582 increased genes, 1,055 genes were bound by CBP, supporting the idea that CBP is an important factor in activity-dependent transcription. Furthermore, 338 was bound by CoRest-C, 254 of which showed colocalization with CBP and Rpd3.
Conclusions: Our study represents activity-dependent transcription in mushroom body in Drosophila, which is mediated by Kdm4B.

overall_design: nuclear RNA-seq in mushroom body nuclei from WT Drosophila


title: MOXD1 is a gate-keeper of organ homeostasis and functions as a tumor-suppressor in neuroblastoma

status: Public on Sep 06 2023

city: Lund

first: Stina

last: Andersson

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: Neuroblastoma is a childhood cancer believed to result from dysfunctional development. Its origin during embryogenesis remains poorly understood. The lack of appropriate models has hindered in-depth mapping of early tumor-driving events. Here, we identify a novel tumor suppressor gene associating with worse outcome in MOXD1-deprived high-risk patients, by applying bulk and single cell RNA sequencing data of neuroblastoma and human fetal adrenal glands. Trunk neural crest-specific MOXD1 discriminates cell populations during normal and tumor development, with implications for deciphering neuroblastoma cell origin. We created an embryonic conditional knockout model and show that cell type-specific loss of MOXD1 leads to disrupted organ homeostasis and failed adrenal gland formation, home for neuroblastoma. We show that MOXD1 is a tumor suppressor gene in zebrafish, chick, and mice in vivo models.

overall_design:
To elucidate the transcriptional changes associated with MOXD1 overexpression, we overexpressed MOXD1 in SK-N-BE(2)c cells and performed RNAseq of in vitro grown cells (SK-N-BE(2)cCTRL (n=3) and SK-N-BE(2)cMOXD1-OE (n=3)).
We then implanted SK-N-BE(2)cCTRL cells to five mice and SK-N-BE(2)cMOXD1-OE cells to five mice. At experimental endpoint (volume >1800mm3), tumors were dissected and subjected to RNAseq.

first: Elina

last: Fredlund

first: Sofie

last: Mohlin


title: Effect of ELF3 and NLRP7 depletion on gene expression in JEG-3 cells

status: Public on Sep 05 2023

city: Cambridge

first: Bowen

last: Gu

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology Department

institute: Harvard University

summary: The distinct Class I MHC expression pattern in extravillous trophoblasts (EVT) endows them with immune-tolerant properties that enable successful pregnancy. Notwithstanding, it remains elusive how this process is elaborately regulated. Previously, we identified ELF3 as a transcription factor that governs high level HLA-C expression in EVT. In this study, we found that ELF3 also binds to the enhancer region of two NLR genes, NLRP2 and NLRP7, transactivating NLRP7 expression while suppressing expression of NLRP2. We confirmed that NLRP2 suppresses HLA-C expression while in this study we described a novel role for NLRP7 promoting HLA-C expression in trophoblasts. These two NLR genes, highly expressed in trophoblasts, are thus fine-tuned by ELF3 and enable proper expression of HLA-C in trophoblasts.

overall_design: To investigate the role of ELF3 and NLRP7 in regulating HLA-C expression in JEG-3 cells, we generated ELF3 and NLRP7 knockout JEG-3 cell lines. We then performed comparative gene expression analysis of WT and ELF3 or NLRP7 knockout cells

first: Jack

last: Strominger

first: Torsten

middle: B

last: Meissner


title: Reconstruction of 3-dimensional tissue organization at the single-cell resolution [ST]

overall_design: Human foreskin samples were fixed using FFPE protocol and then sectioned and analyzed using 10X Visium v1 FFPE ST protocol


title: Single-cell lineage tracing of ispinesib-resistant glioma cells

city: New York

first: Peter

middle: A.

last: Sims

address: 3960 Broadway

institute: Columbia University Medical Center

summary: To study the dynamics of GBM resistance and identify potential synergistic targets , we transfected PDGFR-amplified, patient-derived glioma neurospheres (TS543) with a barcoded lineage tracing library (CellTag), and treated the neurospheres with ispinesib. These genetically-modified, patient-derived neurospheres, which recapitulate key aspects of GBM heterogeneity, allow for surveillance of resistant phenotype on multiple timescales, and the barcode lineage tracing allows us to selectively analyze clones that are destined for resistance in the drug-naïve setting. We analyzed the phenotypes of the glioma cells during the long-term ispinesib treatment with single-cell RNAseq (scRNAseq), assess the stability and survival impact of drug-resistant phenotypes in the absence of drug and in orthotopic xenografts, and identified molecular markers of resistant clones in the drug-naïve setting to nominate effective drug combination.

overall_design: TS543 were seeded at ~1000 cells and were transduced with CellTag virus-laden media or normal media. TS543 were propagated for three weeks before start of treatment. TS543 were treated with 75 nM ispinesib or with vehicle DMSO. Media with ispinesib or DMSO were replenished every two or three days. Viability of TS543 were monitored as guidepost for resistance. Dead cells were removed with Dead Cell Removal Kit from Miltenyi Biotec, and scRNA-seqs were initially performed at three-day interval, and later at two- and four-week intervals.  Orthopotic cell transplantations were performed on six-year-old CrTac:NCr-Foxn1nu female mice with latest time point of TS543 treated with DMSO or ispinesib, ten mice per cohort. Mice were clinically monitored daily and sacrificed once endstage criteria were met. One mouse from each cohort was used for scRNAseq

first: Yim

last: Cheng

first: Wenting

last: Zhao

first: Matei

last: Banu

last: Canoll


title: Analysis of light induced secondary seed dormancy in Aethionema arabicum, wild type and rgl2 mutant in Cyprus accession

city: Wien

first: Zsuzsanna

last: Mérai

address: 1030 Wien Dr. Bohr-Gasse 3.

