title: Leukemic cells expressing NCOR1-LYN are sensitive to dasatinib in vivo in a patient-derived xenograft mouse model

status: Public on Mar 21 2020

city: Kyoto

first: Toshihiro

last: Tomii

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural Univercity of Medicine

summary:
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a distinct subtype of B-ALL with a poor prognosis. Rearrangement of LYN is a recurrent genetic abnormality in Ph-like ALL, but functional analysis of LYN-related fusion genes identified in ALL has not been reported. In this study, we performed functional analysis of the NCOR1-LYN fusion gene identified in a pediatric Ph-like ALL patient to establish its potential for molecular targeted therapy. Retroviral transduction of interleukin (IL)-3-dependent Ba/F3 cells with NCOR1-LYN enabled IL-3-independent proliferation, with constitutive phosphorylation of the tyrosine residues of the LYN kinase domain in the fusion protein. Replacing tyrosine residues with phenylalanine in the LYN kinase domain abolished IL-3 independence. Tyrosine kinase inhibitor dasatinib killed Ba/F3 cells expressing NCOR1-LYN in vitro accompanied by dephosphorylation of the tyrosine residues of the LYN kinase domain in the fusion protein.
In a patient-derived xenograft (PDX) mouse model, generated using leukemic cells from the NCOR1-LYN positive Ph-like ALL patient, dasatinib controlled the growth of leukemic cells in vivo and significantly extended the survival time of the PDX mice (p=0.03). Our data demonstrate that, like other kinase fusions identified in Ph-like ALL, the NCOR1-LYN rearrangement has proliferative activity, and that tyrosine phosphorylation of the LYN kinase domain is critical for IL-3 independent growth. Furthermore, in a preclinical model we demonstrate the efficacy in vivo of dasatinib as therapy for Ph-like ALL with a LYN rearrangement.

overall_design: Ba/F3 cells were transduced with NCOR1-LYN protein by the Retro-X Tet-on Advanced Inducible System (Clontech), and Ba/F3 cells expressing NCOR1-LYN under doxycycline (DOX) dependent manner were established.   To reveal which pathways affected by introducing NCOR1-LYN, Ba/F3 cells expressing NCOR1-LYN induced by DOX (Ba/F3-NCOR1-LYN) and uninduced Ba/F3 cells (mock Ba / F3) were cultured in triplicate, and total RNA was extracted from Ba/F3-NCOR1-LYN and mock Ba/F3.

first: T

last: Imamura

first: K

last: Tanaka

first: I

last: Kato

first: A

last: Mayumi

first: E

last: Souma

first: M

last: Yano

last: Sakamoto

last: Mikami

last: Morita

first: N

last: Kiyokawa

last: Horibe

first: S

last: Adachi

last: Nakahata

first: J

last: Takita

first: H

last: Hosoi


title: Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [RNA-seq]

status: Public on May 01 2020

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

type: Expression profiling by high throughput sequencing

summary: By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.

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

overall_design: Cells expressing HIS6-TEV-3xFLAG tagged Hfq were grown in LB medium from early exponential phase to stationary phase. At various optical densities, cells were UV cross-linked in the Vari-X-linker and harvested by filtration. CLASH was subsequently performed on each sample using the tagged Hfq as bait to enrich for sRNA-terget interactions. The resulting associated RNAs were sequenced on Illumina platforms. We included two biological replicates of the density series. In addition, for each density, we generated two replicates of rRNA-depleted total RNA sequencing data.


title: Next Generation Sequencing (NGS) of miRNAs in rat hippocampal tissues

status: Public on Mar 31 2020

city: Brno

first: Petra

last: Bencurova

address: Kamenice 5

department: Brain and Mind Research

country: Czech Republic

institute: Masaryk University, CEITEC

type: Non-coding RNA profiling by high throughput sequencing

summary: We carried out Massive Parallel Sequencing (MPS) to reveal miRNA expression profiles of  rats with LiCl-pilocarpine induced epileptic status (SE) in adulthood (Postnatal day 60 -P60) and infancy (P12). Hippocampal tissues were collected at 3 stages of epileptogenesis: acute (24 hours), latent (7 days) and chronic (3 months after SE) from 10 animals after SE and 10 controls in each age group (120 in total).  The sequencing platform identified 666 miRNA species, out of which  up to 419 miRNAs were present with the coverage of more than 500 reads altogether in individual groups (onset-age epilepsy stage combinations). We discovered that age of SE induction has impact on miRNA profile throughout all stages of epileptogenesis and infantile-onset of epilepsy leads to changes in smaller number of miRNAs.

overall_design: Examination of samples from 60 animals after SE and 60 controls (10 SE animals and 10 controls in both age groups of acute, latent and chronic epileptogenesis) .

first: Jiri

last: Baloun

first: Sarka

last: Pospisilova

first: Milan

last: Brazdil

first: Hana

last: Kubova

first: Jakub

last: Hynst

first: Jan

last: Oppelt


title: RNA-seq of ID4 knockdown Comma-Dβ mammary epithelial cells

status: Public on May 07 2020

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: The goal of this study was to determine the genes regulated by ID4 in mammary epithelial cells. ID4 was knocked down by siRNA in the mammary epithelial cell line Comma-Dβ and RNA-seq was performed following 48 hr to determine differentially expressed genes.

overall_design: Cells treated with siRNA targeting ID4 were compared with cells treated with non-targeting (NT) siRNA control. 3 biological replicates were performed.

first: Holly

last: Holliday

first: Daniel

last: Roden

first: Chia-Ling

last: Chan


title: RNA-seq analysis of WT and βOGT KO female islets

status: Public on Apr 10 2020

city: Minneapolis

first: emilyn

middle: U

last: alejandro

state: MN

department: Integrative Biology and Physiology

country: USA

institute: University of Minnesota

summary: We report our results from two runs of RNA-seq analysis on islets isolated from female C57Bl/6J mice with a constitutive deletion of O-GlcNAc Transferase (OGT) specifically in pancreatic β-cells (Rip-cre; Ogt f/f) and controls (Ogt f/f or Ogt f/+)

overall_design: RNA was isolated from snap-frozen islet pellets. Libraries were created using standard Illumina reagents and analyzed using a HiSeq2500.

first: Emilyn

last: Alejandro

first: Amber

middle: D

last: Lockridge

first: Juan

middle: E

last: Abrahante


title: Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation

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

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

overall_design: Refer to individual Series


title: Mec1 is activated at the onset of normal S phase by low dNTP pools impeding DNA replication [sequencing]

status: Public on Mar 17 2020

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Mec1 and Rad53 kinases play a central role during acute replication stress in budding yeast. They are also essential for viability in normal growth conditions, but the signal that activates the Mec1–Rad53 pathway in the absence of exogenous insults is currently unknown. Here, we show that this pathway is active at the onset of normal S phase because dNTP levels present in G1 phase are not sufficient to support processive DNA synthesis and impede DNA replication. This activation can be suppressed experimentally by increasing dNTP levels in G1 phase. Moreover, we show that unchallenged cells entering S phase in the absence of Rad53 undergo irreversible fork collapse and mitotic catastrophe. Together, these data indicate that cells use dNTP shortage to detect the onset of DNA replication and activate the Mec1–Rad53 pathway, which in turn maintains functional forks and triggers dNTP synthesis, allowing the completion of DNA replication.

overall_design: NGS-based analysis of replication origin activity, replication checkpoint activation

first: Romain

last: Forey

first: Ana

last: Poveda

first: Sushma

last: Sharma

first: Ismael

last: Padioleau

first: Claire

last: Renard

first: Robin

last: Lambert

first: Magdalena

last: Skrzypczak

first: Krzysztof

last: Ginalski

first: Armelle

last: Lengronne

first: Andrei

last: Chabes

first: Benjamin

last: Pardo

first: Philippe

last: Pasero


title: Mec1 is activated at the onset of normal S phase by low dNTP pools impeding DNA replication


title: Mec1 is activated at the onset of normal S phase by low dNTP pools impeding DNA replication [microarray]

type: Genome binding/occupancy profiling by genome tiling array


title: Transcriptome regulated by arterial aging in mice

status: Public on Feb 27 2020

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: The goal of this project is to determine the critical genes and pathways associated with physiological aging in mouse aortas.

overall_design: We isolated  aortas  from young (14.5 weeks) and old (92.5 weeks) mice  and extracted total RNA for RNA-seq. Each group inlcudes 5  male mice.  Mouse background is C57BL/6. We want to determine differentially expressed genes in young and old aortas in mice through RNA-seq analysis and thus reveal critical genes/pathways regulated by arterial aging.

first: Ping

last: Gao

first: Pan

first: Mihyun

last: Choi

first: Chegireddy

last: Kavaya

first: Jinjing

last: Zhao

first: Wei

last: Zhang

first: Xiaochun

last: Long


title: Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases

status: Public on Feb 26 2020

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Pluripotent stem cells (PSCs) can transition between cell states in vitro, closely reflecting developmental changes in the early embryo. PSCs can be stabilized in their naive state by blocking extracellular differentiation stimuli, particularly FGF5 MEK signaling. Here, we report that multiple features of the naive state in human and mouse PSCs can be recapitulated without affecting FGF-MEK-signaling.  Mechanistically, chemical inhibition of CDK8 and CDK19 kinases (CDK8/19i) removes their ability to repress the Mediator complex at enhancers. Thus CDK8/19i increases Mediator-driven recruitment of RNA Pol II to promoters and enhancers.  This efficiently stabilizes the naive transcriptional program, and confers resistance to enhancer perturbation by BRD4 inhibition. Moreover, naive pluripotency during embryonic development coincides with reduction in CDK8/19.  We conclude that global hyperactivation of enhancers drives naive pluripotency, and this can be captured in-vitro by inhibiting extracellular FGF-MEK-signaling, or downstream, by CDK8/19i. These principles may apply to other contexts of cellular plasticity.

overall_design: Four human pluripotent stem cell lines (PSCs) were cultured in three conditions ("Primed" vs "CDK8/19i" vs "gr8i") for 16 days/3passages, and then transcriptomic differences between the three groups were assessed by RNAseq.  Culture conditions were either standard primed conditions ("Primed" = mTeSR media with FGF2 and TGFb1, feeder-free, on matrigel), or including additional media supplementation with recombinant human LIF (10 mg/ml) and CDK8/19-small molecule inhibitor at 0,4 mM (= "CDK8/19i" or "8i"); or, for the "gr8i" condition: recombinant human LIF (10 mg/ml), CDK8/19-small molecule inhibitor at 0,4 mM, GSK3-inhibitor CHIR99021 at 1 mM, plus IWR1 at 5 mM.  The four cell lines were D2#2, D2#4, HERVH (HH), and H1.

