title: Dynamics of transcription elongation are finely-tuned by dozens of regulatory factors

status: Public on Aug 11 2021

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Understanding the complex network and dynamics that regulate transcription elongation requires quantitative analysis of RNA polymerase II (Pol II) behavior in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 42 strains of S. cerevisiae, each missing a known elongation regulator including RNA processing factors, transcription elongation factors, histone variants, chromatin modifiers, and chromatin remodelers and chaperones. For each strain, we determined differentially expressed genes, measured levels of antisense transcription, examined sites of high polymerase density, and identified single-nucleotide loci of Pol II pausing. For each elongation phenotype, we found that wild-type Pol II activity sits in the middle of the dynamic range, indicating that elongation is balanced by the opposing effects of many factors. We find that Pol II elongation at sites of RNA processing is co-transcriptionally controlled by key regulators. Furthermore, Pol II pauses frequently across gene bodies at locations that vary across deletion strains. Meta-analysis of all datasets finds that commonly differentially-expressed genes across the deletion strains exhibit more extreme antisense transcription and polymerase pausing, revealing a link between elongation activity and gene regulation. Thus, regulation of transcription elongation impacts co-transcriptional processing and overall gene expression through precisely balancing Pol II activity by a diverse array of factors.

overall_design: We deleted 42 known transcription elongation regulators including RNA processing factors, transcription elongation factors, histone variants, chromatin modifiers, chromatin remodelers and chaperones; transcriptional effects of each deletion were assayed using NET-seq. Nearly all mutant samples were analyzed in at least biological duplicate.

first: Kate

last: Lachance

first: Kevin

last: Harlen

first: Kristine

middle: L

last: Trotta

first: Erin

last: Smith

first: L

last: Churchman


title: A human liver cell-based system modeling a clinical prognostic liver signature combined with single-cell RNA-Seq for discovery of liver disease therapeutics

status: Public on Jul 19 2021

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

country: USA

institute: University of Minnesota Medical School

type: Expression profiling by high throughput sequencing

summary: Abstract: Chronic liver disease and hepatocellular carcinoma (HCC) are life-threatening with limited treatment options. The lack of clinically relevant/tractable experimental models hampers therapeutic discovery. We developed a simple and robust human liver cell-based system modeling a clinical prognostic liver signature (PLS) predicting long-term liver disease progression toward HCC. Using the PLS as a readout, followed by validation in NASH-HCC animal models and patient-derived tumorspheroids, we identified nizatidine, a histamine receptor H2 (HRH2) blocker, for treatment of advanced liver disease and HCC chemoprevention. Perturbation studies combined with scRNA-Seq analyses of patient liver tissues uncovered HRH2+, CLEC5Ahigh, MARCOlow liver macrophages and hepatocytes as nizatidine targets. The PLS model combined with scRNA-Seq of patient tissues enables discovery of urgently needed targets and therapeutics for treatment of advanced liver disease and cancer prevention.

overall_design: We performed bulk RNA sequencing of DMSO differentiated Huh751 at different time points

first: Emilie

last: Crouchet

first: Yujin

last: Hoshida

first: Thomas

middle: F

last: Baumert


title: Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae

status: Public on Jul 17 2021

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

summary: Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population.

overall_design: Cells from intact and regenerating caudal fin were used for single-cell RNA-sequencing (10xGenomics Chromium Platform), and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection (UMAP).

first: Béryl

last: Laplace-Builhé

first: Marine

last: Pratlong

first: Dany

last: Severac

first: Farida

last: Djouad


title: SEROTONIN LIMITS GENERATION OF CHROMAFFIN CELLS DURING ADRENAL ORGAN DEVELOPMENT

status: Public on Jul 28 2021

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: Adrenal gland is the major organ releasing catecholamines and regulating our stress response. The mechanisms balancing adrenal hormone-producing cells and protecting against neuroblastoma or other tumors are still enigmatic. Here we revealed that adrenergic chromaffin cells release serotonin (5HT), which acts upon their immediate progenitor “bridge” cells via 5-hydroxytryptamine receptor 3A (HTR3A). Consistently, the aggressive HTR3Ahigh human neuroblastoma cell lines reduce proliferation in response to HTR3A-specific agonists, suggesting the mechanism of anti-tumor protection. Physiological increase of 5HT in vivo caused prolongation of a cell cycle length in “bridge” progenitors leading to smaller chromaffin population and changing the balance of hormones and behavioral patterns in resulting adult rodents. These behavioral effects and smaller adrenals were mirrored in a progeny of pregnant females subjected to experimental stress, suggesting novel maternal-fetal link controlling developmental adaptations. Finally, these findings corresponded to a size-distribution of adrenals found in wild rodents with different coping strategies.

overall_design: Wnt1-Cre+/-;R26RTomato+/+ E13.5 embryos prenatally treated with 5HTP  (40 mg/kg) or vehicle (PBS) for control at E11.5 and E12.5 were harvested in iced cold PBS for smartseq2 sequencing

first: Polina

last: Kameneva

first: Viktoria

middle: I

last: Melnikova

first: Maria

middle: E

last: Kastriti

first: Anastasia

last: Kurtova

first: Emil

last: Kruykov

first: Aliia

last: Murtazina

first: Artem

middle: V

last: Artemov

first: Tatiana

middle: S

last: Kalinina

first: Nikita

last: Kydryashov

first: Michael

last: Bader

first: Jan

last: Skoda

first: Petr

last: Chlapek

first: Lucie

last: Curylova

first: Lukas

last: Sourada

first: Jakub

last: Neradil

first: Marketa

last: Tesarova

first: Massimo

last: Pasqualetti

first: Patricia

last: Gaspar

first: Vasily

middle: D

last: Yakushov

first: Boris

last: Sheftel

first: Tomas

last: Zikmund

first: Jozef

last: Kaiser

first: Kaj

last: Fried

first: Natalia

last: Alenina

first: Elena

last: Voronezhskaya

first: Igor

last: Adameyko


title: Transcriptional profiles of knockouts of m6A writer and readers in Germinal Center B cells

status: Public on Jul 21 2021

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: We performed RNA-seq (MARS-seq) on germinal center (GC) light zone and dark zone B cells sorted to purity from freshly dissociated mouse popliteal lymph nodes immunized with NP-KLH for 7 to 14 days. Germinal center B cell subsets were gated as follows: Dump (CD8, CD4, F4/80, Gr-1)- B220+ CD38- GL-7+ FAS+. Dark zone GC cells were in addition CD86lo, CXCR4hi; LZ cells were in addition CD86hi, CXCR4lo. Three different mouse models were used: AID-cre Mettl3-flox, AID-cre Ythdf2-flox, Igf2bp3-knockout. We used these data to derive differentially expressed genes between B cell subsets of control and knockout genotypes. We also performed m6A-IP on ex vivo activated wild type B cells and determined the m6A targets in B cells. These studies revealed that the GC response depends on m6A RNA methylation and the functions of specific methyl-readers Ythdf2 and Igf2bp3.

overall_design: mRNA profiles of GC B cells deficient in m6A-machinery enzymes Mettl3, Ythdf2 and Igf2bp3. m6A target profile of ex vivo activated wild type B cells.

first: Amalie

middle: C

last: Grenov

first: Sarit

last: Edelheit

first: Schraga

last: Schwartz


title: Hsf1 promotes hematopoietic stem cell fitness and proteostasis in response to ex vivo culture stress and aging

status: Public on Jul 11 2021

city: La Jolla

first: Robert

last: Signer

state: California

address: 3855 Health Sciences Drive

department: Division of Regenerative Medicine

institute: UCSD

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

overall_design: Refer to individual Series


title: Hsf1 promotes hematopoietic stem cell fitness and proteostasis in response to ex vivo culture stress and aging II

summary: Maintaining proteostasis is key to resisting stress and to promoting healthy aging. Proteostasis is necessary to preserve stem cell function, but little is known about the mechanisms that regulate proteostasis during stress in stem cells, and whether disruptions in proteostasis contribute stem cell aging is largely unexplored. We determined that ex vivo cultured mouse and human hematopoietic stem cells (HSCs) rapidly increase protein synthesis. This challenge to HSC proteostasis was associated with nuclear accumulation of Hsf1, and deletion of Hsf1 impaired HSC maintenance ex vivo. Strikingly, supplementing cultures with small molecules that enhance Hsf1 activation partially suppressed protein synthesis, rebalanced proteostasis, and supported retention of HSC serial reconstituting activity. Although Hsf1 was dispensable for young adult HSCs in vivo, Hsf1 deficiency increased protein synthesis and impaired the reconstituting activity of middle-aged HSCs. Hsf1 thus promotes proteostasis and the regenerative activity of HSCs in response to culture stress and aging.

overall_design: RNA-seq experiment to examine the effects of cell culture on hrmatopoietic stem cell (HSC) gene expression. Also tested is the effect of 17-AAG on wild-type and Hsf1-deficient HSCs.

first: Miriama

last: Kruta

first: Mary

middle: J

last: Sunshine

first: Bernadette

middle: A

last: Chua

first: Yunpeng

last: Fu

first: Ashu

last: Chawla

first: Christopher

middle: H

last: Dillingham

first: Lorena

last: San Jose

first: Bijou

last: De Jong

first: Fanny

last: Zhou


title: Transcriptome analysis of Wild Type and RhoP23H/+ mouse retinal explant in presence of a pharmacological chaperone of rhodopsin, YC-001.

