title: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling

first: Aida

last: Moreno-Moral

summary: Bulk RNA-seq heart left ventricle data from wild type and WWP2 gene mutant mice (after 28 days of angiotensinII treatment)

overall_design: We generated WWP2 mutant mice using CRISPR/Cas9 technology to introduce a 4-bp deletion in exon 2. We treated these mutant and wild type mice with angiotensin II infusion for 28 days and harvested left ventricle heart tissue to carry out bulk RNA-sequencing.

first: Huimei

first: Enrico

last: Petretto


title: BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Pluripotency]

status: Public on Jul 07 2019

city: Neuherberg

first: Fatma

last: Uzbas

address: Ingolstaedter Landstr. 1

department: Institute of Stem Cell Research

country: Germany

institute: Helmholtz Center Munich

type: Expression profiling by high throughput sequencing

summary: We describe a novel workflow named Barcode Assembly foR Targeted Sequencing, which is a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts (rBART-Seq) or genomic regions (gBART-Seq) from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, for generating amplicons with dual indices. Here, we used the rBART-Seq for RNA quantification, and for the analysis of developmental states of thousands of single human pluripotent stem cells maintained in different media (mTeSR™1, KSR-bFGF, and E8).

overall_design: 11 selected transcripts and 4 external RNA spike-ins were co-amplified from single or multiple (2 to 32, incremented 2-fold) undifferentiated H9 human embryonic stem cells (hESCs) or BJ fibroblasts, as well as from four-fold dilution series (4-256 pg/well) of bulk RNA isolated from HMGU1 hiPSCs. The amplicons are barcoded using the rBART-seq method, and multiplexed for sequencing.

first: Florian

last: Opperer

first: Micha

last: Drukker


title: Gene Commanding Height (GCH) hierarchy in the cancer nucleus and cancer-free resection margins from a surgically removed prostatic adenocarcinoma of a 65y old black man

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

summary: We profiled the transcriptomes of the dominan nodule (Gleason score 4+5=9) and of the cancer free resection margins of a surgically removed prostate tumor from a 65y old black man. Normalized to the median of valid spots expression data where used to determine the Gene Commanding Height (GCH) Score for every coding and non-coding transcript adequately quantified in all four cancer and four normal tissue samples. The analysis proved that cancer and normal tissue have distinct gene hiearchies. The top three genes in the cancer region were:  BAIAP2L1 (BAI1-associated protein 2-like 1 ), FAM71E1 (amily with sequence similarity 71, member E1 ) and MAP6D1 (MAP6 domain containing 1 ), while the top three genes in the cancer-free region were: TOR1A (torsin family 1, member A ), MRPS12 (mitochondrial ribosomal protein S12 ) and GTF2H1 (general transcription factor IIH, polypeptide 1).

overall_design:
one gender (male) x one tissue (prostate) x two regions (C65Y = cancer dominant nodule and N65Y = cancer-free (normal) resection margins)
Please note that experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as single channel (i.e. 4 raw data files for total 8 samples). The raw data files are linked as Series supplementary files and indicated in the corresponding sample description field.

middle: A

first: Sanda


title: BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Genotyping]

summary: We describe a novel workflow named Barcode Assembly foR Targeted Sequencing, which is a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts (rBART-Seq) or genomic regions (gBART-Seq) from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, for generating amplicons with dual indices. Here, we used the gBART-Seq for genetic screening of breast cancer patients and identified BRCA mutations with very high precision.

overall_design: 10 regions from BRCA1 and BRCA2 genes were co-amplified from genomic DNA samples of 96 breast cancer patients. The amplicons are barcoded using the BART-seq method, and multiplexed for sequencing.


title: single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: To understand the diversity of expression states in IDH-wildtype Glioblastomas, we profiled 24,131 single cells from 28 patients with GBM by single-cell RNA sequencing (7,930 cells by Smartseq2 and 16,201 by 10X).

overall_design:
Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2 (main text) or 10X (supplementary text).
--------------------------------------------------------------
Authors state "We have difficulties in approving raw data submission to GEO or dbGAP and are therefore submitting at this point only the processed data and the metadata (both attached) and will continue in parallel with the process of granting approval for raw data submission in dbGAP and another repository (DUOS). "

first: Julie

last: Laffy


title: Comparative analysis of global gene expression profiles of Bacillus methanolicus MGA3 during growth with arabitol or mannitol

status: Public on Jul 06 2019

city: Bielefeld

first: Volker

middle: F.

last: Wendisch

address: Universitaetstr. 25

institute: Universitaet Bielefeld

summary: Bacillus methanolicus is a Gram-positive, thermophilic, methanol-utilizing bacterium. As a facultative methylotroph, B. methanolicus is also known to utilize d-mannitol, d-glucose and, as recently discovered, sugar alcohol d-arabitol. While metabolic pathways for utilization of methanol, mannitol and glucose are known, catabolism of arabitol has not yet been characterized in B. methanolicus. In this work we present the elucidation of this hitherto uncharted pathway. In order to confirm our predictions regarding genes coding for arabitol utilization, we performed differential gene expression analysis of B. methanolicus MGA3 cells grown on arabitol as compared to mannitol via transcriptome sequencing (RNA-seq). We identified a gene cluster comprising eight genes that was up-regulated during growth with arabitol as a sole carbon source. The RNA-seq results were subsequently confirmed via qRT-PCR experiments. The transcriptional organization of the gene cluster identified via RNA-seq was analyzed and it was shown that the arabitol utilization genes are co-transcribed in an operon that spans from BMMGA3_RS07325 to BMMGA3_RS07365.

overall_design: Differential gene expression analysis of B. methanolicus MGA3 cultivated with either 15 mM mannitol (control condition) or 15 mM arabitol (test condition) as sole carbon source was performed by RNA-seq. Both conditions were cultivated in biological triplicates previous to cell harvest and sampling.

first: Marina

middle: G

last: Lopez

first: Marta

last: Irla

first: Luciana

middle: F

last: de Brito


title: BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Differentiation]

summary: We describe a novel workflow named Barcode Assembly foR Targeted Sequencing, which is a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts (rBART-Seq) or genomic regions (gBART-Seq) from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, for generating amplicons with dual indices. Here, we used the rBART-Seq to analyze cell subpopulations that emerge during 72 hours of Wnt/β-catenin pathway activation of H9 hESCs using recombinant Wnt protein (rWnt3a), a small molecule inhibitor of GSK-3 (CHIR99021), or Dox-inducible constitutively active β-catenin (ΔN90).

overall_design: 19 selected transcripts and 3 external RNA spike-ins were co-amplified from single cells isolated from differentiating H9 human embryonic stem cells (hESCs) at 0, 24 and 72 hours of Wnt pathway stimulation, as well as from bulk RNA derived from them (10/50 pg/well). The amplicons are barcoded using the rBART-seq method, and multiplexed for sequencing.

first: Dmitry

last: Shaposhnikov


title: Gene expression and alternative splicing profile of MFAP1- and THOC1-depleted human cells

status: Public on Jul 05 2019

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary:
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here we show that human THO interacts with MFAP1, a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent either on transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381, also confer a similar transcription-independent genome instability supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses, that affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a novel functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
HeLa cells were depleted of MFAP1 or THOC1 by siRNA during 72 h and their global gene expression and alternative splicing profiles were analyzed.
Data were used to describe genes that were up- or down-regulated or showed alternative splicing changes after MFAP1 or THOC1 depletion.

overall_design: We analyzed RNA from control cells (siC), MFAP1-depleted cells (siMFAP1) and THOC1-depleted cells (siTHOC1). For each condition, microarray analysis was conducted in triplicate from three different biological replicates (Total = 9 samples). We compared siMFAP1 vs siC, siTHOC1 vs siC and siMFAP1 vs siTHOC1.

first: I

last: Salas-Armenteros

first: M

last: Pérez

first: E

last: Andújar

first: R

last: Luna

first: A


title: The androgen receptor regulates a druggable translational regulon in advanced prostate cancer [RNA-seq]

status: Public on Jul 31 2019

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: The recent advent of highly potent inhibitors of the androgen receptor and androgen biosynthesis has had the unfortunate iatrogenic effect of fueling new lethal prostate cancer phenotypes in patients. In particular, non-neuroendocrine androgen receptor-low castration resistant prostate cancer (AR low CRPC) is increasing in occurrence amongst patients and is uniformly fatal. The mechanisms that promote this phenotype remain poorly understood. Through molecular studies of murine and human models of AR low CRPC, we have identified a new functional interface between the androgen receptor and the translation initiation complex inhibitor 4EBP1. AR directly regulates 4EBP1 expression which translationally represses eIF4F complex formation and a pro-proliferation program. In the context of AR low prostate cancer, de-repression of translation initiation drives the aberrant expression of the pro-proliferation regulon which fuels uncontrolled cell growth. Genetic and pharmacologic inhibition of the downstream eIF4F translation initiation complex reverses the proliferation phenotype in vitro and in vivo. These findings reveal a new previously unrecognized druggable nexus which functionally link the processes of mRNA transcription and translation initiation in a rapidly emerging class of advanced lethal prostate cancer

overall_design:
Androgen receptor low prostate cancer has been on the rise with the advent of potent androgen receptor and androgen biosynthesis inhibitors and is uniformly fatal. The mechanisms underlying disease progression remains unresolved. We have identified a previously unknown direct interaction between the androgen receptor and the translation initiation complex inhibitor 4EBP1 which plays a critical role in protein synthesis rates, mRNA specific translation, and disease progression in vivo. This is mediated through the hyperactivation of the downstream eIF4F translation initiation complex which usurps a network of pro-proliferation mRNAs. Importantly, using both genetic and pharmacologic methods, we demonstrate that dissociation of the eIF4F complex reverses the proliferation program leading to tumor regression. As such, we have identified a new therapeutic paradigm for targeting lethal androgen receptor low prostate cancer.