first: Manuel

last: Serrano

first: Cian

last: Lynch

first: Raquel

last: Bernad

last: Stephan-Otto Attolini


title: Anomalous reverse transcription through chemical modifications in polyadenosine stretches

status: Public on Apr 22 2020

city: Stanford

first: Rhiju

last: Das

state: California

address: 279 Campus Dr, B419 Beckman Center

department: Biochemistry

institute: Stanford University School of Medicin

summary: Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes’ behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2’ hydroxyl acylation, as probed by reverse transcription. Here, re-analysis of these and other publicly available data, capillary electrophoresis experiments on chemically modified RNAs, and nuclear magnetic resonance spectroscopy on A 12 and variants show that this effect is unlikely to arise from an unusual structure of polyadenosine. Instead, tests of different reverse transcriptases on chemically modified RNAs and molecules synthesized with single 1-methyladenosines implicate a previously uncharacterized reverse transcriptase behavior: near-quantitative bypass through chemical modifications within polyadenosine stretches. All tested natural and engineered reverse transcriptases (MMLV; SuperScript II, III, and IV; TGIRT-III; and MarathonRT) exhibit this anomalous bypass behavior. Accurate DMS-guided structure modeling of the polyadenylated HIV-1 3´ untranslated region RNA requires taking into account this anomaly. Our results suggest that poly(rA-dT) hybrid duplexes can trigger unexpectedly effective reverse transcriptase bypass and that chemical modifications in poly(A) mRNA tails may be generally undercounted.

sample_organism:
Human immunodeficiency virus
synthetic construct

overall_design:
Sequencing cDNA truncations/mutations caused by chemical modifications in RNA (in vitro transcribed or chemically synthesized)
There are three overarching samples. Two are of RNA libraries comprised of enzymatically synthesized RNA. The third is of chemically synthesized RNA. For all three, “polyA length” and “reactivity” analyses have been carried out.

first: Wipapat

last: Kladwang

first: Ved

middle: V

last: Topkar

first: Bei

last: Liu

first: Ramya

last: Rangan

first: Tracy

middle: L

last: Hodges

first: Sarah

middle: C

last: Keane

first: Hashim

last: al-Hashimi


title: Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Chicken

status: Public on Feb 09 2020

city: Guangzhou

first: wu

middle: jing

last: wen

state: Guangdong

address: TianHe

department: Department of Animal Genetics, Breeding and Reproduction

country: China

institute: South China Agricultural University

summary: Ma-Huang chicken as a high-quality broiler is one of the most popular chickens in the frozen chicken market. However, some chicken may instead have white or lighter skin, which directly causes economic losses every year. To obtain better insight into the molecular mechanisms associated with the process of pigmentation of yellow-skinned broilers reared under intensive conditions, a total of six-hundred Ma-Huang chickens was randomly selected in a single slaughterhouse, the color measurements were carried out on both cloaca(alive) and five different part after slaughtering adopting the L* a* b* system and using a 3nh-NH310 colorimeter, color values from areas of the chicken skin pear each image automatically retrieved by MATLAB, production and slaughtering traits were also measured, comparative transcriptomic analysis of high yellowness(s_deep) versus low yellowness(s_light) skin was performed using the Illumina Hiseq 4000. Average values of the cloaca(alive), cloaca (hair removal), thigh, shank and abdominal fat were 8.98, 7.66, 2.62, 7.29 and 12.86, respectively. The better production and slaughtering traits were observed in higher skin yellowness chicken. Yellowness values of the cloaca(alive) and after slaughtering were significantly correlated (p < 0.05), suggesting that the color of after slaughtering evaluation may be carried out on cloaca(alive). A total of 19061 unigenes were assembled from the reads obtained from the skin of two groups, 882 unigenes were differentially expressed between s_deep and s_light (Fold change ≥ 2, Adjusted P <= 0.001), 612 that up-regulated and 270 that down-regulated genes in s_deep skin, as compared with s_light skin. Twelve promising candidate genes may play an important role in the pigmentation of chicken skin, i.e. GPR143, PMEL, TYR, CYP11A1, TECRL, ACACB, TLR2B, ALDH1A3, FHL2, TECRL, DUOX2, SMOC1 were included. Furthermore, some important functional pathways were revealed, such as the biological process, cellular component and molecular function, which appear to be much activity in skin pigmentation. Our data provide a valuable resource for identifying genes whose functions are critical to skin pigmentation, facilitate understanding the molecular mechanisms of the skin color variation on yellow-skinned broiler chickens under commercial conditions, accelerate the molecular selection of the specific strain on consistent skin colors which allow reduction in pigment use to achieve the skin acceptance by the consumer.

overall_design: From 600 Ma-Huang chickens, 3 chickens were chosen according to the yellowness of cloaca(alive) from high to low and defined as high yellowness(s_deep) group; another 3 chickens were chosen according to yellowness of cloaca(alive) from low to high and defined as the low yellowness(s_light) group.high yellowness(s_deep) versus low yellowness(s_light) skin was performed using the Illumina Hiseq 4000.

first: Jingwen

last: Wu

first: Genghua

last: Chen

first: Zetong

last: Lin

first: Wen

last: Luo


title: Microarray analysis of lncRNAs and mRNAs in the process of human hyaline chondrocyte dedifferentiation in vitro

status: Public on Feb 25 2020

city: Changchun

first: Lin

state: Jilin

address: 126 xinmin

department: Basic Medical College

institute: Jiin University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Autologous chondrocyte implantation (ACI) is an effective method to treat chronic articular cartilage injury in recent years, which requires a large number of human hyaline chondrocytes. Unfortunately, human hyaline chondrocytes often undergo dedifferentiation in vitro. Thus, it is important to elucidate the mechanism of dedifferentiation for the application of ACI technology. Long noncoding RNAs (lncRNA) play a regulatory role in gene expression in many pathological and physiological processes. However, the role of lncRNAs in human hyaline chondrocyte dedifferentiation remains unclear. The aim of this study was to investigate the expression profiles of lncRNAs in human hyaline chondrocyte dedifferentiation during in vitro culture. First, we cultured human hyaline chondrocytes in vitro and detected the expression of COL1A1, COL2A1, and SOX-9 in passage 1 (P1) and 5 (P5) chondrocytes using quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence, and western blotting. Then, we analyzed the expression profiles of lncRNAs and mRNAs in P1 and P5 chondrocytes by microarray analysis.

overall_design: After passage culture, passage 1 (P1) chondrocytes were used as differentiated chondrocytes, while P5 chondrocytes were used as dedifferentiated chondrocytes. In microarray analysis, A stands for P1 chondrocytes, B stands for P5 chondrocytes, each group includes 3 samples (A1,A2,A3,B1,B2,B3), A1 and B1 obtained in the same individual.


title: Atlas of Brown Adipose Tissue

status: Public on Feb 04 2020

city: Bronx

first: Kosaku

last: Shinoda

state: New York

address: 1301 Morris Park Avenue

department: Endocrinology

institute: Albert Einstein College of Medicine

summary:
Heterogeneity in brown adipocyte populations was observed.
Until recently, thermogenic adipocytes have been considered a homogeneous population. However, studies have pointed to the existence of multiple subtypes, which are distinct in developmental origin, substrate usage and transcriptome. Our current incomplete understanding of cell types in brown and beige adipose tissue and the lack of specific markers constitute a critical barrier to studying their biological functions. Our goal is to use the advances in single-cell genomics to determine  subtypes that constitute adipose tissue under various thermogenic stimuli at the single cell resolution.

overall_design: Identifying populations of brown adipocytes

first: Gabrielle

last: Benitez


title: Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth.

status: Public on Feb 10 2020

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Peripheral whole blood transcriptome profiles of pregnant women with normal pregnancy and spontaneous preterm birth from 10-18 weeks of gestational age enrolled in the Vitamin D Antenatal Asthma Reduction Trial (VDAART).

overall_design:
Comparing the whole blood (PAXgene) transcriptome from 10-18 weeks of gestational age of 16 mothers with normal pregnancies versus 8 mothers with spontaneous preterm birth (<32 weeks of gestation).
Whole blood transcriptome, disease state analysis

first: Hooman

last: Mirzakhani

first: Aishwarya

middle: P

last: Yadama

first: Thomas

middle: F

last: McElrath

first: Augusto

middle: A

last: Litonjua

first: Scott

middle: T

last: Weiss


title: Expression data of progesterone regulated miRNAs in U251 cells, derived from human glioblastoma

status: Public on Jan 25 2020

city: CIUDAD DE MÉXICO

first: DIANA

middle: ELISA

last: VELÁZQUEZ

state: CIUDAD DE MÉXICO

address: CIRCUITO ESCOLAR 33, C.U., COYOACÁN

department: FACULTAD DE QUÍMICA

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO

summary: Glioblastoma multiforme (GBM), a grade IV astrocytoma, is the most common and aggressive brain tumor in adults, characterized by being highly infiltrative, angiogenic, and resistant to chemotherapy and radiotherapy. In previous works, has been determined that progesterone P4 increases proliferation, migration and invasion of cells derived from human GBMs through the interaction with its intracellular receptor (PR). In breast cancer, there exist evidence that P4 regulates the expression of miRNAs with tumor suppressor or oncogenic action, via the classical PR. The signature of miRNAs affected by P4 treatment in cells derived from human GBMs has not been determined. Therefore, we studied the effect of P4 on miRNAs expression pattern in U251 cells derived from a human GBM.

overall_design: Four cell cultures were performed for the total RNA extraction: U251 cell treated with P4, RU486, P4+ RU486 and vehicle (cyclodextrin) for 6 h. The  hybridization on Affymetrix microarrays was carried out in triplicate for each treatment.

first: Diana

last: Velázquez-Vázquez

first: Aylin

last: Del Moral-Morales

first: Jenie

middle: M

last: Cruz-Burgos

first: Eduardo

last: Martínez-Martínez

first: Mauricio

last: Rodríguez-Dorantes

first: Ignacio

last: Camacho-Arroyo


title: In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice [RNA-seq]

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: In most cancers, only a few genes are mutated at high frequencies, while the vast majority are mutated at low frequencies. The functions of these recurrent but infrequent ‘long-tail’ mutations remain largely elusive. Here, we develop in vivo CRISPR screens to assess the transforming potential of 484 long-tail genes in human Head and Neck Squamous Cell 5 Carcinoma (HNSCC).

overall_design: Analyzed differential expression between Adam10, Ajuba KO vs. the WT primary mouse keratinocytes.