status: Public on Jul 10 2021

city: Pittsburgh

first: Abhishek

last: Vats

state: PA

address: BST-3, Room no. 10051, 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

summary:
Purpose: The goals of this study is to analyze the transcriptome change during retinal explant culture treated with pharmacological chaperone of rhodopsin (YC-001).
Methods: The WT and RhoP23H/+ mouse eyes were enucleated at post natal day 15 and retinal explant were cultured for 24 hours followed by the 24 hours treatment with pharmacological chaperone of rhodopsin (YC-001) and dmso vehicle control. Another group of P23H/+ retinal explant was treated further till 9 days.  We compare the transcript of RhoP23H/+ dmso with WT dmso at 24 hour treatment (1 days in vitro (1DIV)). RhoP23H/+ YC-001 were also compared with RhoP23H/+ dmso treated retinal explant at 1DIV and 9DIV.
Results: A total of 338 differentially expressed genes (DEGs) were identified comparing the RhoP23H/+ vs. WT retinal explants with DMSO and 56 DEGs were identified comparing RhoP23H/+ YC-001 treated vs. DMSO treated retinal explant at 1 DIV. Further we observed an increased number of DEGs (8,597) comparing RhoP23H/+ vs dmso vehicle control at 9DIV. DEGs were identified using stringency with >1.5-fold change and  P-value<0.05. Interestingly, we found 40 common genes when comparing RhoP23H/+ YC-001 treated vs. DMSO at 1DIV and 9DIV.
Conclusions: This study used RNA-seq technology which represents the transcriptome of WT and RhoP23H/+ mouse retinal explant with and without pharmacological chaperone of rhodopsin (YC-001). Our NGS results show that YC-001 affect many biological pathways including visual transduction, protein homeostasis pathways and decreases the expression of immune response activation genes, to rescue the rhodospin homeostasis and retinal morphology in the retinal explant of P23H Rho mouse model of retinitis pigmentosa (RP).

overall_design: Retinal explant transcript at 1DIV and 9DIV with and without YC-001 in RhoP23H/+ autosomal dominant RP model.

first: Yuanyuan

last: Chen


title: Gene expression analysis of HER2+ breast leptomeningeal carcinomatosis

status: Public on Jul 05 2021

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary: Patient-derived primary HER2+ Leptomeningeal carcinomatosis (Lepto) cell lines were established. RNA-seq in various breast cancer cell lines were conducted to characterize the established cell lines. Gene expression analysis clearly indicated thatt Lepto cell lines are transcriptionally different from HER2 positive and negative metastatic breast cancer cell lines such as BT474 and MDA-MB-231 cells.

overall_design: Gene expression comparison between HER2+ breast leptomeningeal carcinomatosis and other breast cancer subtypes

first: Antariksh

last: Tyagi

first: Motoki

last: Takaku

first: Arunoday

last: Bhan

first: Rahul

last: Jandial


title: MicroRNA-101-3p Modulates Mitochondrial Metabolism via the Regulation of Complex II Assembly

status: Public on Jul 20 2021

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: MicroRNA-101 (miR-101) is a tumour suppressor that regulates cancer proliferation and apoptotic signalling. Loss of miR-101 increases the expression of the Polycomb Repressive Complex 2 (PRC2) subunit enhancer of zeste homolog 2 (EZH2), resulting in alterations to the epigenome and enhanced tumorigenesis. MiR-101 has also been shown to modulate various aspects of cellular metabolism, however little is known about the mechanisms involved. To investigate the metabolic pathways that are regulated by miR-101, we performed transcriptome and functional analyses of osteosarcoma cells overexpressing miR-101. We found that miR-101 downregulates multiple mitochondrial processes, including oxidative phosphorylation, pyruvate metabolism, the citric acid cycle and phospholipid metabolism. We also found that miR-101 overexpression disrupts the transcription of mitochondrial DNA (mtDNA) via the downregulation of the mitochondrial transcription initiation complex proteins TFB2M and Mic60. These alterations in protein expression disrupt mitochondrial function, with significant decreases in both basal (54%) and maximal (67%) mitochondrial respiration rates. Native gel electrophoresis revealed that this diminished respiratory capacity was associated with reduced steady-state levels of mature succinate dehydrogenase (complex II), with a corresponding reduction of complex II enzymatic activity. Furthermore, miR-101 overexpression reduced the expression of the SDHB subunit, with a concomitant disruption of the assembly of the SDHC subunit into mature complex II. Overall, we describe a new role for miR-101 as a modulator of mitochondrial metabolism via its regulation of multiple mitochondrial processes, including mtDNA transcription and complex II biogenesis.

overall_design: We performed RNA-seq on 143BTK- osteosarcoma cells (ATCC CRL-8303) transfected with either a scrambled negative control miRNA or miR-101 for 120 h with n=4 replicates

first: Sze

last: Lim

first: Yilin

last: Kang

first: Sona

last: Samuel

first: Isabel

last: Lopez-Sanchez

first: Michael

last: Gantier

first: Diana

last: Stojanovski

first: Matthew

last: McKenzie


title: Transcriptome analysis of heat stressed Nicotiana tabacum pollen tubes

status: Public on Jun 26 2021

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Along with lipidomic and metabolomic analyses, we analysed the effect of short-term heat stress on Nicotiana tabacum pollen tubes. Tubes were either grown for 3 hours at room temperature, for 6 hours at room temperature or for 3 hours at room temperature and then 37 °C for another 3 hours.

overall_design: Analysis of three different conditions (3h RT, 6h RT or 3h RT + 3h HS) in triplicates

first: Alexander

last: Rotsch

first: H

last: Krawczyk

first: Till

last: Ischebeck


title: Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells

status: Public on Jun 30 2021

city: Göttingen

first: Le

last: Xiong

address: Fassberg 11

department: Molecular Biology

institute: MPI for biophysical chemistry

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.

overall_design: TT-Seq, ATAC-Seq, ChIP-Seq

first: Erik

last: Tolen

first: Jinmi

last: Choi

first: Sergiy

last: Velychko

first: Livia

last: Caizzi

first: Taras

first: Kenjiro

last: Adachi

first: Caitlin

middle: M

last: MacCarthy

last: Lidschreiber

first: Patrick

last: Cramer

first: Hans

middle: R

last: Schöler


title: Regulation of aged skeletal muscle regeneration by extracellular

status: Public on Jul 01 2021

first: Sruthi

last: Sivakumar

address: 450 Technology drive

summary: Heterochronic blood exchange (HBE) has demonstrated that circulating factors restore youthful features to aged tissues. However, the systemic mediators of those rejuvenating effects remain poorly defined. We show that the beneficial effect of young blood on aged muscle regeneration was diminished when serum was depleted of extracellular vesicles (EVs). Whereas EVs from young animals rejuvenate aged cell bioenergetics and skeletal muscle regeneration, aging shifts EV subpopulation heterogeneity and compromises downstream benefits on recipient cells. Machine learning classifiers revealed that aging shifts the nucleic acid, but not protein, fingerprint of circulating EVs. Alterations in sub-population heterogeneity were accompanied by declines in transcript levels of the pro-longevity protein, α-Klotho, and injection of EVs improved muscle regeneration in a Klotho mRNA-dependent manner. These studies demonstrate that EVs play a key role in the rejuvenating effects of HBE and that Klotho transcripts within EVs phenocopy the effects of young serum on aged skeletal muscle.

overall_design: RNA seq data from skeletal muscle of aged mice injected with saline, young serum, or young serum depleted of EVs

first: Amrita

last: Sahu

first: Zachary

last: Clemens

first: Iliya

last: Lefterov

first: Aaron

last: Barchowsky

first: Radosveta

last: Koldamova

first: Fabrisia

last: Ambrosio


title: Dinucleotide-barcode reporter assay of breast risk variants identified PAX9 as a gene promoting breast cancer procession

status: Public on Jun 16 2021

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

country: China

institute: Shandong University

type: Genome variation profiling by high throughput sequencing

summary: We adapted the DiR barcode-based parallel reporter assay systems strategy to systematically identify the breast cancer related SNPs that affect gene expression by modulating activities of regulatory elements. Among 293 SNPs linked with GWAS-identified breast cancer-risk SNPs, we found seven functional regulatory SNPs in MCF7 cells. Further mechanism study indicates that one SNP regulates gene expression in breast cancer malignancy. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases. Our findings hold great promise in benefiting breast cancer patients with prognostic prediction.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: SNP DiR-seq report analysis in MCF7, ZR-75-1, MDA-MB-453, BT-20, BT-474, MDA-MB-468, T-47D, SK-BR-3 and BT-549 (3 independent replicates, respectively), Input plasmid library before transfection (2 independent replicates in MCF7 cell, 3 independent replicates other eight cell lines).

first: Naixia

last: Ren

first: Yingying

last: Li


title: NSD1-mediated HDAC1 recruitment reduces H3K27ac at active enhancers to safeguard associated gene expression

status: Public on Jun 15 2021

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: Epigenetics, especially histone marks, functions beyond the DNA sequences to regulate gene expression. Depletion of NSD1, which catalyzes H3K36me2, led to both up- and down-regulation of gene expression, indicating NSD1 is associated with both active and repressed gene expression. It’s known that NSD1 regulates the deposition and expansion of H3K27me3, a repressive mark for gene expression, to keep active gene transcription. However, how NSD1 functions to repress gene expression is largely unknown. Here, we found that, when NSD1 was knocked out in mouse embryonic stem cells (mESCs), H3K27ac increased correlatively with the decrease of H3K36me2 at active enhancers, which is associated with mesoderm differentiation genes, leading to elevated gene expression. Mechanistically, NSD1 recruits HDAC1, the deacetylase of H3K27ac, to chromatin. Moreover, HDAC1 knockout (KO) recapitulates the increase of H3K27ac at active enhancers as the NSD1 depletion. Together, we propose that NSD1 deposits H3K36me2 and recruits HDAC1 at active enhancers to serve as a ‘safeguard’, preventing further activation of active enhancer-associated genes.

overall_design: Examination of histone markers in enhancers  in NSD1-/- and HDAC1-/- cells.