RNA-seq of prostrate tissue from either intact or castrated PB-Cre4;PTENLoxP/LoxP mice.

first: Yuzhen

last: Liu

first: Jessie

middle: L

last: Horn

first: Kalyan

last: Banda

first: Asha

middle: Z

last: Goodman

first: Yiting

last: Lim

first: Sujata

last: Jana

first: Alexandre

last: Germanos

first: Yu

middle: C

last: Yang

first: Ilsa

middle: M

last: Coleman

first: Robin

last: Tharakan

first: Elise

middle: Y

last: Cai

first: Takuma

last: Uo

first: Smitha

middle: P

last: Pillai

first: Eva

last: Corey

first: Colm

last: Morrissey

last: Chen

first: Brett

middle: S

last: Carver

first: Stephen

middle: R

last: Plymate

first: Slobodan

last: Beronja

first: Peter

last: Nelson

first: Andrew

last: Hsieh


title: Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy [ATAC-seq]

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: LMNA-DCM accounts for 5-10% of DCM cases and has an age-related penetrance whose onset typically appears between the ages of 30 and 40. However, the precise mechanisms linking the LMNA mutation to increased arrhythmogenicity are still unknown.
Methods: We utilized human iPSC-CMs RNA-seq, ChIP-seq, and ATAC-seq technologies.
Results: The electrophysiological studies of iPSC-CMs identify the LMNA mutation as a cause of increased arrhythmogenicity in mutant iPSC-CMs through abnormal calcium homeostasis. We find that the mutations in LMNA disrupt the global chromatin conformation, resulting in hyper-activation of the platelet-derived growth factor (PDGF) signaling pathway in LMNA-mutant iPSC-CMs. Inhibition of the PDGF signaling pathway can rescue the arrhythmic phenotype of mutant iPSC-CMs.
Conclusions: These findings were corroborated in cardiac tissues from healthy and LMNA-DCM patients, thus confirming a novel mechanism of LMNA-DCM pathogenesis both in vitro and in vivo.

overall_design: ATAC-seq of iPSC-CMs.

first: Jaecheol

last: Lee

first: Vittavat

last: Termglinchan

first: K

last: Ioannis

first: Joseph

last: Wu


title: Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy [ChIP-seq]

overall_design: ChIP-seq of iPSC-CMs.


title: Gene Commanding Height (GCH) hierarchy in the cancer nucleus and cancer-free resection margins from a surgically removed prostatic adenocarcinoma of a 47y old white man

first: Dumitru

last: Iacobas

summary: We profiled the transcriptomes of the cancer nucleus (Gleason score 4+5=9) and of the cancer free resection margins of a surgically removed prostate tumor from a 47y old white man. Normalized to the median of valid spots expression data where used to determine the Gene Commanding Height (GCH) Score for every coding and non-coding transcript adequately quantified in all four cancer and four normal tissue samples. The analysis proved that cancer and normal tissue have distinct gene hiearchies. The top three genes in the cancer region were: LOC145474  (uncharacterized long non-coding RNA), PRRG1 (proline rich Gla (G-carboxyglutamic acid) 1) and ASAP3 (ArfGAP with SH3 domain, ankyrin repeat and PH domain 3), while the top three genes in the cancer-free region were: SFR1 (SWI5-dependent recombination repair 1 ), EDF1 (endothelial differentiation-related factor 1) and RHOD (ras homolog family member D).

overall_design: one gender (male) x one tissue (prostate) x two regions (C47Y = cancer nucleus and N47Y = cancer-free (normal) resection margins)

first: Sanda


title: Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1 and Spp1 in western diet-induced obesity

status: Public on Jul 04 2019

city: Bar Harbor

first: Gareth

last: Howell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: We aim to characterize the transcriptomes of major subsets of brain myeloid cells in mouse models of western diet-induced obesity.

overall_design: Examination of CD11b+CD45lo and CD11b+CD45hi brain myeloid cells

first: Leah

last: Graham

first: Hongtian

last: Yang


title: BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis

first: Fatma

last: Uzbas

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

overall_design: Refer to individual Series


title: Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming [ChIP-Seq]

status: Public on Jul 03 2019

city: San Francisco

first: Nicole

last: Stone

address: 1650 Owens St.

institute: Gladstone Institutes - UCSF

summary: To determine the molecular mechanisms by which expression of Gata4, Mef2c, and Tbx5 (GMT) induces direct reprogramming from a cardiac fibroblast toward an induced cardiomyocyte, we performed a comprehensive transcriptomic and epigenomic interrogation of the reprogramming process. Single cell RNA sequencing indicated that a reprogramming trajectory was acquired within 48 hours of GMT introduction, did not require cell division, and was limited mainly by successful expression of GMT. Evaluation of chromatin accessibility by ATAC-seq supported the expression dynamics and revealed widespread chromatin remodeling at early stages of the reprogramming process. Chromatin immunoprecipitation followed by sequencing of each factor alone or in combinations revealed that GMT bind DNA individually and in combination, and that ectopic expression of either Mef2c or Tbx5 is sufficient in some contexts to increase accessibility. We also find evidence for cooperative facilitation and refinement of each factor’s binding in a combinatorial setting. A random-forest classifier that integrated the observed gene expression dynamics with regions of dynamic chromatin accessibility suggested Tbx5 binding is a primary driver of gene expression changes and revealed additional transcription factor motifs co-segregating with reprogramming factor motifs, suggesting new factors that may be involved in the reprogramming process.

overall_design: Examination of genome-wide occupancy of Gata4, Mef2c, and Tbx5. ChIP-seq analyses were performed with at least three biological replicates per condition.

first: Casey

last: Gifford

first: Deepak

last: Srivastava


title: Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming [SF.ATAC-seq]

overall_design: Examination of genome-wide accessibility following individual and combinatorial exogenous expression of reprogramming factors. ATAC-seq analyses were performed with three biological replicates.


title: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

city: Oxford

first: Anne

last: Turberfield

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford


title: Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming


title: Resetting histone modifications during human parental-to-zygotic transition

city: Beijing

first: Wei

last: Xie

state: Beijing

address: Qinghuayuan

department: School of Life Science

country: China

institute: Tsinghua University

summary: Histone modifications regulate gene expression and development. To address how they are reprogrammed in human early development, we investigated key histone marks in human oocytes and early embryos. Unlike that in mouse, the permissive mark H3K4me3 largely exhibits canonical patterns at promoters in human oocytes. After fertilization, pre-zygotic genome activation (ZGA) embryos acquire permissive chromatin and widespread H3K4me3 in CpG-rich regulatory regions. By contrast, the repressive mark H3K27me3 undergoes global depletion. CpG-rich regulatory regions then resolve to either active or repressed states upon ZGA, followed by subsequent restoration of H3K27me3 at developmental genes. Finally, through combining chromatin and transcriptome maps, we revealed transcription circuitry and asymmetric H3K27me3 patterning during early lineage specification. Collectively, our data unveil a priming phase connecting human parental-to-zygotic epigenetic transition.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We investigated the dynamics of two key histone marks H3K4me3, H3K27me3 in human oocytes and pre-implantation embryos, and H3K27ac in post-ZGA embryos using CUT&RUN.

first: Weikun

last: Xia

first: Jiawei

last: Xu

first: Guang

last: Yu

first: Guidong

last: Yao

first: Ying-Pu

last: Sun


title: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [RNA-seq]

summary: CpG islands (CGI) are associated with the majority of mammalian gene promoters and function to recruit chromatin modifying enzymes. It has therefore been proposed that CGIs regulate gene expression through chromatin-based mechanisms, however in most cases this has not been directly tested. Here, we reveal that the histone H3 lysine 36 (H3K36) demethylase activity of the CGI-binding KDM2 proteins contributes only modestly to the H3K36me2-depleted state at CGI-associated gene promoters and is dispensable for normal gene expression. Instead, we discover that KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CGI-associated gene promoters. We further show that KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters. Together this reveals a demethylase-independent role for KDM2 proteins in transcriptional repression and uncovers a new function for CGIs in constraining gene expression.

overall_design: Mouse embryonic stem cells with conditional loss of KDM2A/B long isoforms (Kdm2a/b-JmjCfl/fl) or conditional removal of KDM2A and/or KDM2B from chromatin (Kdm2a/b-CXXCfl/fl, Kdm2a-CXXCfl/fl and Kdm2b-CXXCfl/fl) were profiled for gene expression using spike-in calibrated nuclear RNA-seq.

middle: H

first: Robert

middle: J

last: Klose


title: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ATAC-seq]


title: Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy

first: Lei

last: Tian


title: Transcriptional effect of vaccination and challenge on porcine tonsil cells

status: Public on Jul 02 2019

city: Uxbridge

first: Ronan

last: McCarthy

state: Middlesex

address: Heinz Wolff Building, Kingston Lane, Brunel University London

institute: Brunel University London

summary: To achieve a greater insight into the host response to vaccination with C-strain, custom porcine microarrays were designed and utilised to analyse the differences in gene expression in host tonsil cells between pigs that were vaccinated with C-strain or given a mock vaccination. These pigs were then subsequently challenged with a virulent strain of CSFV within the window before an adaptive immune response can be mounted. Tonsil cells were harvested for transcriptomic analysis at various time points within the pre-adaptive protection window and analysed to identify subsets of genes that may be integral to this early protection phenotype.