first: Sampath

middle: K

last: Loganathan

first: Ahmad

last: Malik


title: Sequencing-based quantitative mapping of the cellular small RNA landscape

status: Public on Jan 01 2020

city: Cambridge

first: Jennifer

last: Hu

address: 77 Massachusetts Ave

institute: MIT

summary: We report the development of an RNA sequencing method – AQRNA-seq – that minimizes biases and enables absolute quantification of all small RNA species in a sample mixture. Validation of AQRNA-seq library preparation and data mining algorithms using a 963-member microRNA reference library, RNA oligonucleotide standards of varying lengths, and northern blots demonstrated a direct, linear correlation between sequencing read count and RNA abundance.

overall_design:
The goal of the overall design was to develop a new, quantitative RNA-seq method. To evaluate the extent to which ligation and other steps may introduced biases to our results, we used 1) a set of 5 synthetic RNA oligonucleotide species of varying lengths mixed in different abundances (5 samples x 3 replicates each) and 2) an equimolar mixture of 963 synthetic microRNAs (3 replicates) to test the quantitative accuracy of our method - These 18 samples correspond to the data files shared here.
The 5 synthetic RNA oligonucleotide species of varying lengths are:
25-mer: NNCAUUGUUAAGCGAACGGCUGCNN
40-mer: NNNUAUCCUAAUCAUCUUAAUACUACAAUGGACCAUGNNN
60-mer: NNNCGACCCAAGUUGUCUGAUUAAGCAUAUUAAGAGCCGAGGAUCGUAUCGCCACCCNNN
80-mer #1:
UCCUGAUAAUUGCAGAGAAGUGACUUCGUGGGUGUCACCAGUAAUAAGGCAUCGCCAGCUAACAAUCGGUGGGAACGUCA
80-mer #2:
UGUCUUUCACGGAGACUGCGGGUAGCUCUGACAAGCUCCUAUGGUGAUACCACCACGCUCGUAAUGAGAUGGGAUAGUCG

first: Bo

last: Cao

first: Peter

last: Dedon


title: qPCR profiling of mouse immune cell miRNAs

status: Public on Jan 23 2020

city: New York

first: Brian

last: Brown

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: qPCR profiling of miRNA expression across a broad range of mouse immune cells as part of the ImmGen Consortium (www.immgen.org)

overall_design: 141 individual samples representing 63 cell types spanning the mouse immune system were profiled for miRNA expression

first: Samuel

last: Rose

first: Aleksandra

last: Wroblewska


title: Sonic Hedgehog inhibitor cyclopamine effect on JAR cells

status: Public on Dec 31 2019

city: Hangzhou

first: Yibin

last: Pan

address: 3 East Qingchun Road,

institute: Sir Run Run Shaw Hospital

summary: Physiologically, trophoblast progenitor cells differentiate into placental villous cytotrophoblast cells (CTBs). CTBs either differentiate into invasive lineage to yields extravillous cytotrophoblast cells (EVTs), or undergo cell fusion lineage to yields syncytiotrophoblast cells (STBs)，Sonic hedgehog (Shh) together with indian hedgehog (Ihh) and desert hedgehog (Dhh) consist of ligand of hedgehog signaling pathway, which plays pivotal roles in regulating cell proliferation, cell differentiation, organogenesis and development, even involving in tumorigenesis and progression. previous study had summarized and indicatedthat hedgehog proteins played important roles in regulating hematopoiesis, vasculogenesis and angiogenesis during embryogenesis and development. Herein, we investigate the effect of the Sonic Hedgehog morphogen inhibitor Cyclopamine on JAR cells

overall_design: JAR Cells mRNA profiles of with or without treatment of Cyclopamine were generated by deep sequencing, in triplicate

first: Lili

last: Yan

first: Qiaoqiao

last: Chen

first: Cheng

last: Wei

first: Yongdong

last: Dai

first: Xiaomei

last: Tong

first: Haiyan

last: Zhu

first: Meifei

last: Lu

first: Yanling

last: Zhang

first: Xiaoying

last: Jin

first: Xiaona

last: Lin

first: Tai

first: Songying


title: CHD4 regulates super-enhancer accessibility in fusion-positive rhabdomyosarcoma and is essential for tumor growth

status: Public on Dec 20 2019

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: ATP-dependent chromatin remodelers modulate gene expression by regulating genome accessibility and can contribute to tumorigenesis. In fusion-positive rhabdomyosarcoma (FP-RMS), we have previously identified the chromatin remodeler and NuRD subunit CHD4 as an essential gene for tumor survival. Here, we demonstrate that the FP-RMS vulnerability to CHD4 goes beyond its function as a NuRD member. Mechanistically, CHD4 interacts with BRD4 and co-localizes with the tumor driver and fusion protein PAX3-FOXO1 at super-enhancers where it generates a chromatin architecture permissive for the binding of the fusion protein. This allows the positioning of RNA polymerase 2 at promoters and the expression of the oncogenic program of PAX3-FOXO1. Additionally, analysis of genome-wide cancer dependency databases identifies CHD4 amongst the NuRD subunits as general novel cancer vulnerability. Our findings describe, for the first time, CHD4 as a regulator of super-enhancer-mediated gene expression and establish this chromatin remodeler as an unexpected broad tumor susceptibility.

overall_design: ChIP assays were performed using the ChIP-IT High Sensitivity kit (Active Motif), and were performed once per target per cell line per condition.

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Transcriptome profiling (RNA-seq)  analysis of  control and NaIO3-treated RPE cells

status: Public on Dec 26 2019

city: Shanghai

first: zhimin

last: Tang

address: 833 Zhizaoju Road

institute: Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Purpose:  The goal of this experiment is to investigate the relative contributions of various types of cell death in  NaIO3-treated RPE cells
Methods: RPE cell mRNA profiles were generated by deep sequencing, in triplicate, using Illumina  HiSeq 4000.
Results: According to the differential expressions of mRNA genes, among which 661 genes were upregulated and 637 genes were downregulated with significance after NaIO3 treatment . From the Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, it has been identified that ferroptosis ranked as the top pathway in comparison to other types of cell death (apoptosis, and necroptosis) upon NaIO3 treatment, which was additionally validated by the higher FPKM of main regulators in ferroptosis than that in apoptosis. Additionally, it was found that heme oxygenase-1 (HMOX1, also known as HO-1) as well as SLC7A11 (solute carrier family 7 member 11) mRNA were characterized as the most dramatically upregulated genes upon NaIO3 treatment against ARPE-19 cells
Conclusions: Our study represented that ferroptosis serves as a predominant pathogenic factor involved in AMD pathological process.

overall_design: Human ARPE-19 cells (RPE cell line) with or without NaIO3 treatment were collected by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Zhimin

first: Ping

last: Gu


title: Nascent RNA sequencing (PRO-seq) after 200nM romidepsin treatment of H9 cells

status: Public on Dec 12 2019

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

overall_design:
These experiments identify the early changes nascent RNA that results from treating cells with 200nM romidepsin.
Cells were treated with romidepsin for 60 minutes in triplicate

middle: J


title: BMP2 and GSK126 synergize to induce expression of osteogenic genes

status: Public on Dec 01 2019

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

overall_design:
MC3T3 sc4 pre-osteoblasts were treated with BMP2 and GSK126 (Ezh2 inhibitor). Our analysis shows that BMP2 and GSK126 synergistically active expression of osteogenic genes.
MC3T3 sc4 cells were maintained in α-minimal essential medium without ascorbic acid (Gibco) containing 10% fetal bovine serum (Atlanta Biologicals), 100 units/ml penicillin and 100 μg/ml streptomycin (Gibco). Cells were seeded in maintenance medium at a density of 10,000 cells/cm2. Next day, cells were treated with vehicle, 5µM GSK126 (Xcess Biociences Inc.), 10 and 50ng/ml BMP2 (R&D Systems), and combination of GSK126 and BMP2 in osteogenic medium (maintenance medium supplementend with 50μg/ml ascorbic acid (Sigma) and 4mM β-glycerol phosphate (Sigma)). Three days later, old osteogenic medium was replaced with a fresh batch of osteogenic medium supplemented with vehicle, GSK126, BMP2, and combination of GSK126/BMP2. Total RNA was isolated on days one and six of osteogenic differentiation using the Direct-zol™ RNA kit (Zymo Research) and TRIzol reagent (Invitrogen).

first: Amel

last: Dudakovic

first: Andre

last: van Wijnen


title: Hotspot exons are common targets of splicing perturbations

status: Public on Nov 22 2019

city: Providence

first: David

middle: Thomas

last: Glidden

state: RI

address: 70 Ship St.

department: Molecular and Cell Biology

institute: Brown University

summary: RNA-seq of amiloride-treated cell culture was conducted in order to understand the characteristics that make certain exons susceptible to splicing perturbations. Amiloride is a diuretic that acts by inhibiting epithelial sodium channels in the kidney. It also behaves as a non-specific kinase inhibitor, and has been shown to affect splicing in a handful of genes, presumably by altering phosphorylation of splicing factors. Two samples were sequenced (one untreated, one treated). Differential splicing was done using rMATS version 3.2.5.

overall_design: Poly-A+ RNA from HEK293T cells untreated or treated with amiloride (300 µg/mL) for 6 h was isolated and prepared for RNA-seq.

first: Jeramiah

last: Buerer

first: Camillo

last: Sauressig

first: William

middle: G

last: Fairbrother


title: CXCR4 Signaling Has a CXCL12-Independent Essential Role in Murine MLL-AF9-Driven Acute Myeloid Leukemia

status: Public on Nov 15 2019

city: Lund

first: Marcus

last: Järås

address: Universitetssjukhuset

department: Clinical Genetics

country: Sweden

institute: Lund University

summary: Acute myeloid leukemia (AML) is defined by an accumulation of immature myeloid blasts in the bone marrow. To identify key dependencies of AML stem cells in vivo, here we use a CRISPR-Cas9 screen targeting cell surface genes in a syngeneic MLL-AF9 AML mouse model and show that CXCR4 is a top cell surface regulator of AML cell growth and survival. Deletion of Cxcr4 in AML cells eradicates leukemia cells in vivo without impairing their homing to the bone marrow. In contrast, the CXCR4- ligand CXCL12 is dispensable for leukemia development in recipient mice. Moreover, expression of mutated Cxcr4 variants reveals that CXCR4 signaling is essential for leukemia cells. Notably, loss of CXCR4 signaling in leukemia cells leads to oxidative stress and differentiation in vivo. Taken together, our results identify CXCR4 signaling as essential for AML stem cells by protecting them from differentiation independent of CXCL12 stimulation.

overall_design: Mouse MLL-AF9 leukemia cells were transduced with control or Cxcr4 sgRNAs and transplanted into sub-lethally irradiated C57BL/6 mice. The mice were sacrificed on day 10 and RNA sequencing was performed on FACS sorted GFP+ cells. Total number of samples - 11. Replicates - Control_sgRNA - 4, Cxcr4_sgRNA_a - 4, Cxcr4_sgRNA_b - 3.