first: Yuan

first: Yin

last: Tang

first: Yanjun

last: Zhang

first: Yixin

last: Pan

first: Junqi

last: Jia

first: Zhongxing

last: Sun

first: Weiwu

last: Zeng


title: Hsf1 promotes hematopoietic stem cell fitness and proteostasis in response to ex vivo culture stress and aging I

first: Robert

last: Signer

first: Miriama

last: Kruta

first: Mary

last: Sunshine

first: Bernadette

last: Chua

first: Yunpeng

last: Fu

first: Ashu

last: Chawla

first: Christopher

last: Dillingham

first: Lorena

last: San Jose

first: Bijou

last: De Jong

first: Fanny

last: Zhou


title: Metabolically distinct subpopulations of a secondary AML cell line are associated with differences in stemness and drug response

status: Public on Jun 13 2021

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: In recent years fatty acid metabolism has gained greater attention in haematological cancers, such as myeloid dysplastic syndrome (MDS) and secondary acute myeloid leukaemia (sAML), and has been implicated in increased proliferation and drug resistance. We have characterised two populations of FACS-sorted MDS/sAML cells - SKK-1LOW and SKK-1HIGH - that retain distinct fatty acid uptake phenotypes that are stable over time.  Transcriptomic analysis of SKK-1LOW and SKK-1HIGH confirmed differentially expressed genes. Gene ontology analysis revealed gene expression differences principally in fatty acid transport genes and receptor tyrosine kinases, of which KIT was associated with low fatty acid uptake.  SKK-1LOW resembled a leukaemic stem cell sub-population on the level of its immunophenotype and exhibited greater resistance to the hypomethylating agent, azacitadine.  Overall, this study sheds new light on the relatively under-characterised SKK-1 cell line, which may be useful for the study of MDS-to-sAML transformation.

overall_design: Characterisation of an MDS/sAML cell line in the context of metabolism and immunophenotyping.

first: Michael

last: Maher

first: Jeannine

last: Diesch

first: Raquel

last: Casquero

first: Sara

last: Vergara

first: Isabel

last: Granada

first: Marc

last: Sorigué

first: Carles

last: Cantó

first: Marcus

last: Buschbeck


title: Poor Endometrial Proliferation after Clomiphene is Associated with Altered Estrogen Action

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS


title: Poor Endometrial Proliferation after Clomiphene is Associated with Altered Estrogen Action [ChIP-Seq]

summary: We report ESR1 cistromic profiles from endometrial biopsies obtained from infertile women in the late proliferative phase who developed either optimal (≥8mm) or suboptimal (<6mm) endometrial thickness following early follicular phase exposure to 100mg clomiphene citrate for 5 days.

overall_design: ESR1 ChIP-seq was conducted on whole endometrium during the late proliferative phase. In parallel, RNA-seq analyses were conducted on whole endometrium during the late proliferative phase.

first: Leah

last: Bressler

last: Fritz

first: San-Pin

last: Wu

first: Lingwen

last: Yuan

first: Suzanna

last: Kafer

first: Tianyuan

last: Wang

first: Francesco

last: DeMayo

first: Steven

last: Young


title: The transcriptional changes in the Anopheles stephensi transcriptome after blood feeding with CSPwt or CSPmut plasmodium

status: Public on Jun 04 2021

city: ChongQing

first: Jian

last: Zhang

address: Gaotanyan Main Street

institute: Army Medical University (Third Military Medical University)

summary: We report the RNA-seq based analyses of the transcriptional changes in the Anopheles stephensi transcriptome at 7d after blood feeding with CSPwt or CSPmut plasmodium.

overall_design: Comparison of the transcriptome of Anopheles stephensi females at two blood feeding conditions (with CSPwt or CSPmut plasmodium) and one time point.

first: Feng

last: Zhu

first: Hong

last: Zheng

first: Wenyue

last: Xu


title: Chronologically Modified Androgen Receptor in Recurrent Castration Resistant Prostate Cancer and its therapeutic targeting

status: Public on Jun 01 2021

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: We uncovered a novel acetylation event at Lys609 in the Zinc finger DNA binding domain of AR (acK609-AR) that altered global transcription program, bestowing insensitivity for enzalutamide and abiraterone. ACK1 kinase small molecule inhibitor, (R)-9b not only curbed K609-acetylation, but also significantly compromised enzalutamide-resistant CRPC tumor growth.

overall_design: Examination of binding profile of Lys609-acetylated androgen receptor (acK609-AR)  in VCaP prostate cancer cells, and effect upon inhibitor R-9b treatment

first: Nupam

middle: P

last: Mahajan

first: Mithila

last: Sawant


title: Identification of miRNAs that regulate hepatitis B virus replication and are potential biomarkers for therapeutic outcome

status: Public on Jun 24 2021

city: Amsterdam

first: Vladimir

last: Loukachov

state: Noord-Holland

address: Meibergdreef 9

department: Experimental Immunology

country: Netherlands

institute: Amsterdam UMC, location AMC

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Chronic hepatitis B (CHB) infection is a serious health problem worldwide and with the current treatment a functional cure is only achieved in 3-15% of the patients. Therefore it is important to investigate novel biomarkers for treatment outcome and to develop new treatment options for CHB. miRNAs are small, non-coding RNA molecules that are involved in various cellular processes by regulating gene expression at the posttranscriptional level and also play an important role in a variety of infectious diseases. In this study we want to identify novel miRNAs that are involved in hepatitis B replication and could therefore be used as biomarkers and targeted as a potential new therapeutic option.
Methods: miRNA/small RNA NGS was performed on total RNA isolated from 10 matching plasma and liver biopsy of an identification cohort of CHB patients and 10 plasma and liver controls.
Results: We identified 23 and 18 miRNAs that were differentially expressed between controls and CHB patients in plasma and liver respectively, of which five were differentially expressed in both liver and plasma. Of these candidate miRNAs 3 were upregulated in liver and 12 in plasma from CHB and 15 were downregulated in liver and 11 in plasma.

overall_design: miRNA expression profile in plasma and liver samples obtained from chronic hepatitis B infected patients.

first: Karel

last: van Dort

first: Neeltje

last: Kootstra


title: Microarray based prediction of circular RNA expression in multiple sclerosis

status: Public on May 31 2021

city: Olsztyn

first: Marcin

middle: P.

last: Mycko

address: Warszawska 30

department: Department of Neurology

country: Poland

institute: University of Warmia and Mazury in Olsztyn

summary:
The aim was to investigate the total circular RNA profile in patients with relapsing–remitting multiple sclerosis and healthy control.
We analyzed close to 14,000 individual circRNA per sample.

overall_design: Hybridization microarray was used to define the circRNA profile in peripheral blood mononuclear cells (PBMC) from 20 untreated patients with relapsing-remitting multiple sclerosis (10 in relapse, 10 in remission) and 10 healthy controls.

first: Anna

last: Zurawska

first: Igor

last: Selmaj

first: Krzysztof

middle: W


title: Characterisation of the expression profiles during skeletal muscle stem cells (MuSCs) lineage progression

status: Public on May 25 2021

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We compared transcriptome of real quiescent MuSCs and freshly isolated MuSCs with in-situ fixation,FISC cultured for 24hrs,48hrs and 72hrs by RNA-sequencing.

overall_design: RNA-seq was performed in quiescent,freshly isolated or cultured muscle stem cells.

first: Yu

last: Zhao

first: Xiaona

last: Chen

first: Hao

last: Sun

first: Huating


title: Young and Old Pre- and Post-Transplantation ATAC Seq

status: Public on May 23 2021

city: New York

first: Paul

middle: Vincent

last: Dellorusso

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

summary: ATAC-sequencing of paired Y and O mouse HSCs pre and 3mo post lethal irradiation and HSC transplantation

overall_design: For the ATAC-seq analyses of Y and O HSCs pre- and post-transplantation, we utilized a paired approach. For each replicate, pools of 3 to 4 Y B6 mice and 1 O B6 mouse were used to isolated 10,000 pre-transplantation HSCs for ATAC-seq sample preparation and to transplant 1,000 HSCs into 5 lethally-irradiated Y BJ recipient mice alongside 300,000 Sca-1 depleted BJ helper BM cells. Post-transplantation samples were collected 3 months after transplantation from the pooled BM of the 5 recipient mice to obtain 10,000 post-transplantation HSCs for ATAC-seq sample preparation.

first: Emmanuelle

last: Passegué


title: SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 3]

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

summary: The transition from pluripotent to somatic states marks a critical checkpoint in mammalian development. How this is regulated remains largely unresolved. Here we report the identification of SS18 by whole genome CRISPR screen as a checkpoint regulator. SS18 regulates pluripotent to somatic transition or PST by relocating from pluripotent loci to somatic ones accompanied by corresponding chromatin closing-opening and remodeling of SS18-centric protein complexes. Mechanistically, SS18 forms phase separation granules (PSG) with an intrinsically disordered region (IDR) rich in tyrosine (Y), which, once mutated, no longer form PSG nor rescue SS18-/- defect in PST. These results reveal that rapid cell fate decision can be achieved by massive redistribution of chromatin remodeling37 complexes through phase separation.

overall_design: We analyzed the binding sites of Ss18, Brd7, and Pbrm1 in the process of differentiation triggered by JUN in mESCs.