overall_design: In brief, 18 Large White/Landrace crossbreed pigs of 8 to 10 weeks of age were randomly assigned to one of two groups. Five days prior to challenge (day 0), the animals in group 1(n = 9) were vaccinated with 2 ml of C-strain vaccine into the brachiocephalous muscle (as recommended by the manufacturer [Riemser Arzneimittel AG]), and group 2 (n = 9) was intranasally inoculated with 1 ml of mock virus supernatant. On day 5, groups 1 and 2 were inoculated intranasally with 105 TCID50 of CSFV Brescia strain. On day 5 (Challenge Day 0), 8 (Challenge Day 3) and 10 (Challenge Day 5), three animals were euthanized from groups 1 and 2, and the tonsils were collected. Please note that  Sample titles refer to days post challenge.

first: Helen

last: Everett

last: Crooke

first: Falko

last: Steinbach

first: Simon


title: Genome-wide discovery of daily transcriptome, cis-regulatory elements and transcription factor footprints in the monarch butterfly brain [RNA-Seq]

city: College Station

first: Christine

last: Merlin

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary: The Eastern North American monarch butterfly, Danaus plexippus, is notorious for its spectacular seasonal long-distance migration. In recent years, it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and seasonal behavioral outputs. However, unlike Drosophila and the mouse, little work has been undertaken in the monarch to identify clock-controlled output genes and elucidate the regulation of their rhythmic expression. Here, we used RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing to profile the diurnal transcriptome, open chromatin regions, and transcription factor (TF) footprints in the brain of wild-type monarchs and Cryptochrome 2 (Cry2), Clock (Clk), and Bmal1 (named DCyc-like) butterfly mutants with impaired clock function. We identified 366 rhythmic transcripts under circadian clock control belonging to biological processes key to brain function, such as neurotransmission, neuropeptide signaling, and glucose metabolism. Surprisingly, we found no significant time of day and genotype-dependent changes in chromatin accessibility (i.e., cis-regulatory elements) in the brain. Instead, we found the existence of a temporal regulation of TFs occupancy within open chromatin regions in the vicinity of rhythmic genes in the brains of wild-type monarchs, which is abolished in clock deficient mutants. Our data suggest that TFs binding specifically in the middle of the day display pioneer-like activity by increasing the accessibility of the surrounding chromatin, while TFs binding specifically in the middle of the night would bind DNA with a longer residency time without affecting accessibility of the surrounding chromatin. Together, this work identifies for the first time the clock-controlled genes and modes of regulation by which diurnal transcription rhythms are regulated in the monarch brain. It also illustrates the power of ATAC-seq to profile genome-wide regulatory elements and TF binding in unconventional organisms.

overall_design: Determine the identify of clock-controlled genes and their cis-regulatory elements in monarch butterfly brains using RNA-Seq and ATAC-Seq open chromatin profiling.

first: Aldrin

middle: B

last: Lugena

first: Ying

last: Zhang

first: Jerome

last: Menet


title: RNA-seq expression profiling of cortical bone from ephrin B2 deficient and control mice

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Within the bone matrix is an interconnected network of cells termed osteocytes. These cells are derived from bone-forming osteoblasts. This transition requires expression of ephrinB2, but we were intrigued about why this protein continues to be expressed at high levels in mature osteocytes. To determine its function in osteocytes, we developed an osteocyte-specific (Dmp1Cre) ephrinB2 null mouse and found they exhibited a brittle bone phenotype. RNA sequencing was used to compare the expression profiles of osteocytes from ephrinB2 null mouse with those of from control cousins.

overall_design: RNA-seq profiles were obtained from femoral cortical bone from 3 ephrin B2 deficient (Dmp1Cre.EfnB2f/f) mice and 4 control mice (Dmp1Cre). All mice were 12 week old females.


title: RNA-seq analysis of developing pods of CpFatB4- and CpFatB5-expressing transgenic Brassica napus

status: Public on Jul 01 2019

city: Daejeon

first: Hankuil

last: Yi

address: Daehak-ro 99 Yuseong-gu

department: Deparment of Biological Sciences

country: South Korea

institute: Chungnam National University

summary: Differentially expressed genes in developing pods of CpFatB4- and CpFatB5- expressing transgenic Brassica napus in seed specific manner were investigated using RNA-seq method at 8, 25, and 45 days after fertilization

overall_design: Examination of mRNA profiles of developing pods of 2 transgenic plants and a control plant at 3 time points

first: Jeong-Won

last: Nam


title: Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming [scRNA-seq]

first: Nicole

last: Stone

overall_design: Examination of transcriptional dynamics during cardiac reprogramming using single cell RNA sequencing.

first: Casey

last: Gifford

first: Deepak

last: Srivastava


title: Expression data from Ricin-A expressing Drosophila wing discs

city: SANTA FE

first: Andres

last: Dekanty

address: COLECTORA RUTA 168

country: Argentina

institute: IAL CONICET

summary: Coordinated tissue growth is essential for generation of functionally integrated organs during animal development as well as for tissue homeostasis during adult life. Using Drosophila wing as a model system we have demonstrated that impairing growth, by expression of a cold sensitive version of type 2 ribosome-inactivating protein Ricin-A (RA), within defined territories along the wing primordium triggers a Dmp53-dependent reduction of growth in adjacent non-perturbed cells. To identify novel genes and pathways involved in coordinating intra-organ growth we analysed differential gene expression between wing discs expressing RA and control wing discs expressing GFP in the posterior compartment by using engrailed-Gal4.

overall_design: Three independent RNA samples were prepared from wing imaginal discs of late L3 larvae expressing GFP or GFP plus RA under the control of en-gal4. After dissection of wing discs, the posterior GFP-positive compartment was separated under a fluorescence stereoscope and used for RNA extraction and hybridization on Affymetrix microarrays.

first: Duarte

last: Mesquita

first: Juan

last: Sanchez

first: Agustín

last: Arce

first: Marco

last: Milan

first: Andrés


title: Genome-wide discovery of daily transcriptome, cis-regulatory elements and transcription factor footprints in the monarch butterfly brain [ATAC-Seq]


title: Genome-wide discovery of daily transcriptome, cis-regulatory elements and transcription factor footprints in the monarch butterfly brain


title: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity [ChIP-seq]

first: Anne

last: Turberfield

overall_design: Mouse embryonic stem cells with conditional loss of KDM2A/B long isoforms (Kdm2a/b-JmjCfl/fl) or conditional removal of KDM2A/B from chromatin (Kdm2a/b-CXXCfl/fl) were profiled by ChIP-seq.

first: Robert

last: Klose


title: Low cytosolic folate cycling is a hallmark of U251 glioblastoma cells reprogramming towards pluripotency

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

country: France

institute: INSERM

type: Methylation profiling by genome tiling array


title: Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy [RNA-seq]

first: Lei

last: Tian

overall_design: RNA-seq of iPSC-CMs.

first: Jaecheol

last: Lee

first: Vittavat

last: Termglinchan

first: K

last: Ioannis

first: Joseph

last: Wu


title: Low cytosolic folate cycling is a hallmark of U251 glioblastoma cells reprogramming towards pluripotency [RNA-seq]

summary: we report that U251 glioblastoma tumor spheres exhibit low cytosolic folate cycle and a reprogrammmed mitochondrial folate cycle that is presumably oriented towards oxidizing the formyl group to CO2 with the production of TetraHydroFolate and release of NADPH instead of synthesizing formate

overall_design: RNA-Seq comparing tumor spheres and adherent monolayer cells derived from U251 glioblastoma cell line

first: Racha

last: Zgheib

first: ShyueFang

last: Battaglia

first: Sébastien

first: Céline

last: Chéry

first: Guillaume

last: Gauchotte

first: Jean-Louis

last: Guéant

first: Farès

last: Namour


title: Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming [RNA-Seq]

first: Nicole

last: Stone

overall_design: Examination of transcriptomes of induced cardiomyocytes. Bulk RNA-seq analyses were performed with three biological replicates.

first: Casey

last: Gifford

first: Deepak

last: Srivastava


title: Low cytosolic folate cycling is a hallmark of U251 glioblastoma cells reprogramming towards pluripotency [methylation]

summary: What is known is that methionine-dependency is a feature of some cancers. So far, it was attributed to mutations in genes involved in the methionine de novo or salvage pathways.   What is new is that in this work we propose that methionine dependency stems from an altered cellular metabolism. We provide evidence that in U251 glioblastoma cell line, only cancer stem cells -isolated as tumor spheres in non adherent conditions- are methionine dependent and not monolayer cells grown in adherent conditions. Transcriptome wide-sequencing reveals that several genes involved in cytosolic folate cycle are downregulated whereas some transcripts of genes involved in mitochondrial folate cycle are upregulated. Genome wide DNA methylation does not account for these changes in gene expression. Mass spectrometry measurements confirm that tumor spheres display low cytosolic folate cycle unable to produce enough 5-methyltetrahydrofolate to remethylate homocystein to methionine. This decreased 5-methyltetrahydrofolate bioavailability is presumably due to a reprogrammed mitochondrial folate cycle which instead of synthesizing formate, intended to fuel the cytosolic folate cycle, oxidizes the formyl group to CO2 with the attendant reduction of NADP+ to NADPH and release of tetrahydrofolate.  The originality of this work resides in that it replaces methionine deprivation as a useful nutritional strategy in cancer growth control since cancer stem cells are much more tumoregenic than their non stem-like counterparts. Second, it reveals that the primary default responsible of the reprogrammation of folate metabolism originates in the mitochondria. Thus, mitochondrial enzymes could be novel and more promising anticancer targets than dihydrofolate reductase (DHFR), the current target of drug therapy linked with folate metabolism.

overall_design: tumor spheres are compared to adherent monolayer cells, 3 independant biological replicates of each cell types are analyzed, 6 samples are used in total, cells are derived from U251 glioblastoma cell line

first: Pierre

last: Rouyer

first: Fares


title: MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (RNA-Seq)

status: Public on Jun 30 2019

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

summary: We knock down MYCN in human neuroblastoma cell line by RNAi. MYCN knock-down caused global epigenome change, including nucleosome gain on key DNA-repair genes and promoter H3K9ac down regulation.