country: Austria

institute: Gregor Mendel Institute

summary: Light inhibits the seed germination in the Cypriot accession (CYP) of Aethionema arabicum. Extended light illumination also induces a secondary seed dormancy that inhibits the germination even if the seeds were transferred back to darkness. A forward genetic screen identified rgl2 mutant, that show light inhibited germination, but fails to re-enter the secondary dormancy.  This analysis aims to compare the seed transcriptome before or after the dormancy was established by light illumination (100 µmol/m2s; white light). One day light treatment (1dL) inhibits the germination but the seeds are not yet dormant. Seven day (7dL) long light treatment induces dormancy in the WT but not in the rgl2 mutant.

overall_design: WT and rgl2 mutant imbibed seeds were exposed to white light (100 µmol m-2s-1) for 23 hours (1dL) or 7 days (7dL). mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeqV4 with SR50 mode. In total, 12 samples were analyzed (2 genotype x 2 conditions x 3 repetitions)

first: Kai

last: Graeber

first: Ortrun

last: Mittelsten Scheid

first: Gerhard

last: Leubner-Metzger

first: Katarina

last: Lalatovic


title: ER-associated degradation maintains postnatal muscle hypertophy and systemic energy metabolism

status: Public on Jul 17 2023

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: The growth of skeletal muscle relies on a delicate equilibrium between protein synthesis and degradation; however, how proteostasis is managed in the endoplasmic reticulum is largely unknown. Here, we report that the SEL1L-HRD1 endoplasmic reticulum (ER)-associated degradation (ERAD) complex, the primary molecular machinery that degrades misfolded proteins in the ER, is vital to maintain postnatal muscle growth and systemic energy balance. Myocyte-specific SEL1L deletion blunts the hypertrophic phase of muscle growth, resulting in a net zero gain of muscle mass during this developmental period and significant reduction in overall body growth. In addition, myocyte-specific SEL1L deletion triggered a systemic reprogramming of metabolism characterized by improved glucose sensitivity, enhanced beiging of adipocytes, and resistance to diet induced obesity. These effects were partially mediated by the upregulation of the myokine FGF21. These findings highlight the pivotal role of SEL1L-HRD1 ERAD activity in skeletal myocytes for postnatal muscle growth, and its physiological integration in maintaining whole-body energy balance.

overall_design: Gene expression was profiled in gastrocnemius muscle isolated from 8-week-old wildtype and muscle-specific Sel1L-deficient mice.

first: Benedict

last: Abdon

first: Yusheng

last: Liang

first: Debora

last: da Luz Scheffer

first: Mauricio

last: Torres

first: Neha

last: Shrestha

first: Rachel

last: Reinert

first: You

last: Lu

first: Brent

last: Pederson

first: Amara

last: Bugarin-Lapuz

first: Sander

last: Kersten

first: Ling

last: Qi


title: Comparative gene expression profile of canine and human invariant Natural Killer T (iNKT) cells at single cell level [scRNA-seq]

city: Philadelphia

first: Antonia

last: Rotolo

state: PA

address: 3900 Chestnut Street, Apt 521

institute: University of Pennsylvania

summary: We used single cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of peripheral blood-derived canine iNKT cells relative to that of human iNKTs.

sample_organism:
Homo sapiens
Canis lupus familiaris

platform_organism:
Homo sapiens
Canis lupus familiaris

overall_design:
Canine and human iNKT cells were sorted via Magnetic Activated Cell Sorting (MACS) using a human CD1d tetramer loaded with PBS57. >90% T cells were confirmed to be iNKT by flow cytometry. 10,000 cells were immediately processed for scRNA-seq analysis. The remaining cells were expanded for 3-4 weeks in vitro. At the end of expansion, iNKT purity was confirmed by flow cytometry (>90%), prior to processing for scRNA-seq analysis.
Please note that as de-multiplexed raw files are unavailable, mixed sample records were created and individual sample information is provided in the metadata.readme.txt.

first: Eoin

middle: C

last: Whelan

first: Matthew

last: Atherton

first: Irina

last: Kulikovskaya

first: Danuta

last: Jarocha

first: Joseph

last: Fraietta

first: Michele

last: Kim

first: Eric

last: Diffenderfer

first: Keith

last: Cengel

first: Martina

last: Piviani

first: Enrico

last: Radaelli

first: Raimon

last: Duran-Struuck

first: Nicola

last: Mason


title: Gene expression profile at single cell levels of post natal day 7 mouse cerebellar subdural meningeal cells

status: Public on Aug 28 2023

city: Toronto

first: Nenad

last: Pokrajac

state: Ontario

address: 60 Leonard Ave

department: Vision Science

country: Canada

institute: University Health Network

summary: The microenvironment exerts a profound control on tumor initiation in many tissues.  In brain tumors, this process is under studied, in particular how stromal signals exert effects on cancer signaling in pre-tumor cells.  In the cerebellum, canonical Wnt signalling mediated by Norrin/Frizzled4 (Fzd4) activation in endothelial cells in the meninges exerts a potent inhibitory effect on preneoplasia and tumour progression in mouse models of Sonic hedgehog medulloblastoma (Shh-MB). Single cell transcriptome profiling and deep phenotyping of the meninges during the critical period of preneoplasia development revealed that Norrin/Fzd4 signalling maintains the activation of meningeal macrophages (mMΦs), characterized by Lyve1 and CXCL4 expression. mMΦ depletion during this critical period phenocopies the enhanced preneoplasia and tumourigenesis caused by Ndp loss. CXCL4 mediates the anti-tumourigenesis effect of mMΦs, as it antagonizes CXCL12/CXCR4 signaling in granule neuron progenitors, the MB cell of origin, to reduce cell cycle progression and promote migration away from the pre-tumour niche. Taken together, these findings are the first demonstration that mMΦs are key mediators of chemokine-regulated anti-cancer cross talk between the stroma and pre-tumour cells in the control of MB initiation.

