title: Transcriptome analysis reveals intermittent fasting-induced genetic changes in ischemic stroke

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

summary: Intermittent fasting is previously reported to exhibit neuroprotection against experimental ischemic stroke. However, the detailed understanding of protection mechanisms are lacking. By observing the overall transcriptomic changes in each timepoint of ischemic stroke would benefit the understanding of underlying active pathways and mechanisms. Here, we conduct experimental MCAO ischemic stroke on mice exposed to different daily intermittent fasting method to compare not only among the ischemic stroke timepoints but also the efficacy of different intermittent fasting interventions. Our current study presented the transcriptomic changes for the first time in specific timepoints of ischemic stroke as well as under the condition of intermittent fasting. A number of neuroprotective mechanisms-related genes were significantly affected by intermittent fasting conditions in differential manners.

overall_design: After 4 months of exposure to daily 12 or 16 h of intermittent fasting, mice were conducted with MCAO for 1 h to induce experimental ischemic stroke on single hemisphere of the brain. Mid-coronal section of ipsilateral cerebrum was dissected after 1 h of ischemia, or at 3, 12, 24, and 72 h after initiation of reperfusion. Total RNA was extracted from collected brain tissue samples and mRNA sequencing was conducted using Illumina HiSeq 4000 system.

first: Thiruma

middle: V

last: Arumugam


title: STIM1 and STIM2 mediate cancer-induced inflammation in T cell acute lymphoblastic leukemia

status: Public on Jul 11 2018

city: New York

first: Stefan

last: Feske

address: 550 First Avenue

country: USA

institute: NYU Langone Health

type: Expression profiling by high throughput sequencing

summary: T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of T cell progenitors that in most patients is associated with activating mutations in the NOTCH1 pathway. Recent reports have indicated a link between Ca2+ homeostasis in the endoplasmic reticulum (ER), the regulation of NOTCH1 signaling and T-ALL. Here we investigated the role of store-operated Ca2+ entry (SOCE) in T-ALL. SOCE is a Ca2+ influx pathway that is mediated by the plasma membrane Ca2+ channel ORAI1 and its activators STIM1 and STIM2. Deletion of STIM1 and STIM2 in leukemic cells abolished SOCE and significantly prolonged the survival of mice in a NOTCH1-driven model of T-ALL. The survival advantage was unrelated to leukemia development and leukemic cell burden, but was associated with the SOCE-dependent ability of malignant T lymphoblasts to cause inflammation in leukemia-infiltrated organs. Mice with wildtype T-ALL showed a severe necroinflammatory response in their bone marrow, which was absent in mice with Stim1/2-/- leukemia. Several signaling pathways previously linked to cancer-induced inflammation were downregulated in Stim1/2-/- leukemic cells, likely accounting for less aggressive leukemia progression and prolonged survival of mice. Our study shows that T-ALL is associated with inflammation of leukemia-infiltrated organs and that SOCE controls the proinflammatory effects of leukemic T lymphoblasts.

overall_design: Bone marrow leukemic cell were isolated from WT and Stim1/2-/- leukemic mice, 21 days after leukemia induction and their mRNA profiles were generated by deep sequencing, in triplicate.

first: Shella

middle: S

last: Fleur


title: Genome-wide maps of H2Bub and H2B states

status: Public on Jul 12 2018

city: Amsterdam

first: Tessy

last: Korthout

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: The Netherlands Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We compare patterns of H2Bub and H2B across genes in WT, ubp8 KO and Dot1 OE cells

overall_design: Generate profiles of H2Bub and used H2B as a control

first: Hanneke

last: Vlaming


title: Gene expression profile difference among renal location in a stone former

city: Nagoya

first: Kazumi

last: Taguchi

address: Kawasumi-1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: Comparison between renal papilla tissue with and without the presence of calcified Randall’s plaques, and between the papilla, medulla, and cortex regions from within a single recurrent stone forming kidney demonstrated that patterns of gene expression between the papilla, medulla, and cortex that distinguished these three regions from one another. Disease and function analysis of these gene sets demonstrated up-regulation of genes related to urinary/renal disorders, granulocyte response, vascular smooth muscle cell proliferation, dehydration, and renal calcification and down-regulation of genes related to carboxylic acid/ lipid/ fatty acid transport and urine osmolality.

overall_design: Specimen: Needle core biopsy specimens from a recurrent CaOx stone kidney. RNA-sequence was performed by the Illumina HiSeq 4000.

first: Thomas

last: Chi


title: Cancer associated mutants of eIF1A impair Rps3/Rps10 binding and enhance scanning of cell cycle genes [Ribo-Seq]

status: Public on Jul 13 2018

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: The Ribo-seq analysis demonstrated that eIF1A is predominantly essential for translation of genes with long 5'UTR genes including cell proliferation and cell cycle progression genes. eIF1A depletion causes broad stimulation of initiation in 5’UTRs at near-cognate AUG codons that diminshes the translation initiation fidelity

overall_design: Ribo-seq analysis was performed either in contol or eIF1A knockdown MEFs

first: Urmila

last: Sehrawat

first: Shaked

last: Ashkanazi

first: Femke

last: Koning

first: Gil

last: Stelzer

first: Rivka

last: Dikstein


title: Transcriptome profiling of intestinal organoids stimulated with TNF and PGE2

city: Herlev

first: Yuan

last: Li

address: Rebæk Søpark

department: Gastroenterology

country: Denmark

institute: Herlev Hospital, University of Copenhagen

summary: To address the effect of inflammatory stimulation on intestinal epithelial cells, we performed RNA-seq analysis on human colonic epithelial organoids treated with TNF and/or PGE2.

overall_design: Intestinal organoids were cultured for 4 days and treated with TNF (10 ng/ml) with or without PGE2 (1 µM), or treated with PGE2 alone for 48 h. RNA was isolated (n = 3/group), and RNA-seq analysis was performed for the four different groups (Control/TNF/TNF+PGE2/PGE2).

first: Christoffer

last: Soengaard


title: CUT&RUN chromatin profiling of endogenously tagged and native BATF

city: San Francisco

first: Ruby

last: Yu

state: CA

address: 513 Parnassus Ave

institute: UCSF

summary: Primary human CD4+ T cells were isolated and an N-terminal GFP tag was inserted into the endogenous BATF locus. CUT&RUN using anti-GFP or anti-BATF antibodies was performed to assay chromatin occupancy. Libraries were prepared and sequenced on Illumina NextSeq platform.

overall_design: CUT&RUN using BATF or GFP antibodies followed by library preparation and 75 nt paired-end sequencing on Illumina NextSeq machines

first: Theodore

middle: L

last: Roth

first: Alexander

last: Marson


title: Transcriptional properties of estrogen receptor fusion genes.

city: Houston

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: RNA sequencing (RNA-seq) detects estrogen receptor alpha gene (ESR1) fusion transcripts in estrogen receptor positive (ER+) breast cancer but their role in disease pathogenesis remains unclear.  Herein we examined multiple in-frame and out-of-frame ESR1 fusions and found that two, both identified in advanced endocrine treatment resistant disease, encoded stable and functional in-frame fusion proteins.  In both examples, ESR1-e6>YAP1 and ESR1-e6>PCDH11X, the N-terminal, DNA binding and dimerization motifs encoded by exons 2-6 were fused to C terminal sequences from the partner gene.  Functional properties included estrogen-independent growth, constitutive expression of ER target genes, anti-estrogen resistance, induction of cellular motility in vitro and the development of lung metastasis in vivo.  Chromatin immunoprecipitation and RNA sequencing experiments showed both fusions uniquely activated a metastasis-associated transcriptional program.  ESR1-e6>YAP1 and ESR1-e6>PCDH11X-induced growth remained sensitive to a CDK4/6 inhibitor, palbociclib, and a patient-derived xenograft (PDX) naturally expressing the ESR1-e6>YAP1 fusion was also responsive.  Transcriptionally active ESR1 fusions therefore trigger both endocrine therapy resistance and metastatic progression explaining the association with fatal disease progression, although CDK4/6 inhibitor treatment is predicted to be effective.

overall_design: HA-ChIP-seq and RNA-seq of stable T47D breast cancer cell lines expressing HA-tagged ESR1 constructs in hormone deprived media -/+ E2.  HA-ChIP DNA from YFP-HA expressing cells was used as input.

first: Matthew

middle: J

last: Ellis

middle: T


title: Epigenome analysis of decidua tissues from unexplained recurrent spontaneous abortion patients and controls with induced abortions

city: Nanjing

first: Mingming

address: NO.818 Tianyuan East Road, Jiangning District

department: School of public health

country: China

institute: Nanjing Medical University

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of decidua samples from unexplained recurrent spontaneous abortion patients and controls with induced abortions.
The Infinium Human Methylation 850K BeadChip was used to obtain DNA methylation profiles across approximately 853,307 CpGs in decidua samples . Samples included 2 normal pregnant women (non-medical reasons for abortion) and 4 unexplained recurrent spontaneous abortion patients.

overall_design: Bisulphite converted DNA from the 6 samples were hybridized to the Illumina Infinium 850k Human Methylation Beadchip

first: Guizhen

last: Du


title: Genes regulated by TTF-1 in small cell lung cancer cell lines

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

institute: Tokyo University

summary: To investigate genes possibly regulated by TTF-1 in small cell lung cancer cell lines, we compared gene expression profiles of NCI-H209 and Lu139 cell lines electroporated with control and TTF-1 siRNAs.

overall_design: RNA was collected from NCI-H209 and Lu139 cell lines transfected with control and TTF-1 siRNAs.

first: Masafumi

last: Horie

first: Naoya

last: Miyashita

first: Johanna

last: Mattsson

first: Patrick

last: Micke

first: Takahide

last: Nagase


title: A robust qualitative transcriptional signature for the early diagnosis of gastric cancer

status: Public on Jul 10 2018

city: FuZhou

first: Li

last: meifeng

address: xueyuan road

institute: Fujian medical university

summary: Pathological examination of gastroscopy biopsy specimens will make false diagnosis for gastric cancer (GC) due to inaccurate sampling locations and/or insufficient sampling amount. We extracted a robust qualitative transcriptional signature, based on the within-sample relative expression orderings (REOs) of gene pairs, to discriminate both GC tissues and adjacent-normal tissues from non-GC gastritis and normal gastric tissues.The qualitative transcriptional signature can be robustly applied at the individual level to aid the diagnosis of early GC.