overall_design: mRNA gene expression profiles of ctrl/MYCN-kd in human neuroblastoma cell line BE2C..

first: Xinjie

last: Hu

first: Cizhong

last: Jiang


title: MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma

overall_design: Refer to individual Series


title: Human memory Th17 cell populations change into anti-inflammatory cells with regulatory capacity upon exposure to active Vitamin D

status: Public on Jun 28 2019

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

summary: Autoimmune diseases are characterized by an aberrantly activated immune system, resulting in tissue damage and functional disability in patients. An important therapeutic goal is to restore the deregulated immunological balance between pro- and anti-inflammatory T cells. This imbalance is illustrated by elevated levels and activity of memory Th17 cell populations, such as Th17, Th1/Th17 and Th17.1 cells, in various autoimmune diseases. These cells are characterized by the chemokine receptor CCR6, RORC expression and production of IL-17A, IFNγ and TNFα. Using rheumatoid arthritis (RA) as a model autoimmune disease, we here demonstrate that pro-inflammatory memory CCR6+ Th cells can switch into anti-inflammatory cells with regulatory capacity using the active vitamin D metabolite 1,25(OH)2D3. Memory CCR6+ Th cells, excluding Tregs, were sorted from healthy controls or treatment-naïve patients with early rheumatoid arthritis (RA) and cultured with or without 1,25(OH)2D3. Treatment with 1,25(OH)2D3 inhibited pro-inflammatory cytokines such as IL-17A, IL-17F, IL-22 and IFNγ in memory CCR6+ Th cells from both healthy controls and RA patients. This was accompanied by induction of anti-inflammatory factors, including IL-10 and CTLA4. Interestingly, these formerly pathogenic cells suppressed proliferation of autologous CD3+ T cells similar to classical Tregs. Importantly, the modulated memory cells still migrated towards the site of inflammation, modelled by RA synovial fluid, and retained their suppressive capacity in this environment. These data show the potential to reset the pathogenic profile of human memory Th cells into non-pathogenic cells with regulatory capacity.

overall_design: CCR6 positive Th17 cells from 3 independent treatment naive early RA patients were stimulated with anti-CD3/anti-CD28 and exposed with or without Vitamin D for 72 hours.

first: Wendy

last: Dankers

first: Nadine

last: Davelaar

first: Jan

last: van Hamburg

first: Edgar

last: Colin

first: Erik

last: Lubberts


title: IBL-302 PIM/PI3K/mTOR triple kinase inhibitor treatment of patient derived orthotopic xenograft neuroblastoma cells

status: Public on Jun 22 2019

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

country: Sweden

institute: Lund University

summary: neuroblastoma cells derived from PDOX models were treated with the kinase inhibitor.

overall_design: 5 repetitions of control and IBL-302 treated cells were harvest and submitted for RNAseq analysis

first: Sofie

last: Mohlin

first: Karin

last: Hansson

first: Daniel

last: Bexell


title: Deep Multiple-omics Profiling of Brain Tumors Identifies Signaling Networks Downstream of Cancer Driver Genes

city: Memphis

first: Timothy

last: Shaw

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: We profiled the transcriptome in two high-grade glioma (HGG) mouse models driven by mutated receptor tyrosine kinase (RTK) oncogenes, platelet-derived growth factor receptor alpha (PDGFRA), neurotrophic receptor tyrosine kinase 1 (NTRK1). In addition, transcriptome for normal mouse cortex was also profiled. The transcriptome was used to define transcription factor activity by integrating with whole proteome and phosphoproteome datasets.

overall_design:
7 samples with PDGFRA Mutant, 7 samples with TPM3-NTRK1 fusions, 4 normal mouse cortex samples;
[1] A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
[2] A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
[3] Normal brain cortex of athymic nude mice

middle: I

first: Alexander

last: Diaz

first: Suzanne

last: Baker


title: High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage

status: Public on Jun 21 2019

city: Boston

first: Pui

last: Lee

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Womens Hospital

summary: Diffuse alveolar hemorrhage (DAH) is a life-threatening pulmonary complication associated with systemic lupus erythematous and other autoimmune diseases. Little is known about the pathophysiology of DAH and no targeted therapy is currently available. Pristane treatment in mice induces systemic autoimmunity and lung hemorrhage that recapitulates hallmark pathologic features of human DAH. Using this experimental model, we performed high dimensional analysis of lung immune cells in DAH by mass cytometry and single cell RNA sequencing. We found a large influx of myeloid cells to the lungs in DAH and defined the gene expression profile of infiltrating monocytes. Using three models of monocyte deficiency and complementary transfer studies, we established a central role of inflammatory monocytes in the development of DAH. We further found that the myeloid transcription factor interferon regulatory factor 8 (Irf8) is essential to the development of both DAH and type-I interferon-dependent autoimmunity. These findings collectively reveal monocytes as a potential treatment target in DAH.

overall_design: Examination of gene expression in peritoneal cells from 1) wild-type mice treated with PBS, 2) wild-type mice treatd with pristane, and 3) Irf8-deficient mice treated with pristane

first: Peter

middle: A

last: Nigrovic


title: LIX1L stabilization of CCL20 promotes fibrosis

city: 南京

first: xiaoyun

last: zhu

address: 江苏省南京市中国药科大学

institute: China Pharmaceutical University

summary: Expression of LIX1L is increased in fibrotic livers and associated with liver fibrosis stage. We investigated whether increased LIX1L expression promotes Hepatic stellate cells (HSCs) activation and liver fibrosis progression by interacting with Chemokine signaling pathway.

overall_design: LX-2 cells mRNA profiles of 48h transfected with siControl or siLIX1L were generated by RNA sequencing.

first: Hao

last: Zhang

first: Xiaoyun

last: Zhu


title: Human breast cancer cells and cancer-associated fibroblasts: Control vs. Compressed

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

institute: Yonsei University

summary: Transcriptional profiling of the human breast cancer cells and primary breast cancer-associated fibroblasts exposed to compressive stress. Four subtypes of breast cancer cells (BT-474, MCF7, SK-BR-3, MDA-MB-231) and four cases of primary breast cancer-associated fibroblasts (CAF1, CAF2, CAF3, and CAF4) were exposed to a static compressive stress for 24 h.

overall_design: Six compressive stress-conditions (0, 0.386, 0.773, 1.546, 3.866, and 7.732 kPa) for each cell. Control (0 kPa) vs. Compressed cells. Biological replicates: 1 control replicate, 1 compressed replicate.

first: Baek-Gil

first: Nam-Hoon

last: Cho


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Validation]

status: Public on Jun 20 2019

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. This approach enables robust cell-typing of complex tissues and reveals a de novo atlas of cellular and epigenomic diversity across many cell types and cell stages.

overall_design: A high-diversity library of random oligonucleotides were introduced to the dscATAC-seq assay, which was run uniformly with PBMCs at various bead input concentrations. To assess the bead merging algorithm (bap), we used overlap of oligonucleotide tags as an independent true positive means for barcodes pairs to then assess the precision and accuracy of our bead merging algorithm. The summary statistics for both bap1 and bap2 are shown here.


title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ATAC-Seq]

city: Los Angeles

first: magdalena

middle: ewelina

last: potok

address: 4045 Terasaki Life Sciences Building

department: MCDB

institute: UCLA

summary: Deposition of histone variant H2A.Z by the SWR1 chromatin-remodeling complex is critical for the appropriate expression of many genes in eukaryotes, yet, despite its importance, the composition of the Arabidopsis SWR1 complex has not been thoroughly analyzed.  Here we have identified the interacting partners of a conserved Arabidopsis SWR1 subunit, actin-related protein 6 (ARP6). We isolated 9 predicted components, identifying subunits implicated in histone acetylation and interacting partners implicated in chromatin biology. We found that the  methyl-CpG-binding domain 9 (MBD9) subunit functioned synergistically with ARP6 to control flowering time. MBD9, in combination with ARP6, was involved in the SWR1-mediated incorporation of the majority of H2A.Z. MBD6 was further required for deposition of H2A.Z at a distinct subset of loci. MBD9 was preferentially bound to nucleosome-depleted regions at the 5’ of genes containing high levels of activating histone marks. Our data suggests a model for MBD9 in recruiting the SWR1 complex to open chromatin of actively transcribing genes.

overall_design: Examination of open chromatin by ATAC-Seq in WT and mbd9-3 mutant.

first: Magdalena

middle: E

last: Potok

first: Steven

last: Jacobsen


title: Identification and therapeutic rescue of autophagosome and glutamate receptor defects in C9ORF72 and sporadic ALS neurons

first: Justin

last: Ichida

address: 1425 San Pablo Street, BCC 305

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

summary: RNA sequencing analysis of Hb9::RFP human induced motor neurons generated using transcription factor overexpression. The goal of this project is to evaluate the process of APC in rescuing degeneration motor neurons.

overall_design: We determine the effect of InAPC and APC on motor neurons . Motor neurons are generated from fibroblasts by transcription factor-mediated lineage conversion.


title: MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (Mnase-Seq)

first: Weisheng

last: Zheng

overall_design: Mnase-seq of nucleosome positioning in ctrl/N-myc_kd neuroblastoma cell line BE2C

first: Xinjie

last: Hu

first: Cizhong

last: Jiang


title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_MBD9]

overall_design: Mapping MBD9 occupany.


title: RNA Seq to identify novel transcripts originating from orphan CGIs

status: Public on Jun 27 2019

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: To identify novel transcripts originating from orphan CGIs we isolated RNA from undifferentiated embryonic stem cells (ESCs), ESCs differentiated into embryoid bodies (EBs), and ESCs differentiated into neuronal cells; we also used RNA from mature male mouse brain. RNA Seq data were visually analysed for transcripts originating from orphan CGIs.

