title: TMED9-gated CNIH4 and TGFa signaling promotes pro-metastatic states in human primary colon cancer cells

city: Geneva

first: Ariel

last: Ruiz i Altaba

address: 1 rue Michel Servet

department: GEDEV

country: Switzerland

institute: University of Geneva Medical School

summary: How cells in primary tumors initially become pro-metastatic is not understood. A previous genome-wide RNAi screen uncovered colon cancer metastatic suppressor and WNT promoting functions of TMED3, a member of the p24 ER-to-Golgi protein secretion family. Repression of WNT signaling upon knock-down (kd) of TMED3 might thus be sufficient to drive metastases. However, searching for transcriptional influences on other family members here we find that TMED3 kd leads to enhanced TMED9, that TMED9 acts downstream of TMED3 and that TMED9 kd compromises metastasis. Importantly, TMED9 pro-metastatic function is linked to but distinct from the repression of TMED3-WNT-TCF signaling. Functional rescue of the migratory deficiency of TMED9 kd cells identifies TGFa as a mediator of TMED9 pro-metastatic activity. Moreover, TMED9 kd compromises the membrane localization, and thus function, of TGFa. Analyses in three colon cancer cell types highlight a TMED9-dependent gene set that includes CNIH4, a member of the CORNICHON family of TGFa exporters. Our data indicate that TGFA and CNIH4, which display predictive value for disease-free survival, promote colon cancer cell metastatic behavior and suggest that TMED9 pro-metastatic function involves the modulation of the secretion of TGFa ligand. Finally, TMED9/TMED3 antagonism impacts WNT-TCF and GLI signaling, where TMED9 primacy over TMED3 leads to the establishment of a positive feedback loop together with CNIH4, TGFa and GLI1 that enhances metastases. We suggest that primary colon cancer cells can transition between two states characterized by secretion-transcription regulatory loops gated by TMED3 and TMED9 that modulate their metastatic proclivities.

overall_design: CC14 and CC36, two primary colon cancer cells, were treated with control or shTMED9 expressing lentivirus. In addition, CC14 cells were also treated with shTMED3 expressing lentivirus. All the experiments were run in triplicates totaling 15 Samples.

first: Sonakshi

last: Mishra


title: Genome-wide mapping of accessible chromatin in hTert-HME1 cell line treated with control or BRCA2 siRNAs and grown with or without EGF (epithelial growth factor)

status: Public on Jul 02 2019

city: Palo Alto

first: Michael

last: Snyder

state: CA

address: 3165 Porter Dr

department: Genetics

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammary epithelial cell line hTert-HME1 was transfected with Control or BRCA2 siRNAs then passaged four times (12 days), then were grown in mammary epithelial growth medium with or without EGF (epithelial growth factor) for 2 passages (6 days).

overall_design: Control siRNA transfection grown in media +EGF (3 replicates), control siRNA transfection grown in media -EGF (3 replicates), BRCA2 siRNA transfection grown in media +EGF (3 replicates), BRCA2 siRNA transfection grown in media -EGF (3 replicates)

first: Joshua

middle: J

last: Gruber

middle: P


title: Effect of Rgnef knockout in an aggressive ovarian cancer cell line

status: Public on Jul 01 2019

city: La Jolla

first: David

middle: D

last: Schlaepfer

address: 3855 Health Sciences Dr.

department: Moores Cancer Center

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: CRISPR/Cas9-mediated Rgnef knockout was performed in the aggressive ID8-IPs (alternaate name is KMF cells). Gene expression profiles of Rgnef-/- or Rgnef-/- cells re-expressing GFP-Rgnef were generated. Differential downregulation of antioxidant genes was observed in Rgnef-/- cells. Results provide insight into the role of Rgnef in promoting ovarian tumor progression.

overall_design: mRNA profiles of ID8-KMF Rgnef-/- or Rgnef-/- cell re-expressing GFP-Rgnef were generated in triplicate using an Illumina HiSeq 4000.

first: Elizabeth

middle: G

last: Kleinschmidt

first: Nichol

middle: L

last: Miller

first: Duygu

last: Ozmandenci

first: Isabelle

last: Tancioni

first: Carlos

last: Diaz-Osterman

first: Allison

middle: M

last: Barrie

first: Kristin

last: Taylor

first: Aaron

last: Ye

first: Shulin

last: Jiang

first: Denise

middle: C

last: Connolly

first: Dwayne

last: Stupack


title: Mapping of m6A and m5C on HIV with PA-antibody-seq

city: Durham

first: Bryan

middle: R

last: Cullen

state: NC

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

summary: In this GEO submission we include the PA-m6A-seq and PA-m5C-seq datasets for HIV in CEM & 293T cells

last: Courtney


title: Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [III]

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

summary: N6-methyladenosine (m6A) is the most abundant modification on mRNA, and is implicated in critical roles in development, physiology and disease. A major challenge in the field has been the inability to quantify m6A stoichiometry and the lack of antibody-independent methodologies for interrogating m6A. Here, we develop MASTER-seq for systematic quantitative profiling of m6A at single nucleotide resolution, building on differential cleavage by an RNAse at methylated sites. MASTER-seq permitted validation and de novo discovery of m6A sites, calibration of the performance of antibody based approaches, and quantitative tracking of m6A dynamics in yeast gametogenesis and mammalian differentiation. We discover that m6A stoichiometry is ‘hard-coded’ in cis via a simple and predictable code. This code accounts for ~50% of the variability in methylation levels and allows accurate prediction of m6A loss/acquisition events across evolution. MASTER-seq will allow quantitative investigation of m6A regulation in diverse cell types and disease states.

overall_design: 17 samples were analyzed: FTO over expression and control in hESC with triplicates;  AlkBH5 over-expression, FTO over-expression and control in HEK293T with triplicates; Cytosolic fraction of HEK293T with duplicates

first: M

middle: A

first: S

last: Flohr-Edelheit

last: Schwartz


title: HAT1 coordinates histone production and acetylation via H4 promoter binding

first: Michael

last: Snyder

summary: The energetic costs of duplicating chromatin are large and therefore likely depend on nutrient sensing checkpoints and metabolic inputs.  By studying chromatin modifiers regulated by epithelial growth factor, we identified histone acetyltransferase 1 (HAT1) as an induced gene that enhances proliferation through coordinating histone production, acetylation and glucose metabolism.  In addition to its canonical role as a cytoplasmic histone H4 acetyltransferase, we isolated a HAT1-containing complex bound specifically at promoters of H4 genes. HAT1-dependent transcription of H4 genes required an acetate-sensitive promoter element.  HAT1 expression was critical for S-phase progression and maintenance of H3 lysine 9 acetylation at proliferation-associated genes, including histone genes.  Therefore, these data describe a feed-forward circuit whereby HAT1 captures acetyl-groups on nascent histones and drives H4 production by chromatin binding to support chromatin replication and acetylation.  These findings have important implications for human disease, since high HAT1 levels associate with poor outcomes across multiple cancer types.

overall_design:
ChIP-seq data in hTert-HME1 cells:
2 replicates HAT1 ChIP-seq, 2 replicates Rbap46 ChIP-seq, 2 replicates input control; 3 replicates H4K12ac ChIP-seq for shControl cells; 3 replicates of H4k12ac ChIP-seq for shHAT1 cells; 3 replicates of H4k5ac ChIP-seq for shControl cells; 3 replicates of H4k5ac ChIP-seq for shHAT1 cells;
H3K9Ac ChIP-seq data in hTert-HME1 cells: 3 replicates of shControl and 3 replicates of shHAT1

first: Joshua

last: Gruber


title: Characterization of human ILC2 subsets

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

summary: To characterize a novel human ILC2 subset found in peripheral blood, RNAseq was performed. Other ILC subsets from blood and tonsil were also included.

overall_design: ILC subsets were sort purified, and immediately lysed for RNA extraction. RNAseq was performed using SmartSeq technology.

first: Yoichiro

last: Ohne


title: Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution

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

sample_organism:
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [II]

overall_design: 10 samples were analyzed: EBS WT and  Metll3 -/- with two replicates each and ESC WT and Mettld -/- with three replicates

first: Sarit

first: Schraga


title: De novo detection of m6A modification in Saccharomyces cerevisiae at single nucleotide resolution

overall_design: 8 samples are analyzed: IP and background for IME4 mutant and WT with 2 biological replicates for each condition


title: Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [I]

overall_design: 14 samples are analyzed: 10 meiosis time points separated by one hour, two WT positive controls and two deletion negative controls


title: Multiple genes recruited from hormone pathways partition maize diterpenoid defences.

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

institute: University of Georgia

summary: Duplication and divergence of primary pathway genes underlie the evolution of plant specialized metabolism; however, mechanisms partitioning parallel hormone and defence pathways are often speculative. For example, the primary pathway intermediate ent-kaurene is essential for gibberellin biosynthesis and is also a proposed precursor for maize antibiotics. By integrating transcriptional coregulation patterns, genome-wide association studies, combinatorial enzyme assays, proteomics and targeted mutant analyses, we show that maize kauralexin biosynthesis proceeds via the positional isomer ent-isokaurene formed by a diterpene synthase pair recruited from gibberellin metabolism. The oxygenation and subsequent desaturation of ent-isokaurene by three promiscuous cytochrome P450s and a new steroid 5α reductase indirectly yields predominant ent-kaurene-associated antibiotics required for Fusarium stalk rot resistance. The divergence and differential expression of pathway branches derived from multiple duplicated hormone-metabolic genes minimizes dysregulation of primary metabolism via the circuitous biosynthesis of ent-kaurene-related antibiotics without the production of growth hormone precursors during defence.

overall_design: A total of 8 samples were analyzed, comprised of two treatments, SLB 24 h and a 0.1%Tween 20 in H20 control 24 h, all in replicates of four

first: Eric

last: Schmelz


title: Tracing transcriptome  profiles of human oocyte cultured by growth hormone or not in vitro by single cell RNA-seq

status: Public on Jun 29 2019

city: jinan

first: shigang

last: zhao

address: No.44, Wenhua Xi Road

department: center for reproductive medicine

country: China

institute: shandong university

summary: Find the different expression profiles between human oocytes IVM with growth hormone and human oocytes without growth hormone. We collected human oocytes cultured by IVM for 24h with growth hormone or not, prepared single cell cDNAs, and sequenced them by Illumina HiSeq Xten.

overall_design: We get transcriptome of 6 individual oocytes, among them, 3 from the growth hormone group, the other 3 from the control group. We analyzed differential expression profile between the two groups.