overall_design: Primary subdural meningeal cells were from NdpWT; SmoA1+/- and NdpKO; SmoA1+/- from perinatal mice (C57/BL6 background) at age P6-P8 and dissociated and analyzed using scRNASeq.

first: Valerie

last: Wallace


title: M2 macrophages independently promote beige adipogenesis via blocking adipocyte Ets1

status: Public on Jul 01 2023

city: Nanjing

first: Kai

last: Li

address: #818, East Tianyuan Road

institute: Nanjing Medical University

summary: Beige adipocytes accumulates mitochondria and alleviates metabolic disorder via activating energy expenditure. Whether the opposing process of mitochondrial biogenesis and clearance are integrated regulated in beige adipocytes is beyond known. Here we show that DNA binding protein Ets1 suppresses beige adipocyte formation via bidirectional regulation of mitochondrial biogenesis and clearance. The expression level of Ets1 was down-regulated in browning adipocytes, and up-regulated in the subcutaneous fat of obese mice. Adipocyte Ets1 heterozygous knock-in mice showed suppressed beige adipocytes formation under cold stress, while the homozygous knock-in mice are cold intolerance. On the other hand, knocking out Ets1 in adipocytes enhanced energy expenditure and protect the mice from high fat diet induced metabolic disorders. Mechanical assay suggests Ets1 binds to the promoter region of mitochondria complex coding genes and autophagy related genes, transcriptionally suppresses mitochondrial biogenesis and activates its clearance. Our results indicate that Ets1 integrally regulates the balance of mitochondria generation and degradation, hence acts as a pivotal governor of mitochondria content and negatively regulates beige adipocyte formation.

overall_design: Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) for open chromatin in mature beige or white adipocytes derived from SVF cells.

first: Suyang

last: Wu

first: Chen

last: Qiu

first: Xiao

last: Han


title: Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning

city: Seattle

first: Sebastian

middle: Martin

last: Castillo Hair

state: Washington

address: West Stevens Way NE

department: Electrical and Computer Engineering

institute: University of Washington

summary: mRNA therapeutics are revolutionizing the pharmaceutical industry, but methods to optimize the primary sequence for increased expression are still lacking. Here, we design 5’UTRs for efficient mRNA translation using deep learning. We perform polysome profiling of fully or partially randomized 5'UTR libraries in three cell types and find that UTR performance is highly correlated across cell types. We train models on all our datasets and use them to guide the design of high-performing 5’UTRs using gradient descent and generative neural networks. We experimentally test designed 5’UTRs with mRNA encoding megaTALTM gene editing enzymes for two different gene targets and in two different cell lines. We find that the designed 5’UTRs support strong gene editing activity. Editing efficiency is correlated between cell types and gene targets, although the best performing UTR was specific to one cargo and cell type. Our results highlight the potential of model-based sequence design for mRNA therapeutics.

overall_design: Polysome profiling followed by Illumina sequencing of synthetic reporter libraries of in-vitro transcribed mRNA with random 5'UTRs.

first: Stephen

last: Fedak

first: Ban

last: Wang

first: Johannes

last: Linder

first: Kyle

last: Havens

first: Michael

last: Certo

first: Georg

last: Seelig


title: Kinetics of the Arabidopsis organellar and nuclear (post)transcriptomes under drought stress

status: Public on Aug 09 2023

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: We extended the investigation of nuclear transcript changes under drought to an overarching characterization of the post(transcriptome), including alternative splicing of nuclear transcripts, accumulation of organellar (chloroplast and mitochondrion) transcripts, editing and splicing of organellar transcripts, and furthermore, accumulation of transposable elements. To this end, long non-coding (lncRNA-Seq) instead of mRNA-Seq was applied, because the lncRNA-Seq workflow employs library preparation after ribosomal RNA depletion instead of library preparation of enriched mRNAs (mRNA-Seq).

overall_design: Analysis of differential gene expression in Arabdidopsis thaliana Col-0 and pp7l-1 plants before and after onset of drought stress


title: Gene expression profiling and the isocitrate dehydrogenase mutational landscape of temozolomide-resistant glioblastoma

status: Public on Jun 30 2023

city: Kaohsiung

first: Jui-Pei

last: Weng

address: No.70 Lien-hai Road

country: Taiwan

institute: National Sun Yat-sen University

summary: Glioblastoma(GBM), an aggressive brain cancer, occurs frequently compared to other brain tumors. This study aimed to reveal the novel mechanism of temozolomide (TMZ) resistance (chemotherapeutic drug) Meta-Z analysis, Kaplan–Meier (KM) survival analysis, protein-protein interaction (PPI) network establishment, cluster analysis of co-expressed gene networks, and hierarchical clustering of all upregulated and downregulated genes were used. Next-generation sequencing (NGS) and quantitative polymerase chain reaction (q-PCR) analysis revealed the downregulated (TIE1, CACNA2D1, CAPN6, and ADAMTS6) and upregulated (SAA1, SAA2, GDF15, and USP26) genes. Different statistical models were developed for these genes using the Z-score and the KM plot was depicted using a cohort of patient with brain tumors. The maximum number of nodes was observed in the PPI-network for ADAMTS6 and TIE1. The PPI network model of all genes showed 35 nodes and 241 edges. Immunohistochemical staining was performed using GBM with isocitrate dehydrogenase (IDH)-wild-type or IDH-mutant samples and significant upregulation of TIE1 (p<0.001) and CAPN 6 (p<0.05) protein expression was found in IDH-mutant GBM. Structural analysis revealed the IDH-mutant model using mutant residues (R132, R140, and R172). The result of this study will aid the development of novel biomarkers and new therapeutics for brain tumors.