overall_design: 2 biological replicates were used per sample.

first: Martha

middle: V

last: Koerner

first: Adrian

last: Bird


title: Targeting p16-induced Senescence Prevents Cigarette Smoke-Induced Emphysema by Promoting IGF1/Akt1 Signaling in mice

city: Gaithersburg

first: Christopher

middle: Travis

last: Cottage

state: MD

address: 1 Medimmune Way

institute: AstraZeneca

summary: Increased IGF1 signaling in p16 -/- lungs

overall_design: qPCR gene expression profiling.  RNA from lung lysates collected from room air and cigarette smoke treated wild type and  p16 knock out mice

middle: T


title: Comparative Single Cell Transcriptomics Reveals Distinct Cell Fate Transition Statuses during Human Cardiac Reprogramming

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

institute: Medical College of Wisconsin

summary: Direct lineage conversion among various somatic cell types revolutionized the field of stem cell and regenerative medicine. In addition, the platform of cellular reprogramming offered a powerful system to gain new knowledge about cell plasticity and cell fate determination and ultimately challenged previous notions of cell identity. Previously, we successfully utilized single cell transcriptomics to reconstruct the molecular routes of how a murine fibroblast adopts cardiomyocyte fate following a continuum of states. In this study, we employed a comparative single cell transcriptomics approach to study human cardiac reprogramming. In comparison with murine fibroblasts and other human cell types, we identified unexpected heterogeneity in human cardiac fibroblasts that was mainly due to variance in cell cycle status. Trajectories inferred by SLICER suggest molecular routes and pathways taken by human fibroblasts when transiting into CM fate. Importantly, by assigning a “cell fate index” to each single cell on the iCM trajectories resolved from both mouse and human fibroblasts, we discovered species differences in fibroblast plasticity and intermediate cell fate statuses when reprogrammed towards a CM fate. Collectively, our comparative single cell transcriptomics study of human cardiac reprogramming revealed previously unrecognized molecular features of human cardiac fibroblasts and regulatory mechanisms in human cardiomyocyte cell fate control.

overall_design: Primary human cardiac fibroblasts were isolated and reprogrammed with polycistronic human MEF2C, GATA4, TBX5 and miR-133. Single cells were captured using the Fluidigm C1 system with the capacity of up to 96 single cells per experiment. A total of eight individual single-cell experiments were performed. One plate (D0hCF) contained uninfected d0 human primary fibroblasts. Two plates (D3M1 and D3M2) contained d3 MGT+miR-133-transduced cells. The fourth plate (D3UN) contained d3 DsRed-transduced cells (DsRed+ by FACS) mixed with d3 uninfected cells at 3:1 ratio. The rest four plates contained MGT+miR-133-transduced cells mixed with Tdtomato-transduced cells (Tdtomato+ by FACS) at 3:1 ratio, which were collected on d3 (D3M3), d5 (D5M1), d7 (D7M1), and d9 (D9M1), respectively. Control RNA spike-ins were added to the plate before cell lysis and processed in parallel to cellular RNA. Lysate from 704 wells containing single cells were selected for mRNA sequencing (raw data files) and a total of 652 high-quality single-cell transcriptomes were analyzed after QC (processed data).

first: Ziqing

last: Liu

first: Yang

last: Zhou

first: Li

last: Qian


title: Role of a-DR3 on group 3 innate lymphoid cells

status: Public on Jun 26 2019

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: In order to examine the role of a-DR3 on group 3  innate lymphoid cells, we treated Rag1-/-Rorcgfp/+ mice with a-DR3 (4C12) and examine the gene expression in ILC3s with RNA-seq analysis.

overall_design: Littermate groups of Rag1-/-Rorcgfp/+ mice were treated with PBS or 1μg of α-DR3 (4C12). ILC3 (Lin-GFP+) cells from large intestinal LPLs were purified by flow cytometry on day 3.

first: Jingyu

last: Li

first: Wenli

last: Shi

first: Yan

last: Ji


title: Dramatic changes in gene expression in adherent C. fasciculata reveal potential mechanisms for insect-specific adhesion of kinetoplastid parasites

city: Media

first: Megan

last: Povelones

state: PA

address: 25 Yearsley Mill Road

department: Sciences

institute: Penn State Brandywine

summary: Kinetoplastids are a group of parasite species, several of which cause important diseases in human and livestock. Nearly all of these pathogenic species are transmitted by insect vectors, in which the parasites undergo a specific developmental program. One shared event undergone by multiple species is adherence to insect tissue. This adhesion occurs by means of a hemidesmosome-like structure that is thus far uncharacterized. We have used the monoxenous parasite Crithidia fasciculata, which exclusively infects mosquitoes, to study this process of parasite adhesion in the insect. We have transcriptionally profiled adherent and swimming forms of the parasite that have been generated in vitro, and compared these profiles to the adhesive form in the mosquito. Using a dual-RNAseq approach, we have also identified several genes that are differentially regulated in infected versus uninfected mosquitoes, including several immune genes. This indicates that the mosquito is responding to the presence of the parasites.

sample_organism:
Crithidia fasciculata
Aedes aegypti

platform_organism:
Crithidia fasciculata
Aedes aegypti

overall_design: We isolated RNA from three flasks containing exclusively swimming C. fasciculata, and from three flasks containing exclusively adherent C. fasciculata. One of the replicates of adherent cells was excluded for technical reasons. We also infected three separate generations of mosquitoes with C. fasciculata, isolated RNA, and compared them RNA from age-matched uninfected controls.

first: John

last: Filosa

first: Corbett

last: Berry

first: Gordon

last: Ruthel

first: Stephen

middle: M

last: Beverley

first: Wesley

middle: C

last: Warren

first: Chad

last: Tomlinson

first: Peter

last: Myler

first: Elizabeth

last: Dudkin

middle: L

first: Michael


title: Zika infected neural stem cells

status: Public on Jun 18 2019

city: La Jolla

first: Tariq

last: Rana

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DNA methylation profilings of Blood Cell collected from CELSS 180-day experiment

city: Shenzhen

first: Yuan

last: Quan

state: Guangdong

address: Space Institute of Southern China, Shenzhen, Guangdong

department: Lab of Epigenetics and Advanced Health Technology

institute: Space Institute of Southern China

summary: In this study, we designed a space simulation study, named “4 Subjects 180-Day Controlled Ecological Life Support System (CELSS) Integration Experiment”, which took place in Shenzhen, China, from June to December 2016. In this experiment, four subjects  (3 males and 1 female) lived for 180  days in an enclosed simulated cabin, and multiple-sampling-point DNA methylation data was collected to conduct the epigenic  analysis. Peripheral whole blood cells were extracted from all 4 subjects on the 12 sampling points (Pre45, Pre15, R2, R30, R60, R75, R90, R105, R120, R150, R175 and Post30 mission day during the experiment).

overall_design: A longitudinal epigenetic profiling of 4 subjects in “4 Subjects 180-Day Controlled Ecological Life Support System (CELSS) Integration Experiment”. 48 samples of blood cell DNA methylation profiling were obtained by  Illumina HumanMethylation450 BeadChip, across 12 sampling points during the 180 days mission for all the 4 subjects

first: Fengji

last: Liang

first: Yuexing

last: Zhu

first: Ying

last: chen

first: Zi

last: Xu

first: Fang

last: Du

first: Ke

last: Lv

first: Hailong

last: Chen

first: Lina

last: Qu

first: Ruifeng

first: Hong-Yu

last: Zhang

first: Jianghui

last: Xiong

first: Yinghui


title: Identification of factors involved in JAK/STAT-dependent cell competition

first: Erika

last: Bach

state: NY

department: Biochemistry and Molecular Pharmacology

institute: NYU Grossman School of Medicine

summary: We report the transcriptional profiles obtained by next-generation sequencing (NGS) of FACS-purified cells from the dpp-domain of wing imaginal discs from mid-third instar Drosophila melanogaster larvae. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of dpp-domain cells that have elevated JAK/STAT signaling or elevated Myc expression compared to control cells.

overall_design: Examination of differentially-regulated genes in two types of wing imaginal disc cells, those with elevated JAK/STAT signaling and those with elevated Myc, compared to controls.

first: Poojitha

last: Sitaram


title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.

first: magdalena

last: potok


title: MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (ChIP-Seq)

first: Weisheng

last: Zheng

institute: Tongji University

summary: We knock down MYCN in human neuroblastoma cell line by RNAi. MYCN knock-down caused global epigenome change, including nucleosome gain on key DNA-repair genes and promoter H3K9ac down regulation.

overall_design: ChIP-seq of 6 histone modifications in ctrl/N-myc_kd neuroblastoma cell line BE2C

first: Xinjie

last: Hu

first: Cizhong

last: Jiang


title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_H2AZ]

overall_design: Examination of H2AZ profiles in SWR1 mutants.

first: Magdalena

last: Potok

first: Steven

last: Jacobsen


title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_H3Ac]

overall_design: Mapping of histone H3 acetylation in WT


title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [RNA-Seq]

overall_design: Total RNA was extracted from 13 DAG shoots grown on 1%MS supplemented with 1% sucrose under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of three seedlings. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo). For RNA-Seq, 1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina).


title: SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3-BASED GLIOMA PATIENT STRATIFICATION AND APPLICATION IN PRECISION ONCOLOGY