overall_design: Examination of 21 GC specimens from seven GC patients. For each patient, three specimens were sampled from three different tumor locations.

first: Haidan

last: Yan

first: Meifeng


title: Hijacking of the macrophage epigenetic machinery involving H3K4 trimethylation and lncRNA HOTAIR, facilitates survival of Mycobacterium tuberculosis

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

country: India

institute: Bose Institute

summary: Genome wide differential association of H3K4me3 in Human macrophages after infection with both virulent and avirulent strains of Mtb

overall_design: Studying H3K4me3 modification in Mtb infected (4hrs) and uninfected macrophage

first: Manikuntala

last: Kundu

first: Zhumur

last: Ghosh

first: Madavan

last: Vasudevan

first: Arijita

last: Subuddhi


title: Zinc Finger Protein 521 regulates early hematopoiesis through cell extrinsic mechanisms in the bone marrow microenvironment

city: Denver

first: James

middle: R

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

summary: Zinc finger protein 521 (ZFP521), a DNA-binding protein containing 30 Krüppel-like zinc fingers, has been implicated in the differentiation of multiple cell types, including hematopoietic stem and progenitor cells (HSPC) and B lymphocytes. Here, we report a novel role for ZFP521 in regulating the earliest stages of hematopoiesis and lymphoid cell development through soluble microenvironmental proteins. Mice with inactivated Zfp521 genes (Zfp521-/-) possess reduced frequencies and numbers of hematopoietic stem and progenitor cells, common lymphoid progenitors, and B and T cell precursors. Notably, ZFP521 deficiency changes BM microenvironment cytokine levels and gene expression within resident HSPC, consistent with a skewing of hematopoiesis away from lymphopoiesis and towards granulopoiesis. These results advance our understanding of ZFP521’s role in normal hematopoiesis, justifying further research to assess its potential as a target for cancer therapies.

overall_design: RNA-seq transcriptome analysis of two independent RNA samples each from wild type or Zfp521 knockout HSC pools from mice.

first: C

last: Fleenor

first: T

last: Arends

first: H

first: J

last: Åhsberg

first: K

last: Okuyama

last: Kuruvilla

first: S

last: Cristobal

first: P

last: Pandey

last: Danhorn

last: Rabe

first: D

last: Straign

middle: M

last: Espinosa

last: Warming

first: E

last: Pietras

first: M

last: Sigvardsson


title: Reduced MEK inhibition preserves genomic stability in naïve human ES cells

first: Bruno

last: Di Stefano

department: Molecular and Cellular Biology

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Reduced MEK inhibition confers a growth advantage and reduces genomic instability in naïve human ES cells (RRBS-seq data set)

summary: Human embryonic stem cells (hESCs) can be captured in either a primed state resembling the post-implantation epiblast or in a naïve state resembling the pre-implantation epiblast. Naïve culture conditions allow study of pre-implantation development ex vivo but reportedly lead to chromosomal abnormalities, compromising their utility in research and potential therapeutic applications. Although MEK inhibition is essential for the naïve state, here we show that reduced MEK inhibition facilitates the establishment and maintenance of naïve hESCs that retain naïve-specific transcriptional and DNA methylation patterns yet accrue fewer chromosomal abnormalities. We further show that hESCs cultured under these modified conditions are less prone to apoptosis and proliferate more rapidly. Our results point to the importance of residual MAPK signaling and provide a simple modification to current protocols to enable robust growth and genomic stability in naïve hESCs.

overall_design: RRBS-seq

first: Kendell

last: Clement

first: Hongcang

last: Gu

first: Konrad

last: Hochedlinger


title: KLF5 controls glutathione metabolism to suppress p190-BCR-ABL+ B-cell lymphoblastic leukemia

city: Cincinnati

first: Jose

last: Cancelas

state: OH

address: 3333 Burnet Ave, ML 7013

institute: Cincinnati Children's Hospital Medical Center

summary: High-risk B-cell acute lymphoblastic leukemia (B-ALL) remains a therapeutic challenge despite advances in the use of tyrosine kinase inhibitors and chimeric- antigen-receptor engineered T cells.  Lymphoblastic-leukemia  precursors are highly sensitive to oxidative stress. KLF5 is a member of the Krüppel-like family of transcription factors. KLF5 expression is repressed in B-ALL, including BCR-ABL1+ B-ALL. Here, we demonstrate that forced expression of KLF5 in B-ALL cells bypasses imatinib resistance not associated with mutations of BCR-ABL. Expression of Klf5 impaired leukemogenic activity of BCR-ABL1+ B-cell precursors in vitro and in vivo. The complete genetic loss of Klf5 reduced oxidative stress, increased regeneration of reduced glutathione and decreased apoptosis of leukemic precursors. Klf5 regulation of glutathione levels was mediated by its regulation of glutathione-S-transferase Mu 1 (Gstm1), an important regulator of glutathione-mediated detoxification and protein glutathionylation. Expression of Klf5 or the direct Klf5 target gene Gstm1 inhibited clonogenic activity of Klf5∆/∆ leukemic B-cell precursors and unveiled a Klf5-dependent regulatory loop on glutamine-dependent glutathione metabolism. In summary, we describe a novel mechanism of Klf5 B-ALL suppressor activity through its direct role on the metabolism of antioxidant glutathione levels, a crucial positive regulator of leukemic precursor survival.

overall_design: p190-BCR-ABL+ Leukemic B-cell precursors mRNA profiles of WT and Klf5Δ/Δ mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2500

first: Cuiping

last: Zhang

first: Angelo

last: D'Alessandro

first: Ashley

last: Wellendorf

first: Fatima

last: Mohmoud

first: Juana

last: Serrano-Lopez

first: John

last: Perentesis

first: Kakajan

last: Komurov

first: Gabriela

last: Alexe

first: Kimberly

last: Stegmaier

first: Jeffrey

last: Whitsett

first: Lee

last: Grimes


title: scRNA-seq of a suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality

city: Seattle

first: Lucas

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

summary: Modern genetic approaches are powerful in providing access to diverse types of neurons within the mammalian brain and greatly facilitating the study of their function. We describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically-defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain. Here, we characterize the transcriptome of a subset of these new lines by scRNA-seq.

overall_design: scRNA-seq of 4,776 cells from primary visual cortex (VISp) and anterior lateral motor cortex (ALM) in the mouse brain.

first: Tanya

last: Daigle

first: Linda

last: Madisen

first: Travis

middle: A

last: Hage

first: Matthew

last: Valley

first: Ulf

last: Knoblich

first: Rylan

last: Larsen

first: Marc

last: Takeno

first: Lawrence

last: Huang

first: Hong

first: Rachael

first: Maya

last: Mills

first: Alice

last: Bosma-Moody

first: La'Akea

last: Siverts

first: Miranda

last: Walker

last: Graybuck

first: Zizhen

last: Yao

first: Olivia

last: Fong

first: Thuc

middle: N

last: Nguyen

first: Emma

last: Garren

first: Garreck

last: Lenz

first: Mariya

last: Chavarha

first: Julie

last: Pendergraft

first: James

last: Harrington

first: Karla

middle: E

last: Hirokawa

last: Harris

first: Rusty

last: Nicovich

first: Medea

last: McGraw

first: Douglas

last: Ollerenshaw

last: Smith

first: Christopher

last: Baker

first: Jonathan

last: Ting

first: Susan

last: Sunkin

first: Jerome

last: Lecoq

first: Michael

middle: Z

last: Lin

first: Edward

last: Boyden

first: Gabe

last: Murphy

first: Nuno

last: da Costa


title: Transgenerational effect of Chlordecone [ChIP-seq]

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1

summary: The environmental factors such as pesticides could affect the developmental processes and cause the phenotypic changes. Moreover, the changes could be transferred to a subsequent generation via gametes. In this project we studied whether the pesticide chlordecone could cause the developmental effects and cause the transgenerational inheritance in outbred mouse strain. Mice were treated during development at dose 100 µg/kg/day and the progeny of exposed mice were crossed for three generations. The testes of the third generations males were used for anti-H3K4me3 ChiP-seq analysis. We used two biological replicates for each condition.

overall_design: H3K4me3 ChIP-seq on testes.

last: Hao

first: Fatima

last: Smagulova


title: Genome wide DNA methylation analysis of arsenic exposure and non-exposure population and patients with skin lesions

city: Buffalo

first: Jie

last: Wang

state: NY

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

summary: Genome wide DNA methylation profiling of arsenic exposure and non-exposure population and patients with skin leisons. The Illumina Infinium HumanMethylation450 BeadChip (HM450K) was used to obtain DNA methylation profiles across approximately 450,000 CpGs in genomic DNA extracted from blood buffy coat samples. Samples included 66 arsenic exposure individuals, 35 non-exposure individuals and 18 arsenical skin lesion patients.

overall_design: Bisulphite converted DNA from the 119 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip (HM450K).

first: Xusheng

last: Chen


title: Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [ChIP-Seq]

status: Public on Jul 09 2018

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: we report that regional expression of the Hoxc genes is regulated by antagonistic switch between repression and activation epigenetic modification. In freshly isolated dermal cells from P50 telogen Wt/Wt ear skin, no enrichment of H3K27ac was detected at Hoxc cluster, consistent with their lack of expression; in contrast, robust peaks of this marker are observed in 3’ region of the Hoxc cluster in dorsal skin dermal cells. Secondly we looked at H3K27 trimethylation (H3K27me3), a marker for polycomb-dependent gene repression, which antagonizes H3K27ac. Concomitantly, we found that H3K27me3 spread across the entire Hoxc cluster in adult ear skin dermal cells but was restricted to the 5’ region of the Hoxc cluster in adult dorsal skin dermal cells . In adult dorsal skin dermal cells, we found three occupied CTCF binding sites inside Hoxc cluster. The rostral CTCF binding site marks the discontinuity point of H3K27me3 modification at the intergenic region between Hoxc11 and Hoxc10 in dorsal skin dermal cells. This indicates the CTCF binding event within Hoxc cluster might forge a topological barrier that can insulate activation region from repression region and therefore lead to the region specific expression of the Hoxc cluster genes.To directly test whether there is ectopic interaction between Hoxc cluster and the active domain in proximal-TAD, we used circularized chromosome conformation capture (4C) with Hoxc4 as bait. In Wt/Koa ear skin dermal cells, there are clear ectopic interactions of Hoxc4 with the remaining active regulatory landscape in proximal-TAD; on the other hand, all of the interactions of Hoxc4 remained inside the distal-TAD with repressive domain in Wt/Wt ear skin.