first: Shigang

last: Zhao


title: Single cell RNAseq of human innate lymphoid cells (ILC)

summary: Single cell RNAseq of human ILCs to investigate potential heterogeneity within ILC subsets

overall_design: ILC2s (Lin-CD127+CRTH2+), ILC3s (Lin‒ CRTH2‒ c-Kit+) and CD56high NK cells isolated from human peripheral blood by cell sorter and mixed at 8:1:1 ratio. Total 4264 cells were analyzed using the microfluidics based single-cell RNAseq platform (scRNA-seq).

first: Alison

last: Humbles

first: Jincheng

last: Wu


title: Cytokine and receptor expression in skin draining lymph nodes after skin immunization

status: Public on Jun 28 2019

city: Vancouver

first: Jan

middle: Peter

last: Dutz

state: BC

address: 950 West 28th Avenue

department: Dermatology & Skin Science

country: Canada

institute: University of British Columbia

summary:
Topical (epicutaneous, e.c.) application of the adjuvant CpG ODN during immunization leads to a robust immune response compared to when subcutaneous (s.c.) administration. Dendritic cells are hematopoietically derived cells that are important in cross-presenting to and activating CD8 T cells. Dermal dendritic cells are one of the two major dendritic cell subsets found in the skin which mobilize from the skin to draining lymph nodes to present to T cells upon activation. Dermal dendritic cells are found in skin draining lymph nodes around 24 hours post immunization. To determine how the immune system respond differently between e.c. versus s.c. administration of CpG ODN, we evaluated changes in the skin draining lymph node environment upon the two routes of adjuvant application. Expression chemokines and chemokine receptors were assessed with real-time qPCR.
To determine the changes in the skin draining lymph node environment (cytokine and cytokine receptor levels) upon immunization via real time RT-PCR.

overall_design: Adult C57bL/6 mice were immunized via subcutaneous injection of chicken ovalbumin (OVA) in the presence or absence of the adjuvant CpG ODN 1826 administered subcutaneously or epicutaneously. Skin draining lymph nodes were harvested for analysis.

first: Jacqueline

last: Lai

first: Wing-Ki

last: Cheng

first: Patrick

last: Hopkins

first: Douglas

last: Carlow


title: Expression data from young and senescent melanocytes

status: Public on Jun 30 2019

city: Linköping

first: Karin

last: Öllinger

address: Medicinska fakulteten

department: Experimental Pathology, Department of Clinical and Experimental Medicine

country: Sweden

institute: Linköping University

summary:
Malignant melanoma might develop from melanocytic nevi in which the growth-arrested state has been broken. We analyzed the gene expression of young and senescent human melanocytes in culture.
In this dataset we include the expression data of young and senescent human melanocytes.

overall_design: 8 samples in total, 4 samples of young and 4 samples of senescent melanocyte from the same donor are RNA isolated, purified and subsequent analysed on the Affymetrix using the Titan ST1.1

first: Petra

last: Wäster

first: Kyriakos

last: Orfanidis


title: RNA sequencing data of human prostate cancer cells treated with androgen

status: Public on Jun 24 2019

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

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

summary: To analyse and understand the differentially expressed genes following treatment with synthetic androgen (R1881)

overall_design: LNCaP or LAPC4 cells were plated in RPMI 1640 media with no phenol red and with 5% charcoal stripped serum, sodium pyruvate, penicillin and streptomycin. After 48h (to allow adnrogen deprivation), fresh media was added, with 96% ethanol or the synthetic androgen R1881 (10nM concentration). 24h later, cells were harvested for RNA purification using the QIAGEN RNeasy plus purification kit. RNA was then enriched for mRNA and then sequenced.

first: Raghavendra

middle: T

last: Karthik Poluri


title: SLIRP mediated rRNA 2'-O-methylation

city: Riverside

first: LIN

last: LI

state: California

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

type: Methylation profiling by high throughput sequencing

summary: SLIRP is a versatile protein that can interact with stem-loop structure in RNA and with G quadruplex DNA. By using a quantitative proteomic experiment, we found that SLIRP interacts with the majority of the human helicase proteome. We found that these interactions facilitate 2'-O-methylation of rRNA and promote protein translation. Hence, we uncovered a novel function of SLIRP protein and offered novel mechanistic insights into its function as a RNA chaperone and into the regulation of 2'-O-methylation of rRNA.

overall_design: We performed the RiboMethSeq in 293T cells with or without knockdown of SLIRP. Three replicates were done for each experiments.

first: Lin

last: Li

first: Yinsheng

last: Wang


title: Follicular Regulatory T Cells Regulate the Development of Cytotoxic-like Follicular Helper T Cells

city: Indianapolis

first: Alexander

last: Dent

state: IN

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

summary: T follicular regulatory (TFR) cells are found in the germinal center (GC) response and help shape the antibody (Ab) response. Whether TFR cells have a suppressive role, a helper role or both types of roles in the GC is unclear. Here, we addressed TFR cell function using 3 different strains of TFR cell mutant mice. After immunization, GC B cells but not T follicular helper (TFH) cell positively correlated with TFR cell levels. Using a gene profiling approach, we found that TFH cells from TFR-deficient mice showed strong up-regulation of granzyme B (Gzmb) and other effector CD8 T cell genes, many of which were Stat4 dependent. This aberrant cytotoxic T cell gene profile was increased in TFR-deficient mice crossed on a pro-inflammatory background. We detected Gzmb+ and Eomesodermin+ TFH cells and a higher rate of apoptotic GC B cells in the absence of TFR cells. Klrg1+ TFH cells expressed higher Gzmb and less IL-4 and IL-21. Our data show that TFR cells repress the development of abnormal cytotoxic TFH cells that correlate with a lower GC and Ab response. This data shows a novel mode of helper function for TFR cells in the GC response.

overall_design: RNA sequenced from freshly isolated TFH cells of different mice with presence or loss of TFR cells

first: Markus

last: Xie

first: Shuyi

last: Fang

first: Jun


title: Aberrant regulation of epigenetic modifiers contributes to the pathogenesis in patients with selenoprotein N-related Multiminicore Disease

status: Public on Jun 27 2019

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

institute: University of Basel

summary: Congenital myopathies are early onset, slowly progressive neuromuscular disorders of variable severity. They are genetically and phenotypically heterogeneous and mainly caused by mutations in several genes including RYR1, TTN, MYH7 and SELENON4-6. Recessive mutations in either RYR1, encoding a protein involved in calcium homeostasis and excitation–contraction coupling (ECC) or SELENON (previously known as SEPN1), encoding the endoplasmic reticulum glycoprotein selenoprotein N, being the most common identifiable causes of multiminicore disease (MmD). Although recessive SELENON mutations are causative of MmD, the mechanism by which they alter muscle function is still unclear. Here, we extensively investigated skeletal muscle physiological, biochemical and epigenetic modifications in order to understand the pathomechanism of disease. Epigenetic changes including DNA methylation, histone modification and non coding RNA expression are now recognized as playing a major role in the pathophysiology of many human diseases including cancer, Rett, Prader-Willi, Angelmann syndromes, and many more. In the present investigation we found several modifications that are common between patients harbouring recessive RYR1 and SELENON mutations, including depletion of RYR1, ATP2B2, STAC3 and ATP2A1 transcripts, and increased levels of class II HDACs and DNA methyltransferases. Our findings provide insights to design new molecularly based strategies for drug targeting in patients with congenital myopathies characterized by reduced RyR1 protein content.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina HumanMethylation850 BeadChip.

first: Christoph

last: Bachmann

first: Francesco

last: Zorzato

first: Susan

last: Treves


title: Cockayne syndrome group B deficiency reduces H3K9me3 chromatin remodeler SETDB1 and exacerbates cellular aging

status: Public on Jun 22 2019

city: Baltimore

first: Jong-Hyuk

last: Lee

address: 251 Bayview BLVD

institute: National Institute of Health

summary: Cockayne syndrome (CS) is an accelerated aging disorder, caused by mutations in the CSA or CSB genes. In CSB-deficient cells, poly (ADP ribose) polymerase (PARP) is persistently activated by unrepaired DNA damage and PARP consumes and depletes cellular nicotinamide adenine dinucleotide (NAD), which leads to mitochondrial dysfunction. Here, the distribution of poly (ADP ribose) (PAR) was determined in CSB-deficient cells using ADPr-ChAP (ADP ribose-chromatin affinity purification), and the results show striking enrichment of PAR at transcription start sites (TSS), depletion of heterochromatin, and downregulation of H3K9me3-specific methyltransferases SUV39H1 and SETDB1. Induced-expression of SETDB1 in CSB-deficient cells downregulated PAR and normalized mitochondrial function. The results suggest that defects in CSB are strongly associated with loss of heterochromatin, downregulation of SETDB1, increased PAR in highly-transcribed regions, and mitochondrial dysfunction.

overall_design: H3K9me3 ChIP or ADPr-ChAP was performed from CSB-deficient (CS1AN) /control cells (CS1AN expressing wild type CSB) or doxycyclin-induced SETDB1 expressing CSB-deficient cells.

first: Tyler

last: Demarest

first: Mansi

last: Babbar

first: Edward

middle: W

last: Kim

first: Mustafa

middle: N

last: Okur

first: Supriyo

last: De

first: Deborah

last: Croteau

first: Vilhelm

last: Bohr


title: Extensive ChIP-seq analysis for VDR, pCREB, H3K4me1, H3K9ac, H3K36me3 from kidney, thyroparathyroid (TPTG), and peripheral blood monocytes (pBMCs) from wildtype (C57BL/6), M1-IKO, M21-IKO, VDR-KO, and Cyp27b1-KO mice.

status: Public on Jun 20 2019

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: ChIP-seq was performed in triplicate on isolated tissues (kidney, thyroparathyroid (TPTG), peripheral blood monocytes) from hormone treated (vehicle, 1,25(OH)2D3, FGF23, or PTH) mice from wildtype (WT), M1-IKO, M21-IKO, VDR-KO, or Cyp27b1-KO mice as indicated in the sample listings. The pBMC samples were isolated from untreated mice and subsequently treated ex vivo in cell culture with the indicated concentrations of 1,25(OH)2D3 or forskolin. Studies are published under PMID 28808057 and PMID 31053643.

first: Nancy

last: Benkusky

first: J

last: Pike


title: Balanced immunity to Lassa virus glycoprotein and nucleoprotein is associated with full protection of macaques after a single shot of different vaccines

city: Paris

first: James

last: Di Santo

address: 28 Rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: Lassa fever is a major threat in Western Africa. The large number of people living at risk for this disease calls for the development of a vaccine against Lassa virus (LASV). We compared the efficacy of measles-based and Mopeia-based vaccine platforms against LASV in cynomolgus monkeys. The vaccines were well tolerated and protected the animals from Lassa virus infection and disease after a single immunization but with different efficacy. Analyses of immune responses demonstrated that complete protection was associated with early and robust T-cell responses against LASV but not humoral responses nor neutralizing antibodies. Transcriptomic and proteomic analyses performed during the immunization phase confirmed the role of early innate immunity and T-cell priming in vaccine efficacy and showed specific profiles detectable as early as two days after immunization. The most efficient candidate, measles vector expressing simultaneously LASV glycoprotein and nucleoprotein, will be soon evaluated in phase I clinical trial.