overall_design: To investigate rarely discussed RNAs, it includes messenger RNA (mRNA) and long non-coding RNAs (lincRNA), which related to chemotherapeutic-resistant GBM. We generated a TMZ-resistant GBM8401 cell line, which is through 140 days of continuous 200 μM TMZ-treatment, to simulate GBM chemotherapeutic resistance. We performed gene expression profiling analysis using data obtained from RNA-seq of two different cells. Comparative gene expression profiling analysis of RNA-seq for GBM8401 cells and TMZ-resistant GBM8401 cell line.

first: Wu-Fu

last: Chen

first: Jimmy

middle: M

last: Chuang

first: San-Nan

last: Yang

first: Nan-Fu

first: Manojit

last: Bhattacharya

first: Hsin-Tzu

last: Liu

first: Kuldeep

last: Dhama

first: Chiranjib

last: Chakraborty

first: Zhi-Hong

last: Wen


title: Analysis of inter-chromosomal rDNA-associated contact changes in K562 erythroleukemia cells after erythroid differentiation caused by incubation in the presence of hemin [4C]

status: Public on Sep 11 2023

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

institute: Engelhardt Institute of Molecular Biology

summary: Expression of the clusters of rDNA genes influences pluripotency, but the underlying mechanisms are not known yet. The clusters shape inter-chromosomal contacts with numerous genes controlling differentiation in human cells. The fact suggests the possible role of these contacts in formation of 3D chromosomal structures and regulation of gene expression in development. We used human leukemia K562 cells induction to erythroid differentiation in order to study the genome-wide changes in inter-chromosomal rDNA-associated contacts.

overall_design: Comparative analysis of genome-wide inter-chromosomal rDNA-associated contact changes by 4C experiments for K562 cells untreated and incubated for 108h with 50 μM concentration of hemin.

first: Yuri

last: Kravatsky


title: 'A CRISPR-Cas9 mutation in sox9b long intergenic noncoding RNA (slincR) affects zebrafish development, behavior, and regeneration

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

department: Environmental Molecular Toxicology

institute: Oregon State University

summary: transcriptomic data for 48 hpf Wildtype, slincRosu3 (sg6; slincR +18 bp mutant) and BigD (slincR -131 bp mutant) zebrafish embryos developmentally exposed to TCDD.

overall_design: Two treatments- Controls ("0") and 1 ng/mL TCDD ("1") -exposed from 6-48 h post fertilization (hpf). Embryos collected at 48  hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq-500 platform, with 100 bl PE

first: Subham

last: Dasgupta

first: Jane

middle: K

last: La Du

first: Gloria

last: Garcia

first: Sizhen

last: Li

first: Konoha

last: Tomono-Duval

first: Yvonne

last: Rericha

first: Liang

last: Huang

middle: L


title: Hox gene activity directs physical forces to differentially shape chick small and large intestinal epithelia

status: Public on Jul 06 2023

city: Boston

first: Hasreet

last: Gill

address: 77 Avenue Louis Pasteur, NRB 360

department: Genetics

institute: Harvard Medical School

summary: Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis.

overall_design: To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut.

first: Sifan

last: Yin

first: Nandan

last: Nerurkar

first: John

last: Lawlor

first: ChangHee

last: Lee

first: Tyler

middle: R

last: Huycke

first: L

last: Mahadevan

first: Clifford

middle: J

last: Tabin


title: The molecular basis of specific functions of Brachyury and Eomes for mesoderm and endoderm lineage specification

status: Public on Jul 26 2023

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

institute: University Freiburg

summary: The Tbx factors Eomesodermin (Eomes) and Brachyury instruct endoderm and mesoderm specification. Both Tbx factors have common large overlap in chromatin binding sites, however their embryonic phenotypes of mutants largely differ. In this study, we delineate the distinct binding patterns and gene target sets of Eomes and Brachyury providing a molecular model of distinct fate specification programs.

overall_design:
Wildtype (WT) embryonic stem cells (ESCs) and ESCs deficient for Eomes or Brachyury were differentiated for 5 days as embryoid bodies (EBs) treated with Activin A. EOMES-GFP and BRACHYURY-GFP expression was induced by the addition of doxycycline (Eomes-GFP and Brachyury-GFP was introduced into the doxycycline-inducible locus (TRE) of EoKO, BraKO ESCs; hereafter EoKO+EoGFP, BraKO+BraGFP). Differentiated EBs were characterized by RNA-seq, ChIP-seq and ATAC-seq. 3 and 4 biological replicates were used for RNA-seq of ESCs or embryos, respectively, and biological duplicates were used for ChIP- and ATAC-seq.
In addition, the inability of Brachury to rescue the EomesΔEpi (epiblast-specific deletion of Eomes) phenotype was shown by RNA-seq of EomesBraΔEpi E7.5 embryos (knock-in allele of Brachyury coding sequence into the first exon of the Eomes genomic locus (EomesBraΔEpi); EomesBra/+, Sox2:Cre males were crossed with EomesCA/CA females to generate EomesBraΔEpi).

first: S

first: K

last: Schüle

first: J

last: Weckerle

first: G

last: Kim

first: M

last: Tekman


title: Npas4 CUT&Tag in amygdala tissue after discriminative fear conditioning

status: Public on Jul 05 2023

city: Pohang-si

first: Dahun

last: Um

address: 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673

department: Life science

institute: Pohang University of Science and Technology(POSTECH)

summary: Npas4 CUT&Tag dataset, Adult male WT C57BL/6J mice underwent discriminative fear conditioning and immediately injected saline. 90 minutes after fear conditioning, The amygdala tissue was extracted for further experiment. Npas4 CUT&Tag was performed to elucidate possible downstream targets which contributes regulation of fear expression during fear retreival.