overall_design: Examination of gene expression in wt/wt ear epidermal cells, wt/wt dorsal epidermal cells, and wt/koa ear epidermal  cells; Examination of gene expression and 2 histone modification in wt/wt ear dermal cells, wt/wt dorsal dermal cells, and wt/koa ear dermal cells; examination of CTCF binding in wt/wt ear dermal cells and wt/wt dorsal dermal cells; examination of chromatin interaction using Hoxc as viewpoint in wt/wt ear dermal cells and wt/koa ear dermal cells.

first: Zhou

last: Yu

first: Huanwei

last: Huang

first: Ting


title: Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [4C]


title: Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters

city: Los Angeles

first: Arnold

last: Berk

address: 611 Charles E. Young Dr.

institute: UCLA

summary: While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300 as reported by Pelka et al. 2009, and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.

overall_design: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC) were infected with an Ad5-based vector expressing wild-type E1A (wt) at an MOI Of 20; a mixture of the wt E1A-expressing vector at an MOI of 5 with an Ad5 mutant containing an E1A deletion (dl312) at an MOI of 95; or an Ad5 mutant expressing E1A with multi-alanine substitutions in regions involved in p300 binding at an MOI of 100.  H3K9ac, H3K18ac, H3K27ac, TBP and Pol2 association were subsequently examined on the HAd5 genome by ChIP-seq.

first: Emily

last: Hsu

first: Mario

last: Pennella

first: Nathan

last: Zemke

first: Carol

last: Eng


title: mRNA Seq of mouse tissues 9 weeks after RYGB or sham surgery [9 weeks]

city: Jerusalem

first: Danny

last: Ben-Zvi

state: Israel

address: Ein Kerem

institute: Hebrew University of Jerusalem

summary: In this study we sought to characterize the long tern response to RYGB surgery using diet induced obese mice. Controls were sham operated mice. Mice were age, sex, weight and diet matched.

overall_design: diet induced obese male C57BL6 mice were subjected Roux en Y Gastric Bypass surgery or sham surgery. Both groups were then transferred to an elemental liquid diet and then gradually returned to high fat diet. Sham operated mice were weight matched by restriction of food. Mice were fasted overnight and sacrificed at 10am.

first: Nicholas

last: Stylopoulos


title: Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [RNA-Seq]


title: Time-dependent molecular responses differ between gastric bypass and dieting but are conserved across species

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: mRNA Seq of mouse tissues 9 days or 9 weeks after RYGB or sham surgery [9 days]

summary: In this study we sought to characterize the acute response to RYGB surgery using diet induced obese mice. Controls were sham operated mice. Mice were age, sex, weight and diet matched.

overall_design: diet induced obese male C57BL6 mice were subjected Roux en Y Gastric Bypass surgery or sham surgery. Both groups were then transferred to an elemental liquid diet. Mice were fasted overnight and sacrificed at 10am.


title: Genome-wide maps of chromatin state in iBMDM (immortalized bone-marrow-derived macrophages) cells without or with virus infection

status: Public on Jul 07 2018

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

summary:
iBMDM cells were infected with VSV (Vesicular Stomatitis Virus) or HSV-1 (Herpes Simplex Virus 1)  for 8 hours, followed by CHIP-seq analysis with H3K27AC antibody.  We find that chromatin state changed with virus infection, some enhacer and superenhancer were induced to promote anti-viral gene expression.
Conclusions: virus infection induce enhancer and superenhancer activation.

overall_design: iBMDM cells were infected with VSV or HSV-1 for 8 hours, then cells were fixed and lysed, chromatin DNA were immunoprecipitated with H3K27AC antibody, followed by CHIP-seq analysis.

first: Lili

first: Fuping

last: You


title: Effect of hyperfractionated irradiation (HFRT) of prostate primary basal cells (PrEPs) on the transcriptome

city: Innsbruck

first: Fabian

last: Guggenberger

state: Tirol

address: Anichstrasse 35

department: Department of Urology

country: Austria

institute: Medical University of Innsbruck

summary: We irradiated PrEPs derived from four patients undergoing radical prostatectomy according to a HFRT protocol (20 single treatments). Transcriptome was analysed by NextGen sequencing. Gene expression profiling revealed a dysregulation of 3468 genes at mRNA level (1470 upregulated and 1998 downregulated). We could characterize cells surviving the lethal effects of radiation by two gene expression signatures showing that these cells have low expression of genes related to DNA damage response and Interferon signaling pathways. These findings could be exploited to develop new drugs for radiotherapy improvement.

overall_design: PrEPs derived from 4 patients undergoing radical prostatectomy were irradiated with either 0.5 or 1 Gray (Gy) for 5 times a week (4 weeks in total) using a linear accelerator. An untreated control group was included. Cells were allowed to recover for one week before all groups received a final 1 Gy treatment 24 hours before harvesting total RNA and RNA sequencing. Bioinformatical analysis was conducted on irradiated samples versus control group.  Group A = 1 Gy irradiation,  group B = 0.5 Gy irradiation, group CTRL = 0 Gy irradiation.

first: Harmen

last: van de Werken

first: Holger

middle: H

last: Erb

first: Giuseppe

last: Cappellano

first: Kristina

last: Trattnig

first: Florian

last: Handle

first: Sarah

last: Peer

first: Georg

last: Schäfer

first: Guido

last: Jenster

first: Zoran

last: Culig

first: Ira-Ida

last: Skvortsova

first: Frédéric

last: Santer


title: Cecal transcriptome by Next Generation Sequencing of WT C57Bl/6 mice treated with water (vehicle) or with antibiotics (AIMD) to induce microbiome depletion .

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Antibiotic induced microbiome depletion (AIMD) has been used frequently to study the role of the gut microbiome in pathological conditions. However, unlike germ-free mice, the effects of AIMD on host metabolism is unknown. We investigated the effects of AIMD in normal-chow fed mice to understand its effects on gut homeostasis, luminal signaling, and metabolism. We show that AIMD, which decreases luminal Firmicutes and Bacteroidetes species, decreases baseline serum glucose levels, reduces glucose surge in a tolerance test, and improves insulin sensitivity without altering adiposity. These occur in the setting of decreased luminal short-chain fatty acids (SCFAs), especially butyrate, and secondary bile acid (BA) pool, which affects whole-body BA metabolism. In mice, AIMD alters cecal gene expression and gut GLP-1 signaling. Extensive tissue remodeling and decreased availability of SCFAs shift colonocyte metabolism toward glucose utilization. Hence, AIMD alters whole-body glucose homeostasis by potentially shifting colonocyte energy utilization from SCFAs to glucose.

overall_design: Cecum mRNA profile of WT C57Bl/6 mice treated for 30 days with a cocktail of antibiotics twice daily by oral gavage (AIMD) or water (vehicle).

first: Amir

last: Zarrinpar

first: Amandine

last: Chaix

first: Satchidananda

last: Panda


title: Comparison of single cell expression in yound and old mouse aorta endothelial cells

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

summary: We report single cell expression in mouse young and old aorta endothelial cells. These data provide insight in the gene expression related to regeneration of mouse aorta endothelial layer.

overall_design: Single cell RNA sequencing was done on a young mouse (8 weeks) and an old mouse (18 months), 10X Genomics Single Cell 3′ v2 was used.

first: M

last: Iruela-Arispe


title: Reduced MEK inhibition confers a growth advantage and reduces genomic instability in naïve human ES cells (RNA-seq data set)

first: Bruno

last: Di Stefano

address: 1 Baylor Plaza

overall_design: RNA-seq

first: Shan

last: Sabri

first: Kathrin

last: Plath

first: Konrad

last: Hochedlinger


title: Diurnal oscillations in human salivary microRNA and microbial transcription

status: Public on Jul 06 2018

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigated daily oscillations in salivary miRNA and microbial RNA to explore relationships between these components of the gut-brain-axis and their implications in human health. Nine subjects provided 120 saliva samples at designated times, on repeated days. Samples were divided into three sets for exploration and cross-validation. Identification and quantification of host miRNA and microbial RNA was performed using next generation sequencing. Eleven miRNAs and 11 microbial RNAs demonstrated consistent diurnal oscillation across the first 2 sample sets and accurately predicted collection time in the hold-out set based on multivariate logistic regression modeling. Associations among five circadian miRNAs and four circadian microbial RNAs were observed.

overall_design: Salivary miRNA and microbial taxon profiles of 120 human samples were generated by shotgun sequencing, using Illumina NextSeq 500.


title: Metabolic signaling directs the reciprocal lineage decisions of αβ and γδ T cells

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Development of ab and gd T cells requires coupling of environmental signals with metabolic and redox regulation by mTORC1

overall_design: Single Cell analysis of Lineage-negative thymocytes in RAPTOR deficient and wild type cells from Thymus

first: Kai

last: Yang

first: Daniel

middle: B

last: Blanco

first: Xiang

last: Chen


title: Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions

first: huanwei

last: huang

overall_design: Refer to individual Series


title: Gene expression profile of juvenile R6/1 and N171-82Q brains

status: Public on Jul 05 2018

city: Alicante

first: Luis

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

summary: Transcriptional dysregulation in Huntington’s disease (HD) is an early event that affects the expression of genes involved in survival and neuronal functions throughout the progression of the pathology. In the last years, extensive research has focused on epigenetic and chromatin-modifying factors as a causative explanation for such dysregulation, offering attractive targets for pharmacological therapies. In this work we examined the gene expression profiles in cortex, striatum, hippocampus and cerebellum of juvenile R6/1 and N171-82Q mice, two models of fast progressive HD, to retrieve the early transcriptional signatures associated with this pathology.These profiles showed significant coincidences with the transcriptional changes in the conditional knockout for the lysine acetyltransferase CBP in postmitotic forebrain neurons.

