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

city: Heidelberg

first: Lukas

last: Mathur

address: Meyerhofstraße 1

department: Genome Biology

institute: EMBL

summary: K562 cells were perturbed with drug combinations for 12h in droplets. Subsequently cells were processed to generate libraries for RNA-Seq.

overall_design: Small drug screens followed by RNA-Seq, with 16 combinatorial treatment conditions (small_scale_matrix).  The barcoding scheme on the microfluidic pipeline was changed and therefore  a total of six raw files (2x 3 replicates). For each replicate in the two screen, an additional separate control was performed called DMSO_[1-3]_dT or DMSO _[1-3]_BIO.

first: Bence

last: Szalai

first: Jonathan

last: Laundry

first: Vladimir

last: Benes

first: Christoph

last: Merten


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

status: Public on May 20 2021

country: Germany

type: Expression profiling by high throughput sequencing

overall_design: Large scale drug screen was performed, in which 3x 420 combinatorial treatment conditions were generated and analysed by RNA-Seq  (large_scale_matrix). For each replicate one additional control was performed called DMSO_DMSO_ctrl.

middle: J

middle: A


title: MAML3 overexpression in neuroendocrine cell lines

city: Aurora

first: Nikita

last: Pozdeyev

state: CO

address: 1890 N. Revere Court | Mailstop F600

department: Biomedical Informatics

country: USA

institute: University of Colorado

summary: The goal of this study was to determine differentially regulated pathways in neuroendocrine cells (SK-N-SH, BON-1, QGP-1) that over-expressed full length or exon 1 deleted MAML3 compared with vector control.

overall_design: SK-N-SH, BON-1 and QGP-1 cells were transfected with vector control, FL MAML3 or dEx1 MAML3. Three biological replicates were plated in triplicate. On day three post transfection, RNA was harvested using Trizol (Invitrogen) and 1mcg total RNA was submitted to the Genomics and Microarray Core at the University of Colorado for library prep using an Illumina TruSeq mRNA library kit (Illumina, San Diego, CA, USA). Sequencing was performed on a NanoSeq 6000 (Illumina). During analysis, adapter sequences were removed with the help of Trimmomatic trimmer, and the “Tuxedo” pipeline was used for transcript expression analysis, as previously described. RNAseq reads were aligned to the hg19 reference genome with HISAT2; stringtie was used for transcriptome assembly and transcript abundance estimation.

first: Lauren

last: Fishbein


title: ANXA10 Promotes Melanoma Metastasis by Suppressing the Ubiquitination of PKD1 Mediated by E3 Ligase TRIM41

city: Nanjing

first: Zichun

last: Hua

address: Xianlin Road 163# Nanjing University Xianlin Campus

department: School of Life Science

country: China

institute: Nanjing University

summary: Melanoma is a highly metastatic type of cancer which requires novel and effective targeted therapies. Annexin A10 (ANXA10), a member of annexin family, is a calcium and phospholipid binding protein. Considerable evidences indicate that ANXA10 is involved in tumor progression, but little is known about the involvement of ANXA10 in melanoma. In this study, we reported that ANXA10 expression was significantly up-regulated and correlated with melanoma progression. Knockout of ANXA10 profoundly reduced cell migration and metastatic activity of melanoma. Mechanistic investigations showed that ANXA10 knockout induced N- to E-cadherin switch by upregulating SMAD6, an inhibitory SMAD in TGF-β/ SMAD pathway. The negative regulation of ANXA10 on SMAD6 was dependent on PKD1. We demonstrated that ANXA10 interacted with PKD1 and inhibited E3 ligase TRIM41-mediated PKD1 degradation. In B16F10 melanoma cells, the protein levels of ANXA10 and PKD1 were negatively correlated with SMAD6, but positively related to cell migration. In addition, a negative correlation of ANXA10 and SMAD6 levels was also observed in clinical samples, which was associated with melanoma progression. Our findings suggest that ANXA10/PKD1/ SMAD6 axis might be new targets of therapeutic strategies for melanoma metastasis.

overall_design: Total mRNA profiles of two B16F10 cell lines of wild type (WT) and ANXA10 Knock out (A10KO) .

first: Xuerui

last: Zhang

first: Zhaoqing

last: Hu

first: Xinran

last: Wang


title: ORAI1 establishes resistance to SARS-CoV-2 infection by regulating tonic type I interferon levels

city: Irvine

first: Arunachalam

last: Ramaiah

state: CA

address: McGaugh Hall

department: Ecology and Evolutionary Biology

institute: University of California, Irvine

summary: We report RNAseq analysis of control, ORAI1KO and STIM1 KO (knockout) HEK293-ACE2 cells under uninfected (mock) and SARS-CoV-2-infected conditions

overall_design: Control, ORAI1KO and STIM1 KO (knockout) HEK293-ACE2 cells were either uninfected or infected with SARS-CoV-2 at MOI 1.0 for ~20 hrs

first: Beibei

last: Wu

first: Gustavo

last: Garcia

first: Yousang

last: Gwack

first: Vaithilingaraja

last: Arumugaswami

first: Sonal

last: Srikanth


title: Transcriptome profiling of mouse retina organoids at defined days in culture

city: Leipzig

first: Jana

last: Schor

state: Saxony

address: Permoserstr. 15

department: Molecular Systems Biology

institute: Helmholtz Centre for Environmental Research

summary:
Methods: Mouse retinal organoids (MRO) profiles at day 20, 22, 25, and 30 in culture under control conditions. MROs were generated using the previously established trisection protocol (Völkner et al. 2016, 2019). Single-end sequencing with 30 Mio reads per sample was performed at a length of 75 bases on HiSeq2500 (Illumina). The sequence reads that passed quality filters were analyzed at the transcripts level.
Results: Our histologic studies indicate that MROs complete retinogenesis at day 20, and mature including development of a stratified structure with outer and inner plexiform layers and synapses within day 20 to 30. Further, immunostaining and ultrastructural studies showed that photoreceptors neurons mature, including nascent outer segment formation. However, MRO maturation is still incomplete and MRO start to undergo some pathologic changes starting at day 30 and progressing upon longer term culture. Transcriptome analysis support and extend this based on differential changes in temporal gene expression: For example. regulators of retinal development and proliferation cease over time. Further, genes involved in the formation of photoreceptor outer segments, synaptogenesis, and phototransduction machinery increase. Starting at day 30, gene involved in reactive gliosis and retinal neuroprotection are upregulated indicating pathologic changes at the molecular level.
Conclusions: Transcriptome analysis of MROs support and extend our findings at the histological level, indicating that MROs reproducibly undergo several stages in culture, i.e. complete retinogenesis, mature on the cellular and molecular level, and develop some pathologic changes.

overall_design: Mouse retinal organoids (MRO) profiles at day 20, 22, 25, and 30 in culture under control conditions (n=6 MRO per timepoint from N=1 independent experiment), generated on HiSeq2500 (Illumina).

first: Manuela

last: Völkner

first: Mike

middle: O

last: Karl


title: High-throughput sequencing of Lactobacillus casei BL23 sRNAs

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: In the present study we characterized the sRNA profile of Lactobacillus casei BL23 using conventional and mDOT-seq approaches. In total 307 potential sRNAs were identified, 28 of which were validated by Northern hybridization. As a major portion of predicted sRNAs were shown to be conserved among the related species of Lactobacillus casei group (LCG), the results obtained in this study could serve as a valuable resource for achieving a better understanding of LCG physiology or even improving their applications in industry and medicine.

overall_design: Nine samples were prepared and analysed covering three different library preparations (two for mDOT-seq and one conventional) with three biological replicates each.

first: Milda

last: Mickutė

last: Kvederavičiūtė

first: Giedrius

last: Vilkaitis


title: Sequencing of miRXplore Universal Reference (Miltenyi Biotec) RNA using mDOT-seq

type: Non-coding RNA profiling by high throughput sequencing

summary: In present study we optimized and validated the mDOT-seq approach with miRXplore Universal Reference (Miltenyi Biotec) RNA. The results revealed that the 3' adapters with alkyne moieties attached to the fifth carbon atom of the second cytosine or uracil in ACTC and CUCC sequences, respectively, are best suited for the preparation of RNA sequencing libraries.

overall_design: Using mDOT-seq eight samples with four different 3' alkyne-adapters (two experimental replicates each) were prepared and analysed.


title: EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer [ATAC-seq].