first: Ramprasad

last: Ramakrishnan


title: Transcriptome analyses of human pancreatic islets and pseudoislets

status: Public on Nov 21 2019

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

summary: We have observed an improvement of glucose-stimulated insulin secretion upon the formation of pseudoislets. Transcriptome analyses of islets and pseudoislets from the same human donor were performed to determine the functional improvement. We identified 38844 transcripts and revealed that unlike islets, pseudoislets were deprived of exocrine and endothelial cells. In addition, the mRNA levels of proteins related to apoptosis and inflammation as well as the components of extracellular matrix were less abundant in pseudoislets.

overall_design: human islets preparations and pseudoislets from 4 different human donors

first: Susanne

last: Ullrich

first: Estela

last: Lorza-Gil

first: Andreas

last: Dahl

first: Marie

last: Gauder


title: Decoding neuronal diversity by single cell Convert-seq

city: Yokoham

first: Joachim

middle: Felix

last: Luginbühl

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

summary: The conversion of cell fates is controlled by hierarchical gene regulatory networks (GRNs) that induce remarkable alterations of cellular and transcriptome states. The identification of key regulators within these networks from myriad of candidate genes, however, poses a major research challenge. Here we present Convert-seq, combining single-cell RNA sequencing (scRNA-seq) and pooled (mutiplexed) ectopic gene expression with a new strategy to discriminate sequencing reads derived from exogenous and endogenous transcripts. We demonstrate Convert-seq by associating hundreds of single cells at multiple time-points during direct conversion of human fibroblasts to induced neurons (iN) with exogenous and endogenous transcriptional signatures. Convert-seq simultaneously identified GRNs that modulate the emergence of parallel developmental trajectories during iN conversion and predicted combinatorial interactions of exogenous transcription factors controlling iN subtype specification. Validation of iN subtypes generated by novel combinations of exogenous transcription factors establish Convert-seq as a broadly applicable workflow to rapidly identify key transcription factors and GRNs orchestrating the direct conversion of virtually any cell type.

overall_design: Single-cell transcriptomes of human fibroblasts reprogrammed into induced neurons via chemicals or ectopic expression of transcription factors at multiple time-points

first: Jay

middle: W

last: Shin


title: Characterization of plasmids mediating carbapenem resistance in Klebsiella pneumoniae in Pretoria, South Africa

status: Public on Oct 17 2019

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

summary: The study aimed to characterize plasmids mediating carbepenem resistance in Klebsiella pneumoniae in Pretoria, South Africa. We analysed 56 K. pneumoniae isolates collected from academic hospital around Pretoria. Based on phenotypic and molecular results of these isolates, 6 representative isolates were chosen for further analysis using long reads sequencing platform. We observed multidrug resistant phenotype in all these isolates, including resistance to aminoglycosides, tetracycline, phenicol, fosfomycin, floroquinolones, and beta-lactams antibiotics. The blaOXA-48/181 and blaNDM-1/7 were manily the plasmid-mediated carbapenemases responsible for carbapenem resistance in the K. pneumoniae isolates in these academic hospitals. These carbapenemase genes were mainly associated with plasmid replicon groups IncF, IncL/M, IncA/C, and IncX3. This study showed plasmid-mediated carbapenemase spread of blaOXA and blaNDM genes mediated by conjugative plasmids in Pretoria hospitals.

overall_design: Six carbapenem-resistant K. pneumoniae isolates were sequenced using PacBio sequencer; PRJNA565241

first: N

last: Mbelle

first: J

middle: O

last: Sekyere


title: Gene expression signatures for Ibrutinib resistance in  Diffuse Large B-cell Lymphoma (ABC-DLBCL)

status: Public on Nov 01 2019

city: columbus

first: Lalit

last: Sehgal

state: Ohio

department: Hematology

institute: The Ohio State University

summary: To understand the acquired resistance mechanism in DLBCL the cell lines (OCI-Ly1, Oci-Ly10 and HBL-1) were treated with Ibrutinib over time to generate resistant clone.

overall_design: The gene expression profile was measured in parental and Ibrutinib resistant clones after 8 months. All the gene expression data for parental is labeled in triplicate marked (A-C) and for the ibrutinib resitance is labeled as (Res).

first: Sehgal

last: Lalit


title: The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy

status: Public on Sep 10 2019

city: SAINT LOUIS

first: Parker

middle: C

last: Wilson

state: MO

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

summary: We report the early transcriptional changes in human diabetic nephropathy by single nucleus RNA sequencing

overall_design: Single nucleus RNA sequencing of 3 early human diabetic kidney samples and 3 controls. Samples represent non-tumor tissue in patients undergoing nephrectomy for renal mass.

first: Benjamin

middle: D

last: Humphreys


title: Expression profiling in Prostate cancer cells treated with DOT1L inhibitor

status: Public on Aug 09 2019

city: CHICAGO

first: Rajita

last: Vatapalli

state: IL

address: 303 E SUPERIOR, 6-250

institute: Northwestern University

summary: We performed expression profiling of prostate cancer cells, LNCaP and PC3 cells that were treated with the specific DOT1L inhibitor EPZ004777 (1uM) for 8 days. We found that unique genes were differentially expressed in both cell lines.

overall_design: Examination of expression changes upon EPZ004777 treatment

first: Sarki

last: Abdulkadir


title: Transcriptional analysis of NK cells in human lung

status: Public on Jul 08 2019

city: Stockholm

first: Jakob

last: Michaelsson

address: Alfred Nobels allé 8, ANA Futura, level 7

department: Department of Medicine

institute: Karolinska Institutet

summary: Subsets of NK cells in human lung have a transciptional signature consistent with being tissue-resident NK cells

overall_design:
Two biological replicates were analyzed for each subset and from each donor
-----------------------------------------------
Authors state "Raw sequence data has been deposited at EGA (accession number EGAD00001000002) and will be released upon acceptance of manuscript."


title: Copy number variations analysis by CytoscanHD array of 33 human pleural mesothelioma cell lines

status: Public on Jul 17 2019

city: Nantes

first: Jean-Francois

last: Fonteneau

address: 8 quai Moncousu BP70721

institute: INSERM

summary:
We performed a cytoscanHD array to analyze copy number variations in the genome of 33 human pleural mesothelioma cell lines established from patient pleural effusion.
We were particularly interested in the analysis of the p21.3 region of chromosome 9 which contains CDKN2A tumor suppressor genes and the gene encoding type I interferons that are often deleted and confer sensitivity to oncolytic Measles virus

overall_design: Copy number analysis of Affymetrix CytoscanHD arrays was performed for 33 human pleural mesothelioma cell lines

first: Christophe

last: Blanquart

first: Stephane

last: Minvielle


title: Treatment of melanoma cell lines with CCG-222740

status: Public on Jul 16 2019

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

summary: The Ras/MEK/ERK pathway has been the primary focus of targeted therapies in melanoma, given that it is aberrantly activated in almost 80% of human cutaneous melanomas (~50% BRAFV600 mutations and ~30% NRAS mutations). While targeted therapies have yielded success in BRAFV600 mutant melanoma patients, such therapies have been ineffective in NRAS mutant melanomas in part due to their cytostatic effects and primary resistance in this patient population. Here, we demonstrate that increased Rho/MRTF-pathway activation correlates with high intrinsic resistance to trametinib, a MEK inhibitor, in a panel of NRAS mutant melanoma cell lines. Combination of trametinib with the Rho/MRTF-pathway inhibitor, CCG-222740, synergistically reduced cell viability in NRAS mutant melanoma cell lines in vitro. Furthermore, the combination of CCG-222740 with trametinib induced apoptosis and reduced clonogenicity in the highly trametinib-resistant SK-Mel-147 cells. These findings suggest a role of the Rho/MRTF-pathway in high intrinsic trametinib resistance to a subset of NRAS mutant melanoma cell lines and highlights the potential of concurrently targeting the Rho/MRTF-pathway and MEK in NRAS mutant melanomas.

overall_design:
Melanoma cell lines were treated with the MRTF pathway inhibitor CCG-222740 and RNA-Seq was performed to measure gene expression.
mRNA profiles of various melanoma cell lines treated with 10 uM CCG-222740 for 0, 2, 6, or 24 hours.

first: Richard

last: Neubig


title: Podoplanin-expressing macrophages (PoEMs) promote lymphangiogenesis and favour lymphatic metastasis in breast cancer

status: Public on Oct 03 2019

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49

country: Belgium

institute: VIB

summary: RNAseq was performed on PoEMs (CD11b+, F4/80+, PDPN+) vs. non-PoEMs (CD11b+, F4/80+, PDPN-) sorted from orthotopically inoculated 4T1 tumors in WT mice.

overall_design: Study on the role of PDPN+ tumor-associated macrophages in lymphangiogenesis and matrix remodelling.

first: Paweł

last: Bieniasz-Krzywiec

first: Rosa

last: Martín-Pérez

first: Manuel

last: Ehling

first: Melissa

last: García-Caballero

first: Sotiria

last: Pinioti

first: Samantha

last: Pretto

first: Roel

last: Kroes

first: Chiara

last: Aldeni

first: Mario

last: Di Matteo

first: Hans

last: Prenen

first: María

middle: V

last: Tribulatti

first: Ann

last: Smeets

first: Agnes

last: Noel

first: Oscar

last: Campetella

first: Giuseppe

last: Floris

first: Jo

last: Van Ginderachter


title: H3K79me2 ChIP-seq in prostate cancer cells

first: Rajita

last: Vatapalli

summary: We report the application of ChIP sequencing technology for high-throughput profiling of H3K79me2 in prostate cancer cells. We generated genome-wide maps of LNCaP and PC3 cells that were treated with the specific DOT1L inhibitor EPZ004777. We find that lysine 79 dimethylation is sensitive to DOT1L inhibition in both cell lines, however the enrichment of K79 methylated peaks differed between the two cell lines.

overall_design: Examination of H3K79me2 modifications in 2 cell lines

first: Sarki

last: Abdulkadir


title: Analysis of differentially expressed genes in intrahepatic HBsAg accumulating mice

status: Public on Oct 16 2019

city: Nagoya

first: Ian

last: Baudi

state: Aichi

address: Kawasumi, Mizuho

department: Virology

institute: Nagoya City University Graduate School of Medical Sciences

summary: Search for distinct genes whose expression correlates with  IFN⍺ mediated liver injury in HBsAg-Tg mice. IFN treatment  induces liver injury from 8 hours post IFN treament, peaking at 24 hours,  in HBs transgenic mice and not in the non-transgenic (control) mice

overall_design: snap-frozen liver samples were obtained from groups of four HBsAg-Tg (Tg) and control mice (CTL) sacrificed prior to (0 hour) and 2, 4, 8 and 24 hours after treatment with 5MU/kg of IFN⍺. RNA was analysed from duplicate biological replicates . Groupings A-E correspond to the timepoints 0,2,4,8 and 24 hours.