overall_design: 3 vaccines, 5 time points (day 0, 2, 4, 9 and 14 after immunization), 4 replicates per condition

first: Sylvain

last: Baize

first: Natalia

last: Pietrosemoli


title: Spliceosomal disruption of the non-canonical BAF complex in cancer

status: Public on Jun 19 2019

city: Seattle

first: Guo-Liang

last: Chew

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary: SF3B1 is the most commonly mutated RNA splicing factor in cancer, but the mechanisms by which SF3B1 mutations promote malignancy are poorly understood. Here, we integrated pan-cancer RNA sequencing to identify mutant SF3B1-dependent aberrant splicing with a positive enrichment CRISPR screen to prioritize splicing alterations that functionally promote tumorigenesis. We identify that diverse, recurrent SF3B1 mutations converge on repression of BRD9, a core component of the recently described non-canonical BAF (ncBAF) complex. Mutant SF3B1 recognizes an aberrant deep intronic branchpoint within BRD9, thereby inducing inclusion of an endogenous retrovirus-derived poison exon and BRD9 mRNA degradation. BRD9 depletion causes loss of ncBAF at CTCF-bound loci and promotes melanomagenesis. We demonstrate that BRD9 is a potent tumor suppressor in uveal melanoma, such that correcting BRD9 mis-splicing in SF3B1-mutant cell lines and patient-derived melanoma xenografts with antisense oligonucleotides (ASOs) or by directly targeting its poison exon with CRISPR-directed mutagenesis profoundly suppresses tumor growth. Our results implicate disruption of ncBAF in the diverse malignancies characterized by SF3B1 mutations, identify a single aberrant splicing event which functionally contributes to the pathogenesis of SF3B1-mutant cancers, and suggest a mechanism-based therapeutic for these malignancies.

overall_design: Gene expression and chromatin association by components of the non-canonical BAF complex in different cancer cell lines (K562, MEL270) under genetic and chemical perturbations

first: Daichi

last: Inoue

first: Bo

last: Liu

first: Brittany

last: Michael

first: Joey

last: Pangallo

first: Drew

last: D’Avino

first: Khrystyna

last: North

first: Lillian

last: Bitner

first: Ariele

last: Block

first: Amanda

last: Moore

first: Stanley

first: Akihide

last: Yoshimi

first: Luisa

last: Escobar-Hoyos

first: Hana

last: Cho

first: Justin

last: Taylor

first: Sydney

middle: X

last: Lu

first: Yu

last: Chen

first: Cigall

last: Kadoch

first: Omar

last: Abdel-Wahab

first: Robert

middle: K

last: Bradley


title: ATAC sequencing and RNA sequencing of L4-L6 mouse Dorsal Root Ganglia upon dorsal column axotomy plus injection of the histone deacetylase inhibitor MS275

city: Miami

first: Matt

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary:
Purpose: compare the response of DRG neurons to a central axonal injury in presence of histone deacetylase inhibitor by measuring accessible chromatin and transcription
Results: we found that MS-275 was able to induce changes in chromatin accessibility and gene expression. In particular, an increased accessibility correlated with changes in gene expression, and a decreased accessibility correlated with gene downregulation

overall_design: Method: ATACseq and RNAseq from sciatic mouse L4-L6 DRG tissue 24 hours after the following treatments: a) spinal cord dorsal column axotomy (DCA) plus 12 mg/kg MS275 intraperitoneal injection b) spinal cord dorsal column axotomy (DCA) plus vehicle (3.2% Tween80, 20% PEG300, 4% DMSO) intraperitoneal injection. MS275 or vehicle were injected intraperitoneally at the time of the injury and 2 h before sacrifice. Pool of sciatic DRGs from 1 mouse was used for each ATACseq sample. Pool of sciatic DRGs from 2 mice were used for each RNAseq sample.DRG were collected and used fresh for ATAC-seq. DRG were collected in RNase later reagent, and crushed with RNase free micropestle for RNA extraction. Biological triplicates of each condition were generated.

first: Ilaria

last: Palmisano

first: Simone

last: Di Giovanni


title: H3K9ac, H3K27ac, H3K27me3 ChIP sequencing and ATAC sequencing of L4-L6 Dorsal Root Ganglia upon spinal or sciatic axonal injury

summary:
Purpose: compare the epigenetic response of DRG neurons to an axonal injury in the peripheral vs central nervous system by measuring accessible chromatin and several histone marks
Results: we found that after peripheral axonal injury there is a much greater number of epigenetic changes than after central spinal injury, and that these epigenetic changes after peripheral axotomy tended toward increased chromatin accessibility.

overall_design:
Method: ATACseq, H3K9ac, H3K27ac and H3K27me3 ChIP-seq from sciatic L4-L6 DRG tissue 24 hours after the following treatments: a) spinal cord dorsal column axotomy (DCA), b) laminectomy (Lam), c) sciatic nerve axotomy (SNA), and  d) sham sciatic nerve surgery (Sham). Pool of sciatic DRGs from 10 mice were used for each ChIPseq sample. Pool of sciatic DRGs from 1 mouse was used for each ATACseq sample. DRG were collected and flash frozen. Biological duplicates and input controls of each surgical paradigm were generated for each histone mark in the ChIPseq experiments. Biological triplicates of each condition were generated for the ATACseq experiments.

Please note that each processed data file was generated from each condition (i.e. replicates pooled together) and is available on the corresponding 'rep1' sample records.


title: Sufficiency analysis of estrogen responsive enhancers using synthetic activators

status: Public on Jun 26 2019

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

summary: Multiple regulatory regions bound by the same transcription factor have been shown to simultaneously control a single gene’s expression. However, it remains unclear how these regulatory regions combine to regulate transcription. Here we test the sufficiency of promoter-distal estrogen receptor α (ER)-binding sites (ERBS) for activating gene expression by recruiting synthetic activators in the absence of estrogens. Targeting either dCas9-VP16(10x) or dCas9-p300(core) to ERBS induces H3K27ac and activates nearby expression in a manner similar to an estrogen induction, with dCas9-VP16(10x) acting as a stronger activator. The sufficiency of individual ERBS is highly correlated with their necessity, indicating an inherent activation potential. By targeting ERBS combinations, we found that ERBS work independently to control gene expression. The sufficiency results contrast necessity assays that show synergy between these ERBS, suggesting that synergy occurs between ERBS in terms of activator recruitment, whereas directly recruiting activators leads to independent effects on gene expression.

overall_design: ChIP-seq to analyze binding of synthetic transcription factors as well as changes in H3K27ac

first: Matthew

last: Ginley-Hidinger


title: A new arsenal for deciphering waterlogging/drainage  responses: 195 dense time-series RNA-seq dataset from sesame

city: Wuhan

first: Jun

last: You

address: Xudong 2nd Road

institute: Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences

summary: In this study, we reported the RNA-seq profiling of two contrasting genotypes under waterlogging and recovery.

overall_design: The plants were grown in pots and subjected to waterlogging treatment at the flowering stage for 36 h and subsequently, 12 h drainage. Root samples were collected in triplicate at 22 time points under waterlogging/drainage treatments and at 10 time points in the control condition.

first: Xiurong

last: Zhang


title: Immature low-density neutrophils exhibit metabolic flexibility that facilitates breast cancer liver metastasis

city: Montréal

first: Brian

last: Hsu

state: QC

address: 1160 Pine Avenue West

department: Medicine

institute: McGill University

summary: Neutrophils play a key role in the control of metastatic progression. Neutrophils are phenotypically heterogeneous and can exert either anti- or pro-metastatic functions. Here, we demonstrate that tumor cells capable of forming liver metastases induce an accumulation of neutrophils in the peripheral blood and liver parenchyma. Cancer cell-derived G-CSF, in concert with other factors, mobilizes immature low-density neutrophils that promote liver metastasis. In contrast, mature high-density neutrophils inhibit the formation of liver metastases. Transcriptomic and metabolomic analyses of high- and low- density neutrophils reveal engagement of numerous metabolic pathways specifically in low-density neutrophils. Low-density neutrophils exhibit enhanced global bioenergetic capacity, through their ability to engage mitochondrial-dependent ATP production, and remain capable of executing pro-metastatic neutrophil functions, including NETosis, under nutrient-deprived conditions. Together, these data reveal that distinct pro-metastatic neutrophil populations exhibit a high degree of metabolic flexibility, which facilitates metastatic progression and the formation of liver metastases.

overall_design: 4 samples of Naïve neutrophils (bone marrow), 4 samples HDNs (from peripheral blood of liver metastasis bearing mice), 4 samples LDNs (from peripheral blood of liver metastasis bearing mice)

first: Peter

last: Siegel


title: Single-cell transcriptomics of the embryonic mouse pancreas

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Single Cell Discoveries

summary: Data accompaning to van Gurp et al. Development 2019. single-cell sequencing of the developing mouse pancreas followed by Seurat analysis to discover genes important for alpha and beta cell differentiation.

overall_design: Single-cells from mouse embryonic pancreas at E12.5, E13.5, E14.5, E15.5 and E18.5 were isolated and enriched for MIP-GFP and sorted into 384-well plates. Afterwards, SORT-seq was performed and single-cell transcriptomics profiles were obtained.

first: Leon

last: van Gurp

middle: J

first: Alexander

last: van Oudenaarden

first: Eelco

last: de Koning


title: Inferring dynamic regulatory programs in non-stationary expression time courses with applications to early human neural development

status: Public on Jun 25 2019

first: Randolph

middle: Scott

last: Ashton

address: 330 N. Orchard Street

department: Biomedical Engineering

institute: University of Wisconsin Madison

summary: We generated RNA-seq data to measure transcriptional profiles of twenty hPSC-derived NSC populations, representing distinct regions of the developing human hindbrain and rostral cervical spinal cord. These cells are differentiated using a protocol that induces collinear activation of region-specific HOX genes during exposure to FGF8 and Wnt signaling (Lippmann et al, 2015 PMID:25843047). By transitioning to media containing retinoic acid after varying durations of Wnt signaling, NSCs are generated with unique rostrocaudal identities that uniformly express the neuroectodermal marker Pax6 and form N-cadherin+ rosette structures in vitro.

overall_design: The data consist of RNA-seq measurements taken from hPSC-derived NSCs that were exposed to CHIR99021 for differents amount of time (2-72hr) prior to retinoic acid treatment. Each time point is represented in triplicate, with the exception of 48 hours, for which one replicate (48_B1) was filtered due to excessive zero-count genes.