overall_design: Prefrontal cortices, striata, hippocampi and cerebella were dissected from mutant mice alongside with wild-type littermates. Total RNA was extracted and hybridized to Affymetrix MoGene 1.0 ST arrays. One array consisted on a pool of 3-4 RNA samples and three arrays were used per condition (genotype-tissue-age).

first: L


title: LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

city: Vancouver

first: Matthew

middle: C

last: Lorincz

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: De novo DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAme associated with polymorphic LITs. Notably, many CGI promoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Total RNA-seq in mouse and rat oocytes; H3K36me3 ChIP-seq in mouse oocytes

first: Julie

last: Brind'Amour

first: Hisato

last: Kobayashi

first: Julien

last: Albert

first: Kenjiro

last: Shirane

first: Akihiko

last: Sakashita

first: Aaron

last: Bogutz

first: Tasuku

last: Koike

first: Mohammad

last: Karimi

first: Louis

last: Lefebvre

first: Tomohiro

last: Kono


title: ER ChiP-Seq Mcf7 10nM E2

city: Boston

first: Thomas

last: Westerling

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer institute

summary: Cells starved 3 days in phenol red free DMEM with 10% charcoal dextran treated FBS, then treated for 45min with 10nM E2

overall_design: 2 independed biological replicates where processed for libraries. Sequenced independently and analyzed in parallel on the same pipeline. Experiment was done using ER ChIP library vs input library generated from the prepared non-enriched chromatin. Processed peak datafile represents ChIP/Treat vs Input/Control, replicate1 and replicate 2 kept separate and requiring called peaks in both replicates.


title: Increased lactate secretion by cancer cells sustains non-cell-autonomous adaptive resistance to MET and EGFR targeted therapies.

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

summary: Microenvironment is known to influence cancer drug response and sustain resistance to therapies targeting receptor-tyrosine kinases. However if and how tumor microenvironment can be altered during treatment, contributing to resistance onset is not known. Here we show that, under prolonged treatment with tyrosine kinase inhibitors (TKIs), EGFR- or MET-addicted cancer cells displayed a metabolic shift towards increased glycolysis and lactate production. We identified secreted lactate as the key molecule able to instruct Cancer Associated Fibroblasts (CAFs) to produce Hepatocyte Growth Factor (HGF) in a NF-KB dependent manner. Increased HGF, activating MET-dependent signaling in cancer cells, sustained resistance to TKIs. Functional targeting or pharmacological inhibition of lactate dehydrogenase prevented and overcame in vivo resistance, demonstrating the crucial role of this metabolite in the adaptive process. This non-cell-autonomous, adaptive resistance mechanism was observed in NSCLC patients progressed on EGFR TKIs, demonstrating the clinical relevance of our findings and opening novel scenarios in the challenge to drug resistance

overall_design: RNA-seq analysis of 2 different samples, each one with 2 biological replicates (4 sequencing runs in total).

first: Karrin

last: Ferrari

first: Daniel

last: Fernandez-Perez


title: NMD-degradome sequencing reveals ribosome-bound  intermediates with 3'-end nontemplated nucleotides

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

summary: Transcriptome-wide methodology is developed to capture and sequence decay intermediates deriving from direct NMD targets. Results demonstrate that mammalian-cell NMD generates decay intermediates in a process that involves the covalent addition of nontemplated U, C, G and A nucleotides to 3'-ends. Variations of this methodology demonstrate that these decay intermediates arise co-translationally.

overall_design: A transcriptome-wide method that captures and sequences the decay intermediates (DIs) deriving from direct NMD targets that we call NMD-Degradome Sequencing (NMD-DegSeq). Unlike methods that identify NMD targets by their upregulation upon the downregulation of one or more NMD factors, which cannot distinguish between direct and indirect NMD targets, our method identifies direct NMD targets based on their co-immunoprecipitation (co-IP) with p-UPF1.

first: Tatsuaki

last: Kurosaki

first: Keita

last: Miyoshi

first: Jason

last: Myers


title: Expression data from young adult, aged, and post-mortem mouse satellite cells

status: Public on Jul 04 2018

city: Paris

first: Shahragim

last: Tajbakhsh

state: Ile de France

address: 25 rue du docteur Roux

department: Stem cell and development

institute: Institut Pasteur Paris

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


title: Expression data from young adult, and aged mouse satellite cells

summary: Transcriptomic analysis of FACS-sorted Pax7nGFP quiescent skeletal muscle satellite cells cells from young,  and old mice. Results provide knowledge about the molecular mechanisms underlying age-related skeletal muscle satellite cells homeostasis.

overall_design: Mouse quiescent satellite cells were selected at different age of the adult life for RNA extraction and hybridization on Affymetrix microarrays

first: Siham

last: Yennek

first: Sébastien

last: Mella


title: Alveolar Macrophages after Murine Lung Transplant

city: Chicago

first: Stephen

middle: Francis

last: Chiu

state: IL

address: 251 E Huron

department: Thoracic Surgery

institute: Northwestern University Feinberg School of Medicine

summary: The objective of this study was to examine transcriptional changes in alveolar macrophages early after reperfusion in a model of murine lung transplant.

overall_design: 12 total samples are analyzed - 4 naïve controls, 4 from 2 hours post-reperfusion, 4 from 24 hours post-reperfusion

middle: F


title: TBK1 suppresses RIPK1-driven apoptosis and inflammation during development and in aging

first: Daichao

last: Xu

address: 240 Longwood Ave.

department: Cell Biology

institute: Harvard Medical School

summary: Aging is a major risk factor for both genetic and sporadic neurodegenerative disorders. However, it is unclear how aging interacts with genetic predispositions to promote neurodegeneration. Here we investigate how partial loss-of-function of TBK1, a major genetic cause for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) comorbidity, leads to age-dependent neurodegeneration. We show that TBK1 is an endogenous inhibitor of RIPK1 and the embryonic lethality of Tbk1-/- mice is dependent on RIPK1 kinase activity. In aging human brains, another endogenous RIPK1 inhibitor, TAK1, exhibits a marked decrease in expression. We show that in Tbk1+/- mice, the reduced myeloid TAK1 expression promotes all the key hallmarks of ALS/FTD, including neuroinflammation, TDP-43 aggregation, axonal degeneration, neuronal loss and behavior deficits, which are blocked upon inhibition of RIPK1. Thus, aging facilitates RIPK1 activation by reducing TAK1 expression, which cooperates with genetic risk factors to promote the onset of ALS/FTD.

overall_design: mRNA profiles of primary microglia derived from 2-day old wild type (WT), Tbk1+/-, Tbk1+/-;Ripk1D138N/D138N, Tak1ΔM/+,  Tbk1+/-;Tak1ΔM/+ and Tbk1+/-;Tak1ΔM/+;RIpk1D138N/+ mice were generated by bulk RNA sequencing, in triplicate.

first: Junying

last: Yuan


title: Programmed Cell Death Ligand 1 (PD-L1) Signaling Regulates Macrophage Proliferation and Activation

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: We used in vitro and in vivo models to investigate PD-L1 signaling in macrophages and the effects of PD-L1 antibody treatment on Tumor associated macrophage responses

overall_design: RNAseq was performed on mouse bone marrow derived macrophages treated with PD-L1 antibody

first: Genevieve

last: Hartley

first: Lyndah

last: Chow


title: Transcriptome of human white and brown adipose tissue biopsies

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

country: Germany

institute: Technical University of Munich

summary:
We analyzed coding transcript abundance in paired biopsies of white and brown adipose tissue obtained from the supraclavicular region of 15 healthy subjects.
In a prior experiment measuring 18F-deoxyglucose uptake by PET-CT, 9 subjects displayed active brown fat and 6 did not.

overall_design: Paired white and brown fat biopsies from 15 human probands, 9 brown fat positive and 6 brown fat negative judged by 18FDG-PET-CT.

first: Mueez

last: U Din

first: Teema

last: Saari

first: Juho

last: Raiko

first: Nobu

last: Kudomi

first: Stefanie

last: Maurer

first: Ez-Zoubir

last: Amri

first: Martin

last: Klingenspor

first: Olof

last: Solin

first: Pirjo

last: Nuutila

first: Kirsi

last: Virtanen


title: RNA-seq analysis of  transcriptomes of Noc4L deficient and the Nco4L sufficient Treg cells

first: Xueping

last: Zhu

address: 1 st West Beichen, Chaoyang

institute: Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of sciences

summary: To gain in depth transcriptional information about the Noc4L deficient and Noc4L sufficient Tregs, we performed RNA-seq analysis to compare the transcriptomes of Noc4L deficient (CD4+GFP+CD62Lhigh, cKO) and Noc4L sufficient (CD4+GFP+CD62Lhigh, Het) Tregs activated in vitro with Dynabeads for 48 hours or 72 hours. We found ~25 unique genes with differential expression between the Noc4L deficient and Noc4L sufficient Treg cells when activated for 48 hours in vitro. And ~100 unique genes with differential expression between the Noc4L deficient and Noc4L sufficient Treg cells when activated for 72 hours in vitro in two times experiment.

overall_design: Transcriptional profiles of Noc4L sufficient (CD4+GFP+CD62Lhigh,Het) and Noc4L deficient (CD4+GFP+CD62Lhigh,cKO) Treg cells isolated from Foxp3CreNoc4l+/fl (Het) or Foxp3CreNoc4lfl/fl (cKO) mice then activated with Dynabeads for 48 hours or 72 hours were generated by RNA-sequencing.

first: Xuyu

last: Zhou


title: Role of TBP in chromatin accessibility (ATAC-seq)

city: Berkeley

first: Sheila

last: Teves

state: California

address: 475D Li Ka Shing Center

department: Molecular Cell Biology

institute: UC Berkeley

summary: To test the role of TBP in promoting chromatin accessibility through the cell cycle, we performed ATAC-seq analysis.

overall_design: As starting material for ATAC-seq, we used asynchronous mouse embryonic stem cells or Nocodazole-synchronized mitotic ES cells before and after TBP degradation.