overall_design: Fear conditioning + saline group

first: BumJIn

last: Ko

first: Rumeysa

last: Dogan


title: the effect of UIFSP on gene expression of WS1 cells after UVB exposure

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

summary: to investigate the function mechanism of UIFSP pretreatment in WS1 cells exposure to UVB,and how UIFSP regulate cell gene expression and signal transduction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data was used,which WS1 cells were divided into four groups, cell treated without UVB, cell exposed to UVB without UIFSP treatment, cell exposed to UVB with TAT-UIFSP 5 treatment,cell exposed to UVB with TAT-UIFSP 6 treatment.(Human skin fibroblast,WS1 cells grown in Dulbecco’s Modified Eagle Medium (DMEM, BI, Israel) supplemented with 1% antibioticsand 10% fetal bovine serum (FBS, BI, Israel) at 37 °C in a humidified incubator with 5% CO2. Before the UVB irradiation, cells were pre-treated with and without TAT-conjugated UIFSPs for 48 h. Cells were exposed to designated intensities of UVB (30 mJ/cm2) under a thin layer of PBS.)

first: Shuyu

last: Zhang

first: Tingyi

last: Yang


title: Dissociation Protocols used for Sarcoma Tissues Bias the Transcriptome observed in Single-cell and Single-nucleus RNA sequencing.

status: Public on Jul 21 2023

city: Houston

first: Danh

last: Truong

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: To determine whether sarcomas – tumors of mesenchymal origin – are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma, Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins.

overall_design: In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing’s sarcoma (ES), and desmoplastic small round cell tumor (DSRCT). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ Prep. These three protocols are described herein as Warm, Cold, and Nuclei protocols. For the OS specimens, we used the same Nuclei protocol and a different Warm protocol optimized for OS. For DSRCT and ES specimens, we performed the additional Cold protocol, using the cold-active protease, as we had more specimens available. Each sarcoma subtype included three PDX specimens derived from different patients. In total, we analyzed 125,831 whole-cells and nuclei across the three sarcoma subtypes and three dissociation protocols.

middle: D

first: Vidya

last: Gopalakrishnan

first: Nancy

last: Gordon

first: Najat

last: Daw

first: Joseph

middle: A

last: Ludwig


title: Prophage induction can facilitate the in vitro dispersal of multicellular Streptomyces structures - Transcriptome of Streptomyces ambofaciens ATCC 23877 grown 30 h on solid media (HT, SAF, ONA, MMM, MMM+NAG)

city: Gif-sur-Yvette

first: Stéphanie

middle: Germaine

last: Bury-Moné

address: 1 Avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell

summary:
The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). Likewise, to find the expression conditions of a complete prophage of Streptomyces ambofaciens ATCC 23877 (named 'Samy' phage/prophage), we conducted a similar approach by analyzing the transcriptomes in five solid media (HT, SAF, ONA, MMM, MMM+NAG).
The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). Likewise, to find the expression conditions of a complete prophage of Streptomyces ambofaciens ATCC 23877 (named 'Samy' phage/prophage), we conducted a similar approach by analyzing the transcriptomes in five solid media (HT, SAF, ONA, MMM, MMM+NAG).

overall_design: Around 2.10^6 spores (in 5 µl) of Streptomyces ambofaciens ATCC23877 were spotted on a sterile cellophane covering the plate and grown during 30 h at 28°C. Experiments were performed in duplicate (MMM, MMM+NAG) or in triplicates (HT, SAF, ONA).

middle: G


title: Microbial Energy Metabolism Fuels a CSF2-dependent Intestinal Macrophage Niche within Solitary Isolated Lymphoid Tissues via purinergic signaling.

status: Public on May 02 2023

first: Arthur

last: Mortha

address: 1 King's College Circle

institute: University of Toronto

summary: Gene expression comparison across CD11b+ cells from Csf2-sufficient and deficient mice.

overall_design: Steady state isolated CD11b+ cells from colon lamina propria or solitary isolated lymphoid tissues collected from 5 wild type or  Csf2-/- mice

first: Pailin

last: Chiaranunt


title: A single-cell atlas of bovine skeletal muscle tissue reveals mechanisms underlying differences in quality between Wagyu and Brahman beef.

city: Cleveland

first: Fulai

last: Jin

address: 10900 Euclid Avenue  Biomedical Research Building

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University, Cleveland

summary: Wagyu cattle are renowned for their premium beef characterized by abundant intramuscular fat (IMF). In contrast, Brahman, a popular breed in the southern coastal area of the US, generally produces tough meat with scarce IMF. However, the mechanisms underlying the differential meat quality between the two breeds are still largely unknown. Using single-cell RNAseq (scRNAseq), we identified many tissue-resident and immune cell types in Wagyu, Brahman, and Wagyu/Brahman crossbred cattle muscle. Multiple fibro/adipogenic progenitor (FAP) subpopulations were identified, including an endomysial adipogenic subpopulation and a perimysial fibrogenic subpopulation. Further analysis comparing individual FAP subpopulations between Wagyu and Brahman identified stronger pro-adipogenic gene expression in Wagyu adipogenic FAP subpopulation and higher pro-fibrogenic gene expression in Brahman fibrogenic FAP subpopulation. Overexpression of CFD, a gene upregulated in Wagyu adipogenic FAPs, enhanced the adipogenic efficiency of FAPs. Moreover, the expression of CFD in FAPs was positively correlated with the IMF content. Interestingly, the expression of CFD was identified in human FAPs but not FAPs of mouse models of intramuscular adipogenesis, suggesting that CFD is a species-specific regulator of IMF formation. Using a mouse line that allows lineage-tracing of FAPs expressing Postn, a gene upregulated in Brahman FAPs, we found that Postn expression was specifically activated during fibrogenic but not adipogenic programming. Cell-cell communication analysis revealed robust interactions between FAPs and other cell types, further suggesting the critical role of FAPs in bovine skeletal muscle growth, development, and homeostasis.