first: Ethan

last: Lippmann

last: McIntosh

first: Mitchell

last: Probasco

first: Peng

last: Jiang

first: Scott

last: Swanson

first: Ron

last: Stewart

first: James

last: Thomson

middle: S


title: Transcriptional profile analysis of uninfected or VSV-infected scrambled siRNA (siControl) and DDX23 knockdown (siDDX23) A549 cells

status: Public on Jun 18 2019

city: Guangzhou

first: Shaochun

last: Yuan

address: 132 Waihuan East Road

institute: Sun yat-sen university

summary: DExD/H-box helicases play essential roles in RNA metabolism, and emerging data suggest that they have additional functions in antiviral immunity across species. However, little is known about this evolutionarily conserved family in antiviral responses in lower species. Here, by isolation of poly(I:C)-binding proteins in amphioxus, an extant basal chordate, we found that DExD/H-box helicases DHX9, DHX15 and DDX23 to be responsible for cytoplasmic dsRNA detection in amphioxus. Since the antiviral roles of DDX23 have not been characterized in mammals, we performed further poly(I:C) pull down assays and found human DDX23 bind to LMW poly(I:C) through its N-terminal region, suggesting that DDX23 is an evolutionarily conserved dsRNA sensor. Knockdown of human DDX23 enhanced replication of VSV and reduced activation of the NF-κB and IRF3. Moreover, when stimulated with poly(I:C) or VSV, human DDX23 translocated from nucleus to cytoplasm and formed complexes with TRIF or MAVS to initiate downstream signaling. Collectively, this comparative immunological study not only defined DDX23 as an emerging nuclear pattern recognition receptor (PRR) for innate sensing of RNA virus, but also extended the essential role of the DExD/H helicase family in viral RNA sensing from mammals to basal chordate.

overall_design: The RNA sequencing studies were performed with A549 cells transfected with scrambled siRNA (siControl ) or siDDX23 targeting DDX23 gene for three days following 12 hours infection with VSV (MOI=3) or uninfected. Total RNA was isolated using TRIZOL Reagent (Invitrogen). cDNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and then sequenced with HiSeq 2000 system (Illumina Inc.). The expression of transcripts was quantified as reads per kilobase of exon model per million mapped reads (RPKM). Subsequently, gene enrichment analysis was conducted using the DAVID tool.

first: Jie

last: Ruan


title: circRNA expression profiles for Human colorectal carcinoma and adjacent normal tissues

status: Public on Jun 01 2019

first: Ri-Xin

last: Chen

state: Guangdong

address: No. 106, Zhongshan Er Road

institute: Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences

summary: We have employed circRNA microarray expression profiling as a discovery platform to identify the dysregulated circRNAs in CRC.

overall_design: Human colorectal carcinoma and adjacent normal tissues were collected and circRNA microarray were applied.

first: Rixin


title: Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs

status: Public on Jun 15 2019

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main Street

department: Biology

institute: Whitehead Institute for Biomedical Research

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

overall_design: Refer to individual Series


title: Analysis of gene expression changes in MLL-rearranged leukaemia cell lines with induced resistance against CCI-006

city: Randwick

first: Klaartje

last: Somers

address: High Street gate 9

country: Australia

institute: Children's Cancer Institute, Lowy Cancer Research Centre, UNSW

summary: Gene expression analysis of two MLL-r leukaemia cell lines (SM6p2 and SM6p3) and the parental PER-485 MLL-rearranged leukaemia cell line they were derived from by continuous culturing in CCI-006. SM6p2 and SM6p3 thereby developed induced resistance against the compound. The aim of this experiment was to identify any gene expression changes in SM6p2 and SM6p3 cells induced by continuous culturing in CCI-006, thereby potentially providing insight into the mechanisms of primary and induced resistance of MLL-rearranged leukaemia cell lines against the cytotoxic compound CCI-006.

overall_design: RNA was isolated from untreated PER-485, SM6p2 and SM6p3 cells while in exponential growth phase.

first: Daria

last: Chudakova

first: Victoria

last: Wen

first: Bing

last: Liu

first: Michelle

last: Henderson

first: Chelsea

last: Mayoh


title: Analysis of changes in gene expression upon CCI-006 treatment and resistance development of the MLL-rearranged leukaemia cell line PER-485


title: Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33

city: Beijing

first: Bofeng

address: Haidian District

department: School of Life Science

institute: Tsinghua University

summary: The epigenome of a cell is established and maintained by chromatin modifiers and remodelers, which are recruited to the chromatin by specific transcription factors. In this report, we show that nodal cross-talks with the epigenome through TRIM33-H3K18ac to mediate mesendodermal genes expression. The chromatin accessibility at mesendodermal genes depends on TRIM33. Moreover, histone acetylation is essential for TRIM33 recruitment to many nodal target genes involved in mesendodermal differentiation. The distribution pattern of the H3K18ac mark changes from foci to expanded domains at the mesendodermal genes promoter during embryonic stem cells (ESCs) differentiation to embryoid bodies (EBs). This could be the cue to facilitate TRIM33 colocalized with Smad2/3 at chromatin in EBs but not in ESCs. TRIM33 interacts with the H3K18ac “writer” p300 dependent on nodal signaling, providing a positive feedback to promote activation of mesendodermal genes and association with HDAC1 plays a negative role in activation of mesendodermal genes.

overall_design: ESCs were cultured on gelatin coated plates with 15% serum ESC culture medium  and d2.5 EBs were cultured on bacteria plates without gelatin with 15% serum ESC culture medium withdrawl LIF. TRIM33 WT or KO ESCs and d2.5 EBs were harvested for ATAC-seq; TRIM33 WT or KO d2.5 EBs treated with activin A (50 ng/ml, R&D Systems) for 2hs or SB431542 (10 μM, TOCRIS) for 1h were harvested for RNA-seq and TRIM33 WT ESCs were harvested for RNA-SEQ.E14 ESCs were harvested for H3K18ac ChIP-seq, E 14 d2.5 EBs treated with activin A (50 ng/ml, R&D Systems) for 2hs or SB431542 (10 μM, TOCRIS) for 1h were harvested for H3K18ac ChIP-seq and H3K27ac ChIP-seq.

first: Maoguo

last: Luo

first: Wei

last: Xie

first: Qianran

last: Xi


title: Massively parallel splicing reporter assay on designed sequence libraries

status: Public on Jun 03 2019

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

institute: University of Haifa

summary: We designed 4 oligonucleotide libraries containing either a retained intron, a cassette exon, tandem 5' or tandem 3' splice sites, cloned them into dedicated reporter constructs, transfected and integrated these constructs in the genome of K562 cells, and performed targeted RNA sequencing to determine RNA splicing ratios and a FACSseq approach to determine protein isoform ratios.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Massively parallel reporter assay for alternative splicing

first: Eran

last: Segal


title: Comparative transcriptomics between species to assess the immune mechanisms underlying the increased reactogenicity of the four component meningococcal capsular group B vaccine when given concomitantly with routinely-administered vaccines

status: Public on Jun 06 2019

city: Oxford

first: Dylan

last: Sheerin

address: Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital

department: Paediatrics

country: United Kingdom

institute: University of Oxford

summary: Whole blood RNA-seq and single cell RNA-seq on neutrophils was leveraged to explore gene expression changes induced in mice 24 hours after immunisation with a second dose of a licensed vaccine against capsular group B, meningococcus, the same vaccine in combination with routinely-administered vaccines, routine vaccines on their own, or a PBS control immunisation.

overall_design: mRNA was profiled from RNA extracted from mouse neutrophils or whole blood, 6 samples per group (neutrophils pool from each sample to yield one sample per group for single cell sequencing) , using an Illumina HiSeq4000 or NovaSeq, respectively.


title: Hepatic arginase deficiency fosters dysmyelination during postnatal CNS development

city: Los Angeles

first: Gerald

last: Lipshutz

state: CA

address: 650 CE Young Drive, Box 957054, UCLA School of Medicine

department: Surgery

institute: UCLA

summary:
Deficiency of arginase is associated with hyperargininemia, and unlike the other disorders of the urea cycle, the major mechanism of metabolism of nitrogen in terrestrial mammals, are characteristic and prominent features that include spastic diplegia/tetraplegia, clonus, and hyperreflexia; loss of ambulation, intellectual disability and progressive neurological decline are other signs. To gain greater insight into the unique neuromotor features, we performed gene expression profiling of the motor cortex of a well-characterized murine model of the disorder. Co-expression network analysis suggested an abnormality with myelination, which was supported by limited existing human data. Utilizing electron microscopy, marked dysmyelination was detected in 2-week-old homozygous ARG1 knockout mice. The corticospinal tract was found to be adversely affected, supporting dysmyelination as the cause of the unique neuromuscular features and implicating oligodendrocyte impairment in a deficiency of hepatic ARG1. Following neonatal hepatic gene therapy to express ARG1, the subcortical white matter, pyramidal tract, and corticospinal tract all showed a remarkable recovery in terms of myelinated axon density and ultrastructural integrity with active wrapping of axons by nearby oligodendrocyte processes.
These findings support the following conclusions: first, arginase deficiency is a leukodystrophy affecting the brain and spinal cord while sparing the peripheral nervous system; and second, neonatal AAV hepatic gene therapy can rescue the defects associated with myelinated axons, strongly implicating the functional recovery of oligodendrocytes after restoration of hepatic arginase activity. These findings support the consideration of early restoration of hepatic arginase activity in those afflicted with arginase deficiency.

overall_design: 6 samples for each genotype - Arg1 knock out (KO), virally treated Arg1 KO (TR), Arg1 heterozygous (HE), and wild type (WT). 24 samples total.

first: Jillian

last: Haney


title: Gene expression analysis of a MLL-rearranged leukaemia cell line, PER-485, treated with small molecule CCI-006.

summary: A phenotypic cell-based high-throughput screen identified a novel small molecule, CCI-006 with selective cytotoxic activity against MLL-rearranged leukaemia cell lines. The aim of this experiment was to identify the mechanism of action of CCI-006 by investigating the gene expression changes induced in a MLL-rearranged leukaemia cell line following a short incubation with the compound.

overall_design: RNA was isolated from PER-485 cells treated with 5 μM CCI-006 or DMSO for 3 hours


title: ATAC-seq of BCSCsSETD4 and BCSCsGFP

status: Public on May 22 2019

city: Hangzhou

first: sen

last: ye

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

institute: Zhejiang University

summary: We report the ATAC-SEQ results of BCSCsSETD4 and BCSCsGFP. To explore epigenetic regulation mechnism in BCSC quiescence, Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) were performed in BCSCsSETD4 and BCSCsGFP. Quiescent BCSCsSETD4 showed marked enrichment of H4K20me3 modifications relative to BCSCsGFP.