first: Robert

last: Tjian


title: LRH-1 Mitigates Intestinal Inflammatory Disease by Maintaining Epithelial Homeostasis and Cell Survival

city: San Francisco

first: James

last: Bayrer

state: CA

address: 550 16th St, 5th Floor, Box 0136

department: Pediatrics

institute: UCSF

summary: We report the gene expression changes in murine small intestinal organoids following deletion of LRH-1 (NR5A2) and humanization by expression of human LRH-1 in mouse LRH-1 knockout organoids.

overall_design: Comparison of wild type (FF), LRH1 knockout (IKO), humanized (hLRH), and AAV-control (GFP) profiles

first: Bayrer

last: James

first: Suzawa

last: Miyuki

first: Ingraham

last: Holly


title: Expression data from young adult, and post-mortem mouse satellite cells

first: Shahragim

last: Tajbakhsh

summary: Transcriptomic analysis of FACS-sorted Pax7nGFP quiescent skeletal muscle satellite cells cells from old, and post-mortem mice. Results provide knowledge about the molecular mechanisms underlying age-related skeletal muscle satellite cells homeostasis.

overall_design: Mouse quiescent satellite cells were extracted from old mice (24-26 weeks old), and from mice two and four days after death for RNA extraction and hybridization on Affymetrix microarrays

first: Francesca

last: Pala

first: Sébastien

last: Mella


title: A stable mode of bookmarking by TBP recruits RNAPolymerase II to mitotic chromosomes


title: Human iPSC-EC differentiation

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: We performed large-scale single-cell RNA-seq on human iPSCs subjected to endothelial cell differentiation.

overall_design: Examined two time points of iPSC-EC differentiation.

first: David

last: Paik

first: Joseph

last: Wu


title: Analysis of genome wide changes in RNA polymerase II occupancy in murine cells during heat shock and recovery

city: Boulder

first: Jennifer

last: Kugel

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

summary: The goal of this study was to reveal changes in genome-bound RNA polymerase II in response to heat shock, and monitor the recovery of bound RNA polymerase II as cells return to homeostasis.

overall_design: RNA polymerase II ChIP-seq from murine cells under three conditions: control, heat shock, and heat shock followed by recovery.

last: Cardiello

last: Goodrich


title: Transcriptional signature of murine tracheal brush cells identified by RNA-Seq

status: Public on Jul 03 2018

first: Lora

last: Bankova

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

summary:
Purpose: Tracheal epithelial brush cells are rare chemosensory cells defined by their expression of elements of the bitter taste transduction system, and known to activate the cholinergic nervous system in the murine lung. Similar chemosensory cells in the intestine can generate lipid mediators and pro-inflammatory cytokines but whether brush cell can contribute to airway inflammation is unknown. Furthermore, despite the advances in understanding chemosensory cell effector functions, the receptors that mediate chemosensory cell activation and expansion beyond taste receptors in any compartment remain largely unknown.
Methods: In this study, we isolated tracheal brush cells by FACS from naïve ChATBAC-eGFP mice with knockin of eGFP within a BAC spanning the acetylcholine transferase locus, marking brush cells in the epithelium and performed transcriptome profiling using low input RNA sequencing.  We compared tracheal brush cells to EpCAM+ epithelial cells and CD45+ hematopoetic cells in naive mice.
Results: When compared to EpCAM+ EpCs and to CD45+ cells in the airway, principal component analysis demonstrated that brush cells grouped quite distinctly. This brush cell distinction relative to EpCAM+ cells, was further reflected in the striking number of highly differentially expressed genes. This included 1305 genes expressed at 4-fold or higher levels in EpCAM+eGFP+ cells (brush cells), of which 418 genes were expressed at 32-fold or higher levels in brush cells.
Conclusions: Our study represents the first detailed analysis of the transcriptome of tracheal brush cells and identifies a unique set of genes that are primarily expressed in brush cells including the bitter taste transduction system, synthenic machinery for several pro-inflammatory lipid mediators and HoxA2 transciptional factors.

overall_design: Examination of gene expression of tracheal brush cells (ChAT-eGFP), EpCAM+ (EpCAM) tracheal epithelial cell and CD45+ hematopoetic cells in naïve mice.

first: Nora

last: Barrett

first: Daniel

last: Dwyer


title: Tuft cells play a suppressive role in pancreatic injury and tumorigenesis [ChIP-seq]

city: San Diego

first: Chi-Yeh

last: Chung

address: 10770 Science Center Drive

institute: Pfizer Inc.

summary: We perfromed POU2F3 ChIP-seq on intestinal tuft cells

overall_design: ChIPmentation method (Schmidl et al., 2015) was perfromed on dissociated, FACS isolated intestinal tuft cells

first: Geoffrey

last: Wahl

first: Kathleen

last: DelGiorno


title: Tuft cells play a suppressive role in pancreatic injury and tumorigenesis

overall_design: Refer to individual Series


title: BAR-Seq to study history-dependent behavior

city: Leuven

first: Abbas

last: Jariani

address: Gaston Geenslaan 1, box 2471

department: KU Leuven - VIB Centre for Microbiology

country: Belgium

institute: KU Leuven - VIB

summary: Sequencing of the barcodes of pooled yeast deletion collection in carbon source shifts to identify the genes affecting history dependent behavior.

overall_design: The yeast deletion was pooled together and pregrown in maltose. They were washed and grown in glucose for different durations. They were washed back to maltose again. Samples were taken regularly and the barcodes were amplified and sequenced. on Illumina. Each deletion has two barcodes (Up and Down) around the deleted gene.

first: Bram

last: Cerulus


title: Role of TBP in reactivation of transcription following mitosis [RNA-Seq]

first: Sheila

last: Teves

summary: We performed nascent chromatin-associated RNA analysis as a time course following mitosis to determine how transcription is reactivated globally as cells enter G1.

overall_design: We used asynchronous mouse embryonic stem (ES) cells, or Nocodazole-synchronized mitotic ES cells as starting material. Mitotic cells were then released into fresh media for 30 or 60 minutes to allow entry into G1. After extracting nascent chromatin-associated RNA, we used stranded single end sequencing and mapped the reads to the mm10 genome.

first: Robert

last: Tjian


title: Arid1a restrains Kras-dependent changes in acinar cell identity

city: New York

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Mutations in members of the SWI/SNF chromatin remodeling family are common events in human cancer, but the mechanisms whereby disruption of SWI/SNF components alters tumorigenesis remain poorly understood.  To model the effect of loss of function mutations in the SWI/SNF subunit Arid1a in pancreatic ductal adenocarcinoma (PDAC) initiation, we directed shRNA triggered, inducible and reversible suppression of Arid1a to the pancreas of mice in the setting of oncogenic KrasG12D.  Arid1a cooperates with Kras in the adult pancreas as postnatal silencing of Arid1a following sustained KrasG12D expression induces rapid and irreversible reprogramming of acinar cells into mucinous PDAC precursor lesions. In contrast, Arid1a silencing during embryogenesis, concurrent with KrasG12D activation, leads to retention of acinar cell fate. Together, our results demonstrate Arid1a as a critical modulator of Kras-dependent changes in acinar cell identity, and underscore an unanticipated influence of timing and genetic context on the effects of SWI/SNF complex alterations in epithelial tumorigenesis.

overall_design: Identification of the transcritpional changes induced upon dox-inducible Arid1a knockdown in mutant Kras pancreatic epithelial cells: Arid1a-downregulated vs Arid1a-expressing mutant Kras-pancreatic epithelial cells were FACS-sorted from pancreata from p48Cre;RIK;LSL-KrasG12;TRE-shRNA mice (harbouring Arid1a shRNAs -6421 or 1803- or control Renilla shRNA -713-) at day 5 post- doxycycline treatment. Mice were placed on doxycycline diet at 5 weeks of age to induce expression of the indicated shRNAs. 3 biological replicates (independent mice) were used per shRNA condition (713, 6421, 1803).

first: Geulah

last: Livshits

first: Scott

middle: W

last: Lowe


title: Gene expression profiling in Dis3l2-null and wild-type nephron progenitor cells

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern Medical Center Dallas

summary:
Purpose: Loss of DIS3L2 in humans is associated with congenital overgrowth in Perlman syndrome, as well as with the development of Wilms tumors.  DIS3L2 is an exoribonuclease with a demonstrated preference for 3’-uridylated RNA substrates.  However, its targets relevant to human disease are poorly understood.  Our goal was to address transcriptomic changes in DIS3L2 deficient mouse nephron progenitor cells, a cell type of the developing kidney with demonstrated relevance to Wilms tumorigenesis.
Methods: RNA-seq libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequenced using 50 base pair single-end reads on an Illumia HiSeq2500 at the McDermott Center Next Generation Sequencing core at UT Southwestern.  Samples were 2 biological replicates of wild-type and 3 of Dis3l2-null from embryos of the same litter.
Results:  Upregulated genes included replication-dependent histone mRNA and small non-coding Polymerase III transcripts, as expected from previous reports, as well as Igf2, a gene that has not previously been established to be regulated by DIS3L2 and whose upregulation is associated with overgrowth and Wilms tumor development.
Conclusions:  These data implicate Igf2 as a promising candidate for the overgrowth and Wilms tumorigenesis observed in DIS3L2-deficient disease states.

overall_design: Gene expression profiles of Dis3l2 null or wild-type primary nephron progenitor cells were determined by RNA-seq.

first: Ryan

last: Hunter

first: Yangjuan

last: Liu

first: Hema

last: Manjunath

first: Asha

last: Acharya

first: Benjamin

last: Jones

first: He

last: Zhang

first: Beibei

last: Chen

first: Harini

last: Ramalingam

last: Hammer

first: Yang

last: Xie

first: James

last: Richardson

first: Dinesh

last: Rakheja

first: Thomas

last: Carroll


first: Richard

last: Koche

overall_design: Identification of the chromatin acessibility changes induced upon dox-inducible Arid1a knockdown in mutant Kras pancreatic epithelial cells: Arid1a-downregulated vs Arid1a-expressing mutant Kras-pancreatic epithelial cells were FACS-sorted from pancreata from p48Cre;RIK;LSL-KrasG12;TRE-shRNA mice (harbouring Arid1a shRNA -6421- or control Renilla shRNA -713-) at day 5 post- doxycycline treatment. Mice were placed on doxycycline diet at 5 weeks of age to induce expression of the indicated shRNAs. Each biological replicate is an independent animal.