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: Neuroinflammatory astrocyte subtypes in the mouse brain

status: Public on Jun 03 2021

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Transcriptomic analysis reveals the mechanism of watercore occurrence and its accelerating fruit decay

status: Public on May 19 2021

city: 扬州

first: 东贺

last: 刘

address: wenhuilu

department: Yuanzhi College

institute: yzau

summary: purpose：The purpose of this study was to compare the transcriptome data of the diseased and the non diseased pear to verify the changes of different physiological indexes of the diseased pear   Methods：By sequencing the transcriptome of the treatment group and the control group, the differences of genes related to glycoalcohol metabolism and cell wall physiological pathway metabolism between the two groups were compared. Verification by fluorescence quantitative PCR

overall_design: MRNA sequencing of normal and diseased pear pulp after 120 days of ripening

first: Xiao

last: Liu

first: Chunlei

last: Wang

first: Donghe


title: UTX Impairs Cartilage Anabolism and Aggravates Osteoarthritis by Deregulating PRC2-IGF2-Wnt10a Axis

city: Kaohsiung

first: Wei

middle: Shiung

last: Lian

address: No.123, Dapi Rd., Niaosong Dist.,

department: Department of Medic al Research

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: This study is the first manifesting a deregulation among UTX, PRC2, and H3K27me3 assembly adverse to cartilage integrity and osteoarthritis development.

overall_design: Examination of H3K27me3 histone modifications of chondrocyte in WT and Col2α1-UTX KO mice.

first: Wei Shiung

first: Feng Sheng


title: Single-cell Transcriptomic Analysis of the Mouse Crista Ampullaris

status: Public on May 18 2021

city: Seattle

first: Olivia

last: Bermingham-McDonogh

state: WA

address: 1959  NE Pacific St box 357420

department: Biological Structure

institute: University of Washington

summary: scRNA-seq on E18, P3 and P7 mouse cirsta ampullaris

overall_design: Cristae, including the ampullae, were dissected from E16 (n=6), E18 mice (n = 5), P3 mice (n = 8) and P7 mice (n= 12) in ice cold Hank’s buffered salt solution. Pooled cristae were then dissociated by treatments with collagenase and papain. Libraries for scRNA-seq were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA) per the manufacturer’s instructions. Reads were aligned to mm10 and filtered using the Cell Ranger pipeline.

first: Brent

last: Wilkerson

first: Heather

middle: L

last: Zebroski

first: Connor

last: Finkbeiner

first: Alex

last: Chitsazan

first: Kylie

last: Beach

first: Nilasha

last: Sen

first: Renee

last: Zhang


title: Transcriptional characterization of mononuclear phagocytes (MNP) in blood and BAL of healthy and sarcoidosis patients

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

summary: Pulmonary sarcoidosis is an inflammatory disease characterized by granuloma formation and heterogeneous clinical outcome. TNF is a proinflammatory cytokine contributing to granuloma formation and high levels of TNF have been shown to associate with progressive disease. Mononuclear phagocytes (MNPs) are potent producers of TNF and highly responsive to inflammation. In sarcoidosis, alveolar macrophages (AMs) have been well studied. However, MNPs also include monocytes/monocyte-derived cells and dendritic cells (DCs) that despite their central role in inflammation are poorly studied in sarcoidosis. We performed in-depth phenotypic, functional and transcriptomic analysis of MNPs subsets from blood and bronchoalveolar lavage (BAL) fluid from 108 sarcoidosis patients and 30 healthy controls.

overall_design: 108 sarcoidosis patients and 30 healthy volunteers were included in the study and gave written informed consent. All patients were newly diagnosed with pulmonary sarcoidosis as defined by WASOG guidelines based on clinical signs, chest radiography findings, an elevated CD4/CD8 T cell ratio in BAL, or non-caseating granulomas in tissue biopsies. Blood and BAL was processed within one hour after retrieval for further applications. Peripheral blood mononuclear cells (PBMCs) were isolated from blood using Ficoll density gradient centrifugation.

first: Rico

last: Lepzien

first: Anna

last: Smed-Sörensen


title: SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 2]

first: kuang

last: junqi

overall_design: We analyzed the H3K27ac  and the dynamic changes of bingding sites of Ss18 and Brg1 in the process of differentiation triggered by JUN in mESCs with or without treatment of small molecules PFI-3 and BI-9564.

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: Transcriptional profiles of placentas from systemic lupus erythematosus and normal full-term pregnancies.

status: Public on Jun 12 2021

city: Jinan

first: Zhao

middle: Ying

last: jie

address: 07 Wenhua xi road, Jinan, Shandong

department: Department of rheumatology

institute: Qilu hospital Shandong University

summary: We report transcriptional profiles of placentas from systemic lupus erythematosus pregnancies and normal full-term pregnancies. We recruited 8 pregnant patients with SLE, and 8 age-matched healthy pregnant women as normal controls. RNA-seq strand-specific libraries were constructed using the VAHTS Total RNA-seq (H/M/R)Library Prep Kit. Differentially expressed genes were identified using Cuffdiff. The P-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.The differentially expressed genes were selected using the following filter criteria: FDR <0.05 and fold-change >2.

overall_design: Examination of 8 placentas from systemic lupus erythematosus and 8 from normal full-term pregnancies.

first: Huihui

last: Li

first: Lintao

last: Sai

first: Qiang

last: Shu

first: Yingjie

last: Zhao


title: SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 1]

overall_design: We analyzed H3K27ac binding during differentiation and the dynamic changes of binding sites of Ss18 in the process of differentiation triggered by JUN in mESCs, EB and EpiSCs.


title: Poor Endometrial Proliferation after Clomiphene is Associated with Altered Estrogen Action [RNA-Seq]

first: Franco

last: Demayo

summary: We report transcriptomic profiles from endometrial biopsies obtained from infertile women in the late proliferative phase who developed either optimal (≥8mm) or suboptimal (<6mm) endometrial thickness following early follicular phase exposure to 100mg clomiphene citrate for 5 days.

overall_design: RNA-seq analyses were conducted on whole endometrium during the late proliferative phase. In parallel, ESR1 ChIP-seq was conducted on whole endometrium during the late proliferative phase.

first: Leah

last: Bressler

first: Marc

last: Fritz

first: San-Pin

last: Wu

first: Lingwen

last: Yuan

first: Suzanna

last: Kafer

first: Tianyuan

last: Wang

first: Francesco

last: DeMayo

first: Steven

last: Young


title: Differentiation of cortical brain organoids and optic nerve-like structures from retinal confluent cultures of pluripotent stem cells.

status: Public on May 12 2021

city: Sydney

first: Anai

last: Gonzalez-Cordero

state: NSW

address: 214 Hawkesbury Road, Westmead

institute: Children’s Medical Research Institute and University of Sydney

summary: single-cell RNA sequencing of a 3-month-old cortical organoid (CO)

overall_design: Advances in the study of neurological conditions have been possible due to induced pluripotent stem cell technologies and the generation of neural cell types and organoids. Numerous studies have described the generation of neural ectoderm-derived retinal and brain structures from pluripotent stem cells. However, the field is still troubled by technical challenges, including high culture costs and organoid-to-organoid variability. Here, we describe a simple and economical protocol that reproducibly gives rise to the neural retina and cortical brain regions from confluent cultures of stem cells. The spontaneously generated cortical organoids were isolated and cultured in suspension conditions for maturation and are transcriptionally comparable to organoids generated by other methods and to human foetal cortex. Furthermore, these organoids show spontaneous functional network activity with proteomic analysis and electron microscopy demonstrating the presence of synaptic components and maturity. The generation of retinal and brain organoids in close proximity also enabled their mutual isolation. Further culture of this complex organoid system demonstrated the formation of optic nerve-like structures connecting retinal and brain organoids, which might facilitate the investigation of the mechanisms of neurological diseases of the eye and brain.

first: Milan

last: Fernando

first: Scott

last: Lee

first: Jesse

last: Wark

first: Di

last: Xiao

first: Hani

last: Kim

first: Grady

last: Smith

first: Ted

last: Wong

first: Erdahl

last: Teber

first: Pengyi

last: Yang

first: Mark

middle: E

last: Graham


title: SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [RNA-Seq]

first: kuang

last: junqi

summary: The transition from pluripotent to somatic states marks a critical checkpoint in mammalian development. How this is regulated remains largely unresolved. Here we report the identification of SS18 by whole genome CRISPR screen as a checkpoint regulator. SS18 regulates pluripotent to somatic transition or PST by relocating from pluripotent loci to somatic ones accompanied by corresponding chromatin closing-opening and remodeling of SS18-centric protein complexes. Mechanistically, SS18 forms phase separation granules  (PSG) with an intrinsically disordered region  (IDR) rich in tyrosine  (Y), which, once mutated, no longer form PSG nor rescue SS18-/- defect in PST. These results reveal that rapid cell fate decision can be achieved by massive redistribution of chromatin remodeling37 complexes through phase separation.

overall_design: We analyzed the transcriptome expression profiles  (RNA-seq) in WT and Ss18-KO mESCs during the process of JUN triggered differentiation

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets

status: Public on May 20 2021

city: Heidelberg

first: Lukas

last: Mathur

address: Meyerhofstraße 1

department: Genome Biology

institute: EMBL


title: Young and Old Mouse Parabiosis Hematopoietic Stem Cell RNA Sequencing

status: Public on May 17 2021

first: Paul

last: Dellorusso

summary: RNA sequencing of hematopoietic stem cells isolated from young (8-12 week) and old (24-27 month) BL6 mice from experimental groups that are intended to describe the transcriptomic consequences of parabiosis on the function of old hematopoietic stem cells.

overall_design: 35 samples were processed, of which 30 met library and sequencing quality thresholds to be included in our analysis. These 30 samples represent eleven different biological groups. Some groups have only two biological replicates (YISOB6, YISOBJ, OHETB6X), but most have a minimum of three biological replicates per group (YB6CNT, YBJCNT, YHETBJ, OHETB6, OISOB6, OB6CNT). Two biological groups only had one replicate (OISOBJ and OBJCNT) and were not utilized for statistical differential expression testing unless they were merged with another sample group.

first: Evgenia

last: Verovskaya

first: Theodore

last: Ho

first: Emmanuelle

last: Passegué


title: Targeted ileal transcriptomic analysis in paediatric IBDs.

city: Southampton

first: Sarah

last: Ennis

state: Hampshire

address: Southampton General Hospital, SO16 6YD

department: Human Development and Health

country: United Kingdom

institute: University of Southampton

summary: We employed contemporary targeted autoimmune RNA sequencing (HTG molecular diagnostics, Autoimmune panel) to ileal tissue derived from 96 paediatric IBD, Crohn's disease, Ulcerative colitis patients and controls. Weighted-gene-co-expression-network-analysis (WGCNA) was performed and differentially expressed genes (DEGs) were determined. We integrated clinical data to determine co-expression modules associated with time to relapse.

overall_design:
Transcriptomic analysis of ileal biopsies of 96 control, treatment-naïve, established Crohn's disease and Ulcerative colitis.