overall_design: Examination of the chromatin structure using ATAC-seq in BCSCsSETD4 and BCSCsGFP.

first: Ye

last: Sen

first: Ding

last: Yan-Fu

first: Jia

last: Wen-Huan

first: Feng

last: Jing-Yi

first: Zhu

last: Qian

first: Liu

last: Xiao-Li

first: Cai

last: Sun-Li

first: Huang

last: Xue-Ting

first: Yang

last: Yao-Shun

first: Lu

last: Qian-Yun

last: Jin-Shu

last: Sheng-Nan

last: Guo-Ping

first: Wang

last: Yue-Hong

first: Zhou

last: Jiao-Jiao

first: Chen

last: Yi-Ding

last: Wei-Jun


title: Axiom Genome-Wide Chicken Array of Broiler Chickens

status: Public on May 25 2019

city: Newark

first: Behnam

last: Abasht

state: DE

address: 531 South College Avenue

department: Animal and Food Sciences

institute: University of Delaware

summary:
DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals.
The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).

overall_design: Commercial broiler chickens (all males) from a cross (BCD) between three commercial broiler pure lines were sampled at 29 days of age from the field in the Delmarva region of the United States and transferred into individual cages for feed efficiency measurement. Line B and C chickens were all males from a high breast meat yield purebred line of broiler breeder chickens raised on the floor, in pens of 300, by Heritage Breeders in the Delmarva region of the United States.

last: Abast


title: Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle

status: Public on May 29 2019

city: Adelaide

first: Thazin

middle: Nwe

last: Aung

state: South Australia

address: Frome

institute: University of Adelaide

summary: We have used computational and experimental biology approaches to identify candidate mechanisms of action of a traditional Chinese medicine; Compound Kushen Injection (CKI), in a breast cancer cell line in which CKI has been shown to cause apoptosis. Because CKI is a complex mixture of plant secondary metabolites, we used a high-performance liquid chromatography (HPLC) fractionation and reconstitution approach to define chemical fractions required for CKI to induce apoptosis in MDA-MB-231 cells. Our initial fractionation separated major from minor compounds, and showed that the major compounds accounted for little of the activity of CKI. By systematically perturbing the major compounds in CKI we found that removal of no single major compound could alter the effect of CKI on cell viability and apoptosis. However, simultaneous removal of two major compounds identified oxymatrine and oxysophocarpine as critical compounds with respect to CKI activity. We then used RNA sequencing and transcriptome analysis to correlate compound removal with gene expression and phenotype data. We determined that many compounds in CKI are required for its effectiveness in triggering apoptosis but that significant modulation of its activity is conferred by a small number of compounds. In conclusion, CKI may be typical of many plant based extracts that contain many compounds in that no single compound is responsible for all of the bioactivity of the mixture and that many compounds interact in a complex fashion to influence a network containing many targets.

overall_design: High-depth paired-end RNA-seq from MDA-MB-231 cell line. Each sample contains 3 biological replicates. N_2(where N represents the total number of compounds in CKI, N_2 represents removal of Omt and Ospc from CKI which is N-OmtOspc), N_3 represents removal of Mac, Omt and Ospc from CKI (hence N-MacOmtOspc), OO represents two compounds only: Omt and Ospc, MOO represents three compounds only: Mac, Omt and Ospc, N_Mac represents removal of Mac from CKI (hence N-Mac), N_Nme represents removal of Nme from CKI, N_Omt represents removal of Omt from CKI, and N_Tri represents removal of Tri from CKI. See the manuscript doi: https://doi.org/10.1101/462135 for more details.

first: David

last: Adelson


title: CeRNA Expression Profiling Identifies KIT Related circRNAs-miRNA-mRNA Networks in Gastro-intestinal Stromal Tumors

status: Public on May 21 2019

city: hefei

first: ning

last: jia

address: No.81 meishan road, shushan district

institute: Anhui medical university

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

summary: Gastrointestinal stromal tumors (GISTs) are the most common human sarcomas and typically locate in the stomach or small  intestine. circular RNAs (circRNAs) were identified to plays vital roles in tumor oncogenesis and progression. To investigate the involvement of differentially expressing genes and circRNAs in GIST , transcriptomic analyses of differential expression genes and circRNAs were performed for discrimination of GISTs from normal tissues. The RNA samples were extracted from three GIST samples and three adjacent mucosa for microarray profiling and performed in Agilent-078298 human ceRNA array for gene and circRNAs expression profiling analysis. On average, we detected expression of 17,000 transcripts.Under the criteria fold change > 2 or < 0.5, we obtained a total of 5770 circRNAs and 1815 mRNAs were differentially expressed in GISTs. Hierarchy cluster analysis also indicated that the 6 samples were distributed into two clusters, 3 GIST samples in one cluster and 3 normal samples in another cluster. Then,qRT-PCR validation of the DEGs in GIST tissue and adjacent tissues.The results revealed that grouping was reasonable and the data can be directly applied to further analysis.

overall_design: 3 gastrointestinal stromal Tumors and adjacent tissues

first: Jin

last: Wang

first: Hanxing

last: Tong


title: IL-6 mediated transcriptional programming of CD4+ T cells in early rheumatoid arthritis

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

institute: Newcastle University

summary: We hypothesised that sustained exposure of naïve CD4+ T cells to IL-6 might imprint them with a distinct transcriptional programme, whose molecular and functional consequences following subsequent TCR ligation was relevant to disease development. Preexposure of healthy naïve CD4+ T-cells to pathophysiological levels of the cytokine caused induction of STAT3 target genes known to discriminate RA patients from disease controls in the clinic. After TCR stimulation IL-6 pre-exposed cells exhibited enhanced proliferative capacity, activation and a propensity towards Th1 differentiation, compared to non-exposed cells.

overall_design: Naïve or memory CD4+ T-cells were isolated from 3 healthy donors and cultured with 0.5ng/ml IL-6 and equimolar sIL-6R for 72 hours prior to washing and stimulation with 0.2μg/ml anti-CD3 and 1μg/ml for 6 days.  anti-CD28 for 4 hours. RNA was extracted for global gene expression analysis at baseline (t0), after 6 hours or 72 hours exposure to IL-6 (t1,t2) and 4 hours post-TCR stimulation (t3)

first: Laura

last: Ridgley

first: Nicola

last: Maney

first: Amy

middle: E

last: Anderson

first: Najib

last: Naamane

first: Andrew

last: Skelton

first: Catherine

last: Lawson

first: Paul

last: Emery

first: John

middle: D

last: Isaacs

first: Ruaidhri

last: Carmody

middle: G


title: Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component.

status: Public on May 30 2019

first: Dylan

last: Sheerin

summary: Whole blood RNA-seq was leveraged to explore gene expression changes induced in mice 24 hours after immunisation with a second dose of a licensed vaccine against capsular group B meningococcus, one of the vaccines components, or one of several comparator groups.

overall_design: mRNA was profiled from RNA extracted from mouse whole blood, 5-6 samples per group, using an Illumina HiSeq4000


title: Effects of Meflin(islr) depletion on the global gene expression profiles in mouse MSCs

status: Public on May 15 2019

city: Nagoya

first: Yasuyuki

last: Mizutani

state: Aichi

address: showa-ku, turumai-cho, 65

department: Gastroenterology

country: Japan

institute: Nagoya University Graduate School of Medicine

summary: Comparison of global gene expression profilles between control and Meflin(islr)-depleted mouse MSCs

overall_design: Three different target sequences used for shRNA-mediated knockdown of mouse Meflin(islr). These Meflin(islr) shRNAs were transduced to primary cultured mouse MSCs by a retroviral expression system

first: Atsushi

last: Enomoto


title: ChIP-seq analysis of adult human kidney cortex

status: Public on May 03 2019

city: Madison

first: Mark

last: Meyer

address: 1415 Linden Dr.

institute: University of Wisconsin-Madison

summary:
Human kidney was obtained from the University of Wisconsin Madison Organ Procurement Program from a deceased 69 year old female patient and the cortex was dissected from 3 different cortex locations.

Associated publication abstract:

Targeted genomic deletions identify diverse enhancer functions and generate a kidney-specific, endocrine-deficient Cyp27b1 pseudo-null mouse

Vitamin D3 is terminally bioactivated in the kidney to 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) via cytochrome P450 family 27 subfamily B member 1 (CYP27B1), whose gene is regulated by parathyroid hormone (PTH), fibroblast growth factor 23 (FGF23), and 1,25(OH)2D3. Our recent genomic studies in the mouse have revealed a complex kidney-specific enhancer module within the introns of adjacent methyltransferase like 1 (Mettl1) and Mettl21b that mediate basal and PTH induced expression of Cyp27b1 and FGF23- and 1,25(OH)2D3-mediated repression. Gross deletion of these segments in mice has severe consequences on Cyp27b1 regulation and skeletal phenotype, but does not affect Cyp27b1 expression in non-renal target cells (NRTCs). Here, we report a bimodal activity in the Mettl1 intronic enhancer with components responsible for PTH-mediated Cyp27b1 induction and 1,25(OH)2D3-mediated repression and additional activities, including FGF23 repression, within the Mettl21b enhancers. Deletion of both submodules eliminated basal Cyp27b1 expression and regulation in the kidney, leading to systemic and skeletal phenotypes similar to those of Cyp27b1-null mice. However, basal expression and lipopolysaccharide-induced regulation of Cyp27b1 in NRTCs was unperturbed. Importantly, dietary normalization of calcium, phosphate, PTH, and FGF23 rescued the skeletal phenotype of this mutant mouse, creating an ideal in vivo model to study non-renal 1,25(OH)2D3 production in health and disease. Finally, we confirmed a conserved chromatin landscape in human kidney that is similar to that in mouse. These findings define a finely balanced homeostatic mechanism involving PTH and FGF23 together with protection from 1,25(OH)2D3 toxicity that is responsible for both adaptive vitamin D metabolism and mineral regulation.

overall_design: For the ChIP-seq, 3 different dissections of cortex were taken and analyzed in triplicate for VDR, pCREB, H3K4me1, and H3K27ac.