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cells utilize epigenetic alterations to acquire autonomous capabilities for tumor maintenance. Here, we show that pancreatic ductal adenocarcinoma (PDA) cells hijack super-enhancers (SEs) to activate the EVI1 gene with its tumor-intrinsic program. We demonstrate that SE is the vital cis-acting element to maintain aberrant EVI1 transcription in PDA cells. Related to disease progression and inferior survival outcomes in human PDA, functional experiments further show that EVI1 upregulation is the cause of aggressive tumor phenotypes. In particular, EVI1 mediates the resistance to anchorage-independent growth and enhanced motility in vitro, with efficient tumor propagation in vivo. EVI1-dependent activation of gene expression program attributes to these phenotypes, by which EVI1 drives the stepwise configuration of the active enhancer chromatin. In sum, our findings support the promise that EVI1 is a crucial driver of oncogenic transcription program in PDA cells. Further, we emphasize the instructive role of epigenetic aberrancy in establishing PDA tumorigenesis.

overall_design: ATAC-seq of mouse PDA cells with EVI1 gain- or loss-of-function

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Gut microbiota analysis in WT and Il17d-deficient mice treated with or without colitis

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Microbiota dysbiosis has been reported to contribute to the pathogenesis of colitis, to demonstrate whether IL-17D protects against DSS-induced colitis through regulation of microflora, we performed 16S rRNA sequencing in feces from WT and Il17d-deficient mice. Our data indicate that Il17d deficiency results in microbiota dysibiosis in both steady state and DSS-induced colitis.

overall_design: Fresh mouse fecal samples were collected and microbial DNA was isolated from stools of WT and Il17d-deficient mice treated with or without colitis by using QiAamp DNA Stool Mini Kit (QIAGEN) according to manufacturer’s instructions. DNA concentration was checked with Nanodrop (Thermo Scientific). The V4 regions of the bacteria 16S rRNA gene were amplified by PCR using primers 515F-806R. The 16S rDNA amplicons were sequenced on an Illumina (HiSeq 2500) platform by Beijing Genomics Institute.

first: Jinling

last: Huang


title: Targeting triple negative breast cancer with combination therapy of epidermal growth factor receptor-targeted chimeric antigen receptor T cell and CDK7 inhibitor

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: Epidermal growth factor receptor-targeted chimeric antigen receptor T cell (EGFR CAR-T) is potent and specific in suppressing triple-negative breast cancer (TNBC) cell growth in vitro and in vivo. However, a subset of mice soon acquired resistance, which limits the potential use of EGFR CAR-T. The aim of this study is to find a way to overcome the observed resistance. Transcriptomic analysis results revealed that EGFR CAR-T treatment led to the induction of a cohort of immunosuppressive genes, presumably through Interferon gamma (IFNγ signaling, in EGFR CAR-T-resistant TNBC tumors. EGFR CAR-T-induced immunosuppressive genes were found to be associated with EGFR CAR-T-activated enhancers and especially sensitive to THZ1, a CDK7 inhibitor, out of a panel of small molecules targeting epigenetic modulators screened. Accordingly, combination therapy of THZ1 and EGFR CAR-T suppressed immune resistance and tumor growth and metastasis in TNBC tumor models including human MDA-MB-231 cells-derived xenografts, TNBC patient-derived xenografts, and mouse EMT6 cells-derived allografts in mice. Taken together, we demonstrated that CAR-T therapy-induced immune resistance can be overcome by transcriptional modulation using epigenetic inhibitors, providing a therapeutic avenue for treating TNBC in the clinic.

overall_design: RNA-seq was performed to identify differential genes in MBA-MB-231 in different condition.

first: Lin

last: Xia

first: Zao-zao

last: Zheng

first: Jun-yi

last: Liu

first: Yu-jie

last: Chen

first: Jian-cheng

first: Guo-sheng

last: Hu

first: Su-ling

first: Wen-xin

last: Luo

first: Ning-shao

first: Wen


title: EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer [RNA-seq].

overall_design: RNA-seq of mouse PDA cells with EVI1 gain- or loss-of-function


title: EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer.

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

overall_design: Refer to individual Series


title: Gene expression analysis of neurons differentiated from iPS cells generated from the fibroblasts of monozygotic twins discordant for schizophrenia

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

summary: Schizophrenia is heterogenious and polygenic disorder, and thus obtaining geneticly close control samples are valuable to increase the effect size. We obtained skin biopsies from five identical twin pairs discordant for schizophrenia and reprogrammed the cells to induced pluripotent stem cells (iPSCs). They are all Finnish/Caucasians, and the study was approved by ethical commitee in Finland. As schizophrenia affects mostly cognitive functions, we differentiated iPSCs to cortical neurons, moslty excitatory glutamatergic neurons and performed RNA sequencing for transcriptomic changes in neurons from patients with schizophrenia.

overall_design: Ribo-depleted RNA was sequenced with Illumina Next-seq 500 from iPS derived neurons

first: Jari

last: Koistinaho

last: Tiihonen


title: Comparison of transcriptional profiles of (1) intestinal ILC3s isolated from WT and IL-17D-deficient mice; (2) CD93+ILC3s and CD93-ILC3s from WT mice

summary: IL-17D/CD93 axis was essential for ILC3s hemostasis. In order to further understand how IL-17D-CD93 axis regulate ILC3s function, we conducted RNA-seq analysis of ILC3s.

overall_design: Cell suspension were isolated from intestine of WT or  IL-17D-deficient mice under steady state and ILC3s (live CD45lowCD3negCD19negCD90.2high) were sort purified. CD93+ or CD93- ILC3s were sorted from WT mice. RNA was isolated and RNA-seq was performed using BGISEQ-500 platform by BGI Genomics and successfully mapped to mouse genome.

first: Xiaohong

last: Zhao


title: Interleukin-17D regulates group 3 innate lymphoid cell function through its receptor CD93

sample_organism:
Mus musculus
Microbiota

platform_organism:
Mus musculus
Microbiota


title: miRNA expression of cultured 4T1 cells sorted by the grade of ALDH activity

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

summary: The expression of miRNA was investigated in  cultered 4T1 cells sorted by the grade of ALDH activity.

overall_design: miRNA expression of cultered 4T1 cells sorted by the grade of ALDH activity.　The expression of miRNA in high ALDH activity 4T1 cells was revealed compared with low ALDH activity 4T1 cells.

first: Naoya

last: Matsunaga

first: Kaori

last: Yasuda

first: Atsushi

last: Doi


title: EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer [ChIP-seq].

first: Jae Seok

last: Roe

overall_design: ChIP-seq of mouse PDA organoids or cells with EVI1 gain- or loss-of-function

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Single Cell sequencing analysis of adult AT1 Yap/Taz KO and wild-type lung epithelium

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The goal of this study was to compare wild-type adult homeostatic lung epithelium to Hopx-creERT2-induced Yap/Taz KO in adult AT1 cells. Three adult mice with identical genotypes and either sex were pooled after fluorescence-activated cell sorting and loaded into the 10X Chromium scRNA sequencing library generation pipeline.

overall_design: Three samples of adult mouse epithelial cells and three samples of adult Hopx-creERT2;Yap/Taz KO lineage traced mice were pooled respectively for library preparation.

first: Ian

last: Penkala

first: Micheal

middle: P

first: Edward

middle: E

last: Morrisey


title: BRD4 inhibition boosts the therapeutic effects of epidermal growth factor receptor-targeted chimeric antigen receptor T cells in glioblastoma

first: Jiancheng

last: Ding

summary: Glioblastoma (GBM) is the deadliest brain malignancy without effective treatments. Here, we report that epidermal growth factor receptor-targeted chimeric antigen receptor T cells (EGFR CAR-T) are effective in suppressing the growth of GBM cells in vitro and xenografts derived from GBM cell lines and patients in mice. However, mice soon acquire resistance to EGFR CAR-T cell treatment, limiting its potential use in the clinic. To find ways to improve the efficacy of EGFR CAR-T cells, we performed genomics and transcriptomics analysis for GBM cells incubated with EGFR CAR-T cells, and found that a large cohort of genes including immunosuppressive genes as well as enhancers in vicinity are activated. BRD4, an epigenetic modulator functioning on both promoter and enhancer, is required for the activation of these immunosuppressive genes. Accordingly, inhibition of BRD4 by JQ1 blocks the activation of these immunosuppressive genes. Combination therapy with EGFR CAR-T cells and JQ1 suppresses the growth and metastasis of GBM cells, and prolonged survival in mice. We demonstrate that transcriptional modulation by targeting epigenetic regulators could improve the efficacy of immunotherapy including CAR-T, providing a therapeutic avenue for treating GBM in the clinic.

overall_design: RNA-seq was performed to identify differential genes in U87 in different conditions.

first: Lin

last: Xia

first: Jun-yi

last: Liu

first: Zao-zao

last: Zheng

first: Yu-jie

first: Jian-cheng

first: Ya-hong

first: Guo-sheng


title: Treatment Naïve and Follow-Up Pediatric Ulcerative Colitis Rectal Gene Expression

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: PROTECT is a multicenter pediatric inception cohort study of response to standardized colitis therapy. In order to more explicitly model progression to colectomy within one year of diagnosis, we performed differential expression analysis between baseline rectal RNAseq biopsies of 21 patients who progressed to colectomy, and 310 who did not. We report rectal gene expression of pediatric patients with ulcerative colitis at diagnosis and at one year follow-up.

overall_design: 418 rectal biopsies were obtained from pediatric ulcerative colitis patients during colonoscopy. Transcriptome profiling was performed with RNA-Seq.

first: Lee

last: Denson

first: Jeffrey

last: Hyams

first: Greg

last: Gibson


title: Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

summary: Two highly pathogenic human coronaviruses that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) have evolved proteins that can inhibit host antiviral responses, likely contributing to disease progression and high case-fatality rates. SARS-CoV-2 emerged in December 2019 to cause a global pandemic. Recent studies have shown that SARS-CoV-2 is unable to induce a robust type I interferon (IFN) response in human cells, leading to speculations about the ability of SARS-CoV-2 to inhibit innate antiviral responses. However, innate antiviral responses are dynamic in nature and gene expression levels rapidly change within minutes to hours. In this study, we have performed a time series RNA-seq analysis to identify early virus-host processes. SARS-CoV-2 infection upregulated transcripts for type I IFNs and interferon stimulated genes (ISGs) after 12 hours. Furthermore, we analyzed the ability of SARS-CoV-2 to inhibit type I IFN production and downstream antiviral signaling in human cells. Using exogenous stimuli, we discovered that SARS-CoV-2 is unable to modulate IFNb production and downstream expression of ISGs, such as IRF7 and IFIT1. Thus, data from our study indicate that SARS-CoV-2 may have evolved additional mechanisms, such as masking its nucleic acid from cellular immune response sensors to mount a dampened innate antiviral response. Further studies are required to fully identify the range of immune-modulatory strategies of SARS-CoV-2.