**Raw Data Not Provided**

first: James

last: Ashton

first: Konstantinos

last: Boukas

last: Davies

first: Imogen

last: Stafford

first: Andres

middle: F

last: Vallejo

first: Rachel

last: Haggarty

first: Tracy

last: Coelho

first: Akshay

last: Batra

first: Nadeem

last: Afzal

first: R

last: Beattie

first: Marta

last: Polak


title: Transcriptional profiling of short telomere iPS derived sorted SFTPC+ iAT2 cells

status: Public on May 07 2021

city: Philadelphia

first: Rafael

middle: Jesus

last: Fernandez

address: 422 Curie Boulevard

institute: University of Pennsylvania

summary: Dyskeratosis congenita (DC) is a rare genetic disorder characterized by deficiencies in telomere maintenance leading to very short telomeres and the premature onset of certain age_Related diseases, including pulmonary fibrosis (PF).  PF is thought to derive from epithelial failure, particularly that of type II alveolar epithelial (AT2) cells, which are highly dependent on Wnt signaling during development and adult regeneration.  We use human iPSC-derived AT2 (iAT2) cells to model how short telomeres affect AT2 cells. Cultured DC mutant iAT2 cells accumulate shortened, uncapped telomeres and manifest defects in the growth of alveolospheres, hallmarks of senescence, and apparent defects in Wnt signaling. The GSK3 inhibitor, CHIR99021, which mimics the output of canonical Wnt signaling, enhances telomerase activity and rescues the defects. These findings support further investigation of Wnt agonists as potential therapies for DC related pathologies.

overall_design: mRNA expression profiles of sorted SFTPC+ iAT2 cells derived from late passage (Px70) iPS cells

last: Fernandez III

first: F Brad

middle: B

last: Johnson

first: John

last: Tobias


title: Endogenous retrovirus control of homeostatic and inflammatory responses to the microbiota [RNA-seq]

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: The microbiota plays a fundamental role in regulating host immunity. However, the processes that initiate homeostatic immunity to the microbiota remain largely unknown. Here, we show that the skin microbiota promotes the discrete expression of defined endogenous retrovirus (ERVs). Keratinocyte-intrinsic responses to ERVs depended on cGAS/STING signaling and promoted the induction commensal specific T cells including CD8+, CD4+ and MAIT cells. Inhibition of reverse transcriptase significantly impacted these responses resulting in impaired homeostatic immunity to the microbiota and associated tissue repair function. Conversely, diets that caused an increase in dietary lipids primed the skin for aberrant ERV expression in response to commensal colonization, leading to tissue inflammation. Together, our results support the idea that the host may have coopted its endogenous virome as a means to communicate with the exogenous microbial microbiota, resulting in a multikingdom dialogue that controls both tissue homeostasis and inflammation.

overall_design: Four week old mice were placed on a high fat or control diet for 6 weeks prior to association with S. epidermidis. Cells were sorted on DAPI– CD45– CD31– CD34– CD49f+ Sca-1+ cells.

first: Yasmine

last: Belkaid

first: Siddharth

last: Krishnamurthy

first: Djalma

last: Souza


title: A cell-based model unravels drivers for hepatocarcinogenesis and targets for clinical chemoprevention

status: Public on Jun 28 2021

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

sample_organism:
Homo sapiens
Rattus norvegicus
Hepacivirus hominis


title: Neuroinflammatory astrocyte subtypes in the mouse brain [Visium]

first: Philip

last: Hasel

summary: Spatial transcriptomics  of saline- and LPS-injected Aldh1l1egfp mice 24 h after injection

overall_design: Brains from 3 saline- and 3 LPS-injected female mice were sectioned to 10 um and used for Visium Spatial Transcriptomics

first: Shane

last: Liddelow


title: Endogenous retrovirus control of homeostatic and inflammatory responses to the microbiota [scRNA-seq]

status: Public on May 05 2021

summary: How the homeostatic dialogue between the host and its microbiota is initiated remains largely unknown. Here, we show that immune response to the skin microbiota is dependent on activity of endogenous retroviruses. Notably, response to the microbiota promotes a discrete transcriptional induction of retroelements. As such, keratinocyte intrinsic sensing of endogenous retrovirus (ERV) derived DNA via cGAS/STING promotes the induction of commensal specific T cells including CD8+, CD4+ and MAIT cells. Consequently, inhibition of reverse transcriptase activity impairs both homeostatic immunity to the microbiota and associated tissue repair function. On the other hand, altered diet and in particular increase in dietary lipids primed the skin for aberrant ERV expression in the context of microbiota exposure leading to tissue inflammation. Together our results support the idea that the host may have coopted its endogenous virome as a means to communicate with exogenous microbiota resulting in a multikingdom dialogue that controls both tissue homeostasis and inflammation.

overall_design: Examination of keratinocytes in control, S. epi treated and S. epi + anti-retroviral drug treated mice in single cell RNA-seq.

middle: S

last: Lima-Junior


title: Endogenous retrovirus control of homeostatic and inflammatory responses to the microbiota [RNA-seq 2]

first: D


title: Endogenous retrovirus control of homeostatic and inflammatory responses to the microbiota

overall_design: Refer to individual Series


title: In Situ Structure of Intestinal Apical Surface Reveals Nanovilli on Microvilli

status: Public on Apr 30 2021

city: Beijing

first: Guangshuo

last: Ou

address: Tsinghua University Haidian District

department: School of Life Science

institute: Tsinghua university

summary: Microvilli are actin bundle-supported membrane protrusions essential for absorption, secretion, and sensation. Microvilli defects cause human diseases, including gastrointestinal disorders and inherited deafness; however, mechanisms controlling microvilli formation and organization remain unclear. Here, we study microvilli by vitrifying the C. elegans larvae and mouse intestinal tissues with high-pressure freezing, thinning them by cryo-focused ion beam milling, cryo-electron tomography, and sub-tomogram averaging. We show that hundreds of previously unrecognized stick-like structures, which we refer to as nanovilli, decorate the lateral surface of C. elegans and mouse microvilli. The C. elegans 37.5-nm long and 4.5-nm wide nanovilli are composed of the protocadherin family protein CDH-8. Loss of nanovilli slows down animal growth and increases the number of Y-shaped microvilli, intermediate structures when a microvillus splits from its tip and separates into two. Our results indicate that nanovilli space microvilli and suggest a microvilli division model through which microvilli assemble with striking uniformity.

overall_design: The  SPLiT-seq of late L3 larvae wild-type worms.

first: Hao

last: Zhu

first: Meijing

last: Li

first: Ruixue

last: Zhao

first: Xueming


title: Alterations in chromosome spatial compartmentalization classify prostate cancer progression [Hi-C]

status: Public on May 01 2021

city: Knoxville

first: Rebeca

last: SanMartin

state: TN

address: 1311 Cumberland Avenue

institute: University of Tennessee Knoxville

summary: Through a systematic analysis of chromosome conformation capture in a cohort of cells that model cancer progression, San Martin et.al. find that rearrangement of the 3D genome structure in prostate cancer is a potential mechanism for disease exacerbation and that genome-wide compartment identity can classify cancer according to progression

overall_design:
Analysis of the 3D genomic structure of a cohort of cell lines in the continuum of prostate cancer, from normal to metastatic
Pleaes note that each processed data *tar file was generated from all replicates and is linked to the corresponding '*HiC-1' sample records.

last: San Martin

first: Prijoyit

last: Das

first: Renata

last: Dos Reis Marquez

first: Xu

last: Yang

first: Rachel

last: McCord


title: Genome wide expression change by MCF-7 cells treated with MST1/2 inhibitor

city: Shenzhen

first: Juntao

last: Xu

state: Guangdong

address: Yuehai Subdistrict, Nanshan District

institute: Philrivers

summary: We aim to the investigate the role of MST inhibitor in breast cancer progression. MCF-7 cells were used as the model.

overall_design: The MCF-7 cells were treated with vehicle or 3 uM MST1/2 inhibitor . After 6 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Jian


title: Transcriptomic analysis of human cancer cell lines treated with the histone deacetylase inhibitor romidepsin

status: Public on Apr 29 2021

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
Global gene expression analysis was performed on 8 cancer cell lines after treatment with romidepsin for 6h, or 6h treatment followed by 12 h incubation with drug free medium. The cell lines were selected based on their response spectrum to romidepsin, and included HUT78, LOXIMVI, M14, A549, MDA231, ACHN, MiaPaca2 and PC3. Differentially expressed genes (DEG) included genes involved in DNA damage repair (DDR) pathways.
The Affymetrix Human Genome U133 Plus 2.0 platform was used for the gene expression profiling.

overall_design: 57 samples were analyzed in triplicate. All 8 cell lines were treated with romidepsin (46 nm/ 25 ng/ml) for 6 hours, or 6h followed by 12 hours incubation in drug-free medium (18h). The romidepsin effect was evaluated against DMSO treated controls

first: Maryam

last: Safari

first: Susan

last: Bates

first: Agnes

last: Basseville


title: PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: The pivotal interplay between light receptors and PHYTOCHROME-INTERACTING FACTORs (PIFs) serves as an essential regulatory hub that perceives and integrates environmental cues into the plant’s transcriptional networks. A critical control component of environmentally-responsive gene networks is the histone variant H2A.Z which provides transcriptional plasticity and prevents undesired gene activation. However, the functional relationship between PIF transcription factors (TFs) and H2A.Z is despite their outstanding importance, only poorly understood. Here, we describe a photo-genomic approach that utilizes the rapid and reversible light-mediated manipulation of PIF7 activity to visualize PIF7 DNA binding and H2A.Z occupancy kinetics on a genome-wide scale. Strikingly, we discovered that PIF shape the H2A.Z landscape in a light quality-dependent manner. We found that DNA binding of PIF7 is not regulated by H2A.Z but most importantly, PIFs initiate H2A.Z eviction and through the direct interaction with EIN6 ENHANCER (EEN), a crucial subunit of INO80 chromatin remodeling complex. Collectively, we describe a PIF-INO80 regulatory module that controls plant growth in response to environmental changes.

overall_design: ChIP-seq and RNA-seq was applied to comprehensively profile the H2A.Z landscape in response to low R:FR light exposure

first: Björn

middle: C

last: Willige

first: Mark

last: Zander

first: Chan

middle: Y

last: Yoo

first: Amy

last: Phan

first: Renne

last: Garza

first: Shelly

last: Trigg

first: Yupeng

last: He

last: Nery

first: Huaming

last: Chen

first: Meng

first: Joanne

last: Chory


title: Genome-wide maps of histone modifications in hematopoietic stem cells in control or H3.3 null LKS cells.