middle: P


title: Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (PAR-CLIP)

first: Hiten

last: Madhani

department: Department of Biochemistry and Biophysics

institute: University of California, San Francisco

summary: In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.

overall_design: PAR-CLIP was conducted on one sample in replicate in S. pombe.

first: Jahan-Yar

last: Parsa

first: Selim

last: Boudoukha

first: Jordan

last: Burke

first: Christina

last: Homer

middle: D


title: Transcriptional alterations in Nucleus Accumbens somatostatin interneurons following exposure to cocaine

first: Efrain

last: Ribeiro

address: 1425 Madison Ave, Icahn bldg. Rm 10-24

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary:
Total RNA-sequencing of FACs isolated nucleus accumbens somatostatin interneuron nuclei
Somatostatin interneuron loss in multiple cortical brain regions has been observed postmortem in humans with several neuropsychiatric disorders and their loss is proposed to underlie some common pathological changes in circuit function across numerous syndromes. However, somatostatin interneurons in the nucleus accumbens (NAc), a key brain reward region, remain poorly understood due to the fact that these cells account for <1% of NAc neurons. Here, we used Flouresence activated cell sorting to isolate nuclei of somatostatin-expressing interneurons in the Nucleus Accumbens from individual SST-TLG498 reporter mice that express membrane bound EGFP-F specifically in somatostatin-expressing neurons. We then performed cell-type specific Total RNA-sequencing to characterize the entire transcriptome of NAc somatostatin interneurons after repeated exposure (7 days) to either saline or cocaine. We identified a wide variety of coding and non-coding transcripts that were expressed at high levels and were differentially expressed between saline and cocaine treated mice. Repeated cocaine administration induces transcriptome-wide changes in gene expression within NAc somatostatin interneurons, with particular regulation of transcripts related to neural plasticity. Our results identify alterations in NAc induced by cocaine in a sparse population of somatostatin interneurons, and illustrate the value of studying brain diseases using cell type-specific whole transcriptome RNA-sequencing to identify novel neurpathophysiology.

overall_design: 10 Saline and 10 Cocaine treated mice were compared for using total RNA-sequencing to identify differences in transcription between the groups

first: Eric

last: Nestler


title: Influenza A virus-derived siRNAs increase in the absence of NS1 yet fail to inhibit virus replication

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: While the issue of whether RNA interference (RNAi) ever forms part of the antiviral innate immune response in mammalian somatic cells remains controversial, there is considerable evidence demonstrating that few, if any, viral small interfering RNAs (siRNAs) are produced in infected cells. Moreover, total inhibition of RNAi by mutational inactivation of key RNAi factors, such as Dicer or Argonaut 2, has been shown to not enhance virus replication. One potential explanation for this lack of inhibitory effect is that mammalian viruses encode viral suppressors of RNAi (VSRs) that are so effective that viral siRNAs are not produced in infected cells. Indeed, a number of mammalian VSRs have been described of which the most prominent is the influenza A virus (IAV) NS1 protein, which has not only been reported to inhibit RNAi in plants and insects but also to prevent the production of viral siRNAs in IAV-infected human cells. Here, we confirm that an IAV mutant that lacks the viral NS1 protein indeed differs from wild type IAV in that it induces the production of readily detectable levels of Dicer-dependent viral siRNAs in infected human cells. However we also demonstrate that these siRNAs have little if any inhibitory effect on IAV gene expression.

sample_organism:
Homo sapiens
Influenza A virus (A/hvPR8/34(H1N1))

overall_design: 293T or Dicer-knockout cells (NoDice) were infected with Influenza A virus PR8 or NS1-mutant PR8, total small RNA from infected cells deep sequenced to determine the presence of viral-derived siRNAs.

first: Edward

last: Kennedy

first: David

middle: G

last: Courtney

first: Bryan

last: Cullen


title: Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

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


title: Eed, a member of the Polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

summary: We used R26R-tdTomato reporter mice activated by the Six2-TGC transgene to isolate cell populations co-expressing GFP and tdTomato by FACS from kidneys of control P0 mice. We observed two distinct populations of cells from control kidneys based on lower or higher tdTomato expression along with high GFP-expression from the Six2-TGC transgene. RNASeq experiment was conducted to analyze the transcriptome of these populations

overall_design: Examination of 2 different populations of cells derived from Six2-expressing kidney by RNA-seq.

first: Sandrine

last: Ettou

first: Dhawal

last: Jain

last: Kreidberg


title: mRNA profiles of JMJD3 overexpression NB4 cells

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

institute: Shanghai JiaYin Biological technology co., LTD

summary:
Next Generation Sequencing Facilitates Quantitative Analysis of NB4 cells transduced with control or JMJD3-expression vector.

JMJD3, a stress-inducible H3K27 demethylase, plays a critical regulatory role in the initiation and progression of malignant hematopoiesis. However, how this histone modifier effects in a cell type-dependent manner remains unclear. Here, we show that in contrast to its oncogenic effect in preleukemia state and lymphoid malignancies, JMJD3 relieves the differentiation-arrest of certain subtypes (such as M2 and M3) of acute myeloid leukemia (AML) cells. RNA-sequencing and ChIP-PCR analyses revealed that JMJD3 exerts anti-AML effect by directly modulating H3K4 and H3K27 methylation levels to activate the expression of a number of key myelopoietic regulatory genes. Mechanistic exploration identified a physical and functional association of JMJD3 with C/EBPb that presides the regulatory network of JMJD3. Thus, the leukemia regulatory role of JMJD3 varies in a disease phase- and lineage-dependent manner, and acts as a potential oncorepressor in certain subsets of AML largely by coupling to C/EBPb-centered myelopoietic program.

overall_design: mRNA profiles of NB4 cells were generated by deep sequencing, using  Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.

first: Shan-he

last: Yu

first: Jiang

last: Zhu


title: Gene expression in microglia of WT and Trem2(-/-) mice upon treatment with cuprizone, Covi-Ox, or both

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

summary:
Eight groups of mice of two genetic backgrounds (WT or Trem2(-/-)) were fed one of the four diets: 1) regular chow; 2) chow supplemented with Covi-ox T-70; 3) chow supplemented with cuprizone; 4) chow supplemented with both Covi-Ox and cuprizone
After this, the differences in the brain of experimental animals were characterized with microscopy and microarray analysis of gene expression.

overall_design: Mice were fed the diet ad libitum. Mice fed cuprizone and tocopherols were placed on the Covi-ox T70 with additional tocopherols diet for 2 weeks prior to feeding with Covi-ox T70 and cuprizone together for either 4 additional weeks or 7 weeks followed by 1 week of normal chow diet. Mice fed cuprizone only were maintained on normal chow for 2 weeks and then changed to cuprizone containing feed for 4 weeks or 7 weeks followed by 1 week of normal chow diet. After the mice were sacrificed, microglia were sorted, and gene expression was analyzed.

first: Tyler

last: Ulland

first: Yaming

last: Wang

first: Ivan

last: Arbuzov

first: Wilbur

last: Song

first: Vasiliki

last: Lampropoulou

first: Monika

last: Bambouskova

first: Fadi

last: Towfic

first: Susan

last: Gilfillan

first: Ekaterina

last: Loginicheva

first: Brian

last: Edelson

first: Ben

last: Zeskind

first: Marco

last: Colonna

first: Maxim

last: Artyomov


title: TBP in mitotic bookmarking and reactivation of transcription [ChIP-Seq]

first: Sheila

middle: S

last: Teves

summary: To test of TBP binds in the same genomic regions in mitosis compared to interphase cells, we performed Chromatin ImmunoPrecipitation coupled with sequencing (ChIP-seq).

overall_design: We used asynchronous mouse embryonic stem (ES) cells, or Nocodazole-synchronized mitotic ES cells as starting material for ChIP-seq. The cells were crosslinked with 1% formaldehyde, digested with MNase, and lightly sonicated to solubilize digested chromatin. This served as input for the ChIP. After extracting DNA from the ChIP experiment, we used paired end sequencing and mapped the reads to the mm10 genome. We then performed in silico size selection for reads under 100 bp and analyzed for enrichment at the TSS

first: Robert

last: Tjian


title: Casein Kinase 2 Mediated Phosphorylation of Spt6 Modulates Histone dynamics and Regulates Spurious Transcription (ChIP-Seq)

city: Québec

first: Amine

last: Nourani

state: Québec

address: 9, rue McMahon 3734-1

institute: Centre de recherche du CHU de Québec-Université Laval

summary: CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. Interestingly, strand-specific RNA-seq analyses show that CK2 inhibits global cryptic promoters driving both sense and antisense transcription. This further indicates a role of CK2 in the modulation of chromatin during transcription. Next, we showed that CK2 interacts with the major histone chaperone Spt6, and phosphorylates it in vivo and in vitro. CK2 phosphorylation of Spt6 is required for its cellular levels, for the suppression of histone H3 turnover and for the inhibition of spurious transcription. Finally, we show that CK2 and Spt6 phosphorylation sites are important to various transcriptional responses suggesting that cryptic intragenic and antisense transcript production may have an impact on cell adaptation to environmental cues. Altogether, our data indicate that CK2 mediated phosphorylation of Spt6 regulates chromatin dynamics associated with transcription, and prevents aberrant transcription.

overall_design: Cells from CK2ts mutant strain and its respective WT were grown at 30°C in YP-Raffinose, arrested in G1 and then 2% galactose was added to induce Flag-H3 synthesis and shifted to 37ºC for 1h. Cultures were cross-linked by adding formaldehyde to a final concentration of 1%. Yeast lysates were generate by bead beating with glass beads of 0.5 mm diameter, and chromatin solubilization was performed by sonication (average DNA fragment size of 350-500 bp). Immunoprecipitation (IP) of Rpb1 was performed using 2-3 μg of the 8WG16 anti-CTD antibody per IP (Covance, MMS-126R). The Flag Immunoprecipitations were done using 10 μL of anti-Flag agarose beads per IP (Sigma, A2220). ChIP-seq experiments were performed fallowing following TruSeq DNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads (McGill University and Génome Québec Innovation Centre, Montréal, Canada). The sequenced reads were aligned to the S-cerevisiae genome assembly R64-1-1 (GCA_000146045.2) using bowtie v0.12.8 (Langmead et al., 2009). Coverage was calculated using bedtools (http://bedtools.readthedocs.io/) (Quinlan et al., 2010) and was normalized into reads per million (RPM).