first: Masanori

last: Isogawa

first: Masaya

last: Onishi


title: Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis [MNase-Seq]

status: Public on Nov 07 2019

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: During mammalian spermatogenesis, male germ cells undergo dramatic reorganization of chromatin, whereby 90-99% of histones are evicted and replaced by protamines.  This reorganization prominently features histone acetylation to loosen chromatin structure.  Given the potential role of retained histones in fertility and early embryonic development, the genomic location of retained nucleosomes is of great interest.  However, the ultimate position and mechanisms underlying nucleosome eviction/retention are poorly understood, including several studies utilizing MNase-seq methodologies, but reporting remarkably dissimilar locations. Here, we utilized ATAC-seq to determine the location of retained nucleosomes in mouse sperm and found enrichment at promoters, but also retention at inter- and intragenic regions, and repetitive elements.  We further investigated nucleosome eviction/retention by generating pre-meiotic, germ cell specific, conditional knockout mice for the histone acetyltransferase Gcn5, a key histone acetyltransferase.  Gcn5cKO germ cells exhibited abnormal chromatin dynamics during spermiogenesis, including diminished nucleosome eviction leading to increased histone retention in sperm.  These mice exhibited severe reproductive phenotypes: abnormal sperm production, sperm morphology, and ultimately, male infertility.  Our findings demonstrate Gcn5 mediated histone acetylation promotes chromatin accessibility and nucleosome eviction in spermiogenesis, and that loss of histone acetylation leads to defects that disrupt male fertility and potentially, early embryogenesis.

overall_design:
Includes MNase-seq from two stages of spermatogenesis (meiotic spermatid, round spermatid) in SV129 mice at three concentrations of MNase (0.5U, 1U, 2U) with 2 replicates for each (stage,concentration) condition

Please note that each 'bed' processed data is generated from both replicaes and is linked to the corresponding rep1 sample records.

first: Lacey

last: Luense

first: Greg

first: Enrique

middle: L

last: Shiao

first: Richard

last: Rangel

first: Angela

middle: H

last: Weller

first: Marisa

middle: S

last: Bartolomei

first: Shelley

last: Berger


title: Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis [ATAC-seq]

overall_design: Includes paired-end ATAC-seq from four stages of spermatogenesis (meiotic spermatid, round spermatid, elongating spermatid, and mature sperm) in three separate genetic backgrounds: SV129 mice (two technical repeats of two biological replicates for meiotic, round, and elongating spermatids and six biological replicates for mature sperm), C57BL6 GCN5+/+ mice (2 biological replicates each) and C57BL6 GCN5-/- mice (Stra8-CRE homozygous flox'd alleles) (2 biological replicates each)


title: Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

summary: Myc is a family of regulator genes and proto-oncogenes that code for transcription factors. Gene expression of CTCF in human cancer cells and control uncover the disrupted enhancer-promoter regulation of MYC in human cancer cells.

overall_design: In situ Hi-C experiments constructed on two CTCF AID homozygous knock-in clones 27 and 35.

first: Judith

last: Hyle

first: Yang

last: Zhang

first: Shaela

last: Wright


title: Nogo maintains muscle integrity and regulates muscle regeneration via modulating Nogo-A expression

status: Public on May 31 2019

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

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

department: Newbiology

country: South Korea

institute: DGIST

summary: Nogo, also called RTN4, functions through three isoforms including Nogo-A, -B, and -C. Although Nogo-A is a well-known CNS inhibitor and the level of Nogo-A is increased in muscles of ALS patients, its role in the regulation of skeletal muscle homeostasis and regeneration is still vague. In this study, we analyzed various pathological muscle condition of human and mouse model, and discovered significant increase of Nogo-A and myogenic factors. To understand the role of Nogo in skeletal muscle, muscle transcripts from Nogo+/+ and Nogo-/- mouse were analyzed and observed intensified gene expression involved in adipocyte differentiation and lipid metabolism, and reduced gene expression related to muscle differentiation and structure organization suggesting muscle disorder from muscle replacement with fat deposition. Skeletal muscle structure from Nogo null mice displayed dystrophic phenotypes including impaired myofiber structure and immune cell infiltrations, and dysregulated homeostatic features such as higher level of MyoD, procaspase 3, CHOP, and AKT compared to wild-type muscle. Notexin-injured Nogo deficient muscle resulted higher level of immune cell infiltration but defective in IL-6 production, a well-known myokine from immune cells, and abnormally upregulated regenerative muscle fibers than normal muscle. Therefore we hypothesized that increased Nogo-A in pathological conditions may regulate muscle regeneration. Then differentiating C2C12 cells and induced myogenic stem cells(iMSC) showed upregulated Nogo-A and Myogenin, and Nogo-A silencing in C2C12 cells abrogated the capability to differentiate into myotubes. In conclusion, Nogo functions to maintain muscle homeostasis and integrity, and altered Nogo-A expression in pathological muscle condition mediates muscle regeneration. These understanding suggests Nogo-A as a novel differentiation target for the treatment of myopathies at clinical set.

overall_design: mRNA expression profiles of gastrocnemius muscle tissues of WT and Nogo KO mice were examined by Illumina Hi-seq 2500

first: Kyu-Shik

last: Jeong

first: Daehee

last: Hwang


title: Mechanism of virus attenuation by codon pair deoptimization

status: Public on Jan 01 2020

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: Determination of translation efficiency of recoded neuramindase mRNA transcripts in transiently transfected HEK 293T cells.

overall_design: Expression plasmids containing recoded IAV neuramindase were transfected into HEK 293T cells and translational dynamics of neuraminidase mRNA was determined by ribosome footprint-profiling experiments

first: Nicole

last: Groenke

first: Jakob

last: Trimpert

first: Sophie

last: Merz

first: Andelé

last: Conradie

first: Hongwei

last: Haza Zhang pis

first: Orsalia-Georgia

last: Hazapis

first: Sebastian

last: Rausch

first: Markus

last: Landthaler

first: Nikolaus

last: Osterrieder

first: Dusan

last: Kunec


title: Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping

status: Public on May 14 2019

first: Chunliang

last: Li

summary: In human cells, CTCF’s role in genomic organization and global transcription regulation is less clearly defined due to the lack of available tools to efficiently deplete CTCF.  Here, we used an auxin-inducible degron system to conditionally deplete CTCF in a human B-cell lymphoblastic leukemia (B-ALL) cell line, SEM. Cut & Run ChIP-seq showed acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ~1.8 Mb downstream.

overall_design: CUT&RUN ChIP-seq was performed on auxin-inducible degron system to conditionally deplete CTCF in a human B-cell lymphoblastic leukemia (B-ALL) cell line, SEM, using antibodies against CTCF for a pulldown assay

first: Judith

last: Hyle


title: Transcriptome profiles of B cell subsets from healthy and SLE subjects

status: Public on May 17 2019

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: SLE is characterized by the production of autoantibodies that arise from the B cell lineage.  Therefore, we sought to assess the epigenetic and transcriptome profiles of distinct B cell subsets known to be expanded in SLE from healthy and SLE subjects.  These data define the differentiation heirarchy of B cell subsets and the epigenetic and transcriptional consequences of SLE on human B cells.

overall_design:
Five distinct B cell subsets were FACS isolated from a cohort of SLE and HC subjects.  For a subset of subjects, circulating Antibody Secreting Cells (ASC) were also isolated for comparisons.  Cells were FACS sorted into lysis buffer and RNA purified and transcriptome profiles determined by RNA-seq.

**Please note that the associated raw data has been replaced on May 2021 as an incomplete dataset was included in the initial submission.***

first: C

first: J

last: Boss


title: Dtx3L and Androgen Signaling in Prostate Cancer

status: Public on Jul 06 2019

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Gene expression in VCaP prostate cancer cells treated with or without androgen was analyzed. VCaP cells containing a dox-inducible shRNA against Dtx3L were compared with and without dox induction (Dtx3L knockdown), in the presence or absence of androgen.

overall_design: RNA was extracted from VCaP cells with a Dox-inducible Dtx3L shRNA, either untreated or treated with androgen for 24 hours (2 nM, R1881). Two conditions were sequenced with 3 replicates for each condition. Data from dox-treated (Dtx3L knockdown) VCaP cells (+/- R1881) was analyzed together with data from control (no dox) VCaP cells (+/- R1881).

last: Yang

first: D

first: Bryce

last: Paschal


overall_design: CaptureC libraries constructed on two CTCF AID homozygous knock-in clones 27 and 35.

first: Yang

last: Zhang

first: Shaela

last: Wright


title: Identifying pre-disease signals before metabolic syndrome in mice by dynamical network biomarkers

status: Public on Jun 24 2019

city: Toyama

first: Makito

last: Oku

address: 2630 Sugitani

department: Research Center for Pre-Disease Science

institute: University of Toyama

summary: The establishment of new therapeutic strategies for metabolic syndrome is urgently needed because metabolic syndrome, which is characterized by several disorders, such as hypertension, increases the risk of lifestyle-related diseases. One approach is to focus on the pre-disease state, a state with high susceptibility before the disease onset, which is considered as the best period for preventive treatment. In order to detect the pre-disease state, we recently proposed mathematical theory called the dynamical network biomarker (DNB) theory based on the critical transition paradigm. Here, we investigated time-course gene expression profiles of a mouse model of metabolic syndrome using 64 whole-genome microarrays based on the DNB theory, and showed the detection of a pre-disease state before metabolic syndrome defined by characteristic behavior of 147 DNB genes. The results of our study demonstrating the existence of a notable pre-disease state before metabolic syndrome may help to design novel and effective therapeutic strategies for preventing metabolic syndrome, enabling just-in-time preemptive interventions.

overall_design: Gene expression in adipose tissues of three groups of mice---TSOD mice (metabolic syndrome model, untreated), TSNO mice (control), and BTS-treated TSOD mice (metabolic syndrome model with treatment)---were measured at 3, 4, 5, 6, and 7 weeks of age. 3 to 5 biological replicates were included.