overall_design: We infected triplicated human lung epithelial cells (Calu-3) at a multiplicity of infection (MOI) for SARS-CoV-2 of 2, with comparison to triplicated uninfected controls. One hour post infection, the inoculum was removed and the clock was set to zero. We extracted and sequenced poly-A enriched RNA at 0, 1, 2, 3, 6 and 12 hours post infection (hpi) using an Illumina HiSeq 2500 with 2 x 50 bp chemistry to a minimum of 21.9 million clusters per replicate. Paired-end sequencing reads were mapped to the human reference transcriptome (GRCh37.67) obtained from the ENSEMBL database using the ‘quant’ function of Salmon, transcript counts summarized at the gene-level using the corresponding transcriptome GTF file mappings obtained from ENSEMBL, and count data normalized using DeSeq2's 'estimateSizeFactors' function using the default 'median ratio method’.

first: Arinjay

last: Banerjee

first: Patrick

last: Budylowski

first: Daniel

last: Richard

first: Hassaan

last: Maan

first: Jennifer

last: Aguiar

first: Nader

last: El-Sayes

middle: R

last: Agostino

first: Benjamin

last: Tremblay

first: Sam

last: Afkhami

first: Mehran

last: Karimzadeh

first: Lily

last: Yip

first: Mario

last: Ostrowski

first: Jeremy

last: Hirota

first: Robert

last: Kozak

first: Terence

last: Capellini

first: Matthew

middle: S

last: Miller

first: A

middle: G

first: Bo

last: Wang

middle: C

last: Doxey

first: Samira

last: Mubareka

first: Karen

last: Mossman


title: KIF15 promotes AR and AR-V7 protein stabilization in contribution to enzalutamide resistance of prostate cancers

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

institute: shandong university


title: Patient-Derived Mutant Forms of NFE2L2/NRF2 Drive Aggesssive Murine Hepatoblastomas

city: pittsburgh

first: Edward

middle: V.

last: Prochownik

address: 4401 Penn Avenue

department: Section of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh

summary: The pediatric liver cancer hepatoblastoma (HB) often expresses mutant forms of b-catenin and dysregulates the Hippo tumor suppressor pathway. Murine HBs can be generated by co-expressing b-catenin mutants and the constitutively active Hippo effector YAPS127A. Some human HBs also express mutant forms of NFE2L2/NRF2 (NFE2L2), a bHLH transcription factor that tempers oxidative and electrophilic stress. In doing so, NFE2L2 either suppresses or facilitates tumorigenesis in a context- and time-dependent manner. We show here that two patient-derived NFE2L2 missense mutants, L30P and R34P, markedly accelerate HB growth in association with diffuse cyst formation, an otherwise uncommon feature of human HB. Surprisingly, we found that any two members of the mutant b-catenin-YAPS127A-L30P/R34P triad were tumorigenic, thus providing direct evidence for NFE2L2’s oncogenicity. Each tumor group showed distinct features but shared a similarly deregulated set of 22 transcripts, 10 of which perfectly correlated with survival in human HBs. 17 transcripts also correlated with survival in multiple cancers.  One of the most deregulated transcripts encoded Serpin E1, a serine protease inhibitor with roles in fibrinolysis, tumor growth and extracellular matrix formation. The combination of mutant b-catenin-YAPS127A-Serpin E1 neither accelerated tumor growth nor generated cysts but did promote large-scale necrosis that was often associated with the cysts seen in mutant b-catenin-YAPS127A-L30P/R34P tumor, albeit on a lesser scale. These findings establish the direct oncogencity of NFE2L2 mutants and identify key transcripts, including Serpin E1, that impact tumor growth and other HB features.

overall_design: RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.  Samples for sequencing were prepared using an NEB NEBNext Ultra Directional RNA Library Prep kit according to the directions provided by the vendor (New England Biolab, Beverly, MA) and sequencing was performed on a NovaSeq 600 Instrument (Illumina, Inc., San Diego, CA) by Novagene, Inc. (Sacramento, CA).

first: Huabo

middle: V


title: KIF15  confers resistance to enzalutamide in castration resistant prostate cancer [RNA-Seq]

summary: The aim of this research was to confirm the regulatory effect of KIF15 on gene expression in castration resistant prostate cancer.

overall_design: In this research, there were six samples examed including sample of negative control cells (C4-2B-ENZR-NC) and sample of KIF15 knocked down cells (C4-2B-ENZR-siKIF15).

last: Han


title: Evaluation of Repair Activity  by Quantification of Ribonucleotides in the Genome

status: Public on May 21 2021

city: Bunkyo-ku

first: Tetsushi

last: Iida

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Biological Visualization

institute: The Institute for Quantitative Biosciences (IQB), The University of Tokyo

summary: Ribonucleotides incorporated in the genome are a source of endogenous DNA damage, and also serve as signals for repair. Although recent advances of ribonucleotide detection by sequencing, the balance between incorporation and repair of ribonucleotides has not been elucidated. Here, we describe a competitive sequencing method, Ribonucleotide Scanning Quantification sequencing (RiSQ-seq), which enables absolute quantification of misincorporated ribonucleotides throughout the genome by background normalization and standard adjustment within a single sample. RiSQ-seq analysis of cells harboring wild-type DNA polymerases revealed that ribonucleotides were incorporated non-uniformly in the genome with a 3’-shifted distribution and preference for GC sequences. Although ribonucleotide profiles in wild-type and repair-deficient mutant strains showed a similar pattern, direct comparison of distinct ribonucleotide levels in the strains by RiSQ-seq enabled evaluation of ribonucleotide excision repair activity at base resolution and revealed the strand bias of repair. The distinct preferences of ribonucleotide incorporation and repair create vulnerable regions associated with indel hotspots, suggesting that repair at sites of ribonucleotide misincorporation serves to maintain genome integrity and that RiSQ-seq can provide an estimate of indel risk.

sample_organism:
Sinsheimervirus phiX174
Saccharomyces cerevisiae BY4741

overall_design:
A detailed description of each sample, experiment design and the corresponding processed data file is provided in the sample description field.

DRA Study accession (DRPnnnns have not been assinged):
DRA04327, DRA004328, DRA004329, DRA004330, DRA004331, DRA004332, DRA004917

RiSQ_seq_reference.fa = sequence data used for bedgraph files. From original EF4.68 assembly, chromosome numbers were changed from Roman to Arabic numerals and add Ty1 consensus sequence and rDNA repeat unit sequence.
RiSQ_seq_genes.gtf = annotation data of genomic elements used in this study.
STD_target.fa = reference sequences of standard fragments used in this study.
STD_*.tsv = fragment composition from standard fragment (STD) data analysis
Mapping_bias.bed = information of mapping biased region

first: Naoko

first: Jun

last: Sese

first: Takehiko

last: Kobayashi


title: DUX/DUX4 activation is coupled to p53 signaling in embryos, 2C-like cells, and FSHD patient cells

city: Salt Lake City

middle: John

last: Grow

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Profiling AT1 and AT2 cells throughout alveolar development

first: Michael

last: Morley

summary: This experiment profiled the transcriptomes of developing AT1 and AT2 cells from the beginning of embryonic alveolar development through the end of alveologenesis at 6 weeks of age.

overall_design: Analysis of AT1 and AT2 cell transcriptomes at critical transition points during lung development from e15.5 to P42.

first: Ian

last: Penkala

first: Micheal

last: Morrisey


title: KIF15  confers resistance to enzalutamide in castration resistant prostate cancer [array]

overall_design: In this research, there were two samples examed including sample of negative control cells (22Rv1-NC) and sample of KIF15 knocked down cells (22Rv1-siKIF15).


title: Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: Setd2 methylate the nucleosome to form H3K36me3. Here we utilized the Cryo-EM to elucidate the structure of SETD2/Set2 bound with nucleosomes. Through this structure analysis, we found that histone H1 may interfere the enzymatic activity of SETD2/Set2 by inhibiting their binding affinity.

overall_design: To compare the enrichment of H1.4 and H3K36me3 in the genome

first: Yingying

last: Liu

first: Yanjun

last: Zhang

first: Han

last: Xue

first: Mi

last: Cao

first: Zongkai

last: Mou

first: Yanli

last: Yao

first: Shuyang

last: Sun

first: Jing

last: Huang


title: Integrated Analysis of Omics Data Reveal AP-1 as a Potential Regulation Hub in the Inflammation-Induced Hyperalgesia Rat Model

status: Public on May 19 2021

city: Suzhou

first: Lei

last: Wei

state: Jiangsu

address: Suzhou Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu

type: Methylation profiling by high throughput sequencing

summary: Inflammation-associated chronic pain is a global clinical problem, affecting millions of people worldwide. However, the underlying mechanisms that mediate inflammation-associated chronic pain remain unclear. A rat model of cutaneous inflammation induced by Complete Freund’s Adjuvant (CFA) has been widely used as an inflammation-induced pain hypersensitivity model. We present the transcriptomics profile of CFA-induced inflammation in the rat dorsal root ganglion (DRG) via an approach that targets gene expression, DNA methylation, and post-transcriptional regulation.

overall_design: Deciphering the chronic pain model using multiomics ways

first: Xiang

last: Zhu

first: Intanx

last: Life

first: Feng

last: Li


title: Analysis of delayed changes in expression of miRNA in rat kidneys: role of miR-34a

city: Milwaukee

first: Meetha

last: Medhora

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Radiation oncology

institute: Medical College of Wisconsin

summary: We used a rat model of whole body (except one hind limb that was shielded) x-ray irradiation to profile the microRNA (miRNA) in kidneys at 35 days after radiation. Small RNA from normal and irradiated (with or without lisinopril) Wistar rat kidneys were analyzed by next-generation sequencing and the changes by radiation and lisinopril were identified by deRNA-seq. MiR-34a-5p was increased after irradiation.