city: New York

first: Shahin

last: Rafii

state: New York

address: 413 East 69th Street

institute: Weill Cornell Medicine

summary: In order to understand the epigenetic events following the deletion of histone variant H3.3 in mouse hematopoieitc stem cells both in vitro or in vivo (Rosa26creERT2+ H3.3Af/f, H3.3B -/- mice), we sorted cKit+Sca1+Lin- HSPCs and utilized an MNase based native ChIP protocol to characterize the four types of histone modifications H3K27me3, H3K9me3, H3K27ac and H3K4me3 changes. Matching with the biased granulocyte-macrophage progenitor differentiation potential of H3.3 null HSPCs, we found that there is significant global gain of H3K27me3 marks when H3.3 is deleted. Conversely, there is a predominant loss of H3K9me3 marks globably in H3.3 null HSPCs. We hypothesize that the gain of H3K27me3 marks is what udnerlines the dimished stemness and lineage differentiation capacities toward red blood cell lineages, the mimicing of GMPs for H3.3 null HSPCs. On the other hand, loss of H3K9me3 at ERV regions derepssed ERVs and induces interferon responses. The H3K9me3 reduced/ERV regions may serve as enhancer regions for transcription factors to bind and might confer the H3.3 null HSPCs adaptive advantage for enhanced survival.

overall_design: Examination of 4 different histone modifications in LKS cells in vivo in H3.3BKO or H3.3A, H3.3B double KO (DKO) mice. Examination of H3.3 enrichment in wild type LKS cells in vitro or in vivo.

first: Peipei

last: Guo


title: Expression data from wild type or KLF15 knockout mouse skeletal muscle after immobilization

status: Public on Apr 22 2021

city: kobe

first: Yu

last: Hirata

address: chuo-ku, kusunoki-chou, 7-5-2

country: Japan

institute: Kobe University

summary:
Evidence suggests that immobilization is a promoting factor of sarcopenia; mechanism how immobilization accelerates the development of sarcopenia is not known. We have recently established a model of immobilization-induced skeletal muscle mass loss in mice.
We used microarrays to detail the global programme of gene expression underlying skeletal muscle atrophy in immobilized mice and identified up-regulated  or down-regulated genes during this process.

overall_design: Gastrocnemius muscle were selected at 3 days after immobilization of wild type or skeletal muscle specific KLF15 knockout mice for RNA extraction and hybridization on Affymetrix microarrays.

first: Wataru

last: Ogawa


title: A combinatorial atlas of RNA Polymerase III subunit occupancy in human THP-1 cells

status: Public on Apr 18 2021

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

summary: We present a genome-wide map of RNA Polymerase III subunit localization in human THP-1 monocytes and THP-1 derived macrophages after 72 hr exposure to PMA, as well as profiles of POLR3G and POLR3GL occupancy in THP-1 monocytes after 4 hr exposure to Pol III drug inhibitor ML-60218; 27 uM

overall_design: Chromatin IP (ChIP) experiments were performed against specific RNA Polymerase III subunits, including POLR3A, POLR3B, POLR1D, POLR3C, POLR3G, POLR3GL, POLR3D, and POLR3E, as well as TFIIIB subunit BRF1, and TFIIIC subunit GTF3C1

first: Michael

last: Snyder


title: SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

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


title: SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ATAC-Seq]

summary: The transition from pluripotent to somatic states marks a critical checkpoint in mammalian development. How this is regulated remains largely unresolved. Here we report the identification of SS18 by whole genome CRISPR screen as a checkpoint regulator. SS18 regulates pluripotent to somatic transition or PST by relocating from pluripotent loci to somatic ones accompanied by corresponding chromatin closing-opening and remodeling of SS18-centric protein complexes. Mechanistically, SS18 forms phase separation granules (PSG) with an intrinsically disordered region (IDR) rich in tyrosine (Y), which, once mutated, no longer form PSG nor rescue SS18-/- defect in PST. These results reveal that rapid cell fate decision can be achieved by massive redistribution of chromatin remodeling37 complexes through phase separation.

overall_design: We analyzed the chromatin accessibility in mESCs during the process of JUN triggered differentiation

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: Hedgehog-Responsive PDGFRa(+) Fibroblasts are Necessary for Maintenance of a Unique Pool of Alveolar Epithelial Progenitor Cells During Alveologenesis

status: Public on Apr 15 2021

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

summary: The adult lung alveolus is a flexible 3D structure composed of multiple epithelial, endothelial, and mesenchymal cell types. Two highly specialized alveolar type I (AT1) and type II (AT2) cells, derived from epithelial progenitors, form the inner lining of the alveolus. During alveologenesis, the increasing demand for epithelial cells to cover the surface of the expansive number of alveoli is met by proliferating progenitor cells. There is presently little information about the identity of this population, and the niche microenvironment that controls its proliferation. We show that during alveologenesis genetic inactivation of TGFreceptors in hedgehog-responsive, PDGFRa(+) mesodermal cells previously identified as secondary crest myofibroblasts or SCMF reduces their number, and depletes a unique pool of proliferative epithelial progenitors, without significantly impacting differentiation of cells existing the pool. SCMF are a source of both extracellular matrix and secreted trophic molecules and may thus constitute a key component of the epithelial progenitor niche during alveologenesis. Paralleling the mouse model, we found evidence of reduced proliferation of SFTPC(+) progenitors in lungs of human preterm infants who died with bronchopulmonary dysplasia or BPD.  SCMF are a transient cell population, which are depleted at completion of alveologenesis, making them a unique stage-dependent niche mesodermal cell type in mammalian organs.

overall_design: scRNAseq of PN14 lungs from wild type (Ctrl) and Tgfbr1&2-/- mice (Mut).

first: Feng

first: Parviz

last: Minoo


title: LNCap cell nucleosome footprint elicits  novel noncanonical GATA2 pioneer model

status: Public on Apr 14 2021

city: San Antonio

first: Tianbao

last: Li

state: Texas

address: 7703 Floyd Curl

department: Molecular Medicine

institute: University of Texas Health Science Center at San Anotnio

summary: Purpose: The dynamic nucleosome reorganization is the interplay among nucleosome and regulated by pioneer factors, which can access target DNA sequences on nucleosomes.The goals of this study are revealing the dynamic nucleosome footprint and how GATA2 is capable of resetting crowding array to primed, or accessible edge nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by MNase to Mono-nucleosome and ChIP/ChIP-exo was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and nucleosomes could unwrapped and be more accessible in pioneer factor GATA2 binding sites. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and analysis of the relationship between pioneer factor GATA2 and nucleosome reorganization in whole genomic DNA. These results demonstrated GATA2 play a critical role in an AR-independent manner in prostate cancer.

overall_design: LNCaP cells was used as cell model, Mnase-seq and Mnase-ChIP-seq were applied for mono-nucleosome profiling and ChIP-exo of GATA2 compariing in vehicle and DHT conditions.

first: Qi

last: Liu

first: Victor

last: Jin


title: Intrapericardial administration of secretomes from endometrial-derived mesenchymal stromal cells: effects on immune-related genes in a porcine model of myocardial infarction

status: Public on Apr 09 2021

city: Madrid

first: Juan

middle: Carlos

last: Silla-Castro

address: Melchor Fernandez Almagro 3

department: Bioinformatics

institute: CNIC

summary: Using a porcine model of acute myocardial infarction, we explored the potential effect of secretomes from endometrial-derived mesenchymal stromal cells (endMSCs) and from IFNγ/TNFα-primed endMSCs on immune-related genes in the infarcted tissue.

overall_design: Infarcted tissues from pigs administered with placebo (n = 4), secretomes from endometrial mesenchymal stromal cells (S-enMSCs) (n = 4), and secretomes from IFNγ/TNFα-primed  endometrial derived  mesenchymal stromal cells (S-enMSCs*) were collected at 7 days post-therapy for RNA extraction and Affymetrix microarrays. Differentially gene expression analysis between biogroups were performed and immuno-related genes were determined.

first: Esther

last: López Nieto

first: Javier

last: García Casado


title: RNA-seq for HepG2 cell line with AUF1 knockdown.

first: Guan

last: Guiwen

state: Beijing

address: 38 Xueyuan Road, Haidian District

institute: Peking University

summary: Although several studies indicate that ARE-specific RNA binding proteins (ARE-BPs) contribute to the development of cancer, the detailed functions and mechanisms of ARE-BPs have not been fully elucidated. By using a bioinformatics analysis of two well-established hepatocellular carcinoma (HCC) datasets, we identified the AU-rich binding factor 1(AUF1), one of the well-known ARE-BPs, was abnormally highly expressed in HCC and the high expression of AUF1 was correlated with poor prognosis of HCC patients. The prognostic value of AUF1 expression was also confirmed in our HBV-related HCC cohorts. Gain and loss of function analyses demonstrated that AUF1 promoted HCC tumorigenesis both in vitro and in vivo. Mechanistically, we found that aldoketo reductase family 1 member B 10(AKR1B10) was a critical target of AUF1 and was essential for sustaining the AUF1-induced proliferation of HCC cells. AUF1 stabilized AKR1B10 mRNA by binding to the 3'UTR region of AKR1B10. Additionally, we confirmed that E2F1 enhanced AUF1 expression in HCC through the transcription level, and in HBV-related HCC, HBx could up-regulate E2F1 expression and promote the expression of AUF1. Our study reveals a novel role of AUF1 in promoting hepatocarcinogenesis via the post-transcriptional regulation of AKR1B10 expression and proposes that the HBx/E2F1/AUF1/AKR1B10 pathway may serve as a potential therapeutic target in HCC.

overall_design: AUF1 was knock down by siRNA in HepG2 cell lines for 48 hours.