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

summary: Intratumoral heterogeneity is a hallmark of glioblastoma (GBM) tumors, thought to negatively influence therapeutic outcome. Previous studies showed that mesenchymal tumors fare more poorly than the proneural subtype. We focused on STAT3 because its activation precedes the proneural-mesenchymal transition. We first established a STAT3 gene signature that stratifies GBM patients into STAT3-high and -low cohorts. STAT3 inhibitor treatment selectively mitigated STAT3-high cell viability and tumorigenicity in orthotopic mouse xenograft models. Additionally, we defined the mechanism underlying resistance in STAT3-low cells by combining STAT3 signature analysis with kinome screen data on STAT3 inhibitor-treated cells. This allows us to draw connections between kinases affected by STAT3 inhibitors, their associated transcription factors and target genes. We demonstrate that dual inhibition of IGF-1R and STAT3 sensitized STAT3-low cells and improved survival in mice. Our study underscores the importance of serially profiling tumors so as to accurately target individuals who may demonstrate molecular subtype switching

overall_design: The mRNA extracted from STAT3 KD and NT GPCs, were hybridized on Affymetric HG U133Plus2 microarrays

first: Carol

last: Tang

first: Melanie

last: Tan

first: Christopher

last: Beng Ti


title: Bcl6 binding sites and neurogenic activity in in vitro cortical progenitors

city: Leuven

first: Pierre

last: Vanderhaeghen

address: O&N4 Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven


title: Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2 [RNA-Seq]

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

summary: Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and transcriptional waves with Oct6 and an Oct4 mutant defective in the dimerization with Sox2 (Oct4defSox2). We find that initial silencing of the somatic program proceeds indistinguishably with or without Oct4. Oct6 mitigates the mesenchymal-to-epithelial transition and derails reprogramming. These effects are a consequence of differences in genome-wide binding, as the early binding profile of Oct4defSox2 resembles Oct4, whilst Oct6 does not bind pluripotency enhancers. Nevertheless, in the Oct6-SK condition many otherwise Oct4-bound locations become accessible but chromatin opening is compromised when Oct4defSox2 occupies these sites. We find that Sox2 predominantly facilitates chromatin opening, whilst Oct4 serves an accessory role. Formation of Oct4/Sox2 heterodimers is essential for pluripotency establishment; however, reliance on Oct4/Sox2 heterodimers declines during pluripotency maintenance.

overall_design: We analyzed the gene expression profiles of Oct4,Oct6 and Oct4 mutant with two interface mutations leading to a disruption of the DNA dependent dimer with Sox2 (Oct4I21Y/D29R  in manuscript termed Oct4defSox2 and data in GEO is submitted by name "YR") at different time points (Days 0, 1, 3, 5, 8) during the somatic cell reprogramming by RNA-seq. In addition we also sequenced a 'POU-free' control where Oct4 was replaced by GFP in a GFP-SK cocktail.

first: Vikas

last: Malik

first: Ralf

last: Jauch


title: The Circadian Protein Nocturnin Regulates Metabolic Adaptation in Brown Adipose Tissue

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Fine-tuning of transcriptional responses can be critical for long-term outcomes in response to an environmental challenge. The circadian protein Nocturnin belongs to a family of proteins that include exonucleases, endonucleases and phosphatases and is most closely related to the CCR4 family of deadenylases that regulate the cellular transcriptome via control of polyA tail length of RNA transcripts. In this study, we investigate the role of Nocturnin in regulating the transcriptional response and downstream metabolic adaptations during cold exposure in brown adipose tissue. We find that Nocturnin exhibits dual localization within the cytosol and mitochondria, and loss of Nocturnin causes changes in expression of networks of mRNAs involved in mitochondrial function. Furthermore, Nocturnin-/- animals display significantly elevated levels of TCA cycle intermediates indicating that they have distinct metabolic adaptations during a prolonged cold exposure. We conclude that cold-induced stimulation of Nocturnin levels can regulate long-term metabolic adaptations to environmental challenges.

overall_design: We performed mRNA-seq analysis on brown fat (BAT) isolated from wild-type and Nocturnin-/- littermates at room temperature or after a 4-hour cold exposure. For cold exposure experiments, age-matched 10-20 week old young adult WT and Nocturnin-/-  mice were randomly assigned to cold (6C) or room temperature (22C) groups. Mice were single housed for the duration (4hrs) of the experiment and food was removed in order to minimize individual variation. N=4-5 mice per condition.

first: Yasemin

last: Onder

first: Isara

last: Laothamatas

first: Stefano

last: Berto

first: Katharina

last: Sewart

first: Gokhul

last: Kilaru

first: Bogdan

last: Bordieanu

first: Jeremy

last: Stubblefield

first: Prashant

last: Mishra

first: Carla

last: Green


title: Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2 [ATAC-Seq]

overall_design: We analyzed the chromatin accessibility  profiles of Oct4,Oct6 and an Oct4 mutant with two interface mutations leading to a disruption of the DNA dependent dimer with Sox2 (Oct4I21Y/D29R  in manuscript termed Oct4defSox2 and data in GEO is submitted by name “YR”) in replicates at days 1 and 5 of retrovirus based somatic cell reprogramming to iPSC  in highly efficient chemically defined iCD1 medium


title: Systematic Analysis of Allelic Silencing Defines the Interplay of Key Pathways in Xist-mediated Chromosome Inactivation

status: Public on Jun 17 2019

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome silencing through the stepwise recruitment of factors that modify underlying chromatin structure.  Whilst considerable progress has been made towards defining key silencing factors and the elements to which they bind, their relative contribution to silencing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in ES cell-based models. We show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of low expressed genes.  Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin.  LBR and the Rbm15-Mettl3/14 m6A-methyltransferase complex, previously proposed to have a central role, make at most a minor contribution to gene silencing.  We integrate our findings in a comprehensive model for Xist-mediated chromosome silencing.

overall_design: We isolated chromatin-associated RNA (ChrRNA) to analyze the allelic ratio, aiming to understand Xist-mediated Silencing. The ChrRNA was isolated from cells with trangenic Xist model (iXist-Chr3) or endogenous Xist model (iXist-ChrX) derived from mouse embryonic stem cells. Xist is composed of several repetitive elements, which act by interacting with different factors. Cell lines with different factor knockout or Xist domain deletions were generated. The allelic ratios were systematically and comprehensively compared.

first: G

first: T

last: Nesterova

first: H

last: Coker

last: Pintacuda

first: Q

last: Pan

last: Zhang

first: J

middle: S

last: Bowness

first: B

last: Bloechl

first: N

last: Brockdorff


title: m6A-seq profiling in WT, WtapKO and Mettl3KO mESCs

type: Methylation profiling by high throughput sequencing

summary: By m6A-seq, we examined the m6A pattern on Xist, which immediately after the A-repeat region. The cell line, integrating multiple copy of Xist on chr3, with m6A core machinery knockout (Wtap and Mettl3) were generated.  We also profiled m6A-seq in transgenic Xist line, and observed a global reduction of m6A level, validated by m6A-LC-MS/MS. Unexpectedly, we haven’t observed reduced m6A level on Xist m6A region downstream of A-repeat in transgenic Xist line.

overall_design: M6A profiling in WT, WtapKO, and Mettl3KO male mESC cells, in which Xist RNA was randomly integrated into Chr3 under the TetOn promoter. After dox treatment, Xist expressed from chr3 locus and leads to chr3 inactivation.  We are aiming to understand how m6A pattern was on Xist and how m6A modification on Xist affect Xist-mediated chromosome silencing.


title: AGO-iCLIP-seq analysis of Zika infected neural stem cells

first: Tariq

last: Rana

summary: AGO-iCLIP-seq was utilized to characterize the RNAs bound to AGO in human neural stem cells infected with Zika virus strains Paraiba at MOI 1. miRNAs and mRNAs were analyzed to determine changes in RNAs loaded into the RISC 4 days post-infection.

overall_design: Examination of AGO bound RNAs in human neural stem cells infected with  Zika virus Paraiba with 3 experimental replicates per group.

first: Jason

last: Dang


title: miRNA expression changes in HC-T116 cells before and after SHU00238 treatment

status: Public on Jun 13 2019

city: Shanghai

first: Rui

last: Chen

address: Nanchen Road 383

institute: Shanghai University

summary:
newly developed isoxazole derivative SHU00238 suppressed cell proliferation and promoted cell apoptosis in vitro， SHU00238 treatment significantly inhibited colonic tumor growth in vivo.
we used microarrays to detail the miRNA expression in HCT116 cell line underlying the influence of SHU00238

overall_design: Two group of total RNA from HCT116 with or without SHU00238 treatment were subjected to hybridization to Affymetrix miRNA4.0 arrays，i.e.SHU00238（238），control（con)


title: miRNA analysis of Zika infected neural stem cells

summary: small RNA-seq was utilized to characterize the transcriptome of human neural stem cells infected with Zika virus strains MR766 and Paraiba at MOI 1. Coding and noncoding genes were analyzed to determine transcriptional changes 3 days post-infection.

overall_design: Examination of miRNA expression of human neural stem cells infected with  Zika virus MR766 and Paraiba with 2 experimental replicates per group.


title: Expression data of isp-1(qm150);ctb-1(qm189) mutant, exposed to klf-1 RNAi during development or adulthood

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

institute: Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases

summary: We showed that KLF-1 is needed for longevity of isp-1(qm150);ctb-1(qm189) mutant specifically in adulthood. We aimed to determine the expression changes that occur specifically upon adulthood klf-1 RNAi compared to developmental RNAi that did not affect the lifespan of isp-1(qm150);ctb-1(qm189) mutant.

overall_design: isp-1(qm150);ctb-1(qm189) mutant was exposed to klf-1 RNAi either until L4 larval stage, after which it was switched to control L4440 plates, or swicthed at L4 larval stage to klf-1 RNAi plates from control L4440 plates. Worms were then grown until fifth day of adulthood and collected for RNA isolation. In parallel, isp-1(qm150);ctb-1(qm189) mutant and wild type N2 worms were grown on control L4440 plates their whole life and collected at the fifth day of adulthood. Three biological repeats were obtained for each sample.