first: J

last: Pike


title: Unravelling of the novel melanin biosynthesis-signalling networks in Cryptococcus neoformans

city: Seoul

first: Kyung-Tae

last: Lee

address: Yonsei-ro 50, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: Melanin is an antioxidant polyphenol pigment, which is required for the pathogenicity of many human and plant fungal pathogens. Nevertheless, its comprehensive regulatory mechanism still remain elusive. In this study, we systematically analyzed melanin-regulating signaling pathways in Cryptococcus neoformans. Here we identified four core melanin-regulating TFs, Bzp4, Usv101, Mbs1, and Hob1, which are required for induction of the laccase gene (LAC1). Bzp4, Usv101 and Mbs1 independently regulate LAC1 induction while Hob1 controls Bzp4 and Usv101 expression. Both Bzp4 and Usv101 are translocated from the cytoplasm into the nucleus upon nutrient starved condition, while Mbs1 is constitutively localized in the nucleus. Notably, the cAMP pathway is not involved in regulation of the four TFs, while the HOG pathway negatively regulates induction of BZP4 and LAC1. As potential kinases upstream of the core TFs, we identified the nine core kinases, whose deletion leads to defective melanin production and LAC1 induction. Deletion of GSK3 or KIC1 abolishes induction of LAC1 and BZP4, and also perturbs nuclear translocation of Bzp4. Notably, Gsk3 also regulates the expression of HOB1, USV101, and MBS1, indicating that it is a critical melanin-regulating kinase. Finally, the RNA-sequencing based transcriptome analysis of the wild-type and bzp4Δ, usv101Δ, hob1Δ, and mbs1Δ strains under nutrient rich and starved conditions reveals that the core melanin-regulating TFs govern redundant and distinct classes of genes, which are involved in a variety of biological processes.

overall_design: SET1 (WT and bzp4Δ mutant) and SET2 (WT and hob1, mbs1, usv101 mutants) strains were inoculated into 50 ml of YPD liquid medium and cultured overnight at 30°C in a shaking incubator. Cells were subcultured in 80 ml fresh YPD medium until OD600 indicated 0.6 to 0.8. 40 ml of the culture was placed in a liquid nitrogen tank as a basal sample (nutrient-rich samples) and remaining 40 ml was spun down, washed three times with phosphate-buffered saline, and resuspended in 40 ml of YNB medium containing ammonium sulfate without glucose. After resuspension, cells were further incubated at 30°C in a shaking incubator for 2 h (nutrient-starved samples). Incubated cells were spun down, frozen in liquid nitrogen and lyophilized overnight to extract the total RNA. R1, R2, R3 indicated the biological replicates.

first: Dongpil

first: Yong-Sun

last: Bahn


title: TNF induces Glucocorticoid Resistance by reshaping the GR Nuclear Cofactor Profile: Investigation of TNF mediated effects on the GR mediated gene expression

status: Public on May 06 2019

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Glucocorticoid resistance (GCR) is defined as an unresponsiveness to the anti-inflammatory properties of glucocorticoids (GCs) and their receptor, the glucocorticoid receptor (GR). It is a serious problem in the management of inflammatory diseases and occurs frequently. The strong pro-inflammatory cytokine TNF induces an acute form of GCR, not only in mice, but also in several cell lines, e.g. in the hepatoma cell line BWTG3, as evidenced by impaired Dexamethasone (Dex)-induced GR-dependent gene expression. We report that TNF has a significant and broad impact on the transcriptional performance of GR, but no impact on nuclear translocation, dimerization or DNA binding capacity of GR. Proteome-wide proximity-mapping (BioID), however, revealed that the GR interactome is strongly modulated by TNF. One GR cofactor that interacts significantly less with the receptor under GCR conditions is p300. NFκB activation and p300 knockdown both reduce transcriptional output of GR, whereas p300 overexpression and NFκB inhibition revert TNF-induced GCR, which is in support of a cofactor reshuffle model. This hypothesis is supported by FRET studies. This mechanism of GCR opens new avenues for therapeutic interventions in GCR diseases

overall_design: Examination of GR induced gene expression in 4 conditions (1 control: NI and 3 treated: DEX, TNF, TNFDEX) starting from 3 biological replicates

first: Karen

last: Dendoncker

first: Jolien

last: Vandewalle

first: Melanie

last: Eggermont

first: Joanna

last: Lempiäinen

first: Evelien

last: Van Hamme

first: Sylviane

last: Dewaele

first: Sofie

last: Vandevyver

first: Marlies

last: Ballegeer

last: Souffriau

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Tineke

last: Vanderhaeghen

first: Rudi

last: Beyaert

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Marc

last: Van Montagu

first: Claude

last: Libert


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Smad7-/- E15.5 tooth germ Transcriptomes

status: Public on May 08 2019

city: New Orleans

first: Yiping

last: Chen

state: LA

address: 6400 Freret

department: CMB

institute: Tulane University

summary: Smad7 is known to regulate both Smad-dependent and Smad-independent TGF-β signaling pathways but is also extensively involved in crosstalks with other signaling pathways. To investigate the underlying molecular mechanism, we conducted RNA-Seq analysis on E15.5 molars from Smad7 mutant and control mice.

overall_design: Tooth germ mRNA profiles of E15.5 wild type (WT) and Smad7-/- mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 550.

first: Zhi

last: Liu

first: Tian


title: R-spondin 3 regulates stem cell plasticity and recovery of damaged colon epithelium

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: The gastrointestinal epithelial crypts are clonal units with a high cell turnover, driven by a small population of long-lived, Lgr5-expressing stem cells located in the crypt base. Despite this, depletion of Lgr5+ cells does not lead to severe pathology. Instead, other cell populations, such as secretory and enterocyte precursors are able to de-differentiate, replace Lgr5+ cells, and regenerate the crypt. However, the signals that regulate this epithelial plasticity are not well understood. Here we illuminate the hierarchical organization and regulation of stem cell plasticity in the colonic crypt. Using in vivo lineage tracing, we find that the classic Wnt target gene Axin2 is expressed in colonic Lgr5+ cells and adjacent Lgr5-negative cells that give rise to entire crypts upon Lgr5+ cell depletion. The identity of Lgr5+ cells is controlled by by R-spondin 3 (Rspo3) produced by myofibroblasts and the recovery of Lgr5+ cells upon depletion required functional Rspo3 signaling. In contrast, expression of Axin2 and the reserve stem cell function of Axin2+ cells is not dependent on Rspo3. Accordingly, upon knockout of Rspo3, Lgr5-negative Axin2+ cells are able to compensate the loss of the Lgr5+ cell compartment and maintain epithelial integrity. In contrast, Rspo3 is essential for maintaining epithelial integrity in the context of injury of the entire Axin2+ cell pool, as observed in the context of DSS colitis. We demonstrate that DSS induces a progressive loss of the Lgr5+ stem cells as well as Axin2+ Lgr5-negative reserve stem cell compartment. While Rspo3 deficient animals are unable to withstand this injury, in Rspo3 competent animals, crypt homeostasis and regeneration are fueled by the remaining Axin2-negative, differentiated cells. These cells can be reprogrammed by Rspo3 to proliferate and act as stem cells. Thus, we identity Rspo3 as a major regulator of the Lgr5 stem cell signature. While loss of this signature can be compensated by Rspo3-independent reserve stem cells under healthy conditions, it is essential for re-establishment of epithelial integrity upon crypt injury.

overall_design:
Tamoxifen (Sigma) was injected intraperitoneally into mice either as single dose or on three consecutive days (4 mg/25 g bodyweight, diluted in 200 µl corn oil) at the indicated time points to deplete Rspo3 expression.
C57BL/6 Axin2CreErt2/Rosa26-tdTomato cells were sorted using the BD FACSAria II.  Cells were sorted for tdTomato, DAPI and ESA expression.  Td Tomato was used as positive marker for Axin2 expressing cells.
Microarray experiments were performed as dual-color hybridizations on Agilent whole mouse catalog 4x44K (Agilent-014868) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Christine

last: Harnack

first: Hilmar

last: Berger

first: Thomas

last: Meyer

first: Michael

last: Sigal


title: Chromatin-informed inference of transcriptional programs in gynecologic cancers [RNA-Seq]

status: Public on May 01 2019

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

summary: RNA-seq of MDA-MB-436 cells  in control cells (shRen) and upon knockdown of MITF ( shQa, sh962) were generated by deep sequencing in duplicates

overall_design: 6 samples, 2 replicates

first: Osmanbeyoglu

last: Hatice

first: Leslie

last: Christina


title: Effects of a food grade, phenol-enriched maple syrup extract on hippocampus and hepatic tissue from diet-induced obese C57BL/6 mice.

city: Kingston

first: Marisa

last: Pfohl

state: RI

address: Pharmacy Building, 7 Greenhouse Road

department: BPS

institute: University of Rhode Island

summary:
Introduction: Diet-induced obesity is associated with hepatic lipid accumulation, increased circulating levels of endotoxin, and chronic low grade inflammation. Hepatic lipid accumulation and resulting non-alcoholic fatty liver disease (NAFLD) can exacerbate systemic inflammation further contributing to neurodegenerative effects. Maple Syrup Extract (MSX), could be a potential source of beneficial phytonutrients capable of mitigating these adverse inflammatory processes from occurring.  Methods: A pilot scale diet-induced obesity study with male C57BL/6 mice fed either a standard diet (10% kcal from fat) or a high fat diet (45% kcal from fat) with or without MSX at a dose of 0.5% w/w incorporated into feed for 12 weeks. Livers and whole hippocampi were excised for multiplex gene expression analysis of inflammatory, fatty liver, and neurodegenerative disease associated genes. Livers were scored for lipid accumulation and lipid moieties were quantified.
Results: In hepatic tissue, MSX protected against lipid accumulation and inflammatory progression. MSX supplementation significantly reduced lipid accumulation scores as well as gene expression of lipid uptake, storage, and inflammatory associated genes.  In the hippocampus, MSX supplementation in HFD feed significantly reduced the gene expression of pro-inflammatory, death receptor ligands, anti-oxidant response enzymes, macrophage receptors, and leptin receptor.  Conclusions: In the liver, MSX prevents gross hepatic lipid accumulation and suppresses both pro-inflammatory and lipid storage associated genes. In the hippocampus, MSX may act on pro-inflammatory gene expression but TNF mediated death receptor pathways in addition to modulating leptin receptor signaling.

overall_design: We analyzed a total of 12 samples, using 3 biological replicates per treatment group. Relative gene expression was compared between the low fat diet (LFD) controls, high fat diet (HFD) controls, low fat-MSX (L-MSX), and high fat-MSX (H-MSX) treatment groups.

first: Christoph

last: Schorl


title: Regulation of yeast chromosome III architecture and mating-type switching by a Sir2/condensin-bound region of the recombination enhancer [HiC-Seq]

status: Public on May 23 2019

city: New York

first: Ryan

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

summary: Saccharomyces cerevisiae switches its mating type (MATa or MATalpha) through gene conversion using one of two possible donors, HMLalpha or HMRa, both of which are maintained by the SIR silencing complex as heterochromatic cassettes on opposing ends of chromosome III. In MATa cells, HMLalpha on the left arm is preferentially chosen as the donor through a mechanism requiring a cis-acting sequence called the recombination enhancer (RE). The left half of the RE is required for this donor preference activity, whereas the right half has been implicated in regulating chromosome III structure. In this study we have identified a MATa-specific Sir2 and condensin binding site within the right half of the RE that maintains chromosome III in a switching-competent conformation by preventing MATa from interacting with the default HMRa donor on the right arm. Within the RE, Sir2 strongly represses transcription of a small MATa-specific gene of unknown function (RDT1). Upon expression of HO endonuclease to induce the switching process, Sir2 redistributes from the RE to the double-stranded DNA break site at MATa, thus derepressing RDT1 transcription to coincide with the timing of mating-type switching. Condensin is also displaced from the RE in response to the HO-induced break, likely contributing to the transient change in chromosome III conformation required for effective switching without disruption of HML and HMR heterochromatin.