first: Emmanuelle

last: Gouot

first: Wajid

last: Bhat

first: Anne

last: Rufiange

first: Eric

last: Fournier

last: Paquet


title: Casein Kinase 2 Mediated Phosphorylation of Spt6 Modulates Histone dynamics and Regulates Spurious Transcription (RNA-Seq)

overall_design: Cells from CK2ts and spt6-7SA mutant strains and a WT strain were grown in YPD to an OD600 of 0.5 at 30°C and shifted to 39°C for 2h before RNA extraction. Total RNA was extracted using the hot-phenol method. Prior to library preparation, total RNA was depleted for ribosomal RNA using the Ribo-zero Gold yeast kit (Epicentre-Illumina). RNA-seq experiments were performed following TruSeq stranded total RNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads on an Illumina Hi-Seq2000 (McGill University and Génome Québec Innovation Centre, Montréal, Canada). The sequenced reads from each sample were preprocessed with Trimmomatic (Bolger et al., 2014) and aligned with bwa (Li et al., 2009) to S.cerevisiae genome assembly R64-1-1 (GCA_000146045.2) and the numbers of reads for each exon annotated in Ensembl Release 77 was calculated for both the sense and antisense strands using SAMtools.


title: KDM5 histone demethylases repress innate immune response via suppression of STING

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

summary: Tri-methylation on histone H3 lysine 4 (H3K4me3) is enriched near transcription start sites and correlates with active transcription. Like other histone marks, methylation on H3K4 is catalyzed by the respective methyltransferases and erased by demethylases. Lysine demethylase 5 (KDM5) family of Fe (II) and α-ketoglutarate-dependent dioxygenases removes the methyl groups from H3K4me3. All four family members of KDM5 demethylases (KDM5A-D) share sequence identity, have similar in vitro kinetic parameters, and display functional redundancy. To determine the effects of complete depletion of KDM5 activity, we treated MCF7 cells with DMSO, or two pan-KDM5 specific inhibitors, KDM5-C70 (our lab code 443) and CPI-48 (our lab code 278) and performed RNA sequencing to determine gene expression changes after KDM5 inhibitor treatment.

overall_design: RNA sequencing of MCF7 cells treated with DMSO or KDM5 inhibitors.

first: Lizhen

last: Wu


title: The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types

status: Public on Jul 02 2018

first: Yuheng

last: Lu

state: NY

address: 417 East 68th Street


title: Tuft cells play a suppressive role in pancreatic injury and tumorigenesis [RNA-seq]

first: Chi-Yeh

last: Chung

summary: We perfromed RNA-seq on pancreatic and intestinal tuft cells and bone marrow derived macrophages

overall_design: The transcriptomes of pancreatic and intestinal tuft cells and bone marrow derived macrophages were profiled. Three biological replicates for each cell type.

first: Geoffrey

last: Wahl

first: Kathleen

last: DelGiorno


title: The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types (PolyA-Seq)

summary: Numerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3’UTR usage analysis using polyadenylation (polyA)-Seq in activated miR-155-sufficient and  deficient macrophages, dendritic cells, T and B lymphocytes, we identified numerous targets differentially bound by miR-155. While alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in a majority of cases identical 3’UTR isoforms were differentially regulated across cell types, suggesting ApA-independent and cellular context-dependent miR-155-mediated gene regulation reminiscent of sequence-specific transcription factors. Our study provides comprehensive maps of miR-155 regulatory RNA networks and offers a valuable resource for dissecting context-dependent and -independent miRNA-mediated gene regulation in key cell types of the adaptive and innate immune systems.

overall_design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS.

first: Alexander

middle: Y

last: Rudensky


title: Comprehensive RNA-Seq profiling in PBMCs of ALS patients and healthy controls

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Coding and long non-coding RNA metabolism is now revealing its crucial role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we performed Illumina RNA-seq analysis on Peripheral Blood Mononuclear Cells (PBMCs) from Sporadic and mutated ALS patients (mutations in FUS, TARDBP, SOD1, C9Orf72 and VCP genes) and healthy controls. Our aim is the whole-transcriptome characterization of PBMCs content, both in terms of coding and non coding RNAs, in order to compare the disease state to the healthy controls, both for sporadic patients and for mutated patients. Out dataset is a starting point for the omni-comprehensive analysis of coding and long non coding RNAs, from an easy to withdraw, manage and store tissue that shows to be a suitable model for RNA profiling in ALS.

overall_design: whole transcriptome RNA-Seq profiling in PBMCs of ALS and healthy donors

first: Susanna

last: Zucca

first: Stella

last: Gagliardi

first: Cecilia

last: Pandini

first: Luca

last: Diamanti

first: Matteo

last: Bordoni

first: Daisy

last: Sproviero

first: Maddalena

last: Arigoni

first: Martina

last: Olivero

first: Orietta

last: Pansarasa

first: Mauro

last: Ceroni

first: Cristina

last: Cereda


title: Temporal activation of NR5A2 and RARγ induce functional human naïve pluripotent state via modulating TGFβ pathway

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

summary: Rejuvenated primed human pluripotent stem cells, naïve cells, are accessible through the manipulating transcription factors, singaling pathways or a combination of both. However, there is a notable challenge in the functions of naïve hPSCs. Here, we show that the brief treatment with two chemical agonists (2a) of nuclear receptors NR5A2 and RARγ along with 2i and lif (2a2iL) is sufficient to induce naive pluripotency during the reprogramming of fibroblasts and pre-established hPSCs as well as the generation of new cell lines from preimplantation embryos. These cells manifested global naive-specific critera especially the contribution into the human-mouse chimeras. We demonstrated that TGF-β pathway activity is potentially critical for induction and maintenance of 2a2iL naive hPSCs. Consequently, transient activation of TGF-β resulted in generation of naive hPSCs in 2iL condition. These results represent a naive pluripotent state which is in a top point of developmental potential equivalent with preimplantation human embryo.

overall_design: Primed and naïve hESCs mRNA profiling in two cell lines.

first: Adeleh

last: Taei

first: Tahereh

last: Kiani

first: Zeinab

last: Taghizadeh

first: Sharif

last: Moradi

first: Azam

last: Samadian

first: Sepideh

last: Mollamohammadi

first: Stefan

last: Guenther

first: Azimeh

last: Akhlaghpour

first: Behrooz

last: Asgari

first: Mostafa

last: Najar-Asl

first: Razieh

last: Karamzadeh

first: Thomas

last: Braun

first: Hassani

last: Seyedeh-Nafiseh

first: Hossein

last: Baharvand


title: SOX9 is dispensable to initiate epigenetic remodeling and activation of marker genes at the onset of chondrogenesis (RNA-Seq)

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

country: USA

institute: Cleveland Clinic Lerner Research Institute

summary: Using whole-transcriptome and whole-epigenome sequencing approaches for wild-type and Sox9-deficient mouse embryo limb buds, we here identify genes specifically expressed and likely involved in precartilaginous condensation. We show that SOX9 directly upregulates these genes and well-known early-cartilage markers, and that its actions in chondrogenic cells have little impact on neighboring cell types. Intriguingly, we find that SOX9 helps remove epigenetic signatures of transcriptional repression and establish active-promoter and active-enhancer marks at precartilage- and cartilage-specific loci, but is not absolutely required to initiate these changes and activate transcription. Altogether, these findings widen our current knowledge of SOX9 targets in early chondrogenesis and call for new studies to identify the pioneer and transactivating factors that act upstream of or along with SOX9 to prompt chromatin remodeling and specific gene activation at the onset of chondrogenesis and other processes.

overall_design: RNAs were isolated from 3-4 biological replicates of control and Sox9-deficient mouse limb buds at E11.5 and E12.5 for RNA-seq experiments.

first: Veronique

last: Lefebvre


title: SOX9 is dispensable to initiate epigenetic remodeling and activation of marker genes at the onset of chondrogenesis

overall_design: Refer to individual Series


title: Expression profiling of mouse bone marrow skeletal progenitors with osteogenic and adipogenic potential and adipogenic progenitors treated with IFNγ.

city: Dresden

first: Konstantinos

last: Anastassiadis

address: Tatzberg 47

department: Biotechnology Center

institute: Technische Universitaet Dresden

summary: Bone marrow stromal cells (BMSCs) were isolated from the femora and tibiae of irtTA-GBD*-TAg transgenic mice. Using cellular cloning we established skeletal progenitors with unipotent osteogenic and adipogenic properties. Previous RNA-seq analysis of more progenitor types revealed differential expression in members of the Interferon-gamma (IFNγ) signaling pathway. Treatment of adipogenic progenitors with IFNγ inhibited adipogenesis and promoted osteogenesis. RNA-seq analysis of osteogenic, adipogenic and IFNγ treated adipogenic clones revealed factors controlling the osteogenic versus adipogenic commitment of bone marrow skeletal progenitors.

overall_design: Expression profiling (RNA-seq) of three biological replicates representing skeletal progenitors with osteogenic potential, adipogenic potential and adipogenic progenitors after treatment with IFNγ for 3 days

first: Maria

last: Rostovskaya


title: Single-molecule nascent RNA sequencing reveals regulatory domain architecture ant promoters and enhancers

city: Ithaca

first: Jacob

middle: Michael

last: Tome

address: 416 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: CoPRO adapts PRO-cap for paired end sequencing, and includes a total of three different libraries that were enriched for either capped nascent RNAs only, uncapped nascent RNAs only, or both.  With paired end sequencing, each read tells us where an RNA polymerase molecule initiated, and then where its active site is located.  Comparison of the libraries for different capping states allows us identify the precise location of pausing, and of where nascent RNAs become capped across the tens of thousands of initiation sites that we detect.  The paired nature of the data enabled identification of sites of transcription initiation with unprecedented precision: we could use the pattern of pausing and elongation as a sensitive way of calling real initiation sites, and filter out termination by comparing capped and uncapped treatments.  Because CoPRO maps nascent RNA, it is not affected by the post-transcriptional stability of the initiation and pausing events detected.  Thus, it puts non-coding transcription (such as eRNAs and upstream divergent RNAs) on an equal footing with longer lived RNAs like mRNA and lncRNAs.  With our comprehensive maps of transcription initiation, we are able to compare the architecture of initiation sites with other features of the genome.  For this purpose, we chose human K562 cells for direct comparison with dozens of publically available genome-wide datasets.