overall_design: To determine the cellular composition of skeletal muscle tissue, we performed scRNAseq using cells isolated from the Longissimus dorsi muscle of 4-month old full-blood Wagyu, purebred Brahman, and Wagyu/Brahman crossbred (50/50; abbreviated as crossbred hereafter) heifer calves. A total of 32,708 cells passed quality control, including 11,765 from Wagyu, 5,903 from Brahman, and 15,040 from crossbred.

first: Fu

last: Xing


title: Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

status: Public on May 31 2023

city: Cambridge

first: Ernest

last: Laue

address: 80 Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

summary:
Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex.
The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging.
Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity.

overall_design:
Comparison of Hi-C, chromatin binding (CTCF and SMC3), and single molecule imaging experiments +/- MBD3 (a core component of the NuRD complex).
Please note that raw data for the 'MBD3+ ES cell population Hi-C rep2 to rep5' samples is available at:
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6591/
and the Run accession is indicated in the corresponding sample description field.

first: Brian

last: Hendrich


title: Taraxasterol suppresses the proliferation and tumor growth of prostate cancer cells through the FGFR2-PI3K/AKT signaling pathway

city: Dali

first: Jinqiu

state: Yunnan Province

address: Wanhua Street

institute: Dali University

summary: To define the gene expression changes of DU145 cells after Taraxasterol treatment

overall_design: Conducting the high-throughput RNA sequencing to define the gene expression changes of DU145 cells after  Taraxasterol treatment

first: Chulin

last: Xin

first: Guangfen

last: Yin

first: Juan

last: Li


title: Tur1 regulates alternative TSS usage in Cryptococcus

status: Public on Jul 15 2023

city: Paris

first: Guilhem

last: Janbon

address: 25 rue du Dr Roux

institute: Institut Pasteur

summary: Cryptococcus neoformans is a life-threatening basidiomycete fungal pathogen responsible for meningoencephalitis in immunocompromised patients. This yeast can adapt to diverse habitats, efficiently produces virulence factors, and escapes immune surveillance. This implies intricate mechanisms underlying its gene regulation networks, which are yet to be comprehensively understood. Alternative transcription usage regulation has been identified as the major mean formeans of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. We Hhere we re-analysed transcription start site (TSS)-seq data to define genuine TSS clusters in two species of pathogenic Cryptococcus. We identified two types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (aTSS) usage genome-wide when cells switch from exponential phase to stationary phase. Tur1 has been previously shown to be essential for virulence in C. neoformans. Accordingly, we demonstrated here that a tur1? mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the Wild-type (WT) strain.

overall_design: we here performed both spliked RNA-Seq and TSS-Seq on a Cryptococcus neoformans transcription factor mutant strain tur1delta grown in exponential phase or stationnary phase

first: Thi

middle: V

last: DANG

first: Corinne

last: MAUFRAIS

first: Jessie

last: COLIN

first: Frédérique

last: MOYRAND

first: Isabelle

last: MOUYNA

first: Jean-Yves

last: COPPEE

first: Chinaemerem

middle: U

last: ONYISHI

first: Joanna

last: LIPECKA

first: Ida

last: GUERRERA

first: Robin

last: MAY

last: JANBON


title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

status: Public on Apr 28 2023

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution

status: Public on Jun 18 2023

city: Beijing

first: Cong

last: Liu

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

summary: We developed a quantitative method called GLORI to investigate m6A methylation in the mammalian transcriptome at single-base resolution.

overall_design: We provided a detailed description of the specific workflow and intricate details of the GLORI technique.Also, we conducted a detailed evaluation of the performance of GLORI.


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle

status: Public on Jun 22 2023

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

institute: Université de Sherbrooke

summary: Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.

overall_design: Subcellular direct RNA sequencing in human K562 cells.

first: Brendan

last: Smalec

first: Robert

last: Ietswaart

first: Erik

last: McShane

first: Emma

last: West

first: L

middle: S

last: Churchman

first: Albert

last: Xu

first: Ziad

last: Jowhar

first: Chantal

last: Guegler

first: Autum

last: Baxter-Koenigs

first: Becky

last: Xu Hua Fu

first: Luke

last: Gilbert

first: Stephen

middle: N

last: Floor


title: Single-cell RNA-seq and single-cell ATAC-seq of in vitro polarized mouse Th17 and Th1 cells

status: Public on Jun 01 2023

first: Pratiksha

middle: I

last: Thakore

address: 415 Main St

institute: Broad Institute

summary: We generated droplet-based single-cell RNA-seq profiles of non-pathogenic Th17, pathogenic Th17, and Th1 cells after 48 hours in polarization conditions

overall_design: We profiled in vitro polarized and in vivo mouse primary CD4 T cells inon-pathogenic Th17, pathogenic Th17, and Th1 cells harvested after 48h polarization from naive mouse CD4 T cells using single-cell RNA-seq and single-cell ATAC-seq

first: Alexandra

last: Schnell

first: Maryann

last: Zhao

first: Elena

last: Christian

first: Sarah

last: Zaghouani

first: Chao

last: Wang

first: Vasundhara

last: Singh

first: Orit

last: Rozenblatt-Rosen

first: Aviv

last: Regev

first: Vijay

last: Kuchroo


title: Population RNA-seq of in vitro polarized CD4 T cells

summary: To understand the molecular programs driving Th17 heterogeneity and CD4 T cell fate, we profiled in vitro polarized non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells using RNA-seq.