overall_design: S. cerevisiae HiC data for WT, SIR2Δ, and a 100bpΔ of RDT1 promoter region strains.

first: Mingguang

last: Li

first: Manikarna

last: Dinda

first: Stefan

last: Bekiranov

first: Jeffrey

last: Smith


title: Regulation of yeast chromosome III architecture and mating-type switching by a Sir2/condensin-bound region of the recombination enhancer [ChIP-Seq]

overall_design: Biological Duplicate ChIP-Seq libraries of 2 factors in WT and SIR2 deletion backgrounds with Input.


title: Regulation of yeast chromosome III architecture and mating-type switching by a Sir2/condensin-bound region of the recombination enhancer

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

overall_design: Refer to individual Series


title: Single-Cell transcriptomes of murine Bone Marrow Stromal Cells Reveal Niche-Associated Heterogeneity

status: Public on May 17 2019

first: Pawel

last: Durek

institute: Deutsches Rheuma-Forschungszentrum

summary: Bone marrow (BM) stromal cells are important in the development and maintenance of cells of the immune system. Using single cell RNA sequencing, we here explore the functional and phenotypic heterogeneity of individual transcriptomes of 1,167 murine BM mesenchymal stromal cells. These cells exhibit a tremendous heterogeneity of gene expression, which precludes the identification of defined subpopulations. However, according to the expression of 108 genes involved in the communication of stromal cells with hematopoietic cells, we have identified 14 non-overlapping subpopulations, with distinct cytokine or chemokine gene expression signatures. With respect to the maintenance of subsets of immune memory cells by stromal cells, we identify distinct subpopulations expressing IL7, IL15 and Tnfsf13b. Together, this study provides a comprehensive dissection of the BM stromal heterogeneity at the single cell transcriptome level and provides a basis to understand their lifestyle and their role as organizers of niches for the long-term maintenance of immune cells.

overall_design: For single cell library preparation, ex vivo FACS sorted VCAM-1+CD45-Ter119-CD31- BM cells were applied to the 10X Genomics platform using the Single Cell 3’ Reagent Kit V2 (10x Genomics) following the manufacturer’s instructions. Upon adapter ligation and index PCR, the quality of the obtained cDNA library was assessed by Qubit quantification, Bioanalyzer fragment analysis (HS DNA Kit, Agilent) and KAPA library quantification qPCR (Roche). The sequencing was performed on a NextSeq500 device (Illumina) using a High Output v2 Kit (150 cycles) with the recommended sequencing conditions (read1: 26nt, read2: 98nt, index1: 8 nt, index2: n.a.).

first: Richard

last: Addo

first: Frederik

last: Heinrich

first: Gitta

last: Heinz

first: Daniel

last: Schulz

first: Özen

last: Sercan-Alp

first: Katrin

last: Lehmann

first: Cam

middle: L

last: Tran

first: Markus

last: Bardua

first: Mareen

last: Matz

first: Max

last: Löhning

first: Anja

last: Hauser

first: Andrey

last: Kruglov

first: Hyun-Dong

last: Chang

first: Andreas

last: Radbruch

first: Mir-Farzin

last: Mashreghi


title: Chromatin-informed inference of transcriptional programs in gynecologic cancers

first: Hatice

last: Osmanbeyoglu


title: The Catalytic Core of DEMETER Guides Active DNA Demethylation in Arabidopsis

status: Public on May 02 2019

city: kannapolis

first: Tzung-Fu

last: Hsieh

state: NORTH CAROLINA

address: 600 Laureate way

department: Plant and Microbial Biology

institute: North Carolina State University

summary: The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization, and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, and how it is recruited to these differing chromatin landscapes is unknown. The C-terminal DME catalytic core consists of three conserved regions required for catalysis in vitro. We show that the catalytic core of DME guides active demethylation at endogenous targets, rescuing the developmental and genomic hypermethylation phenotypes of DME mutants. However, without the N-terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated.  We used comparative analysis to reveal that the conserved DME N-terminal domains are only present in the flowering plants, whereas the domain architecture of DME-like proteins in non-vascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in all plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N-terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.

overall_design: DNA methylation was measured in C-terminal DME-complemented (dme-2/dme-2; nDMECTD/nDMECTD) or full length DME-complemented (dme-2/dme-2; DMEFL/DMEFL) dme-2 Arabidopsis endosperm

first: Changqing

last: Zhang

first: Yu-Hung

last: Hung


title: SLAM-seq for K562 endogenous mRNA decay

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.

overall_design:
SLAMseq Kinetics Kit - Catabolic Kinetics Module) from Lexogen was performed. Basically, k562 cells were feed with 100uM 4sU for 24h, fresh media containing s4U was changed every 3h. For chasing, old media are removed and cells were washed with PBS three times before adding media without s4U, but 10mM UTP instead, samples were collected at 0, 2, 4, 6h in triplicates for RNA extract and IAA treatment. All the operations were done in red light source to protect 4sU from crosslink. QuantSeq 3’mRNA-seq library were generated and sequenced. The SLAM-seq data was processed with the slam dunk pipeline (https://github.com/t-neumann/slamdunk 0.3.3.) The reads were aligned to the human genome GRCh38. The half-life was estimated according to the SLAM-seq paper; for downstream analyses a cut-off of p-value < 0.05 was applied to the decay rate estimates.
Comparing mRNA levels using QuantSeq and RNA-seq poly-A selection.

first: Qiushuang

last: Wu

first: Ariel

middle: A

last: Bazzini


title: Translation affects mRNA stability in a codon dependent manner in human cells


title: Chromatin-informed inference of transcriptional programs in gynecologic cancers [ATAC-Seq]

summary: Epigenomic data on transcription factor occupancy and chromatin accessibility can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. However, in many cancers, epigenomic analyses have been limited, and computational methods to infer regulatory networks in tumors typically use expression data alone, or rely on transcription factor (TF) motifs in annotated promoter regions. Here, we develop a novel machine learning strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine cell line chromatin accessibility data with large tumor expression data sets and model the effect of enhancers on transcriptional programs in multiple cancers. We generated a new ATAC-seq data set profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and applied PSIONIC to 723 RNA-seq experiments from ovarian, uterine, and basal breast tumors as well as 96 cell line RNA-seq profiles. Our computational framework enables us to share information across tumors to learn patient-specific inferred TF activities, revealing regulatory differences between and within tumor types. Many of the identified TF regulators were significantly associated with survival outcome in basal breast, uterine serous and endometrioid carcinomas. Moreover, PSIONIC-predicted activity for MTF1 in cell line models correlated with sensitivity to MTF1 inhibition.  Therefore computationally dissecting the role of TFs in gynecologic cancers may ultimately advance personalized therapy.

overall_design: Examination of chromatin landscape  in gynecologic and basal breast cancer cell lines

first: Osmanbeyoglu

last: Hatice

first: Leslie

last: Christina


title: SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [ChIP-seq]

city: Beijing

first: Wei

last: Xie

address: Haidian District

institute: Tsinghua University

summary: The oocyte epigenome plays critical roles in mammalian gametogenesis and embryogenesis. Yet, how it is established remains elusive. Here, we report that histone-lysine N-methyltransferase SETD2, an H3K36me3 methyltransferase, is a crucial regulator of the mouse oocyte epigenome. Deficiency in Setd2 leads to extensive alterations of the oocyte epigenome, including the loss of H3K36me3, failure in establishing the correct DNA methylome, invasion of H3K4me3 and H3K27me3 into former H3K36me3 territories and aberrant acquisition of H3K4me3 at imprinting control regions instead of DNA methylation. Importantly, maternal depletion of SETD2 results in oocyte maturation defects and subsequent one-cell arrest after fertilization. The preimplantation arrest is mainly due to a maternal cytosolic defect, since it can be largely rescued by normal oocyte cytosol. However, chromatin defects, including aberrant imprinting, persist in these embryos, leading to embryonic lethality after implantation. Thus, these data identify SETD2 as a crucial player in establishing the maternal epigenome that in turn controls embryonic development.

overall_design:
Mouse GO_P7, GO_P10, GO_P14, FGO, MII oocyte, zygote, late 2-cell, 8-cell and ICM from E3.5 blastocyst were obtained and performed STAR ChIP-seq to determine the H3K36me3 distribution. FGO in Dnmt3L KO mice and Setd2 maternal KO mice were collected and conducted STAR ChIP-seq, STEM-seq and RNA-seq to explore the cross talk between histone modifications. STAR ChIP-seq and RNA-seq were performed in Setd2 maternal KO zygote to test if abnormal H3K4me3 and transcription can be inherited in mutant embryo.
GO = growing oocyte
FGO = full grown oocyte

first: Qianhua

last: Xu

first: Yunlong

last: Xiang


title: Gene expression analysis of immortalized human liver progenitor-like cells in culture

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: We described a highly efficient method to establish the immortalized HepLPC cell, these cell lines could efficiently expand and able to readily differentiate back into metabolically functional hepatocytes. To further characterize them, we compare the global expression profiles among immortalized human liver progenitor-like cells (iHepLPCs), hepatocyte-like cells differentiated from iHepLPCs (iHepLPCs-Hep) and 3D cell spheroids of the iHepLPCs-Hep (iHepLPCs-Hep-3D).

overall_design: Immortalized human liver progenitor-like cells (iHepLPCs)  were cultured in the transition and expansion medium or in the modified hepatic maturation medium for 9 days. 3D cell spheroids of the iHepLPCs-Hep was aggregated by iHepLPCs and then  cultured in the modified hepatic maturation medium for another 9 days. Sample was assayed in double.