overall_design: CoPRO libraries for Capped nascent transcripts only, Uncapped nascent transcripts only, or both Capped and Uncapped nascent transcripts were prepared from K562 cells, each in biological duplicate.  CoPRO libraries for Capped nascent transcripts were prepared from MEF cells with and without 60 minutes of heat shock at 42 Celsius.

middle: M

first: Nathaniel

last: Tippens

first: John

middle: T

last: Lis


title: Expression profiling of clonally derived skeletal progenitors from mouse bone marrow

summary: Bone marrow stromal cells (BMSCs) were isolated from the femora and tibiae of irtTA-GBD*-TAg transgenic mice. Using cellular cloning we established skeletal progenitors with distinct differentiation properties and analysed their transcriptome. Unipotent osteogenic and adipogenic cells expressed specific transcriptional programs whereas bipotent clones combined expression of those genes and did not show a unique signature.

overall_design: Expression profiling (RNA-seq) of two independent clones from different mice representing skeletal progenitors with the following characteristics: tripotent clones (Osteogenic, Adipogenic, Chondrogenic = OAC1 and OAC2); bipotent clones (Osteogenic, Adipogenic = OA1 and OA2); unipotent clones (Osteogenic = O1 and O2; Adipogenic = A1 and A2). Further, we prepared and sequenced pools of several other clones from these two mice, with the following properties: tripotent clones (Osteogenic, Adipogenic, Chondrogenic = OAC3); bipotent clones (Osteogenic, Adipogenic = OA3; Osteogenic, Chondrogenic = OC3; Adipogenic, Chondrogenic = AC3); unipotent clones (Osteogenic = O3; Adipogenic = A3).


title: A Virus-acquired Host Cytokine Controls Systemic Aging by Antagonizing Apoptosis

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

summary: Aging is characterized by degeneration of unique tissues. However, dissecting the interconnectedness of tissue aging remains a challenge. Here, we employ a muscle-specific DNA damage model in Drosophila to reveal secreted factors that influence systemic aging in distal tissues. Utilizing this model, we uncovered a cytokine, Diedel, that when secreted from muscle or adipose can attenuate age-related intestinal tissue degeneration by promoting proliferative homeostasis of stem cells. Diedel is both necessary and sufficient to limit tissue degeneration and extend lifespan. Secreted homologs of Diedel are also found in viruses, having been acquired from host genomes. Focusing on potential mechanistic overlap between cellular aging and viral-host cell interactions and, we found that Diedel is a functionally conserved inhibitor of apoptosis and can act as a systemic rheostat to modulate cell death during aging. These results highlight a key role for secreted antagonists of apoptosis in the systemic coordination of tissue aging.

overall_design: Intact fly thorax and midguts were dissected (at 10 days and 30 days) in PBS. Total RNA was extracted using Trizol reagent and used as template to generate sample libraries for RNA sequencing (using the TruSeq Stranded Total RNA Library Prep Kit). Sample libraries were sequenced using the Illumina HiSeq 2500. Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina’s HCS 2.2.58 and RTA 1.18.64 software with default parameter settings. Between 7 and 12 million (1X50) base pair reads were generated per library and mapped to the Drosophila genome (Release 6).

first: Mohamed

last: Mlih


title: The interferon-induced exonuclease, ISG20, exerts antiviral activity through upregulation of type I interferon response proteins

status: Public on Jul 01 2018

city: Pittsburgh

first: William

last: Klimstra

state: PA

address: 3501 Fifth Ave, 9052 BST3

department: Microbiology and Molecular Genetics

institute: University of Pittsburgh

summary: Type I interferon-stimulated genes (ISGs) have critical roles in inhibiting virus replication and dissemination. Despite advances in understanding the molecular basis of ISG restriction, the antiviral mechanisms of many remain unclear. The 20 kDa ISG, ISG20, is a nuclear 3'-5'exonuclease with preference for single stranded RNA (ssRNA) and has been implicated in the IFN-mediated restriction of several RNA viruses. Although the exonuclease activity of ISG20 has been shown to degrade viral RNA in vitro, evidence has yet to be presented that virus inhibition in cells requires this activity. Here, we utilized a combination of an inducible, ectopic expression system and newly generated Isg20−/− mice to investigate mechanisms and consequences of ISG20-mediated restriction. Ectopically expressed ISG20 localized primarily to Cajal bodies in the nucleus and restricted replication of chikungunya and Venezuelan equine encephalitis viruses. Although restriction by ISG20 was associated with inhibition of translation of infecting genomic RNA, degradation of viral RNAs was not observed. Instead, translation inhibition of viral RNA was associated with ISG20-induced upregulation of over 100 other genes, many of which encode known antiviral effectors. ISG20 modulated the production of IFIT1, an ISG that suppresses translation of alphavirus RNAs. Consistent with this observation, the pathogenicity of IFIT1-sensitive alphaviruses was increased in Isg20−/− mice compared to wild-type viruses, but not in ISG20 ectopic-expressing cells. Our findings establish an indirect role for ISG20 in the early restriction of RNA virus replication by regulating expressionof other ISGs that inhibit translation and possibly other activities in the replication cycle.

overall_design: Two clones each of tet-inducible MEFs overexpressing eGFP (control), Isg20, and Isg20(D94G) were induced by tetracycline removal for 72 hours. rRNA was depleted with RiboMinus Eukaryote kit (Life Technologies) and prepared for Illumina directional 100bp paired-end HiSeq2000 reads.

first: Wiliam

first: Christopher

last: Weiss


title: Casein Kinase 2 Mediated Phosphorylation of Spt6 Modulates Histone dynamics and Regulates Spurious Transcription

first: Amine

last: Nourani

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


title: RNA sequencing analysis of metabolism related genes in MKRN1-null mice tissues.

city: Seoul

first: Jae whan

last: Song

address: Yonsei-ro 50

department: Department of Biochemistry

country: South Korea

institute: College of Life Science and Biotechnology

summary: Analysis of metabolism related gene expression in liver and adipose tissues from MKRN1 knockout mice.

overall_design: Total RNA was obtained from MKRN1 knockout liver and adipose tissues and then RNA-seq was perform.

first: Hyun-Ji

last: Han

first: Min-sik

last: Lee

first: Su

first: Jaewhan


title: ELF1 expression in prostate cells reduces oncogenic ETS functions and promotes senescence and sensitivity to chemotherapy through distinct gene expression programs

city: Bloomington

first: Peter

last: Hollenhorst

state: Indiana

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University


title: ELF1 expression in prostate cells reduces oncogenic ETS functions and promotes senescence and sensitivity to chemotherapy through distinct gene expression programs [ChIP-seq]

summary: Aberrant overexpression of oncogenic ETS factors through chromosomal rearrangments is the most common genomic event in primary prostate tumor and these factors have been well studied. Loss of ELF1, another ETS transcription factor family member, is a common event in prostate cancer, but the function of ELF1 has not been described within the prostate. Studies of ELF1 in different tissue types has determined that it can be important for oncogeneis or tumor suppression. Here, we show that ELF1 is a novel prostate tumor suppressor by hindering oncogenic ETS function at cell migration related genes, but also that ELF1 has the ability to regulate senescence and chemotherapy resistance. Next generation sequencing was used to determine gene expression changes in RWPE-1 cells upon addition of an oncogenic ETS factor and then with the loss of ELF1 through an shRNA knockdown. Genomic binding locations were also determined for ELF1 and ERG, through ChIP-seq to identify any cobound or unique regions. The combination of this data indicates that ELF1 repressed migration related genes which ERG activates, but ELF1 also uniquely binds genes related to cell senescence and activates their transcription. There, these data indicate a novel tumor suppressive mechanism for ELF1 within the prostate and better characterizes its function within this cell type.

overall_design: ChIP-sequencing of ELF1 in two prostate cancer cell lines, RWPE-1 and PC3

first: Justin

middle: A

last: Budka


title: ELF1 expression in prostate cells reduces oncogenic ETS functions and promotes senescence and sensitivity to chemotherapy through distinct gene expression programs [RNA-seq]

overall_design: mRNA profiles of ERG overexpression and ELF1 knockdown in RWPE-1 cells were generated from RNA-sequencing data, in triplicate, using Illumina NextSeq. Knockdowns were stable shRNA expression from a lentiviral construct selected with puromycin and overexpressions were stable retroviral constructs selected with hygromycin.


title: H3K79me3 AND H3K4me3 ChIP Seq

city: Rehovot

first: Rafael

last: Valdés Mas

address: Herzl St 234

institute: Weizmann Institute

summary: H3K79me3 AND H3K4me3 ChIP Seq

overall_design: DNA from human ESC ectopically expressing MLL-AF4, AF4-MLL or both

first: P

last: Menendez

first: C

last: Bueno


title: Three-dimensional brain-like microenvironments facilitate the direct reprogramming of fibroblasts into therapeutic neurons

first: Yoonhee

last: Jin

department: Department of Biotechnology

institute: Yonsei University

summary: We report differential mRNA expression levels in primary mouse embryonic fibroblasts, primary neurons, and induced neuronal cells generated via direct reprogramming method. The induced neuronal cells were cultured on laminin or decellularized brain ECM.

overall_design: Examination of mRNA expression levels in 4 different groups

first: Jung

first: Jin

last: Kim

first: Sungjin

last: Min

first: Soohyun

last: Wi

first: JiHea

last: Yu

first: Gyeong-Eon

last: Chang

first: Ann-Na

last: Cho

first: Yeeun

last: Choi

first: Da-Hee

last: Ahn

first: Sung-Rae

first: Eunji

last: Cheong

first: Yun-Gon

first: Hyong-Pyo

first: Yonghwan

first: Dong

first: Hyun

first: Zhejiu

last: Quan

first: Hoon-Chul

last: Kang

first: Seung-Woo


title: The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types (iCLIP)

city: New York

first: Yuheng

last: Lu

institute: Memorial Sloan Kettering Cancer Center

overall_design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS. Each condition has 4 sequencing replicates.

first: Alexander

last: Rudensky