overall_design: Profile of miRNA in Wistar rat kidneys with and without radiation at 35 days after radiation were generated by next generation sequencing. Rats were randomized into 3 groups (1) nonirradiated controls (0 Gy). (2) Irradiation only group (13 Gy). (3) Irradiation + lisinopril group (13 Gy + lisinopril). Each group contains four or five rats.

last: Gao

first: Pengyuan

first: Jayashree

last: Narayanan


title: Six-hour interval time-course expression data during VISUAL

city: Kobe

first: Tomoyuki

last: Furuya

address: 1-1, Rokkodai-cho, Nada-ku

institute: Kobe University

summary:
We used in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons
To investigate temporal gene expression profiles during ectopic vascular cell defferentiaction processes, we performed GeneChip analysis using VISUAL.

overall_design: Arabidopsis cotyledons cultured with the induction medium were sampled collected from 0 to 72 hours at every 6 hours after inuduction.

first: Yukiko

last: Sugisawa


title: Identification of dachshund-1 (DACH1) transcriptional target genes in podocytes at baseline and in experimental diabetes

city: New York

first: Weijia

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: RNA sequencing was performed to compare glomerular transcriptomes of control and podocyte-specific DACH1 KO mice both under the basal condition and early after STZ-induced diabetes.

overall_design: Glomerular RNA was extracted from ten week old age-matched control and podocyte-specific DACH1 KO mice under the basal condition and RNA sequencing performed. Control and podocyte-specific DACH1 KO mice were also made diabetic by STZ injection and ten days later, glomerular RNA was isolated and RNA sequencing performed. Three different mice from each experimetal group were analyzed.

first: Aili

first: Zhengzi

last: Yi

first: Lewis

last: Kaufman


title: RNA-Sequencing Analysis of ox-LDL-treated Peritoneal Macrophages Transcriptomes

city: 长沙

first: Mengqing

last: jiang

address: tongzipo road 138

department: cardiology

institute: The Third Xiangya Hospital of Central South University

summary: Since previous stduies demostrated that oxidized phospholipids function as caspase-11 agonists to induce noncanonical inflammasome activation in immune cells and the levels of oxidized phospholipids derived from ox-LDL are largely elevated in atherosclerotic lesions. Purpose:RNA-Sequencing analysis of ox-LDL-treated peritoneal macrophages transcriptomes.Methods and results:The principal component analysis gene expression profiles of the control and ox-LDL-treated groups were clearly distinct. Among the DEGs that met the cutoff criteria of a -log10(false discovery rate (FDR)) > 2 and |log2(fold change (FC)| > 2. A total of 1,388 downregulated and 855 upregulated genes were identified. GSEA showed that the dominant upregulated pathways in ox-LDL-treated macrophages were associated with the IL-1-mediated signaling pathway, response to cytokine stimulus, and granulocyte migrationwe discovered that  caspase-11-mediated inflammation signaling was significantly activated in ox-LDL-treated peritoneal macrophages.Conclusions：we verified caspase11associated inflammatory signaling was significantly activated in ox-LDL-treated macrophages.

overall_design: WT mice peritoneal macrophages were isolated  on the third day after thioglycollate infusion and then primed with LPS (100ng/ml) followed by 16 hours of ox-LDL(100ug/ml) stimulation .Total RNA was extracted from 5 biological replicates for each group.

last: Jiang

first: Xuejing

first: Suzhen

last: Liu

first: Yujie

last: Wang

first: Jingjing

last: Cai


title: The expression profile of tomato in response to heat stress.

city: 昆明市

first: zhengxiang

last: feng

address: 云南大学呈贡校区

institute: 云南大学

summary: Transcriptome analysis of tomato fruits under heat stress revealed that most SlCRK genes were downregulated upon heat treatment. GO enrichment analysis of genes that were co-expressed with SlCRK members have identified various stress response related and proteasoma protein catabolic process related genes, which may be involved in heat stress signaling Overall, our results provide valuable information for further research on the roles of SlCRKs in response to abiotic stress, especially heat stress.

overall_design: Analysis of the expression profile of tomato in response to heat stress.

first: Yahui

first: Yingying

last: Zhang

first: Junzhong


title: Prognosis associated mRNA and microRNA in peripheral blood mononuclear cells (PBMCs) from hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF)

first: Shanshan

last: Ms

address: No.79 Qingchun Road

institute: The First Affiliated Hospital, College of Medicine, Zhejiang University

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

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

overall_design: Refer to individual Series


title: Prognosis associated microRNA in peripheral blood mononuclear cells (PBMCs) from hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) [miRNA]

summary: Genome wide microRNA profiling in peripheral blood mononuclear cells (PBMCs) from hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) patients of in different prognoses of 28-day. The Agilent Human miRNA Microarray Kit was used to obtain RNA profiles in 8 survival patients and 8 dead patients in 28-day.

overall_design: To identify short term prognosis associated microRNAs and comprehensively understand their underlying pathologic mechanism, we compared Agilent Human miRNA Microarray data from PBMCs of 16 HBV-ACLF patients (8 survival cases and 8 dead controls in 28-day).

last: Ma

first: Zhaongyang

last: Xie

first: Lanjuan


title: Prognosis associated mRNA in peripheral blood mononuclear cells (PBMCs) from hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) [mRNA]

summary: Genome wide mRNA profiling in peripheral blood mononuclear cells (PBMCs) from hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) patients of in different prognoses of 28-day. The Agilent SurePrint G3 Human Gene Expression ver. 3 8x60K Microarray  was used to obtain RNA profiles in 8 survival patients and 8 dead patients in 28-day.

overall_design: To identify short term prognosis associated mRNA and comprehensively understand their underlying pathologic mechanism, we compared Agilent SurePrint G3 Human Gene Expression ver. 3 8x60K Microarray  data from PBMCs of 16 HBV-ACLF patients (8 survival cases and 8 dead controls in 28-day).

last: Li


title: Expression data from Fibroblast-like Synoviocytes (FLS) isolated from patients with Juvenile Idiopathic Arthritis (JIA) - compares untreated FLS to FLS exposed to conditioned media from Chondrocytes (Ch)

city: Wilmington

first: AnneMarie

last: Brescia

state: DE

address: 1601 Rockland Rd

institute: Nemours

summary:
This dataset was used to determine the influence of conditioned media from Ch and how that influence affects genome-wide gene transcription in fibroblast-like synoviocytes
In this dataset, we include data from untreated fibroblast-like synoviocytes and FLS cultured in chondrocyte-conditioned media, both normal FLS (C ) and JIA FLS (J).

overall_design: 36 samples were analyzed in this study. 3 normal FLS (C ), 3 normal FLS with Ch-conditioned media (CCh), 3 JIA FLS (J), and 3 JIA FLS with Ch-conditioned media (JCh). All normal FLS came from donors. All JIA FLS were obtained from our IRB-approved repository.

first: Megan

last: Simonds

first: Suzanne

last: McCahan


title: Altered Expression Profiles of tRNA-derived fragments in relapsed/refractory multiple myeloma

city: changsha

first: cong

last: xu

state: China

address: No. 138 tongzipo Road, Yuelu District, Changsha

institute: the third xiangya hospital

summary: tRNA related fragments(tRF) and tRNA halves(tiRNA) are novel class of short non-coding RNA derived from tRNAs. Using RNA sequencing, we evaluated the tRFs/tiRNAs expression profiles in relapsed/refractory multiple myeloma and  multiple myeloma patients. Bioinformatics analyses indicated that tRFs/tiRNAs may be involved in the progression and drug-resistance of multiple myeloma.

overall_design: tiRNA and tRF profiles in the bone marrow of relapsed/refractory multiple myeloma and  multiple myeloma patients, using Illumina NextSeq 500 system.

first: Cong

last: Xu

first: Yunfeng

last: Fu


title: mRNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of CFI.