first: Keiichi

last: Koizumi

first: Shusaku

last: Hayashi

first: Akiko

last: Inujima

first: Naotoshi

last: Shibahara

first: Luonan

last: Chen

first: Yoshiko

last: Igarashi

first: Kazuyuki

last: Tobe

first: Shigeru

last: Saito

first: Makoto

last: Kadowaki

last: Aihara


title: A Phase II Randomized Trial of Neoadjuvant Trastuzumab or Lapatinib or the Combination of Trastuzumab and Lapatinib, Followed by Docetaxel and Carboplatin with Trastuzumab and/or Lapatinib in Patients with HER2+ Breast Cancer [treatments]

status: Public on May 08 2019

city: Santa Monica

first: HSIAOWANG

last: CHEN

state: CA

address: 2825 Santa Monica Blvd

department: Medicine

institute: UCLA

summary: Adjuvant docetaxel, carboplatin, and trastuzumab (TCH) is a standard regimen for HER2+ breast cancer. Dual HER2-blockade with lapatinib (L) and trastuzumab demonstrated significant activity in the metastatic and neoadjuvant settings. This study evaluates neoadjuvant TC plus trastuzumab (H) and/or lapatinib (L). This study demonstrated a similar pCR rate with TCH and TCHL and a lower rate of pCR with TCL.  Treatment-related toxicity limited the ability for participants to receive protocol-specified chemotherapy and HER2-targeted therapy in the TCHL Arm.

overall_design:
Microarray experiments were conducted using the 2-color Agilent Whole Human Genome platform. Samples were collected before treatment at the time of diagnosis (baseline samples). Every adequate baseline sample was profiled against a breast tumor mixed reference pool. 110 patients had baseline samples which passed QC.  Samples were also taken after two weeks of treatment with the HER2-targeted biologic. (run-in samples). Each run-in sample was compared to the baseline sample from the same patient. 89 patients had adequate baseline and run-in samples. The Agilent feature extracted data was processed using the Rosetta Resolver Gene Expression system V 7.xx. Data is available for each unique probe on the Agilent platform (total of 41000) and expressed as log 10 ratio of experimental to reference sample.  In the 110 baseline experiments the reference sample is the untreated breast tumor collected at diagnosis and the reference sample is the mixed breast tumor reference.  In the 89 run-in experiments, the experimental sample is the run-in sample taken after two weeks of treatment and the reference sample is the baseline sample taken at diagnosis from the same patient.

NOTE: the assigned treatment group and the final drug response is provided as sample characteristics; T=Docetaxel C=Carboplatin, H=trastuzumab, Ty=lapatinib.  RD=residual disease. PCR=Pathological complete Response defined as the absence of invasive cancer in the breast and axilla

first: Sara

last: Hurvitz

first: Chen

last: Hsiao-Wang

first: Dering

last: Judy

first: Slamon

last: Dennis


title: Next Generation Sequencing Analysis of Prenatal Chlorpyrifos Exposure embryonic kidneys

status: Public on Jun 30 2019

city: Hangzhou

first: Bingjue

last: Li

address: Qingchun Road 79

institute: Zhejiang University

summary:
Purpose: In order to study signaling pathway changes of prenatal chlorpyrifos exposure embryonic kidney development
Methods: By using RNA-seq, we studied the transcriptome of E12.5, E14.5, E16.5 and E18.5 prenatal chlorpyrifos exposure embryonic kidneys and DMSO exposure (control) embryonic kidneys
Results: We show that Notch signaling pathway and aquaporin family had high expression in chlorpyrifos exposure E18.5 kidney. The nephron progenitor markers had low expression in chlorpyrifos exposure embryonic kidneys

overall_design: ICR mice aged 8 weeks were bred using timed matings, the pregnant mice were randomly divided into two groups. Chlorpyrifos (96% purity) was dissolved in dimethyl sulfoxide (DMSO), and CPF 5mg/kg was injected subcutaneously daily in CPF group during gestation day 7.5-11.5. The controls were injected with isovolumetric DMSO at the same time. We collected E12.5, E14.5, E16.5 and E18.5 mouse embryonic kidneys for RNA-seq of the two groups respectively.

first: Chaohong

last: Zhu

first: Wenyu

last: Xiang

first: Jing

last: Qin

first: Lihua

last: Dong

first: Jianghua

first: Hong

last: Jiang


title: Identification of Notch1 regulated genes in A549 NSCLC cell line

status: Public on Sep 30 2019

city: Guangzhou

first: Han

last: Tian

state: Guangdong

address: No.74, Zhongshan Er Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

summary: Notch signaling is an evolutionarily conserved signaling pathway. Notch1 signaling has been shown to potentially paly an important role in cancer development and progression. To illustrate the underlying regulating mechanisms of Notch1 activation in NSCLC, the intracellular domain of Notch1 receptor (NICD1) was overexpressed in A549 cell line and the RNA-sequences were performed.

overall_design: Transcriptomes profiles of A549-NICD1 and A549-vector were generated by Illumina NovaSeq 6000.

first: Lei

last: Liu

first: Shihua

first: Junchao

last: Cai


title: Human islets of varying quality: the good, the (not so) bad and the ugly

status: Public on Jul 27 2019

city: Camperdown

first: Anand

last: Hardikar

state: NSW

address: 92-94 Parramatta Road

institute: University of Sydney

summary: This collection represents whole transcriptome data for human islets that were stratified to high quality (Group 1), intermediary quality (Group 2) and poor quality (Group 3) islets (Wong WKM et al JCI Insight 2019).

overall_design: Randomly selected islet preparations based on their post-isolation quality.

first: Wilson KM

last: Wong

first: Mugdha

last: Joglekar

first: Yi Vee

last: Chew

first: Wayne

last: Hawthorne

first: Anandwardhan

middle: A


title: Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis

first: Gregory

last: Donahue

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

overall_design: Refer to individual Series


title: Bcl-2 overexpression effects in rat neural precursor cells.

status: Public on May 01 2019

city: Seoul

first: Yun Young

last: Lee

address: 222, Wangsimni-ro, Seongdong-gu

department: Department of Biochemistry and Molecular Biology

institute: Hanyang University

summary: Bcl-2 is highly enriched in the nervous system during neural development and plays an important role in modulating cell survival. In addition to its anti-apoptotic function, Bcl-2 has previously been suggested as a mediator of neuronal differentiation. However, the mechanism by which Bcl-2 might influence neurogenesis is not sufficiently understood. We aimed to determine the non-apoptotic functions of Bcl-2 during neuronal differentiation.

overall_design: Two-condition experiments, Vector/-bFGF (Induction of neuronal differentiation) vs rBcl-2/+bFGF (Bcl-2 overexpression)

first: Joong-Soo

last: Han

first: YunYoung


title: Sequencing of Tumor infiltrating macrophages from B16f10 tumors in Wt and IFNγR knockout mice

status: Public on Apr 30 2019

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr.

institute: University of Utah

summary: We report the application of RNA sequencing to determine the transcriptional result of IFNgR deletion upon tumor associated macrophages within the B16f10 tumor microenvironment.

overall_design: Examination of genes regulated by IFNγR signaling in tumor associated macropahges

first: Thomas

last: Huffaker


status: Public on Apr 27 2019

first: Chulwoo

last: Park

address: Anam

institute: Korea univ.

summary: RNA-seq analysis of Deinococcus metallilatus of wild type and mutant No. 6 at exponential phase (24 h)

overall_design: Both strains were cultured in TYG media until 24 h with agitation, and RNAs were extracted

first: Woojun


title: Search for a novel diagnostic marker for liver cancer.

status: Public on Apr 02 2019

city: HeFei

first: Yong

address: 218 Jixi Road

institute: First Affiliated Hospital of Anhui Medical University

summary:
Analysis of the gene expression proﬁles of tumor and normal tissue samples from Hepatocellular carcinoma (HCC).
Find potential secretory protein to serve as diagnostic marker for liver cancer.

overall_design: Expression profiling by array, transformed count, 4 samples.

first: Yeben

last: Qian


title: Sequencing of primary mouse machrophage and Raw 264.7 macrophage cell skewed in M1 or M2 conditions

summary: We report the application of RNA sequencing to determine the transcriptional response of primary bone marrow macorphages and murine macrophage Raw 264.7 cells in response to stimulation with LPS/IFNgamma(M1) or IL-4 (M2) stimulation conditions

overall_design: Examination of gene changes in macrophages stimulated with M1 or M2 conditions

first: Marah

last: Runtsch


title: Intranasal immunization with CpG-B Oligodeoxynucleotides protects CBA mice from lethal equine herpesvirus 1 challenge

status: Public on Feb 21 2019

city: Shreveport

first: Seong

last: Kim

state: Louisiana

address: 1501 Kings Highway

institute: LSU Health Sciences Center

summary: Equine herpesvirus 1 (EHV-1) is the causative agent of a number of equine pathological states, including severe disease of the central nervous system, respiratory infections, and abortion storms. Our results showed that intranasal immunization with CpG-B oligodeoxynucleotides (ODN) protects CBA mice from lethal EHV-1 challenge. IFN-γ and seven interferon-stimulated genes (ISGs) were upregulated 39.4- to 260.3-fold at 8 h postchallenge in the lungs of RacL11-challenged mice that had been immunized with CpG-B ODN. Treatment with 20 ng/ml of IFN-γ reduced EHV-1 yield by 100-fold in MH-S at 4 days post-VZV infection compared to that of untreated cells. However, IFN-γ reduced virus yield by only 2-fold in and mouse fibroblast L-M cells. To identify IFN-γ-stimulated genes that inhibit EHV-1 replication, Affymetrix microarray analyses were performed with IFN-γ-treated MH-S and L-M cells. In MH-S cells, IFN-γ upregulated 551 genes and down-regulated 136 genes as compared to those of untreated cells. In L-M cells, IFN-γ upregulated 225 genes and downregulated 2 genes. Nine genes associated with innate immune response were significantly upregulated only in MH-S cells. Five antiviral ISGs MX1, SAMHD1, NAMPT, TREX1, and DDX60 were upregulated 3.2- to 18.1-fold only in MH-S cells. These results suggest that CpG-B ODN may be used as a prophylactic agent in horses.

overall_design: Murine alveolar macrophage MH-S and mouse fibroblast L-M cells were treated with 0 or 20 ng/ml of murine IFN-γ (Cell Sciences, Canton, MA). The untreated and treated cells were harvested at 8 h post-treatment and used in DNA microarray analyses using the Affymetrix mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA).

first: Akhalesh

last: Shakya

first: Dennis

last: O'Callaghan


title: IFNb/LPS activates convergence of inflammatory gene expression patterns between adipocytes and myeloid cells.