first: Marija

last: Herholz

first: Linda

last: Baumann

first: Peter

last: Frommolt


title: Global gene transcription analysis in response to changes in chromosome supercoiling in Streptomyces coelicolor

status: Public on Jun 14 2019

city: Wroclaw

first: Marcin

middle: Jan

last: Szafran

address: Joliot-Curie 14A

department: Faculty of Biotechnology

country: Poland

institute: University of Wroclaw

summary: Here, we address the transcriptional response to both novobiocin-induced rapid chromosome relaxation or long-term topological imbalance, both increased and decreased supercoiling, in environmental antibiotic-producing bacteria belonging to the Streptomyces genus.

overall_design: RNA was extracted from vegetative hyphae of Streptomyces coelicolor growing for 18h in liquid YEME/TSB medium (30 mL). To induce supercoiling changes S. coelicolor culture was treated with novobiocin in final concentration 10 g/ml for 10 min (rapid chromosome relaxation). For long-term exposure to topological imbalance we used PS04 stain in which TopA level is controlled by thiostrepton addition (long-term high and low DNA supercoling in not induced and induced PS04 strain, respectively)

first: Martyna

last: Gongerowska

first: Tomasz

last: Małecki

first: Marie

last: Elliot

first: Dagmara

last: Jakimowicz


title: Transcriptome analysis of Zika infected neural stem cells

summary: RNA-seq was utilized to characterize the transcriptome of human neural stem cells infected with Zika virus strains MR766 and Paraiba at MOI 1. Coding and noncoding genes were analyzed to determine transcriptional changes 3 days post-infection.

overall_design: Examination of transcriptome of human neural stem cells infected with  Zika virus MR766 and Paraiba with 2 experimental replicates per group.


title: Gene expression changes in mouse breast cancer cells (4T1) after axitinib resistance

status: Public on Jun 12 2019

city: Buffalo

first: John

last: Ebos

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

institute: Roswell Park Cancer Institute

summary: RNA sequencing analysis was used to identify changes in mouse breast cancer cells (4T1) resistant to axitinib (AxR).

overall_design: Mouse breast cancer cells (4T1) resistant to axitinib were derived in vivo after continuous treatment with 100mg/kg/day axitinib from post-surgical metastatic lesions. Resistant cells were maintained in vitro with 0.5μM axitinib for more than 2 months.

first: Michalis

last: Mastri


title: Association of cohesin subunits on chromosomes

status: Public on Jun 11 2019

first: Christophe

last: Chapard

address: South Parks road

department: Biochemistry

summary: Characterisation of the effect of wpl1 and Eco1 on association of Cohesin subunits onto chromosomes in S. cerevisiae

overall_design: Mutants strains calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies)


title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes

first: Ligang

last: Wu

state: Shanghai

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

summary: Small RNAs have important functions. However, small RNAs in primate oocytes remain unexplored. Herein, we develop CAS-seq, a single-cell small RNA sequencing method, and profiled the small RNAs in human oocytes and embryos. We discover a class of ~20-nt small RNAs that are predominantly expressed in human and monkey oocytes, but not in mouse oocytes. They are specifically associated with HIWI3 (PIWIL3), whereas significantly shorter than the commonly known PIWI-interacting RNAs (piRNAs), designated as oocyte short piRNAs (os-piRNAs). Notably, the os-piRNAs in human oocytes lack 2’-O-methylation at the 3’ end, a hallmark of the classic piRNAs. In addition, the os-piRNAs have a strong 1U/10A bias and are enriched on the antisense strands of recently evolved transposable elements (TEs), indicating the potential function of silencing TEs by cleavage. Therefore, our study has identified an oocyte-specific piRNA family with distinct features and provides valuable resources for studying small RNAs in primate oocytes.

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Evaluate the reproducibility and sensitivity of CAS-seq to detect small non-coding RNAs (sncRNAs) in mouse oocyte/testis and three cell lines, including HEK293, A549 and Hela. Compare the profiles of sncRNAs in the oocyte of human, mouse and monkey, and investigate the characteristics of sncRNAs and their function and expression dynamics in human oocyte and early embryos.

first: Qiyuan

last: Yang

first: Ronghong

last: Li

first: Qifeng

last: Lyu

first: Li

last: Hou

first: Zhen

last: Liu

first: Qiang

last: Sun

first: Miao

first: Huijuan

last: Shi

first: Beiying

last: Xu

first: Mingru

last: Yin

first: Zhiguang

last: Yan

first: Ying

last: Huang

first: Mofang

first: Yiping


title: Transcriptome changes caused by Tudor-SN mutations in rice seed

status: Public on Jun 07 2019

city: Pullman

last: Tian

address: Clark hall, IBC, Washington State University

department: IBC

institute: Washington State University

summary: One OsTudor-SN mutant, EM1084, carrying E503K point mutation and one associated WT-OsTSN complemented transgenic (pHL8042/EM1084 ) were applied in this study. EM1084 was obtained by TILLING studies (http://www.shigen.nig.ac.jp/rice/oryzabase). The E503K mutation site in EM1084 lies within the SN3 domain, while the EM1084 complemented transgenic plant was complemented with the full-length WT OsTSN gene driven by native OsTSN promoter. This mutation results in affecting storage protein mRNA localization and, in turn, with a strong reduction in grain weight and storage protein accumulation. Transcriptome analysis on the dehulled 10-14 days old developing seeds from wild type, EM1084 and pHL8042/EM1084 indicates that partial loss of Tudor-SN function caused the differential expression of storage protein genes and relevant genes involved in several essential biological processes during rice development.

overall_design: Total 9 samples were anlyzed, including 3 biological repeats from each genotype,wild type, EM1084 (E503K) and pHL8042/EM1084

first: Hong-Li

last: Chou

first: Thomas

middle: W

last: Okita


title: Transcriptome Signature of Cellular Senescence

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Abstract: Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage, and signaling from activated oncogenes.  At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated protein expression and secretion, DNA damage, and β-galactosidase activity; unfortunately, these traits are neither exclusively nor universally present in senescent cells.  To identify robust shared markers of senescence, we have performed RNA-sequencing analysis across 8 diverse models of senescence triggered in human diploid fibroblasts (WI-38, IMR-90) and endothelial cells (HUVEC, HAEC) by replicative exhaustion, exposure to ionizing radiation or doxorubicin, and expression of the oncogene HRASG12V.  The intersection of the altered transcriptomes revealed 47 RNAs consistently elevated and 26 RNAs consistently reduced across all senescence models, including many protein-coding mRNAs and some long noncoding RNAs.  We propose that these shared transcriptome profiles will enable the identification of senescent cells in vivo, the investigation of their roles in aging and malignancy, and the development of strategies to target senescent cells therapeutically.

overall_design: Transcriptomic analysis of various cell line models of senescence and their respective controls

first: Gabriel

last: Casella

first: Rachel

last: Munk

first: Kyoung

last: Kim

first: Yulan

last: Piao

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Mitofusins Regulate Lipid Metabolism to Mediate the Development of Lung Fibrosis

city: Taipei

first: Kuei-Pin

last: Chung

address: No 7, Chung-Shan South Rd

department: Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

summary: Idiopathic pulmonary fibrosis (IPF) is a devastating chronic lung disease, where lung function decline is gradual and the overall prognosis of patients with IPF is poor with a median survival after diagnosis of approximately 3.8 years. Growing evidence points to the fundamental role for the mitochondrion in alveolar type 2 (AEC2) cell dysfunction in the pathogenesis of IPF. Additionally, single-cell RNA sequencing (RNA-Seq) recently identified MFN2 mRNA as significantly upregulated in AEC2 cells from patients with IPF, suggesting a role for mitochondrial fusion in AEC2 cells and the development of IPF. To investigate the roles of mitofusin 1 (MFN1) and mitofusin 2 (MFN2) of AEC2 cells in the pathogenesis of pulmonary fibrosis, we utilized genetically modified mice harboring MFN1 and/or MFN2 flanked by two loxP sites, and crossed them with Sftpc-CreERT2 mice, in which the AEC2 cell specific Sftpc-promoter drives the expression of tamoxifen-responsive CreERT2. Using this approach, we were able to selectively delete MFN1, MFN2 and both MFN1 and MFN2 together in AEC2 cells of the lung. Profoundly, in the absence of both mitofusins in AEC2 cells, we observe significant morbidity and mortality associated with disordered mitochondrial dynamics, failure of surfactant lipid production and the development of spontaneous pulmonary fibrosis, reminiscent of usual interstitial pneumonitis observed in the lungs of patients with IPF. Furthermore, we showed that mice with MFN1 or MFN2 deletion in AEC2 cells would have deteriorated bleomycin-induced pulmonary fibrosis. The results together confirmed the critical roles of MFN1 and MFN2 in AEC2 cells in protecting the lung from fibrotic process.

overall_design: To explore the detailed transcriptomic responses, we isolated AEC2 cells from control mice (n=3) or mice with MFN1/2 loss (n=3) in AEC2 cells at 6 weeks after tamoxifen-induced target gene deletion. RNA of AEC2 cells was extracted using TRIzol reagent (Invitrogen), and was purified by the RNeasy Plus Mini Kit (Qiagen), together with DNA digestion with the RNA free DNase set (Qiagen). The RNA samples were then submitted to Genomic Resource Core Facility of Weill Cornell Medical College for next generation RNA sequencing. On the other hand, we isolated AEC2 cells from control mice, or mice with MFN1 or MFN2 loss in AEC2 cells, at 5 days after bleomycin or PBS intra-tracheal administration (n=4 per group). RNA extraction and the subsequent RNA sequencing were performed as described above.

first: Suzanne

last: Cloonan

first: Augustine

last: Choi


title: m6A modification of a 3′ UTR site reduces RME1 mRNA levels to promote meiosis