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

institute: University of Turku

summary: Keratinocyte carcinomas (BCC and cSCC) are the most common cancers worldwide. cSCC is considered as the most prevalent metastatic skin malignancy and its incidence is increasing globally. The complement system is a fundamental part of the host immune defense. It is composed of three distinct pathways (classical, alternative and lectin) that get activated sequentially. However, the process of complement activation is rigorously regulated by a series of soluble and membrane-bound inhibitor proteins that protect the host cells from lytic damage. One of these soluble negative regulators is complement factor I (CFI) which is an 88 kDa serine protease that hampers all three complement pathways through blockade of C3- and C5- convertases by cleaving C3b and C4b. Oligonucleotide array (Affymetrix)-based analysis of normal human epidermal keratinocytes (NHEKs; n=5), primary (Prim. cSCC; n=5) and metastatic (Met. cSCC; n=3) cSCC cell lines as well as next-generation-sequencing (SOLiD) based transcriptome profiling of NHEKs (n=4), primary (Prim. cSCC; n=5) and metastatic (Met. cSCC; n=3) cSCC cell lines revealed marked overexpression of CFI in cSCC cells compared to NHEKs (GSE66368 and GSE66412 respectively). Furthermore, we have previously shown that knockdown of CFI inhibits proliferation and migration of cSCC cells and potently impedes growth of cSCC xenograft tumors in vivo. In these respects, we intended to further investigate the functional role and molecular mechanism of CFI in cSCC progression via analyzing the mRNA expression profile of CFI in cSCC cells.

overall_design:
Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most prevalent metastatic skin malignancy and its incidence is increasing globally. The complement system is a fundamental part of the host immune defense. It is composed of three distinct pathways (classical, alternative and lectin) that get activated sequentially. The process of complement activation is rigorously regulated by soluble and membrane-bound inhibitor proteins that protect the host cells from lytic damage. One of these soluble negative regulators is complement factor I (CFI) which is an 88 kDa serine protease that hampers all three complement pathways through blockade of C3 and C5-convertases by cleaving C3b and C4b. Oligonucleotide array (Affymetrix)-based analysis of normal human epidermal keratinocytes (NHEKs; n=5), primary (Prim. cSCC; n=5) and metastatic (Met. cSCC; n=3) cSCC cell lines, as well as next-generation-sequencing (SOLiD) based transcriptome profiling of NHEKs (n=4), primary (Prim. cSCC; n=5) and metastatic (Met. cSCC; n=3) cSCC cell lines revealed marked overexpression of CFI in cSCC cells compared to NHEKs (GSE66368 and GSE66412, respectively). Furthermore, we have previously shown that knockdown of CFI inhibits proliferation and migration of cSCC cells and potently suppresses growth of cSCC xenograft tumors in vivo (Riihilä et al., J Invest Dermatol. 2015 Feb;135(2):579-588). In this respect, we have investigated the molecular mechanism of CFI in cSCC progression via analyzing the mRNA expression profile in cSCC cells after knockdown of CFI expression.
Total RNAs from negative control siRNA and CFI siRNA-treated cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina sequencing.

first: Pegah

last: Rahmati Nezhad

first: Veli-Matti

last: Kähäri


title: Single cell RNA sequencing of CD41+ and CD41- CD34+ HPC in model of RUNX1 insufficiency

city: Philadelphia

first: Brian

last: Estevez

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: To gain insights into the global and local transcriptomic changes underlying defects in adult RUNX1in HSPCs, we then performed scRNA SEQ on sorted CD41a- and CD41a+ HSPCs from cultures expressing NT or RUNX1-targeting lentiviral shRNA.

overall_design: Examination of gene expression in 12 sorted samples from control  (3 CD41- and 3 CD41+) and RUNX1 haploinsufficient (3 CD41- and 3 CD41+) iHPCs based on CD42 expression.

first: Mortimer

last: Poncz


title: tRF and tiRNA  profiles in lung adenocarcinoma.

city: Kunming

first: Wanpu

last: Wang

address: No.157  Jinbi  Road

institute: he First People’s Hospital of Y unnan Province

summary: We investigate tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues using a NextSeq system. Total RNA was extracted from tissues and pretreated to remove the RNA modifications. In patients with lung adenocarcinoma, 338 types of tRFs and tiRNAs were detected via sequencing, 284 of which were not previously reported. Compared with the adjacent tissues, 17 types of tRFs and tiRNAs comprising 34 subtypes were found to be abnormally expressed in lung adenocarcinoma tissues, 20 of which were upregulated and 14 of which were downregulated. Finally, we show that tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues and identify several dysregulated tRFs and tiRNAs.

overall_design: Examination of the expression of tRFs and tiRNAs in three pairs of lung adenocarcinoma and adjacent tissues.


title: CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies [single-cell]

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: Glioblastoma (GBM) is the most prevalent primary malignant brain tumor, containing self-renewing stem-like GBM stem cells (GSCs) that have been a focus of immunotherapies. Chimeric antigen receptor (CAR) T cell therapy has shown evidence of clinical activity, but overall limited responses in patients with GBMs. Here, we interrogated molecular determinants of CAR T cell-mediated GBM killing through whole-genome CRISPR screens in both CAR T cells and patient-derived GSCs. CRISPR screening of CAR T cells identified dependencies for their effector functions, including TLE4 and IKZF2. Targeted knockout of these genes in CAR T cells robustly enhanced antitumor efficacy against GBM patient-derived xenografts (PDXs). Bulk and single cell-RNA sequencing of edited CAR T cells revealed transcriptional profiles of superior effector function and inhibited exhaustion responses. Reciprocal screening of GSCs identified genes essential for their susceptibility to CAR-mediated killing, including RELA and NPLOC4, the knockout of which altered the tumor-immune signaling axis and increased responsiveness of CAR therapy. Overall, CRISPR screening of CAR T cells and GSCs are promising strategies to discover avenues and inform potential combinatorial approaches for enhancing CAR T cell therapeutic efficacy against GBM, and can be extended to reveal key mediators of immunotherapy responses across solid tumors.

overall_design: Selected targets were knocked out using CRISPR-Cas9 in CAR T cells. Cells were then stimulated by co-culture with glioblastoma stem cells, or remained unstimulated in monoculture. Single cell sequencing was performed. Non-targeting sgRNAs were utilized to generate control cells.

first: Dongrui

first: Qi

first: Christine

last: Brown

first: Jeremy

last: Rich


title: Immune phenotyping of patients with acute Vogt-Koyanagi-Harada Syndrome after glucocorticoids therapy

city: Wuhan

first: Han

last: Jiang

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology

summary:
Purpose:This study was designed to systemically characterize and compare the immunological profiles of peripheral blood from patients with VKH and healthy controls. The influence of MP, which has been the most widely prescribed GC in VKH therapy, on immune phenotypes in peripheral blood from VKH patients was also evaluated. Our investigation will offer a better understanding of the function, activation and differentiation status of the leukocyte subpopulations during autoimmune VKH and after GC therapy, and may facilitate a more specific therapeutic regimen for this particular disease, which is a major cause of visual impairment.
Methods:Total RNAs of whole blood cells were extracted in accordance with the manual of PAXgene tube (BD bioscience, San Jose, CA, USA). Preparation of library and transcriptomic sequencing were carried out using Illumina novaseq 6000 (Novogene Bioinformatics Technology Co., Ltd., Beijing, China). Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P value <0.05 found by DESeq2 were assigned as differentially expressed.
Results:The lymphocyte composition in the blood was different in VKH patients and HCs. VKH patients had significantly higher numbers of T cells with more activated, polarized and differentiated phenotype, more unswitched memory B cells and monocytes, as compared to HCs. MP treatment resulted in decreased frequencies of T cells and NK cells, inhibited NK cell activation and T cell differentiation, and more profoundly, a marked shift of monocytes toward an anti-inflammatory phenotype. Collectively, our findings suggest that the occurrence of VKH mainly affects the activation status and numbers of peripheral lymphocytes, and GC therapy with MP not only inhibits T cell activation directly, but also affects monocyte subsets and polarizes monocyte toward a suppressive phenotype, endowing them with the capacity to inhibit the pathogenic immune response.
Conclusion:The comprehensive analysis of blood leukocytes from VKH patients and HCs described in this study reveals a perturbation of the lymphocyte compartment in VKH, exemplified by the increased activation and proliferation of T cells in VKH patients. GC therapy not only affects the proliferation and apoptosis of lymphocytes, especially T cells, but also affects the distribution of monocyte subsets. Our results also indicate that CD56+ monocytes may be regulatory and contribute to the remission of inflammatory autoimmune diseases such as VKH, suggesting that this monocyte subset could represent a potentially useful cellular therapeutic target in certain inflammatory diseases, especially when patients have strong side effects in response to GC therapy.

overall_design: Gene expression in the peripheral blood from VKH patients before (before, n=7) and after (after, n=7) GC treatment for one week, as well as healthy controls (HC, n=7) generated by deep sequencing.

first: Zhaohui

first: Long

last: Yu

first: Ying

last: Zhang

first: Zhou

first: Jianhua

last: Wu

first: Jing

last: Yuan

first: Mengyao

last: Han

first: Tao

first: Junwen

last: He

first: Shan

first: Chenfeng

first: Sha

last: Pan

first: Min

first: Hangyu

last: Liu

first: Haihong

last: Zeng

first: Zhu

last: Song

first: Qiangqiang

first: Shen

last: Qu

first: Junyan

first: Yafei

last: Huang


title: CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies [bulk]

first: Briana

overall_design: Selected targets were knocked out using CRISPR-Cas9 in CAR T cells. RNA sequencing was performed on each sample. Non-targeting sgRNAs were utilized to generate control cells.

first: Dongrui

last: Wang

first: Qi

last: Xie

first: Christine

first: Jeremy


title: Hippocampal CA3 Transcriptional Modules Associated with Granule Cell Alterations and Cognitive Impairment in Refractory Mesial Temporal Lobe Epilepsy Patients

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: In about a third of the patients with epilepsy the seizures are not drug-controlled. The current limitation of the antiepileptic drug therapy derives from an insufficient understanding of epilepsy pathophysiology. In order to overcome this situation, it is necessary to consider epilepsy as a disturbed network of interactions, instead of just looking for changes in single molecular components. Here, we studied CA3 transcriptional signatures and dentate gyrus histopathologic alterations in hippocampal explants surgically obtained from 57 RMTLE patients submitted to corticoamygdalohippocampectomy. By adopting a systems biology approach, integrating clinical, histopathological and transcriptomic data trough weighted gene co-expression network analysis, we were able to identify transcriptional modules highly correlated with age of disease onset, cognitive dysfunctions, and granule cell alterations.

overall_design: A systems biology approach, integrating clinical, histopathological, and transcriptomic data - through WGCNA - to identify transcriptional modules highly correlated with clinical and histopathological traits, in refractory mesial temporal lobe epilepsy patients.

first: Silvia

middle: Y

last: Bando

first: Fernanda

middle: B

last: Bertonha

first: Luciana

last: Pimentel-Silva

first: João

last: Oliveira

first: Marco

last: Carneiro

first: Mariana

middle: H

last: Oku

first: Hung-Tzu

last: Wen

first: Luiz

last: Castro


title: CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies [GSC]

last: Prager

overall_design: Selected targets were knocked out using CRISPR-Cas9 in glioblastoma stem cells. RNA sequencing was performed on each sample. Non-targeting sgRNAs were utilized to generate control cells.

last: Brown

last: Rich


title: CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies


title: mRNA profile of Ch25h null ECs which were treated with PBS or mouse colorectal tumor extracellular vesicles in vitro.