status: Public on Feb 06 2019

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
We examined the transciptomic changes to primary adipocytes resulting from exposure to IFNb and/or LPS, in order to define the mechanisms driving adipocyte inflammatory capacity and resulting transcriptomic convergence with iinflammatory myeloid cells.
Inguinal adipose tissue was obtained from 8 weeks old aged male C57BL/6 mice and stromal vascular fraction was maximally differentiated into primary adipocytes.  Cultured cells were treated with IFNb (200U/ml) or saline for 3 hours and thereafter with LPS (100ng/ml) or saline for 4 hours and then submitted for RNA-sequencing.
Results: We mapped approximately 20 million reads per sample to the mm10 genome, and analyzed all transcripts with >3 reads in 100% of at least one experimental condition.

overall_design: Our study characterizes the transcriptional changes induced by IFNb, LPS and IFNb+LPS through RNAsequencing of adipocytes.  Our results identify that IFNb unlocks a convergence in gene expression patterns between adipocytes and myeloid cells. Further, IFNb priming augments LPS-induced pathways in adipocytes.

first: S

last: Divanovic

first: R

first: C

last: Chan


title: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_ChIP-seq]

status: Public on Feb 27 2019

first: YEQIAO

last: ZHOU

address: 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

summary:
Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells.
Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states.
Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes.
Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.

overall_design: ChIP-seq, RNA-seq and HiChIP in Notch-on, -off, -recovery conditions in TNBC and MCL cell lines to profile Notch transcriptional complex binding, histone modification, Notch target genes and contact between regulatory elements.

first: Yeqiao

last: Zhou

first: Jelena

last: Petrovic

first: Robert

last: Faryabi


title: The Wnt pathway inhibitor, LGK974 has suppressive effects for LPS-induced endotoxemia

status: Public on Mar 01 2019

first: Minwoo

address: 25, Seonyu-ro 13-gil, youngdeungpo-gu

department: Research & Development

institute: ebiogen

summary: We demonstrated that Wnt/β-catenin pathway was activated in in endotoxemic mice, and the modulation of this pathway by LGK974 had beneficial effects by suppressing the inflammation and lethality caused by endotoxemia.

overall_design: C57BL/6 mice (4 weeks old) were used to induce endotoxemia by intraperitoneal injection of 25mg/kg LPS, and liver tissues were collected from the Normal and LPS induced-endotoxemia mice. RNA was extracted from the Liver tissue of each group.

first: Yoosik

last: Yoon

first: Jaewoong

last: Jang


title: DDX3 depletion represses translation of mRNAs with complex 5′ UTRs

status: Public on Mar 25 2019

first: Emanuel

last: Wyler

summary: We describe the subset of transcripts that require DDX3 for efficient translation.

overall_design: Ribosome profiling upon DDX3 knockdown and DDX3 PAR-CLIP was performed from HEK 293 cells.

first: Lorenzo

last: Calviello

first: Srivats

last: Venkataramanan

first: Karol

last: Rogowski

first: Kevin

last: Wilkins

first: Malvika

last: Tejura

first: Bao

last: Thai

first: Jacek

last: Krol

first: Witold

last: Filipowicz

first: Markus

last: Landthaler

first: Stephen

middle: N

last: Floor


title: RNA-sequencing analysis examining how the Vibrio cholerae MARTX toxin and its inidividual effector domains modulate the transcriptome of human intestinal epithelial cells.

status: Public on Jan 23 2019

city: Chicago

first: Karla

middle: Jean Fullner

last: Satchell

address: 303 East Chicago Ave

department: Microbiology-Immunology

institute: Northwestern University

summary: MARTX toxins are large single polypeptide bacterial toxins that translocate multiple cytotoxic and functionally independent effector domains into the cytosol of a target eukaryotic cell. Pandemic Vibrio cholerae El Tor O1 strains secrete a MARTX toxin with three effector domains — the actin crosslinking domain (ACD), the Rho inactivation domain (RID), and the alpha/beta-hydrolase domain (ABH) — to regulate innate immunity and enhance colonization. The goal of this study was to compare changes in the transcriptome of human intestinal epithelial cells (IECs) treated with V. cholerae modified to secret a toxin with only one effector domain to the transcriptome of cells treated with V. cholerae secreting the wild type MARTX toxin that delivers all three effector domains simultaneously. We demonstrate that when all three effectors are delivered there is no change in transcriptional response of IECs compared to untreated cells. However, when only ACD is delivered, transcriptional profiling revealed a significant proinflammatory response is activated. These data suggests that V. cholerae may utilize co-delivery of RID and/or ABH to silence the intestinal immune response to ACD activity. These data provide insight into how the V. cholerae MARTX toxin effector domains function together to alter the innate immune response of IECs during bacterial infection.

overall_design:
mRNA expression profile of T84 human colonic epithielial cells inoculated with N16961ΔhlyAΔhapA V. cholerae containing the wild type MARTX toxin or strains generated to contain MARTX toxins with only a single effector domain.
Each processed file is in .xlsx file type and contain offical gene symbol and description for each gene, read counts for each replicate, fold changes compared to PBS treated controls, and p-values indicating statistically significant or non-significant changes in gene expression compared to PBS treated controls.

first: Patrick

last: Woida


title: A novel computational complete deconvolution method using RNA-seq data

status: Public on Dec 12 2018

city: Cambridge

first: Kai

last: Kang

state: MA

address: 32 Vassar Street

department: CSAIL

institute: MIT

summary: The cell type composition of many biological tissues varies widely across samples. Such sample heterogeneity hampers efforts to probe the role of each cell type in the tissue microenvironment. Current approaches that address this issue have drawbacks. Cell sorting or single-cell based experimental techniques disrupt in situ interactions and alter physiological status of cells in tissues. Computational methods are flexible and promising; but they often estimate either sample-specific proportions of each cell type or cell-type-specific gene expression profiles, not both, by requiring the other as input. We introduce a computational Complete Deconvolution method that can estimate both sample-specific proportions of each cell type and cell-type-specific gene expression profiles simultaneously using bulk RNA-Seq data only (CDSeq). We assessed our method’s performance using several synthetic and experimental mixtures of varied but known cell-type composition and compared its performance to the performance of two state-of-the-art deconvolution methods on the same mixtures. The results showed CDSeq can estimate both sample-specific proportions of each component cell type and cell-type-specific gene expression profiles with high accuracy. CDSeq holds promise for computationally deciphering complex mixtures of cell types, each with differing expression profiles, using RNA-seq data measured in bulk tissue .

overall_design: In brief, total mRNA was prepared from Namalwa (Burkitt’s lymphoma), Hs343T (fibroblast line derived from a mammary gland adenocarcinoma), hTERT-HME1 (normal mammary epithelial cells immortalized with hTERT), and MCF7 (estrogen receptor positive breast cancer cell line). mRNA samples were diluted to 100 ng/μl  and mixed in different proportions (Supplementary Table 2). Global mRNA abundance of the four pure cell lines and of the mixed RNA samples was profiled by RNA-sequencing. Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina). 75-bp single end sequencing was performed on the NextSeq sequencer (Illumina). After obtaining the fastq data, we first ran cutadapt (version 1.12) for trimming adapter sequences. Secondly, we mapped reads to the genome using STAR (version 020201). Lastly, we used featureCounts (version 1.5.1) to generate raw read counts data as the input for our algorithm.

first: Qian

last: Meng

first: Igor

last: Shats

first: David

last: Umbach

first: Melissa

last: Li

first: Yuanyuan

first: Xiaoling

first: Leping


title: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques

city: Philadelphia

first: YEQIAO

last: ZHOU


title: Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

status: Public on Jan 18 2019

city: Ramat Gan

first: Galit

last: Shohat-Ophir

address: The Nanotechnology Building 206, Room C-663

country: Israel

institute: Bar Ilan University

summary: We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using RNA-seq, we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

overall_design: We crossed UAS-unc84-2XGFP transgenic flies with 10 different GAL4 drivers (Dh44-GAL4, NPF-GAL4, NPFR-GAL4, Tdc2-GAL4, Crz-GALl4, TH-GAL4, Trh-GAL4, Fru-GAL4, OK107-GAL4, and elav-GAL4), immunoprecipitated tagged nuclei and extracted RNA. Three independent replicates of each each cross were performed to isolate RNA for RNA-sequencing.

first: Anne

last: Sapiro

first: Anat

last: Shmueli

first: Lee

last: Gilbert

first: Qin

first: Tali

last: Shalit

first: O

last: Yaron

first: Yoav

last: Pass

first: Jin

middle: B


title: A-to-I RNA editing signatures of neuronal populations within the Drosophila brain


title: A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways

status: Public on Nov 28 2018

city: Tokyo

first: Shigeharu

last: Kinoshita

state: Bunkyo

address: 1-1-1,Yayoi, Bunkyo, Tokyo, 113-8657 Japan room 251

department: Aquatic Bioscience

institute: The University of Tokyo

summary: Acromegaly is a pathological condition due to excess growth hormone (GH) secretion. Acromegaly patients exhibit a deterioration of health and many associated complications, such as cardiovascular issues, arthritis, kidney diseases, muscular weakness, and colon cancer. Since these complications are generalized throughout the body, we investigated the effect of GH excess on cellular integrity. Here, we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein (RFP) reporter gene for tracking GH gene expression throughout generations, and performed RNA-Seq data analysis from different organs. Intriguingly, heatmap and Expression2Kinases (X2K) analysis revealed the enrichment of DNA damage markers in various organs. Moreover, H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA-damaged cells. Using Gene Set Enrichment Analysis (GSEA), we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver, such as double-strand break (DSB), homologous recombination repair (HRR), non-homologous end joining (NHEJ), nucleotide excision repair (NER), and translesion synthesis (TLS). Interestingly, the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish (three years old). Thus, our study demonstrates that affection of cellular integrity is characteristic of acromegaly

overall_design: Total mRNA obtained from 1-years old acromegaly zebrafish model muscle, brain, kidney, liver and 3-day old larvae compared to wild-type (WT) zebrafish were generated by deep sequencing using Illumina.

first: Abdalla

middle: K

last: Elbialy

first: Shuichi

last: Asakawa


title: Antagonistic Regulation of Abscisic Acid Inhibited Root Growth By Brassinosteroid is Partially Mediated by BRASSINAZOLE RESISTENT 1 suppressed ABSCISIC ACID INSENSITIVE 5 expression

status: Public on Nov 24 2018

city: Shijiazhuang

first: Wenqiang

last: Tang

state: Hebei Province

address: East 20 NanErHuang Road

department: College of Life Sciences

institute: Hebei Normal University

summary: Plant hormone brassinosteroids (BRs) and abscisic acids (ABA) antagonistically regulate many aspects of plant growth and responses. This study analyzes the molecular mechanisms by which regulate the crosstalk between BR and ABA signaling.Various BR deficient and gain-of-function signaling mutants were used to analyze their responses to ABA inhibited primary root growth. RNA sequencing was performed to identify the ABA regulated root genes that are also regulated by BR signaling components.Our result demonstrated that BR signaling negative regulates plant ABA response, and the crosstalk is mediated by BIN2 and BZR1. RNA sequencing has identified subsets of ABA responsive root genes that were regulated by BIN2 and/or BZR1. ChIP-qPCR and EMSA assays showed that BZR1 could bind directly with several G-box cis-elements on ABI5 promoter, suppress the expression of ABI5 and makes plant insensitive to ABA.These data demonstrated that ABI5 is a BZR1 direct targeted gene. Regulation of ABI5 expression by BZR1 plays important roles in regulating the crosstalk between BR and ABA signaling pathways.