overall_design: We profiled in vitro polarized and in vivo mouse primary CD4 T cells in the following independent experiments: 1) non-pathogenic and pathogenic Th17 cells harvested polarized from naïve CD4 T cells isolated from Il17-eGFP reporter mice, sorted for GFP+ and all cells (Il17eGFP); 2) non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells harvested after 72h polarization from naive mouse CD4 T cells (CD4_diff); 3)  non-pathogenic Th17, pathogenic Th17, and Th1 harvested at time points ranging from 0 to 48 hr after polarization from naive mouse CD4 T cells (Time_course); 4) Il17-expressing Th17 cells from the draining lymph node and central nervous system of mice at the peak of experimental autoimmune encephalomyelitis response (EAE)


title: The role of HYL1 in MIR genes transcription

status: Public on Jun 21 2023

city: Poznan

first: Jakub

middle: Jacek

last: Dolata

address: Uniwersytetu Poznanskiego 6

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

summary: HYL1 (DRB1) is a double-stranded RNA-binding protein involved in miRNA processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the DCL1 protein. In this work, we report a novel function of HYL1 protein in the transcription of MIR genes. DRB1 co-localizes with RNA Polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that HYL1 protein interacts with many transcription factors. Finally, we show that the action of DRB1 is not limited to MIR genes as it impacts the expression of many other genes, the majority of which are involved in plant response to light. These discoveries add DRB1 as another player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.

overall_design:
RNA Polymerase II distribution in hyl1-2

Grant ID: 2022/45/B/NZ1/01273
Grant title: Consequences of posttranslational modifications of HYL1 for plant development
Funding source: National Science Center Poland

first: Dawid

last: Bielewicz


title: The RNA-helicase YTHDC2 serves a late role in spermatocytes during germ cell differentiation

status: Public on Mar 02 2023

city: Stanford

first: Margaret

last: Fuller

address: 279 Campus Drive, Beckman Center B300

department: Developmental Biology

country: USA

institute: Stanford University

summary: Post-transcriptional regulation of gene expression by RNA-binding proteins helps facilitate fast, clean transitions from one cell state to the next during germ cell differentiation. Previously we showed that the RNA helicase YTHDC2 is required for germ cells to properly switch from mitosis to meiosis (Bailey et al., 2017). While YTHDC2 protein is first expressed as male germ cells enter meiosis, when it is needed to shut down the mitotic program, YTHDC2 expression continues to increase and reaches its highest levels later in meiotic prophase, in pachytene spermatocytes. Here we show that YTHDC2 has an additional essential role regulating meiotic progression in late spermatocytes during mouse germ cell differentiation. Inducing conditional knockout of Ythdc2 during the first wave of spermatogenesis, after the germ cells have already initiated meiotic prophase, allowed Ythdc2-deficient germ cells to successfully reach the pachytene stage and properly express many meiotic markers. However, instead of continuing through meiotic prophase and initiating the meiotic divisions, late pachytene spermatocytes failed to transition to the diplotene stage and quickly died. Loss of function of Ythdc2 in spermatocytes resulted in changes in transcript levels for a number of genes by RNA-sequencing compared to control spermatocytes. Our findings suggest that YTHDC2 facilitates proper progression of germ cells through multiple steps of meiosis, potentially via several mechanisms of post-transcriptional RNA regulation.

overall_design: RNA profiles for control and Ythdc2 cKO testes at P14 and P16 were generated by RNA sequencing.

first: Alexis

last: Bailey

middle: T


title: Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes [AML Bulk]

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

summary: RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-Seq and snRNA-Seq, scnRNA-Seq for short), can help characterize the composition of tissues and reveal cells that influence key healthy and disease functions. However, the use of these technologies is challenging because of their relatively high costs and exacting sample collection requirements. Computational deconvolution methods that infer the composition of RNA-Seq-profiled samples using scnRNA-Seq-characterized cell types can expand the benefit of these technologies, but their effectiveness remains controversial. We produced the first systematic evaluation of deconvolution methods on datasets with either known compositions or based on concurrent RNA-Seq and scnRNA-Seq profiles. Our analyses revealed biases that are common to scnRNA-Seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-Seq and scnRNA-Seq profiles can help improve the accuracy of both scnRNA-Seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), combined RNA-Seq transformation and a dampened weighted least squares deconvolution approach to consistently outperform other methods in predicting the composition of cell mixtures and tissue samples. Moreover, our analysis suggested that only SQUID could identify outcomes-predictive cancer cell subtypes in pediatric acute myeloid leukemia and neuroblastoma datasets.

overall_design: We profiled diagnosis and relapse pair samples from 6 pediatric AML patients by bulk RNA-seq (n=12). All patients were treated at Texas Children's Cancer Center and consented to banking of tissue for research.