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Tumor derived vesicles (TEVs) promote Angpt2 expression in Ch25h-/- ECs, while Reserpine reversed TEV induced Angpt2 expression in ECs.

overall_design: Ch25h null ECs isolated from Ch25h k.o mice and pre-treated with Reserpine(10μM for 8hr) followed by PBS or  MC38 derived TEVs treatment (20ug/ml) for 12 hr in vitro.

first: Serge

last: Fuchs

first: Zhen

last: Lu

first: Daniel

last: Beiting


title: Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant

city: London

first: Florian

last: Klimm

address: Exhibition Rd, South Kensington

country: United Kingdom

institute: Imperial College London

summary: Most humans carry a mixed population of mitochondrial DNA (mtDNA heteroplasmy) affecting ~1-2% of molecules, but rapid percentage shifts occur over one generation leading to severe mitochondrial diseases. A decrease in the amount of mtDNA within the developing female germ line appears to play a role, but other sub-cellular mechanisms have been implicated. Establishing an in vitro model of early mammalian germ cell development from embryonic stem cells, here we show the reduction of mtDNA content is modulated by oxygen and reaches a nadir immediately before germ cell specification. The observed genetic bottleneck was accompanied by a decrease in mtDNA replicating foci and the segregation of heteroplasmy, which were both abolished at higher oxygen levels. Thus, differences in oxygen tension during early development can modulate mtDNA segregation, facilitating germ-line purification, and contribute to tissue-specific somatic mutation loads.

overall_design: Single-cell RNA seq for 768 cells from mice embryo.

first: Mikael

last: Pezet

first: Aurora

last: Gomez-Duran

first: Juvid

last: Aryaman

first: Stephen

last: Burr

first: Wei

last: Wei

first: Mitinori

last: Saitou

first: Julien

last: Prudent

first: Patrick

middle: F

last: Chinnery


title: Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells

city: Nijmegen

first: Hendrik

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University Nijmegen

summary:
Introduction: Chronic inflammation and immune dysfunction play a key role in the development of non-AIDS related comorbidities. The aim of our study was to characterize the functional phenotype of immune cells in people living with HIV (PLWHIV).
Methods: We enrolled a cross-sectional cohort study of PLWHIV on stable antiretroviral therapy (cART; n=211) and HIV uninfected controls (n=56). We performed peripheral blood mononuclear cell stimulation to assess ex vivo cytokine production and transcriptomics of monocytes and T lymphocytes upon bacterial, fungal and viral stimulation. We used a linear regression model with age, sex, BMI and seasonality as covariates to compare both cohorts. All p-values are FDR-corrected.
Results: PLWHIV exhibited an exacerbated pro-inflammatory profile in monocyte-derived cytokines, but not of lymphocyte-derived cytokines. Especially the interleukin (IL)-1β response to imiquimod (TLR7), lipopolysaccharide (LPS) and Mycobacterium tuberculosis was increased and correlated with plasma concentrations of high-sensitive C-reactive protein and soluble CD14. The increase in monocyte responsiveness remained stable over-time in subsequent blood sampling. Transcriptome analyses confirmed priming of the monocyte IL1β pathway, consistent with a monocyte trained immunity phenotype. Increased plasma concentrations of β-glucan, a well-known inducer of trained immunity, were associated with increased innate cytokine responses.
Conclusions: Monocytes of PLWHIV on stable cART exhibit a sustained pro-inflammatory immune phenotype with priming of the IL-1β pathway. Training of the innate immune system in PLWHIV is likely to play a role in the long-term HIV complications and forms an attractive therapeutic target for inflammation-related comorbidities.

overall_design:
Analysis of the behaviour of monocytes (as a compartment of innate immune system) from healthy volunteers and HIV positive donors in RPMI cell culture.

**Submitter declares that donor consent does not allow deposit of raw data files**

first: Wouter

middle: A

last: van der Heijden

first: Farid

last: Keramati

first: Andre

middle: J

last: van der Ven

first: Quirijn

last: de Mast


title: Gene expression data from human circulating myeloid-derived suppressor cells

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

summary:
αβT cell- and B cell-depleted HLA-haploidentical haematopoietic stem cell transplantation is a life-saving therapeutic option to treat patients with high-risk leukemia. The G-CSF treatment stimulates mobilization from the bone marrow to blood of hematopoietic stem cells (HSC), and this manipulated graft also contains mature donor-derived NK and γδT cells, both exerting graft-versus-leukemia activity and control of infections at early stages after transplantation.  The G-CSF-induced mobilization in the donor causes relevant increases of different myeloid cells, including polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC). PMN-MDSC are present in high proportions in the graft and exert a sharp inhibition on the effector functions of co-infused mature NK cells. Conversely, low frequencies of PMN-MDSCs are detected in the blood of non-mobilized healthy donors.
We used microarray technology to identify possible differences in the transcriptional programme of PMN-MDSCs isolated from blood of G-CSF mobilized donors as compared to those of non-mobilized healthy individuals.

overall_design: PMN-MDSC were purified after density gradient centrifugation and immune-capture with CD66b beads from blood of 8 mobilized donors upon G-CSF treatment and from 5 non-mobilized donors as control group. Cell purity was confirmed by flow cytometry. After RNA extraction, samples were hybridized on Affymetrix GeneChip microarray.

first: Nicola

last: Tumino

first: Francesca

last: Besi

first: Paola

last: Vacca

first: Lorenzo

last: Moretta


title: RNA m6A reader YTHDF2 facilitates lung adenocarcinoma cell proliferation and metastasis by targeting the AXIN1/Wnt/ β-catenin signaling

city: guangzhou

first: Yin

last: Li

state: State...

address: No.601,Huangpu avenue,tianhe area, guangzhou

institute: The First Affiliated Hospital of Jinan University

summary: Lung cancer is a leading cause of cancer-related mortality worldwide and poor prognosis remains a major problem encountered in its treatment. The dynamic and reversible N6-methyladenosine (m6A) RNA modification has been recently implicated in the tumorigenesis and metastasis of a variety of cancers. However, the biological functions and underlying mechanisms of YTHDF2 in the regulation of lung adenocarcinoma (LUAD) progression remain elusive. Here we report that YTHDF2 expression was significantly increased in lung adenocarcinoma than in adjacent normal tissues. YTHDF2 knockdown drastically inhibited cell proliferation, colony formation, and migration in vitro, and the opposite proved true when YTHDF2 was overexpressed. In addition, YTHDF2 attenuation significantly inhibited tumorigenesis in a murine tumor xenograft model. Through the integrative analysis of RNA-seq, m6A-seq, CLIP-seq, and RIP-seq datasets, we identified a set of potential direct targets of YTHDF2 in lung adenocarcinoma. We further confirmed AXIN1, which encodes a negative regulator of the Wnt/β-catenin signaling, as a direct target of YTHDF2. YTHDF2 promotes AXIN1 RNA decay and subsequently activates the Wnt/β-catenin signaling. Knockout of AXIN1 can sufficiently rescue the inhibitory effect of YTHDF2 depletion on lung cancer cell proliferation, colony-formation, and migration. Collectively, our results uncovered YTHDF2-mediated regulation of the AXIN1/Wnt/β-catenin signaling that contributes to LUAD tumorigenesis, and thus provided insight into the mechanisms underlying lung adenocarcinoma progression.

overall_design: m6A profiles and mRNA profiles of control and knockdown of YTHDF2 A549 cells by deep sequencing

first: Hao

last: Sheng

first: Qiang

last: Wu

first: Feng

last: Ma

first: Jianfang

last: Huang

last: Chen

first: Lianghe

first: Xinghai

last: Zhu

first: Xiaoxi

first: Meng

last: Xu


title: Differentially expressed mRNA and circular RNA in HFD-fed or normal chow-diet-fed mice aortas

city: Shanghai

first: FEI

last: XU

state: Shanghai

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

summary: mRNA and Circular RNA sequencing data of aortas of ApoE-/- male mice fed with high fat diet or normal chow diet for 12 weeks.

overall_design: 6-week-old ApoE-/- male mice were fed high fat diet (HFD) or normal diet (ND) for 12 weeks. After the diet, the mice were sacrificed, mRNA and circular RNA were extracted from mice aortas. Sequencing was conducted and the results were included in this file.

first: Fei


title: Changes in whole heart gene expression resulting from endothelial TLR2 deletion

first: Michael

last: McCoy

address: 9500 Euclid Ave

department: Neuroscience

institute: Cleveland Clinic Foundation

summary: We report the application of bulk RNA sequencing for profiling changes in mouse cardiac lysates as a result of changes in innate immunity function. We generated an inducible endothelial cell toll-like receptor 2 knockout and assessed changes in overall gene expression in the absence of pathogen presence. We find that over 200 genes are differentially regulated between the two genotypes that are solely due to the presence of endogenous signaling within these animals. We also show that the genes that are differentially regulated are tied to the immunity function of the endothelium and that removal of toll-like receptor 2 signaling creates a diminished response by the immune system to wound healing and tumor development. Finally, we demonstrate that other immunomodulatory pathways are further affected, suggesting that changes outside of the endothelium are driven by endothelial-toll-like receptor 2 signaling. This study provides a framework for the application of tissue specific knockouts and profiling the role of endothelial as an innate immunity organ.