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

summary: We performed m6A-seq on 5h meiotic yeast from WT and ime4-cat background (IP and input), and RNA-seq on total and polysome RNA of 5h meiotic yeast from WT, ime4-cat, and rme1-10 backgrounds

overall_design: 12 yeast m6A-seq samples, 18 yeast RNA-seq samples


title: RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens

city: Münster

first: Petya

last: Berger

address: Robert-Koch Straße 41

department: Institute of Hygiene

institute: University of Münster

summary: Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.

overall_design: Exponentially growing E. coli K-12 MG1655, MG1655::φO104 (carrying the Stx2 phage of E. coli O104:H4) and MG1655::φPA8 (carrying the Stx2 phage of E. coli O157:H7 PA8) cells were subjected to strand specific RNA-seq. Three biological replicates per strain were included. DESeq2 analysis based on the reads mapped to the E. coli MG1655 genome was performed to identify examples of differential gene expression in the Stx2 lysogens in comparison to naive E. coli MG1655.

first: Berger

last: Petya


title: Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference.

overall_design: ChIP-Seq against transcriptoin and splicing machinery in mouse embryonic stem cells

first: Yang

last: Guo

first: John

last: Manteiga

last: Henninger

first: Benjamin

middle: R

last: Sabari

first: Alessandra

last: Dall’Agnese

first: Nancy

last: Hannett

first: Jan

middle: H

last: Spille

first: Lena

last: Afeyan

first: Alicia

last: Zamudio

first: Krishna

last: Shrinivas

first: Brian

middle: J

last: Abraham

first: Ann

last: Boija

first: Tim

last: Decker

first: Jenna

last: Rimel

first: Charli

last: Fant

first: Tong

last: Lee

first: Ibrahim

last: Cisse

first: Phillip

last: Sharp

first: Dylan

last: Taatjes


title: Xist-mediated Chromosome Inactivation

first: Guifeng

last: Wei

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

overall_design: Refer to individual Series


title: ATACseq and RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

status: Public on Jun 06 2019

first: Florian

last: Bonkhofer

address: John Radcliffe Hospital/Headley Way

institute: Oxford University


title: RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

summary: The goal of this study is to perform RNAseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034). High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used  to generate SMARTer libraries for low-input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32). Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1). To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).

overall_design: Analysis of 5 different cell types; DN (double negative), SP-kdrl (single positive), DP-R1lo (double positive runx1 low expression), DP-R1med (runx1 medium expressionand) and DP-R1hi (runx1 high expression) in non-injected (Wt) TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. Analysis was also done of the DN and DP-R1hi populations in runx1-morpholino (MO) injected embryos.

first: Rossella

last: Rispoli


title: Expression profile of rat kidney of fetuses with 19 days of gestation under chronic rotation of the photoperiod.

city: Valdivia

first: Carlos

last: Spichiger

state: Región de los Rios

address: Instituto de Bioquímica y Microbiología, campus Isla Teja, UACh

department: Instituto de Bioquímica y Microbiología

country: Chile

institute: Universidad Austral de Chile

summary:
Previously, we reported that of pregnant dams rats exposure to continues light and rotation of photoperiod have detrimental effects on the mother, fetus and adult offspring, with changes in the expression profile of fetal heart and liver.
We investigated whether the chronic rotation of the photoperiod (CPS) during gestation can modify the fetal kidney expression profile at gestational day 19 by Affymetrix microarray analysis.

overall_design: Pregnant rat females were separated randomly into two groups: LD group, pregnant females kept 12:12 photoperiod throughout gestation (n=6 mothers LD), and the second group was CPS (Chronic photoperiod shifting) corresponding to pregnant females (n=6 mothers CPS) kept under a rotation scheme of photoperiod. At E19 we evaluate the global fetal transcriptome by microarray analysis of pooled fetal kidney for each mother.

first: Hans

last: Richter


title: Gene expression from mouse models of B cell lymphomagenesis driven by gp130 signaling

city: Munich

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

summary: This study examines the transcriptional changes invoked by activation of gp130 signaling in different mouse models of B cell lymphomagenesis. In order to study the in vivo effects of aberrant activity of IL-6/IL-6R/gp130-JAK/STAT3 signaling, we designed a transgene that allows conditional expression of L-gp130 by generating a ROSA26 knock-in mouse strain where compound L-gp130 and ZsGreen expression from the CAG promoter is prevented by a loxP- and a rox-flanked stop cassette. Total RNA extracted from purified B cells from young CD19Cre+/- ;L-gp130fl/+ and wildtype control mice was sequenced using unique molecular identifiers (UMI) in a paired end design where read1 corresponds to the cDNA and read2 contains the UMI. Furthermore, aging CD19Cre+/- ;L-gp130fl/+ animals developed tumors located predominantly in mesenteric lymph nodes. Infiltration of CD19;L-gp activated B cells was determined by Flow Cytometry and ZsGreen expression. Total RNA from tumors generally containing >60% ZsGreen+ cells was profiled as described above, for tumors with lower CD19;L-gp activated B cell content FACS was applied. In order to study the effects of activated IL-6/IL-6R/gp130-JAK/STAT3 signaling on Eµ-Myc-driven lymphomagenesis, CD19Cre;L-gp130fl;Eµ-Myc triple transgenic mice were generated and fetal liver hematopoietic stem/progenitor cell (FL-HSPC) grafts were transplanted into lethally irradiated syngeneic mice alongside FL-HSPC from CD19Cre;L-gp130f and Eµ-Myc control mice. Lastly, IL-6/IL-6R/gp130-JAK/STAT3 signaling was activated in the entire hematopoetic system using Vav1Cre resulting in Vav1Cre+/- ;L-gp130fl/+ animals. Independent of the time point of activation during hematopoietic and B cell differentiation, all Cre;L-gp compound mice succumbed to tumors of B cell origin.

overall_design: Bulk gene expression data are presented for (i) purified B cells from wildtype control mice (n=6) and young CD19;L-gp mice (n=4), (ii) tumors detected in aging CD19;L-gp mice with a mature (n=11) and plasma cell phenotype (n=6), respectively, (iii) tumors arising in lethally irradiated syngeneic mice after transplantation of fetal liver hematopoietic stem/progenitor cells from CD19;L-gp;Myc (n=9), CD19;L-gp (n=7) and Eµ-Myc (n=9) mice, respectively, and (iv) malignant B cells from Vav1;L-gp mice (n=13).

first: Anna

middle: K

last: Scherger

first: H

first: Rupert

last: Öllinger

first: Ulrich

last: Keller


title: A cancer associated fibroblast hierarchy driven by mutant p53 induces perlecan deposition in  the pancreatic tumor stroma to permit metastasis and impairs response to chemotherapy

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

institute: Garvan Institute

summary: Heterogeneous sub-populations of cancer cells exist within pancreatic tumors and shape the local stroma. Recent studies have provided evidence that subtypes of cancer-associated fibroblasts (CAFs) also coexist within pancreatic cancer tissues and can both promote and restrain disease progression. Here, we interrogate how cancer cells harboring distinct alterations in p53 (loss or gain-of-function) manipulate CAFs using matched CAFs and cancer cells isolated from the low metastatic KPflC (p53 null) and highly metastatic KPC (gain-of-function p53 mutant) mouse models of pancreatic cancer. We reveal the existence of a p53-driven hierarchy, where cancer cells with a gain-of-function (GOF) mutant p53 educate a dominant population of CAFs that drive the establishment of a pro-metastatic environment for GOF and null p53 cancer cells alike. We also demonstrate that CAFs educated by null p53 cancer cells may be reprogrammed by either GOF mutant p53 cells or their CAFs. Using proteomic characterization of CAF secretomes combined with CRISPR-Cas9 based editing identified perlecan as a key component of this pro-metastatic and resistant environment. Lastly, using longitudinal intravital imaging with a CDK1 FRET reporter and titanium windows, we observe that these dominant CAFs delay cancer cell response to gemcitabine/Abraxane in both GOF and null p53 cancer cells. We also reveal that depletion of perlecan in the stroma combined with chemotherapy prolongs mouse survival, supporting it as a potential novel target for development of anti-stromal therapies in pancreatic cancer.

overall_design: Gene expression analysis of four primary mouse pancreatic tumor cell lines: (i) p53fl (null); (ii) p53 mutant (R172H); (iii) p53fl (null) + vector; and (iv) p53fl (null) + human mutant p53 (R175H).

first: Claire

last: Vennin

first: David

last: Herrmann

first: Paul

last: Timpson


title: KLRG1 and NKp46 expressing CD117+ human innate lymphoid cell precursors are biased to ILC2 and ILC3, respectively

status: Public on Jun 05 2019

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

summary: Recently, circulating multi- and uni-potent human ILC precursors (ILCP) have been found in a lymphocyte population that expresses CD117 and CD127 but lacks CRTH2 and NKp44. However, these ILCPs have not been extensively characterized. We performed an unbiased Hierarchical Stochastic Neighbor Embedding (HSNE) analysis of the phenotype of peripheral blood CD117+ ILCPs which revealed the presence of three major subsets: the first expressed NKp46, the second expressed both NKp46 and CD56, while the third expressed KLRG1. Analysis of their differentiation potential on bulk and clonal levels, cytokine production and the transcriptome revealed that the NKp46+ ILCPs contain high frequencies of ILC3 precursors whereas a minority can differentiate into ILC1/NK-like cells. In contrast, KLRG1+ ILCPs are biased to the ILC2 lineage, but are highly plastic and epigenetically primed to differentiate into other ILC subsets depending on the activation signals they receive.

overall_design: biological replicate (n=3) ATAC-Seq experiments

first: Rudi

last: Hendriks

first: Suzanne

last: Bal