first: Ting

last: Zhang

first: Guangui

last: Guan

first: Fengmin

last: Lu

first: Xiangmei

last: Chen


title: Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA [RNA-seq]

city: Worcester

first: Ye

last: Duan

state: MASSACHUSETTS

address: 373 Plantation Street, Biotech Two, Suite 306

department: Program of Molecular Medicine

institute: Umass Medical School

summary: The C.elegans transcriptomes of single-nt let-7a 3' non-seed mutants (U13A / U18A). In order to identified gene perturbance and determine the post-transcriptional regulation mechanism caused by disrupting 3' non-seed pairing of let-7a, we examined the global gene expression by RNAseq in addition to ribosome profiling of L4 whole animals. To include the deadenylated but temperally stable mRNA in the enrichment, we used a RNase H based ribosomal RNA depletion with antisense oligos specifically designed for C.elegans to enrich mRNA (PMID: 33005886).  lin-41(ma480) was used in the background to filter out downstream regulation related to the lin-41 pathway.

first: Isana

last: Veksler-Lublinsky

last: Ambros


title: Alterations in chromosome spatial compartmentalization classify prostate cancer progression.

first: Rebeca

last: SanMartin

type:
Expression profiling by array
Other


title: Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA


title: Alterations in chromosome spatial compartmentalization classify prostate cancer progression [array]

overall_design: Analysis of the gene expression of a cohort of cell lines in the continuum of prostate cancer, from adenocarcinoma to bone metastatic

last: San Martin

first: Prijoyit

last: Das

first: Renata

last: Dos Reis Marquez

first: Xu

last: Yang

first: Rachel

last: McCord


title: The cGAS/STING pathway suppresses TLR-dependent systemic autoimmunity in TMPD-mediated SLE

status: Public on Mar 26 2021

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical

summary:
The purpose of the study was to identify differentially regulated genes between WT MRL/Lpr strain and cGAS deficeint MRL/Lpr strain.
We utilized Nanostring technology to analze RNA obtained from spleen of these mice.

overall_design: Total RNA was isolated ( Qiazol; Qiagen) and quantitated via a  Nanodrop ND-1000 spectrophotometer ( Thermo Scientific).  Next, 50 ng of RNA was hybridized and quantified with a custom  probe set using t he NanoString nCounter analysis system  (NanoString Technologies). Gene-expression data were  normalized t o housekeeping genes. All values were scaled by a  log2(x – min(x) + 1) function and a heatmap generated using Rbased  software.

first: Zhaozhao

last: Jiang

first: Kate


title: Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA [Ribo-seq]

summary: The C.elegans translatomes of single-nt let-7a 3' non-seed mutants (U13A / U18A). In order to identified gene perturbance caused by disrupting 3' non-seed pairing of let-7a, we examined the global gene expression at tranlational levels of L4 whole animals by ribosome profiling. We found that let-7a U13A mutation results in overexpression135/351 Note for let-7a U13A mutation, lin-41(ma480) was used in the background to filter out downstream regulation related to the lin-41 pathway.

first: Victor


title: Common and rare variant prediction and penetrance of IBD in a large, multi-ethnic, health system-based biobank cohort

status: Public on Apr 07 2021

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

summary:
Background and aims: As genome sequencing technologies rapidly expand in capacity and availability, understanding how genetic background in different populations modifies IBD risk will be an important factor in disease prediction, prevention, and treatment. However, most of the datasets that are used to generate polygenic risk scores (PRS) contain predominantly European ancestry patients.   To address this, we tested different models for prediction of IBD cases using PRS built using association data from multiple races and also assessed the penetrance of rare very early onset IBD (VEOIBD) SNPs.
Methods: PRS were calculated using association data from European, African American, and Ashkenazi Jewish (AJ) studies, as well as a meta-GWAS run using all three association datasets.  PRS were then combined using regression modelling to assess which combination of scores was best able to predict IBD status in European, AJ, Hispanic, and African American BioMe Biobank populations.   Additionally, rare variants were assessed in genes associated with very early onset IBD, taking into account genetic penetrance in each BioMe population, deleteriousness, and evolutionary conservation.
Results: Combining risk scores based on IBD association results from multiple racial populations resulted in improved IBD prediction for every population in BioMe.  We also identified highly penetrant rare variants in previously established VEOIBD genes which were predicted to be deleterious, including SNPs in established risk genes such as NOD2 as well as novel variants, including some in LRBA which appear to be particularly relevant for risk of IBD in African Americans.

overall_design: Single cell seq analysis of paired samples from inflamed rectum and uninflamed sigmoid from same UC diagnosed patient

first: Mamta

last: Giri


title: Time series transcriptomic analysis of sepsis-induced myocardial injury in mice

city: Hangzhou

first: Xiao

last: Yan

address: No.2318 Yuhangtang Road

institute: Hangzhou Normal University

summary: Our study helps to understand the molecular pathogenesis of septic cardiomyopathy in C57BL/6 mice and identifiy genes and pathways that may be potential therapeutic targets for septic cardiomyopathy treatment.

overall_design: Cardiac mRNA profiles of C57BL/6J mice after cecal ligation and puncture (CLP) for 24, 48, and 72 hours

first: Hui-Hua

last: Li


title: The DISARM study: effects of inhaled corticosteroids on bronchial epithelial cell gene expression in COPD

status: Public on Mar 22 2021

city: Vancouver

first: Don

middle: D

last: Sin

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia

summary: The Differential Effects of Inhaled Symbicort and AdvaiR on Lung Microbiota (DISARM) study aimed to determine the effects of inhaled corticosteroids (ICS) on the lung microbiome. The full trial protocol is registered at clinicaltrials.gov (NCT02833480) and the study was approved by the Human Research Ethics Committee of the University of British Columbia and Providence Health Care (H14-02277). Participants were randomized to receive inhaled long-acting beta agonist (LABA) treatment with formoterol, or LABA/ICS combination treatment with formoterol/budesonide or salmeterol/fluticasone propionate, for 12 weeks. Bronchoscopy was performed before and after treatment, and bronchoalveolar lavage fluid and bronchial brushes (6th-8th generation) were collected. This dataset contains RNA-seq data from the bronchial brushes. RNA was extracted from cytological brush specimens stored in QIAzol RNA lysis buffer (QIAGEN, Stockach, Germany) using the RNeasy Plus kit (QIAGEN) according to the manufacturer’s instructions, and specimens were submitted for sequencing at the University of British Columbia Biomedical Research Centre. Sample quality control was performed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Qualifying samples were then prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs, Ipswich, MA, USA). Sequencing was performed on the Illumina NextSeq 500 (Illumina, San Diego, CA, USA) with paired end 42bp × 42bp reads. Samples were sequenced in batches of 24, with batches formed by random selection of samples.

overall_design: Randomized controlled trial. No placebo group was included in the DISARM trial due to the risk of acute exacerbation of COPD during the treatment period. FOR monotherapy is considered the control group. 63 participants with mild to very severe COPD were randomised into 3 groups: FOR (n=21), FOR/BUD (20), or SAL/FLU (n=22). 61 participants have pre-treatment sequencing data available, and 54 participants have both pre- and post-treatment sequencing data available.

first: Xuan

first: Stephen

last: Milne


title: miR-15a reprograms activated hepatic stellate cells back toward quiescence

status: Public on Mar 11 2021

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

summary: Cell reprogramming enables dedifferentiation to generate induced pluripotent stem cells or transdifferentiation to produce desired terminally differentiated cell types. However, the concept of forced reprogramming has not been extended to converting the activation status of specialized cell types such as hepatic stellate cell (HSC) which, once activated, plays a central role in promoting liver fibrosis. We identified miR-15a as a key driver to reprogram activated HSC back toward quiescence, partly by directly targeting Wisp1, to generate what we designate as induced quiescent-like HSC (iqHSC). iqHSCs had a morphologic, transcriptional, and functional phenotype similar to that of truly quiescent HSCs. Finally, performing cell therapy with iqHSCs attenuated hepatic inflammation and fibrosis in mouse models of liver injury induced by toxin, biliary obstruction, or diet.

overall_design: We performed RNA sequencing of hepatic stellate cells in various activation states to predict a set of genes that have a higher likelihood of being targeted by miR-15a.

first: Byeong-Moo

last: Kim

first: Yujin

last: Hoshida

first: Michael

last: Choi


title: Next-generation interaction screening to discover Mla6aa1-161 and Mla6aa1-225, Mla6aa550-956 related protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.

status: Public on Mar 24 2021

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

sample_organism:
Hordeum vulgare
Blumeria hordei

platform_organism:
Hordeum vulgare
Blumeria hordei

overall_design: Refer to individual Series


title: Expression data from MCRedAL Prostate Tumors

status: Public on Apr 06 2021

first: Charles

last: Drake

address: 650 W. 168th Street

country: Mexico

institute: Columbia University

summary:
Prostate tumor cells growth is interconected to androgen signaling. Indeed, the main line of treatment for advanced prostate cancer is focused on inhibiting androgen signaling by either surgical or pharmacological castration (or androgen-ablation, e.g. degarelix).
We used microarrays to detail the global programme of gene expression following androgen-deprivation therapy (ADT) and identified distinct classes of up-regulated genes during this process that could contribute to the development of castration resistance.

overall_design: Prostate tumor cells were isolated for RNA extraction and hybridization on MTA1.0 Affymetrix microarrays. To obtain homogeneous populations of tumors at each treatment group (CS, castration sensitive; and pADT, Post-ADT), we isolated tumor cells from similar tumor size based on their positive expression of the mcherry fluorescent protein and negative expression of CD45, F4/80, and CD11b immune cell markers.

first: Zoila

last: Lopez-Bujanda

middle: G


title: A microarray-based transcriptomic analysis of oral squamous cell carcinoma cell lines with differing responses to cisplatin

status: Public on Mar 09 2021

city: Kuala Lumpur

first: Chua

last: Eng Wee

state: Kuala Lumpur

address: Jalan Raja Muda Abdul Aziz,

department: Faculty of Pharmacy

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: Cisplatin is a commonly used platinum-based chemotherapeutic agent for oral squamous cell carcinoma (OSCC). However, cisplatin efficacy is limited by drug toxicity and the resistance capabilities of cancer cells. Reduced efficacy of anticancer therapy has been recently attributed to the presence of therapy-insensitive subpopulations in heterogeneous tumours, known as cancer stem-like cells (CSCs). CSCs comprise a tumour-forming subpopulation of cells that exhibit stem cell-like features, including the abilities to self-renew and turn into progenitor and differentiated cancer cell lineages, and enhanced therapeutic resistance capabilities, thus driving the continual growth and survival of tumours. Overall, this work was conducted to provide the transcriptomes of the OSCC cell lines with differing responses to cisplatin using a microarray analysis. The data may be analyzed alongside other similar datasets to explore the underlying cisplatin resistance mechanisms in OSCC.