overall_design: Examination of 2 different genotypes resulting from endothelial cell-specific receptor deletions

first: Tatiana

last: Byzova

first: Rakhilya

last: Murtazina


title: Pathogenesis, Clinical and Biological Predictors of Growth in Environmental enteric dysfunction (EED): An Infant Birth Inception Cohort

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

type: Methylation profiling by genome tiling array

summary:
Environmental enteric dysfunction (EED) is a major impediment to the Sustainable Development Goals of improved childhood survival and healthy growth worldwide. Few studies have directly examined the affected intestine, limiting the development of effective interventions.
The Study of Environmental Enteropathy and Malnutrition (SEEM, Pakistan) followed 416 at-risk children prospectively from birth to 24 months of age in a rural district of Pakistan with a high prevalence of undernutrition. The duodenal genome-wide methylome and transcriptome was determined in 52 undernourished SEEM participants refractory to nutritional interventions and 42 North American healthy controls and celiac disease patients. Biomarkers were measured at 9 months and tested for association with growth at 24 months in training (n=166) and validation (n=84) groups within SEEM.

overall_design: DNA methylation was assessed in Duodenal biopsies from undernurished SEEM participants, and north American healthy controls. DNA was extracted, bisulfite converted and genome-wide DNA methylation was interrogated using the HumanMethylationEPIC BeadChip (Illumina).

first: Yael

last: Haberman

first: Najeeha

middle: T

last: Iqbal

first: Sudhir

last: Ghandikota

first: Indika

last: Mallawaarachchi

first: Phillip

last: Dexheimer

first: Najeeb

last: Rahman

first: Rotem

last: Hadar


title: RNA-sequencing from miR-375 knockout and YAP overexpression lung carcinoid (H727) cells.

city: Kingston

first: Neil

last: Renwick

state: ON

address: 88 Stuart Street

institute: Queen's University

summary: We report RNA sequencing data for miR-375 knockout and YAP overexpression lung carcinoid cells (H727). Lung carcinoids are variably aggressive and mechanistically understudied neuroendocrine neoplasms (NENs). Here, we identified and elucidated the function of a miR-375/yes-associated protein (YAP) axis in lung carcinoid (H727) cells. miR-375 and YAP are respectively high and low expressed in wild-type H727 cells. Following lentiviral CRISPR/Cas9-mediated miR-375 depletion, we identified distinct transcriptomic changes including dramatic YAP upregulation.  Similarly, YAP overexpression resulted in distinct and partially overlapping transcriptomic changes, phenocopying the effects of miR-375 depletion in the same models as above. Pathways analysis and confirmatory real-time PCR studies of shared dysregulated targets indicate that this axis controls neuroendocrine related functions such as neural differentiation, exocytosis, and secretion. Taken together, we provide compelling evidence that a miR-375/YAP axis is a critical mediator of neuroendocrine differentiation and tumorigenesis in lung carcinoid cells.

overall_design: Examination of transcriptional changes resulting from miR-375 knockout and YAP overexpression in lung carcinoid cells

first: Xiaojing

last: Yang

first: Jina

last: Nanayakkara


title: Transcript expression level in control and Setd1a-knockdown mouse explant retina

city: Bunkyo-ku

first: Toshiro

last: Iwagawa

address: 7-3-1 Hongo

department: Tokyo University Hospital

institute: University of Tokyo

summary: Knockdown of Kmt2f in a embryonic mouse retina caused increased apoptosis and decreased proliferation. To investigate downstream molecular mechanisms of Kmt2f in retina, RNA-sequencing was performed with control or shKmt2f-expressing retina. Mouse retinas at embryonic dat 17 were electroporated with plasmids and cultured for 2 days. EGFP-expressing cells were purified by a cell sorter, and RNA-seq was carried out.

overall_design: mRNA proflies of control (n = 3) and Setd1a-knockdown (n = 4) explant retina, which were culture for 2 days from embryonic day 17.

first: Xiaoyue

last: Deng

first: Masaya

last: Fukushima

first: Yutaka

last: Suzuki

first: Sumiko

last: Watanabe


title: Analysis of transcriptomes in HUVECs treated with exosomes derived from hypoxia-induced MDA-MB-231

city: Singapore

first: Chwee Teck

last: Lim

state: Singapore

address: T-Lab, #08-03, 5A Engineering Drive 1

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

summary: To study the cancer exosome-induced changes in HUVECs, we characterized the transcriptomes in HUVECs treated with exosomes derived from hypoxia-induced MDA-MB-231. We found the exosomes upregulated the epithelial–mesenchymal transition(EMT)-related and metabolism-related genes in HUVECs.

overall_design: Examination of transcriptomein 2 untreated HUVECs as well as 2 HUVECs treated with exosomes derived from hypoxia-induced MDA-MB-231

first: Pan

last: Zhang

first: Chwee-Teck


title: RNA-seq of human gastric cancer

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh School of Medicine

summary: We compared transcriptomic profiles of gastric carcinomas between patients carrying the ATG16L1 T300A SNP and patients without the SNP.

overall_design: We performed bulk RNA-seq of gastric cancer samples in patients who carry the ATG16L1 T300A SNP and patients who do not.

first: Changqing

last: Ma

first: William

last: Schwarzmann

first: Ta-Chiang

last: Liu


title: RNA-seq data of liver samples in FMT recipient rats

first: Qixin

last: HAN

address: NO.845 Lingshan Road

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: DHEA-shaped gut microbiota was transplantated to pseudo germ- free rats. Glucose intolerance, liver lipid accumulation and dyslipidemia were observed in recipient rats. Therefore, liver gene expression of these recipient rats were investigated.

overall_design: Three replicates each group. Overall,6 samples were analyzed including 3 replicates of control.

last: Han


title: Comparative gene expression analysis of biliary tract cancer cells under organoid culture and adherent culture.

city: Shinjuku-ku

first: Akiyoshi

last: Kasuga

state: Tokyo

address: 35, Shinanomachi

institute: Keio University

summary:
Organoid culture is important for maintenance of epithelial cell characteristics, stemness, and tumorigenic activity of biliary tract cancer initiating cells.
To investigate whether organoid culture maintain cancer stem cell properties of biliary tract cancer initiating cells, we compared the gene expression changes between organoid culture and adherent culture.

overall_design: Using Agilent mouse genome array, we compared global gene expression profiles in biliary tract cancer initiating cells under organoid culture and adherent culture.

first: Takashi

last: Semba

first: Ryo

last: Sato

first: Hiroyuki

last: Nobusue

first: Hideyuki

last: Saya

first: Yoshimi

last: Arima


title: Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma

first: Pushkar

last: Dakle

address: 14 Medical Dr

institute: Cancer Science Institute of Singapore

summary: In esophageal squamous cell carcinoma (ESCC), the core regulatory circuitry is ill-defined and the limited clinical approaches are available currently for the treatment of ESCC. Here, using enhancer profiling and CRC programme, we generated ESCC-dependent epigenomic-transcriptional regulatory circuitry, elaborated the exquisite work model mediated by core TFs and SEs through physical interaction between enhancers and promoter, and identified the crucial target of ESCC regulatory network.

overall_design: By integration of enhancer profiling and chromatin accessibility, we establish super-enhancer (SE) mediated core regulatory circuitry (CRC) for esophageal squamous cell carcinoma (ESCC) and identify tumor cells-dependent SE-associated TFs-TP63, SOX2 and KLF5.

first: Yuan

last: Jiang

first: Yan-Yi

first: Chun-Quan

last: Li

first: Zhang

last: Ying

first: Fullwood

last: MJ

first: De-Chen

last: Lin

first: H.

middle: P

last: Koeffler


title: Impact of aging on gene expression response to x-ray irradiation using mouse blood

city: New York

first: Constantinos

last: Broustas

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

summary:
Background: In the event of an improvised nuclear device or radiological dirty bomb detonation large numbers of people will be exposed to radiation that would require a timely and accurate biodosimetry to identify the highly exposed individuals who would require medical treatment from those who have received low or no radiation (the “worried well”). Gene expression signatures in response to radiation have been derived from mice and human peripheral blood and the impact of a number of variables, such as dose, time, genotype, and gender, on gene expression has been analyzed. However, the impact of aging on radiation gene profiling has not been taken into consideration.
Results: Global gene expression was measured in the blood of young (2 mo) and old (21 mo) male C57BL/6J mice 1 day after they were exposed to 4 Gy x-rays or they were sham irradiated (control) using the Agilent Mouse Whole Genome microarrays. Animals exposed to radiation suppressed expression of DNA repair genes with fold-changes being very similar to the two age groups. A notable exception was Mismatch Repair (MMR) that was significantly enriched among the downregulated genes in irradiated old mice (p = 2.34E-09) compared with irradiated young mice (p = 1.62E-04). Furthermore, cardiac hypertrophy signaling (p < 0.002) and the role of NFAT in cardiac hypertrophy (p = 0.01) were predicted to be enriched among the upregulated differentially expressed genes in irradiated old mice, but not irradiated young mice. In contrast, young mice respond to x-ray exposure by significantly upregulating genes involved in phagosome formation (p = 3.09E-07), phagosome maturation (p = 0.001), and Fcγ receptor-mediated phagocytosis (p = 0.03), all crucial processes that eliminates apoptotic cells and preserve tissue homeostasis.
Conclusions: We show that age is a variable that has the potential to fundamentally alter the transcriptomic profile of irradiated mouse blood. A number of biological processes, including phagocytosis, are differentially represented in young and old mice exposed to x-ray radiation. Our results highlight the significance of age as a variable that can have profound biological effects that will affect medical management and treatment decisions in case of a radiological emergency.