overall_design: Arabidopsis Col, bin2-1 and bzr1-D/bin2-1 were grown vertically on 1/2 MS in chamber for 7 days and then treated with or without 100 μM ABA for 3 h . The roots about 1 cm from the tips were excised and collected for RNA extraction. Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen) and the concentration was quantified on Nanodrop 1000 (Thermo). The mRNA sequencing libraries were constructed with barcodes using the TruSeq RNA Sample Preparation Kit (Illumina). Six barcoded libraries were pooled together and sequenced by Illumina HiSeq2000.

first: Xiaorui

last: Yang


title: Next Generation Sequencing Analysis of Wild Type and SRSF1-MKO Skeletal Muscle  Transcriptomes

status: Public on Oct 01 2018

city: Shanghai

first: Yuguo

last: Liu

address: 320 Yue Yang Road

department: Institute for Nutritional Sciences, SIBS

institute: Chinese Academy of Sciences

summary: Skeletal muscle specific SRSF1 KO mice were generated by mating SRSF1flox/flox and MyoD-Cre mice, Total RNA from muscle sample were analyzed  by Next Generation Sequencing

overall_design: Skeletal muscle RNA from P30 mice were extraced and analyzed.


title: Systematic Identification of Epithelial–Stromal Crosstalk Signaling Networks in Ovarian Cancer

status: Public on Oct 22 2018

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Ovarian cancer is the most lethal malignancy in the United States. While studies on ovarian cancer pathogenesis were mainly focused on the epithelial component of the tumor, understanding in the role of cancer associated fibroblasts (CAFs) in ovarian cancer progression is limited. In the present study, we describe the use of microdissected transcriptome profiles for the identification of cancer–stroma crosstalk networks with prognostic value, which presents a unique opportunity for developing new treatment strategies for ovarian cancer.

overall_design: Transcriptome profiling analyses were performed on laser microdissected cancer associated stroma samples and epithelial tumor samples from high grade serous ovarian cancer patients using the Affymetrix human genome U133 Plus 2.0 microarray. Based on the transcriptome profiles, computer program cell-cell communication explorer (CCCExplorer) was used to predict signaling crosstalks between cancer associated fibroblasts and ovarian cancer cells.

first: Samuel

last: Mok

first: Stephen

middle: T

last: Wong


title: Higher-Order Organization Principles of Pre-translational mRNPs [RIPPLiT]

status: Public on Nov 14 2018

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

summary: We demonstrates that pre-translational mammalian mRNPs fold as linear rod-like structures  with no strong propensity for 5' and 3' end interaction.

overall_design: RNA ImmunoPrecipitation and Proximity Ligation in Tandem (RIPPLiT)

first: Mihir

last: Metkar

first: Hakan

last: Ozadam

first: Bryan

middle: R

last: Lajoie

first: Maxim

last: Imakaev

first: Leonid

last: Mirny

first: Melissa

middle: J

last: Moore


title: Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women

status: Public on Aug 31 2018

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

institute: National Instute of Genomic Medicine

type:
Expression profiling by array
Genome variation profiling by SNP array

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

overall_design: Refer to individual Series


title: Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women [copy number]

summary: Breast cancer is a heterogeneous disease described in well-recognized biological subtypes. Particularly, gene expression profiling has revealed 5 intrinsic subtypes of breast cancer characterized by different biological and clinical features. The diversity of the intrinsic subtypes across human population has been limited described, and there is few information about the genomic architecture of breast tumors in Mexican or Hispanic populations. In this study, we performed PAM50 assay, based in Affymetrix microarray profiling of 128 fresh frozen tumors from Mexican Latino Hispanic population, to describe the overall distribution of subtypes, and characterize the relation to clinicopathologic characteristics. As well, we correlated the mRNA expression patterns with specific copy number alterations (CPA), in order to analyze their role in breast tumors. A total of 100 blood-tumor samples were assayed using Affymetrix 6.0 SNP arrays; segmentation analysis and GISTIC were performed to identify focal amplifications or deletions. The distribution of PAM50 intrinsic subtypes in our cohort was computed to be 44% luminal A, 20% luminal B, 12.0% HER2-enriched, 12% basal-like, and 12% normal-like. Study comparison with the literature mainly TCGA and METABRIC (most of the patients came from Caucasian population), as well as LACE (which describe a population study) show a similar distribution of the intrinsic subtypes within Hispanic and Caucasian populations. Interestingly, basal-like subtype is less represented than in African-American race. The sum of sensitivity and specificity between the clinicopathologic and intrinsic subtype categories across 4 groups (excluding normal-like) was 50% and 87.5%, respectively. Differentially expression profiles within the subtypes reveal a set of genes altered in each group with biological relevance to stablish the phenotypical characteristics of each subtype. Our analyses confirmed the already reported copy number data. Importantly, many of the copy number profiles correlated with mRNA subtype. With this analysis we can conclude that breast cancer intrinsic subtypes have been reproduced in Mexican population contributing to the description of the PAM50 subtypes among multiple ethnic groups based on a gene expression assay. Our observation based in the integrative genomic analysis of mRNA expression and CPA allowed us to define gene circuits and phenotypic characteristics that can explain the heterogeneity of breast cancer subtypes.

overall_design: Breast cancer tumors were collected at the Fundación Mexicana de Fomento para la Prevención Oportuna del Cáncer de Mama, A.C., (FUCAM) during the surgical procedure in adjuvant, togehetr with 5ml of blood. Two training pathologist carefully performed a histopathological review to define percentage of tumoral cells. Also, immunochemistry markers (ER-, PR- and Her2-) were analyzed. Thus tumors with at least 70% of tumoral cells were processed (N=124). Genomic DNA was extracted and hybridize on Affymetrix SNP6 microarrays. To define SCNAs GISTIC algorithm was computed. SNP markers were used to define ancestry

first: R

last: Rebollar-Vega

first: S

last: Romero-Córdoba

last: Rodríguez-Cuevas

first: A

last: Maffuz-Aziz

last: Hidalgo-Miranda


title: Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

first: Galit

last: Shohat-Ophir

summary: We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using microfluidic multiplex PCR and sequencing (mmPCR-seq), we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

overall_design: We crossed UAS-unc84-2XGFP transgenic flies with 10 different GAL4 drivers (Dh44-GAL4, NPF-GAL4, NPFR-GAL4, Tdc2-GAL4, Crz-GALl4, TH-GAL4, Trh-GAL4, Fru-GAL4, OK107-GAL4, and elav-GAL4), immunoprecipitated tagged nuclei and extracted RNA. Three independent replicates of each each cross were performed to isolate RNA subjected to mmPCR-seq for targeted RNA editing analysis.

first: Anne

last: Sapiro

first: Anat

last: Shmueli

first: Lee

last: Gilbert

first: Qin

last: Li

first: Tali

last: Shalit

first: O

last: Yaron

first: Yoav

last: Pass

first: Jin


title: Mouse model of RHOA G17V mutation in Peripheral T-Cell Lymphoma

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary:
Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive lymphoid tumor derived from malignant transformation of T follicular helper (Tfh) cells. Genetically, AITL is characterized by loss of function mutations in the Ten-Eleven Translocation 2 (TET2)  epigenetic tumor suppressor and a highly recurrent mutation (p.Gly17Val, G17V) in the RHOA small GTPase gene
Moreover, RHOA G17V expression in Tet2 deficient hematopoietic progenitors resulted in the specific development of lymphoid tumors resembling human AITL.
Notably, inhibition of ICOS signaling impaired the growth of RHOA G17V-induced mouse lymphomas in vivo, thus providing a potential new rational approach for the treatment of AITL.

overall_design: We analyzed mRNA expression profiles of primary tumor cells expressing Rhoa G17V or Rhoa wild type.

first: Jose

last: Rodriguez-Cortes

first: Ana

last: da Silva Almeida

first: Christine

last: Kim

first: Zachary

last: West

first: Lucile

last: Couronne

first: Laura

last: Belver

first: Govind

last: Bhagat

first: Olivier

last: Bernard

first: Adolfo

last: Ferrando

first: Teresa

last: Palomero


title: miRNA expression in triple negative tumors

first: Sandra

last: Romero-Cordoba

summary: Triple negative breast cancer (TNBC) represents a challenging tumor type due to their poor prognosis and limited treatment options. It is well recognize that clinical and molecular heterogeneity of TNBC is driven in part by post-transcriptional regulators such as miRNAs. To stratify TNBCs, we profiled 1050 miRNAs in 132 adjuvant TNBC tumors and 40 tumors from other immunophenotypes using  an Affymetrix microarray platform. A NMF clustering analysis allowed us to identify 4 TNBC subtypes featuring unique miRNA expression patterns, disease free and overall survival rates and particular gene ontology enrichments (performed with GSEA algorithm). Our agglomerative approach was cross-validated by using two other clustering algorithms (k-means and consensus clustering). TNBC miRNAs subgroups were also correlated with the Lehmann intrinsic subtypes, finding a significant enrichment of immmnomodulartory and basal 1 subtypes in our high risk miRNA subgroups. 3 cell line models (MDA MB 468, MDA MB 231 and HS578T) were classified according to our miRNA signature, recapitulating two different miRNA subgroups. The TNBC tumors were compared against other phenotypes identifying differentially expressed miRNAs that together with the altered miRNAs within the subgroups allowed us to define interesting miRNAs for further functional analysis.

overall_design: Breast cancer tumors were collected from the archives of the Fundación Mexicana de Fomento para la Prevención Oportuna del Cáncer de Mama, A.C., (FUCAM) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain triple negative tumors (ER-, PR- and Her2-) and tumors from other immunophenotype (ER+, PR+ or/and Her2+) by microdissection of tumoral cells for RNA extraction and hybridization on Affymetrix miRNA microarrays.

first: Rosa

last: Rebollar-Vega

first: Sergio

last: Rodriguez-Cuevas

first: Verónica

last: Bautista-Pina

first: Antonio

last: Maffuz-Aziz

first: S

last: Baroni

first: E

last: D'Ippolito

first: M

last: Iorio

first: Alfredo

last: Hidalgo-Miranda