overall_design: Two human OSCC cell lines with different tumour staging, namely H103 and SAS, and an in vitro drug-resistant model derived from the CSCs of SAS cell line were used in this study. The CSCs from SAS cell line were generated via a sphere-forming assay, resulting in SAS tumour spheres with stem cell-like features. Cisplatin sensitivity was determined by measurements of cell viability after 72 h treatments with cisplatin using CellTiter 96 AQueous Non-Radioactive Cell Proliferation Assay (MTS assay; Promega Inc., USA). Briefly, H103 and SAS tumour spheres had reduced sensitivity towards cisplatin, yielding higher IC50 values of cisplatin compared to SAS. Three biological replicates per cell were prepared, with each replicate representing a different passage of the cells. The whole transcriptomic profiles of the cells were obtained from a microarray analysis using the Affymetrix GeneChip Human Clariom S Array (Thermo Fisher Scientific Inc., USA).

first: Amnani

last: Aminuddin

first: Eng

last: Chua


title: Global regulators fine-tune the translation and metabolic machinery in Escherichia coli under proteome-efficient anaerobic fermentation

status: Public on Feb 28 2021

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

institute: Uppsala University

summary: We report high-throughput RNA sequencing of WT,  Δfnr, ΔarcA and Δihf in the exponential phase under anaerobic fermentative conditions

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA was extracted from two biological replicates of WT, Δfnr, ΔarcA and Δihf in the exponential phase under anaerobic fermentation conditions, grown in glucose minimal media conditions. RNA sequencing was done using Illumina Hi-Seq 4000 platform.

first: Mahesh

last: Iyer

first: K

middle: V

last: Venkatesh


title: Type I IFNs exacerbate tuberculosis pathogenesis by inhibiting migration of antigen specific T cells

status: Public on Feb 27 2021

city: Seoul

first: Kyungsoo

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

country: South Korea

institute: Yonsei University

summary: Tuberculosis, a chronic granulomatous disease caused by Mycobacterium tuberculosis (Mtb), often becomes exacerbated upon co-infection with other pathogens, yet the underlying immunological mechanisms remain insufficiently understood. Here, mice were initially infected with the hypervirulent Mtb strain K, and later with lymphocytic choriomeningitis virus to investigate the mechanism of severe pulmonary pathology. Virus infection significantly reduced Mtb-specific IFN-g, increased bacterial loads, and aggravated lung inflammation in the lung of Mtb-infected mice, which did not occur in pre-existence of Th1 response by Bacillus Calmette-Guerin vaccination prior to the co-infection. Blockade of type I IFN receptor signaling reinvigorated Mtb-specific IFN-γ response and ameliorated pathogenesis by upregulating pulmonary CXCL9/10 production. Our results demonstrate that virus-induced type I IFN triggers severe immunopathology by deteriorating migration of Mtb-specific IFN-γ-producing T cells, suggesting the balance between type I and type II IFNs determines either control of Mtb or exacerbation of pathology in the lung upon viral infection

overall_design: mRNA profile of Lung infitrating CD45+ immune cells from Naïve, Mtb only infected, Mtb+LCMV co-infected, Mtb+LCMV+aIFNAR1 co-infected mice at 21 days post Mtb infection

first: Tae-gun

last: Kang

first: Sang-Jun

last: Ha

first: Insuk

last: Lee


title: Next-generation interaction screening to discover Mla6aa1-225 related protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.

status: Public on Mar 23 2021

country: USA

summary: The barley R gene (Mla6aa1-225) dataset was part of a larger Y2H screen (GEO GSE150396) to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. The Mla6aa1-225 bait was mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions.

overall_design: Y2H screening of a cDNA library was coupled to next-generation sequencing to identify and rank positive protein-protein interactions. Screening for the Mla6aa1-225 bait was conducted in triplicate with yeast cells grown in selective and non-selective conditions. NuGEN’s AnyDeplete technology was used to deplete HORVU3Hr1G072260 (zinc finger protein) from the samples. Two constructs of luciferase were used as bait negative controls. Samples were run on three lanes of Illumina’s HiSeq 3000.

first: Sagnik

last: Banerjee

first: Valeria

last: Velasquez-Zapata

first: James

middle: M

last: Elmore

first: Gregory

last: Fuerst

middle: P


title: Myometrial Progesterone Receptor Isoform B Regulates the Phospholipase C Pathway and Suppresses Uterine Contractility

status: Public on Feb 24 2021

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: Uterine contractile dysfunction leads to pregnancy complications such as preterm birth and labor dystocia. Progesterone is necessary to suppress uterine contractions to prevent premature labor. As humans maintain high levels of progesterone throughout parturition, a functional progesterone withdrawal hypothesis suggests that relative levels of myometrial progesterone receptor isoforms PGR-A and PGR-B switch at parturition, where PGR-B promotes a relaxed state and PGR-A result in increased uterine contractility. Our objective is to determine the effects of altered levels of PGR-B and PGR-A in the mouse myometrium on pregnancy and parturition using transgenic mouse models in which the relative levels of these isoforms are altered specifically in the myometrium. Overexpression of PGR-B is associated with a markedly increased gestational length compared to control mice. In both ex vivo and in vivo experiments, myometrium of PGR-B overexpressing mice have prolonged labor, a significant decrease in uterine contractility, and a high incidence of labor dystocia. Conversely, overexpression of PGR-A is associated with an increase in uterine contractility without a change in gestational length. Uterine RNAseq at mid-pregnancy identified isoform-specific downstream targets and genes that were commonly regulated by both PGR isoforms. Gene signature analyses further revealed that PGR-B promotes muscle relaxation and that PGR-A is pro-inflammation. High levels of PGR-B manifest a genetic profile of a blunted phospholipase C pathway that mediates oxytocin and angiotensin II induced muscle contraction. These findings provided in vivo support that PGR isoform levels determine distinct transcriptomic landscapes and pathways in myometrial function and labor.

overall_design: mRNA profiles of uterine tissues at midpregnancy of control, myometrial PGR-A overexpression and myometrial PGR-B overexpression mice were generated by deep sequencing, in quadruplicate, using Illumina NextSeq.

first: San-Pin

last: Wu

first: Lecong

last: Zhou

first: Tianyuan

last: Wang

first: Francesco

last: DeMayo


title: Transcriptome of cct3A(RNAi) planarians at 72 hours of regeneration

status: Public on Apr 26 2021

city: Jena

first: Oscar

middle: Gutierrez

last: Gutierrez

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: We performed RNA-seq of whole starved cct3A(RNAi) planarians and controls at 72hR.

overall_design: Transcriptome profiles of gfp(RNAi) planarians (controls) and cct3A(RNAi) planarians at 72hR were generated by deep sequencing, using Illumina HiSeq2500

first: Óscar

last: Gutiérrez-Gutiérrez

first: Cristina

last: González-Estévez


title: A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome

status: Public on Feb 26 2021

city: Wuhan

first: Shuhong

last: Zhao

address: No.1,Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Although major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and ChIP-Seq analyses. In total, we generated 199 datasets and identified more than 220,000 pig cis-regulatory elements. We find that cis-regulatory elements are more conserved between humans and pigs than that between humans and mice. To further explore the three dimension structure of pig genome, we performed high-throughput chromosome conformation capture (Hi-C) experiment. The rearrangements of TADs between pig and human have apparently contributed to the evolution of head and face phenotypes. Beyond generating a major new benchmark resource for pig epigenetics research, our study provides basic epigenetic comparative data for using pig as a model for human biomedical research.

overall_design: High-throughput sequencing (RNA-seq, ChIP-Seq, ATAC-seq, and Hi-C)of diverse tissues from four pig breeds.

first: Yunxia

first: Ye

last: Hou

first: Yueyuan

last: Xu


title: The tRNA-derived small RNAs (tsRNAs) expression profiles in human aortic vascular smooth muscle cells (HAVSMCs)

status: Public on Jan 12 2021

city: shi jia zhuang

first: shaoguang

last: sun

state: Hebei

address: zhong shan dong lu 361

department: biochemistry and molecular biology

institute: Hebei medical university

summary:
Purpose: Next-generation sequencing (NGS) is the main way to mine ncRNA. The purpose of this study is to screen out tRNA-derived small RNAs (tsRNAs) that are differentially expressed in proliferative and quiescent HASMCs
Methods: tsRNAs profiles of proliferative and quiescent HASMCs were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed Illumina chastity filter were used for the following analysis. Trimmed reads (with 5ʹ, 3ʹ-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences. The alignment statistical analysis was applied to retain the valid sequences for subsequent tsRNAs expression profiles and differential expression analysis.
Results: Using an optimized data analysis workflow, we mapped about 8 million sequence reads per sample to mature-tRNA and pre-tRNA sequences from GtRNAdb and identified 3,891 tsRNAs in the proliferative and quiescent HASMCs. According to the standardized TPM, 887 up-regulated and 951 down-regulated tsRNAs were found in the proliferative HASMCs (fold change > 2, P < 0.05).

overall_design: HASMCs were cultured using Smooth Muscle Cell Medium containing 2% fetal bovine serum, 1% 100 × Smooth Muscle Cell Growth Supplement and 1% 100 × Penicillin/Streptomycin Solution at 37°C in a humidified chamber with 5% CO2 and 95% O2. Quiescent HASMCs were induced by FBS starvation for 24 hours.

first: Shaoguang

last: Sun

first: Jianzhi

first: Bin

last: Li


title: RNA sequencing of Klebsiella pneumoniae and Escherichia coli treated with silver nanoparticles

status: Public on Jan 31 2021

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

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

sample_organism:
Escherichia coli K-12
Klebsiella pneumoniae MGH 78578