first: HeXin

last: Yan

first: ZhenYu

last: Wang


title: Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers (ChIP-seq data set)

status: Public on Apr 15 2019

city: Dallas

first: Eric

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: Fibroblasts can be directly reprogrammed toward a cardiac fate by introducing cardiogenic transcription factors (TFs), although the underlying mechanisms of the cardiac reprogramming process remain unclear. Three cardiac TFs, GATA4, MEF2C, and Tbx5 (referred to as GMT) can activate cardiac genes in fibroblasts and their cardiogenic activity is enhanced by the Hand2 TF and the Akt1 kinase. To understand the mechanistic basis of cardiac reprogramming, we performed a genome-wide analysis of cardiogenic TF binding sites and active enhancers, which were annotated by H3K27ac histone modification, during the reprogramming process. We found that cardiogenic TFs rapidly co-occupy core regulatory elements of cardiac genes and activate myriad cardiac enhancers that are enriched predominantly in Mef2 binding sites. Addition of Hand2 and Akt1 to the GMT reprogramming cocktail expands the spectrum of co-occupied active cardiac enhancers. As reprogramming proceeds over time, reprogramming TFs continue to activate additional cardiac enhancers, which are also enriched for Mef2 motifs, while fibroblast enhancers are silenced. This transition of the enhancer landscape strongly correlated with changes in the fibroblast and cardiac transcriptome. To test the relevance of cardiac reprogramming enhancers to the regulation of cardiogenesis in vivo, we assayed a collection of reprogramming enhancers in transgenic mouse embryos and found that they directed highly specific expression patterns in the developing heart. Our findings demonstrate that Hand2 and Akt1 enhance reprogramming by facilitating cardiac enhancer occupancy and identify Mef2 as a central effector of cardiac reprogramming, which coordinates the actions of accessory factors across a broad landscape of cardiac enhancers.

overall_design: To understand the mechanistic basis of cardiac reprogramming, we profiled cardiogenic TF binding sites and epigeomes (using ChIP-seq) and the transcriptiomes (using RNA-seq), of MEFs treated with reprogramming cocktail compared to embroynic heart tissue.

first: Hisayuki

last: Hashimoto


title: Genomic analysis of lncRNA and mRNA profile in circulating exosomes of patients with rheumatic heart disease

status: Public on Apr 19 2019

city: Changsha

first: Qinghua

last: Hu

state: Hunan

address: Xiangya Road

department: Cardiovascular disease

institute: Central south university

summary: Rheumatic heart disease (RHD) is still a serious life-threatening heart disease in developing countries. Accumulating evidence suggested that circulating exosomes and its cargoes including mRNA, microRNA and long noncoding RNA (lncRNA) play essential roles in cardiovascular diseases, while their roles in RHD remain unexplored. In the present study, we investigated genomic profiles of circulating exosomes harvested from RHD patients. And we performed gene ontology (GO) and pathway analysis to explore potential roles of differentially expressed mRNAs. Furthermore, we identified 5 lncRNAs and their flanking coding genes simultaneously dysregulated in the circulating exosome. Collectively, we provided the first transcriptome analysis identifying lncRNAs and mRNAs in circulating exosomes in RHD patients, and our data provide valuable insights into seeking for potential biomarkers and therapeutic targets for RHD.

overall_design: Microarray expression profiles of mRNAs and lncRNAs in circulating exosomes extracted from 5 RHD patients and 5 normal people were conducted .

first: Luo

last: Yanli

first: Huang

last: lingjin

last: Wanjun

first: Shu

last: Ye

first: Hu

last: Qinghua


title: Gata2 deficiency delays leukemogenesis while contributes to aggressive leukemia phenotype in Cbfb-MYH11 knockin mice

status: Public on Apr 26 2019

city: Bethesda

first: Pu

middle: Paul

last: Liu

state: MD

address: 49 Convent Dr.

department: TFGB

institute: NHGRI/NIH

summary: To clarify the role of Gata2 in the development of Cbfb-MYH11 induced leukemia, we generated conditional Cbfb-MYH11 knockin mice with Gata2 heterozygous knockout. Leukemic cells with Gata2 heterozygous knockout gained higher number of genetic mutations and showed more aggressive phenotype in both primary and transplanted recipient mice. We compared gene expression profilings between Gata2+/+ and Gata2+/f leukemic cells with Cbfb-MYH11.

overall_design: Leukemia mRNA profiles of end stage Cbfb-MYH11 mice with Gata2+/+ and Gata2+/f mice were generated by Illumina sequencing, in triplicate.

first: Satoshi

last: Saida

first: Erika

last: Kim


title: The transcriptomic response to albendazole (ABZ), mebendazole (MBZ), thiabendazole (TBZ), oxfendazole (OxBZ) and fenbendazole (FBZ) in the C. elegans strain CB3474 ben-1(e1880)III

status: Public on Apr 30 2019

city: Calgary

first: John

middle: Stuart

last: Gilleard

state: Alberta

address: 3330, Hospital Dr, NW

department: Faculty Veterinary Medicine

institute: University of Calgary

summary: We have undertaken a detailed analysis of the biotransformation of five of the most therapeutically important benzimidazole anthelmintics - albendazole (ABZ), mebendazole (MBZ), thiabendazole (TBZ), oxfendazole (OxBZ) and fenbendazole (FBZ) - in Caenorhabditis elegans. As a step to identifying nematode enzymes potentially responsible for benzimidazole biotransformation, we characterised the transcriptomic response to each of the benzimidazole drugs using the C. elegans strain CB3474 ben-1(e1880)III in order to minimize general phenotypic and stress responses to the drug. In the case of albendazole (ABZ), mebendazole (MBZ), thiabendazole (TBZ), and oxfendazole (OxBZ) - the shared transcriptomic response was dominated by the up- regulation classical xenobiotic response genes.

overall_design: Three biological replicates of approximately 20,000 larvae C. elegans CB3474 ben-1(e1880)III  exposed to 1.13mM of either albendazole (Sigma Cat# A4673), mebendazole (Sigma Cat# M2523), thiabendazole (Sigma Cat#T8904), oxfendazole (Sigma Cat#34176), fenbendazole (Sigma Cat# F5396) dissolved in DMSO as well as a DMSO negative control.

first: Susan

last: Stasiuk

first: Matthew

last: Workentine


title: IL-21/type I interferon interplay regulates neutrophil-dependent innate immune responses to Staphylococcus aureus

status: Public on Apr 22 2019

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Methicillin-resistant Staphylococcus aureus (MRSA) is a major hospital- and community-acquired pathogen, but the mechanisms underlying host-defense to MRSA remain poorly understood. Here, we investigated the role of IL-21 in this process. When administered intra-tracheally into wild-type mice, IL-21 induced granzymes and augmented clearance of pulmonary MRSA but not when neutrophils were depleted or a granzyme B inhibitor was added. Correspondingly, IL-21 induced MRSA killing by human peripheral blood neutrophils. Unexpectedly, however, basal MRSA clearance was enhanced when IL-21 signaling was blocked, both in Il21r KO mice and in wild-type mice injected with IL-21R-Fc fusion-protein. This correlated with increased type I interferon and an IFN-related gene signature, and indeed anti-IFNAR1 treatment diminished MRSA clearance in these animals. Moreover, we found that IFNβ induced granzyme B and promoted MRSA clearance in a granzyme B-dependent fashion. These results reveal an interplay between IL-21 and type-I IFN in the innate immune response to MRSA.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq analysis using total RNA either from total lung tissues isolated from mouse or from peripheral blood purified from normal donors or AD-HIES patients.

first: Rosanne

last: Spolski

first: Erin

last: West

first: Sharon

last: Veenbergen

first: Sunny

last: Yung

first: Majid

last: Kazemian

first: Jangsuk

last: Oh

first: Zu-Xi

last: Yu

first: Alexandra

middle: F

last: Freeman

first: Steven

middle: M

last: Holland

first: Philip

last: Murphy

first: Warren

last: Leonard


title: Cell layer specific and polysome associated RNA from Arabidopsis thaliana Col0 and hyl1 mutant roots.

status: Public on Apr 24 2019

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

institute: ETH

summary: microRNAs (miRNA’s) regulation target gene expression, often transcription factors and as such control entire transcriptional networks. This control is important for various developmental transitions and stress responses in a wide range of eukaryotic organisms. While miRNA-mediated gene regulation has been investigated over time (temporal) and in whole organs or tissues in multiple different organisms highlighting their importance, there has been a distinct lack of focus on spatial resolution of miRNA biology. Here we present at cell-type specific resolution, miRNA loading and miRNA action within the Arabidopsis root. Our results for the first time demonstrate the multiple novel modes of miRNA action and illustrate the widespread nature of miRNA movement, at a genome scale within a complex eukaryotic organ.

overall_design: 24 samples examined corresponding to HF-RPL18-IP for Col0 or hyl1 mutant plants expressing HF-RPL18 under 35S promoter or specific root cell layer promoter (columella/pACR4, stele/pSHR, endodermis/pSCR, cortex/pCO2 and epidermis/pWER) (2 replicates for each)

first: Chris

last: Brosnan

first: PeiQi

last: Lim

first: Matthias

last: Hirsch-Hoffmann

first: Nicolas

last: Bologna

first: Olivier

last: Voinnet


title: Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers (RNA-seq data set)

first: Eric

middle: N

last: Olson

first: Hisayuki

last: Hashimoto


title: Identification of regulatory networks of microRNAs and their targets in immunity to Colletotrichum gloeosporioides in tea plant (Camellia sinensis L.)

status: Public on Apr 10 2019

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

institute: Anhui Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant Camellia sinensis. MicroRNAs (miRNAs) have been known as key modulators of gene expression in defense responses; however, the role of miRNAs in tea plant during defensive responses to C. gloeosporioides remains unexplored. Six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. 1134 and 596 mRNAs were identified as targets of 389 and 299 novel  and conserved  miRNAs by degradome analysis, respectively. The expression levels of twelve miRNAs and their targets were validated by quantitative real-time PCR. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in translation, carbohydrate metabolism and signal transduction pathways. This study enriches the resources of defense-responsive miRNAs and their targets in C. sinensis, and thus, provides novel insights into the miRNA-mediated regulatory mechanisms underlying immunity responses to biotic stress in tea plant.

overall_design: 8 samples including control and treatment

first: Anburaj

last: Jeyaraj

first: Xuewen

last: Wang

first: Shuangshuang

first: Ran

last: Zhang

first: Ailin

last: Wu

first: Chaoling


title: Comparative genomic hybridization of Shewanella baltica strains

status: Public on Mar 31 2019

city: Norman

first: Jie

last: Deng

state: OK

address: 101 David L Boren Blvd, SRTC 2022

institute: University of  Oklahoma

summary: CGH of 46 Shewanella baltica strains using customized oligonucleotide microarrays

overall_design: Genomic DNAs from a total of 46 Shewanella baltica strains were extracted, labeled with Cy5, and hybridized onto customized arrays.


title: The Cytosine Deaminase AICDA Regulates FGF/ERK Signaling to Achieve the Naïve Pluripotent State During Reprogramming.

status: Public on Apr 03 2019

first: Ritu

last: Kumar

address: 1300 York Avenue

institute: Weill Cornell Medicine