first: Michele

last: Redell


title: Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development

status: Public on May 11 2023

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

institute: University of Geneva

summary: The precisely orchestrated differentiation of chondrocytes during skeleton development is a critical determinant of human height and body shape. Disruptions of this process can cause severe skeletal abnormalities. The ultimate size and shape of each of over 200 bones depends on the intricate spatiotemporal regulation of chondrogenic and chondrocyte differentiation genes, but the genomic architecture coordinating these events remains poorly defined. Here we provide a comprehensive map of transcriptional enhancers specifically active in chondrocytes and show that they provide a mechanistic framework through which noncoding genetic variants can influence human stature. We isolated limb and trunk fetal chondrocytes from mice with a Col2a1 fluorescent regulatory sensor and used RNA-seq to identify 780 genes that are specifically expressed during chondrogenesis. To create cell type-specific enhancer maps, we performed ATAC-seq to map open chromatin regions and ChIP-seq for H3K27ac, an enhancer-associated histone modification, and identified 2'704 putative chondrogenic enhancer regions. Most of these enhancers (74%) showed pan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. We found that chondrogenic enhancers are enriched for the binding of several chondrogenic transcription factors including SOX9. Moreover, we find that genetic variation overlapping chondrogenic enhancers explains a higher fraction of the heritability of human adult height than the one overlapping non-chondrogenic enhancers. Finally, targeted deletions of identified enhancers at the Fgfr3, Col2a1, Hhip and, Nkx3-2 loci each exhibited a significant reduction of cognate gene expression, therefore demonstrating their functional importance. This data provides a comprehensive mapping of the chondrogenic enhancer repertoire, paving the way to interpreting the role of non-coding sequence polymorphisms in phenotypic variation and bone diseases.


title: Defining molecular and cellular landscape behind non-response to Lupus Nephritis drugs

status: Public on May 01 2023

city: GRANADA

first: Daniel

last: Toro

state: Spain

address: Avenida de la Ilustracion

department: Bioinformatics

institute: GENYO

summary:
Lupus nephritis (LN) is one of the more severe systemic lupus erythematosus manifestations with the potential of developing into end stage kidney disease. Mycophenolate mofetil (MMF) and Azathioprine (AZA) are widely used for both induction and maintenance therapy for LN, but the one year complete renal response ranges from 30-40% in most trials. Reasons for non-response are still unknown.  Thus, anticipating lack of drug efficacy in a patient could lead to early introduction of advanced therapies.  A longitudinal cohort comprising gene-expression and clinical data of responder and non-responder samples to MMF, AZA and standar of care drugs (hidroxicloroquine (HC) and HC + glococorticoids (GC) (SOC)) was retrospectively analyzed. Response to drugs was defined over time using SRI-4 scores. Differential gene expression and functional analysis were performed. Response rate was measured based on blood cell proportions. Single-cell RNA sequencing data was analyzed to identify the cell subtypes influencing non-response and their contributing genes.
SLE: Systemic Lupus Erythematosus; MMF: Mycophenolate mofetil; AZA: Azathioprine; HC: Hydroxychloroquine; PHC: Prednisone (Glucocorticoid (GC)) + HC; SOC: Standard Of Care drugs (HC and HC + PHC)

overall_design:
103 and 27 responder and non-responder samples to MMF. 24 and 30 responder and non-responder samples to AZA. 133 and 40 responder and non-responder samples to HC. 173 and 64 responder and non-responder samples to SOC (HC and HC + GC). 20 healthy control samples.
Preprint: https://doi.org/10.21203/rs.3.rs-3783877/v1

first: Raúl

last: López-Domínguez

first: Juan

last: Villatoro-García

first: Concepción

last: Marañon

last: Goldman

first: Michelle

last: Petri

first: Pedro

last: Carmona-Sáez

first: Marta

middle: E

last: Alarcón-Riquelme

last: Toro-Domínguez


title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [ChIP-seq]

first: Lucille

last: Lopez-Delisle

summary: During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the anterior part of the cluster, following Wnt signaling, and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, i.e., with an asymmetric distribution in favor of the anterior part the gene cluster. Chromatin extrusion then occurs with, along with time, successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more posterior-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.

overall_design: ChIP and ChIPmentation data of wt and mutant stembryos

first: Hocine

last: Rekaik

first: Bénédicte

last: Mascrez

first: Célia

last: Bochaton

first: Alexandre

last: Mayran

first: Denis

last: Duboule


title: The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans germ line [ChIP-Seq]

status: Public on May 14 2023

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

institute: Yale University School of Medicine

summary: The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility.  In C. elegans and other nematodes, Type-I piRNA precursor transcripts are expressed from >10,000 small, independently regulated genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. These large domains likely play a significant role in promoting germline-specific expression of piRNAs, but the underlying mechanisms are unclear.  By examining the chromatin environment specifically in isolated germ nuclei, we demonstrate that piRNA clusters are located in closed chromatin, and confirm the enrichment for the inactive histone modification H3K27me3.  The piRNA biogenesis factor USTC (Upstream Sequence Transcription Complex) plays two roles – it promotes a strong association of nucleosomes throughout the domain, and it organizes the local nucleosome environment to direct the exposure of individual piRNA genes. Overall, this work reveals new insight into how chromatin state coordinates transcriptional regulation over large genomic domains, which has implications for understanding global genome organization in the germ line.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27me3, H3K36me3, and H3K9me3 as well as Native ChIP-seq of H3 of isolated germline nuclei in C. elegans.

first: Nancy

last: Sanchez

first: Lauren

last: Gonzalez


title: Alterations in Germinal Center Formation and B Cell Activation during Severe Orientia tsutsugamushi Infection in Mice

status: Public on Jan 16 2023

city: Galveston

first: Lynn

last: Soong

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary:
We performed RNAseq on total RNA extracted from splenic B cells isolated from mice infected with Orientia tsutsugamushi to investigate the dynamic transcriptomic signature of these cells throughout infection.
We then performed differential expression analysis, meta-analysis, and gene set enrichment anaylsis using data obtained by RNA-seq of mock infected (D0) and O. tsutsugamushi-infected mice (D4 and D8).

overall_design: Splenic B cells in mice were isolated using immunomagnetic enrichment and analyzed using RNAseq.

first: Casey

last: Gonzales

first: Yuejin

last: Liang


title: The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans germ line