overall_design: Radiation induced gene expression in  blood from young (2 month) and old (21 month) mice was measured 24 h after 4 Gy of x-rays. Six independent experiments were performed at each age and treatment.


title: Functional Identification of Specialized Basal Ganglia Circuits that Regulate Vocal Motor Sequences

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Production of learned vocalizations requires precise selection and accurate sequencing of appropriate vocal-motor actions. The basal ganglia are essential for the selection and sequencing of motor actions, but the cellular specializations and circuit mechanisms governing accurate sequencing of vocalizations are unknown. Here, we use single-nucleus RNA sequencing and genetic manipulations to map basal ganglia cell types and circuits involved in the production of songbird vocal sequences. We identify cell-type specializations in direct-like and indirect-like basal ganglia pathways, including evolutionary expansion of striatal and arkypallidal cell-types that could facilitate vocal sequencing. We also reversibly reduced the expression of FoxP2 with a viral knockdown. For birds in which FoxP2 was knocked down, striatal neurons exhibited decreased expression of Drd1 and showed an increased ratio of Drd2/Drd1 expression. These findings identify key evolutionary specializations and circuits essential for selection and sequencing of vocal-motor actions necessary for vocal communication.

overall_design: We carried out single-nuclei RNA-sequencing of zebra finch Area X. Each bird received an AAV injection of a hairpin directed to knockdown FoxP2 or a scrambled control hairpin. Two birds for each condition were pooled.

first: Lei

last: Xiao

first: Devin

last: Merullo

first: Marissa

last: Co

first: Ashwinikumar

last: Kulkarni

first: Todd

last: Roberts


title: Effect of Flt3L and DNGR-1 on the biology of tumor-infiltrating type 1 dendritic cells

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: DNGR-1 is a dead cell-sensing receptor specifically expressed in type 1 conventional dendritic cells (cDC1s), but whether it plays a role in antitumor immunity remains unexplored. In our work we have explored the transcriptional profile of tumor-infiltrating cDC1s competent or deficient in DNGR-1,

overall_design: Transcriptomic analysis comparing tumor-infiltrating cDC1s from WT and DNGR-1-deficient mice (Clec9agfp/gfp) hydrodynamically injected with a Flt3L-producing plasmid (FL) or an empty plasmid (control). Three replicates of each of the four conditions, where each replicate was generated from tumors of a pool of 2-3 mice.

first: Francisco

last: Cueto

first: David

last: Sancho


title: Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [RNA-seq]

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

first: Yuan

first: M

last: Fullwood

first: H


title: Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [ATAC-seq]

last: Jiang

first: Yan-Yi

first: Chun-Quan

last: Li

first: Zhang


title: Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [ChIP-Seq Drug]

last: Ying

first: De-Chen


title: Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [ChIP-seq]

last: Lin


title: Genome wide CRISPR screen for Sorafenib resistance in MOLM13 and MV411 cells using Y. Kosuke library

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

type:
Other
Third-party reanalysis

summary: MOLM13 or MV411 cells were generated to express Cas9, infected with CRISPR library (Tzelepis et al 2016) , selected for puromycin resistance and exposed to Sorafenib (50nM), Crenolanib (20nM) or vehicle, DMSO.  Cells were collected at time 0 (post puromycin selection), day 7 and 14 for Sorafenib as well as 14 and 21 for Crenolanib.  DNA was extracted and sgRNA barcodes were amplified. The resulting PCR library was deep sequenced using the Illumina HiSeq 2500 using 6 samples per lane.

overall_design: Performed comparisons of sgRNA read counts between DMSO (FASTQ from GSE130412 processed using the data processing pipeline below) and Sorafenib treated cells at corresponding time points. Addition of MV411 CRISPR sequencing data to be added to existing GSE138343.

first: Alisa

last: Damnernsawad

first: Tamilla

last: Nechiporuk

first: Steve

last: Kurtz

first: Shannon

last: McWeeney

first: Jeffrey

last: Tyner


title: Expression data from A549 human lung adenocarcinoma cells with and without knockdown against CNOT3

city: Bethesda

first: Yo-taro

last: Shirai

state: MD

address: Building 37, Room 3118

department: Center for Cancer Research

institute: NIH

summary:
The physiological importance of mRNA degradation through the CCR4-NOT deadenylase has recently been highlighted. For example, mutation in CNOT3, a gene coding for sCNOT3 subunit of the CCR4-NOT complex, is found to be associated with T-cell acute lymphoblastic leukemia, T-ALL, though its contribution to other cancers has not been reported.
To identify the taget mRNAs of CNOT3 in human non-small cell lung cancer (NSCLC), we performed the microarray analysis using A549 cells with and without knockdown against CNOT3.

overall_design: We established A549 cells stably expressing tetracyclin-induible shRNA against non-targeting control (A549-T-shNTC) or CNOT3 targeting two different sequences (A549-T-shCNOT3-1 or A549-T-shCNOT3-2) using a lentiviral system. We evaluated the mRNA expression of each A549 stable with or without Doxycyclin (DOX; 1 ug/ml) treatment for 72 hours.

first: Chisato

last: Kikuguchi


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

overall_design: Refer to individual Series


title: PACAP Induces Light Aversion in Mice by an Inheritable Mechanism Independent of CGRP

status: Public on May 18 2021

city: Iowa City

first: Benjamin

last: Hing

state: IA

address: 51 Newton Road, BSB 6-509

institute: University of Iowa

summary: Bulk mRNA-seq was used to evaluate gene expression changes of the trigeminal ganglia of CD1 mice that were responsive and non-responsive to PACAP.

overall_design: mRNA from the trigeminal ganglia of mice that were responsive and  non-responsive to PACAP (3 males and 3 females from each group) were prepped using polyA selection and sequenced using Illumina HiSeq with 150 bp paired-end sequencing.

first: Adisa

last: Kuburas

first: Bianca

middle: N

last: Mason

first: Anne-Sophie

last: Wattiez

first: Alyssa

last: Reis

first: Levi

last: Sowers

first: Cristina

middle: M

last: Loomis

first: Leon

last: Garcia-Martinez

first: Andrew

last: Russo


title: Engrailed 1 coordinates cytoskeletal re-organization to induce myofibroblast differentiation

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

summary: Transforming growth factor-β (TGFβ) is a key mediator of fibroblast activation in fibrotic diseases including systemic sclerosis. Here we show that Engrailed 1 (EN1) is re-expressed in multiple fibroblast subpopulations in the skin of SSc patients. We characterize EN1 as a molecular amplifier of TGFβ signaling in myofibroblast differentiation: TGFβ induces EN1 expression in a SMAD3-dependent manner, and, in turn, EN1 mediates the pro-fibrotic effects of TGFβ. RNA sequencing demonstrates that EN1 induces a pro-fibrotic gene expression profile functionally related to the cytoskeleton organization and ROCK activation. EN1 regulates gene expression by modulating the activity of SP1 and other SP-transcription factors, as confirmed by ChIP-seq experiments for EN1 and SP1. Functional experiments confirm the coordinating role of EN1 on ROCK activity and the re-organization of cytoskeleton during myofibroblast differentiation both in standard fibroblast culture systems and in in vitro skin models. Consistently, mice with fibroblast-specific knockout of En1 demonstrate impaired fibroblast-to-myofibroblast transition and are partially protected from experimental skin fibrosis.

overall_design: EN1 and SP1 genomic targets in dermal fibroblasts stimulated with TGFβ with siRNA-induced knockdown of EN1, with fibroblasts stimulated with TGFβ and treated with non-targeting siRNA as controls

first: Andrea-Hermina

last: Györfi

first: Alexandru-Emil

last: Matei

first: Maximilian

last: Fuchs

first: Meik

last: Kunz

first: Jörg

last: Distler


title: Erythropoietin promotes abdominal aortic aneurysm via angiogenesis and inflammatory infiltration in Apoe-/- and wild type mice

city: jinan

first: meng

last: zhang

address: Jinan 250012, Shandong, China

institute: Shandong University

summary: The present study was undertaken to test the hypothesis that EPO may promote the formation of abdominal aortic aneurysm (AAA) via angiogenesis and inflammatory response. We injected EPO in different doses to Apoe-/- and WT mice, used EPO mAb in Apoe-/- mice with AngII stimulation, injected a selective activator of the heterodimer receptors of EPO into Apoe-/- and WT mice, and created CRISPR-mediated EPOR knockout (Epor+/-Apoe-/-) mice. In addition, we measured serum EPO concentration in healthy controls and patients with AAA, and performed a series of in vitro and ex vivo experiments in ECs, SMCs, and macrophages. Our results showed that EPO dose-dependently promoted the formation of AAA, with a high occurrence rate in both Apoe-/- and WT mice, and there was a close relationship between serum concentration of EPO and the incidence of AAA in Apoe-/- and WT mice receiving AngII or EPO treatment. The major mechanism involved angiogenesis, inflammatory response, SMCs apoptosis and collagen degradation via EPO-EPOR-JAK2/STAT5 signaling pathway in vascular cells. Administration of EPO neutralizing antibody suppressed AngII-induced AAA formation, and the incidence of AAA was dramatically reduced in Epor+/-Apoe-/- versus Apoe-/- mice after AngII infusion. In addition, serum EPO concentration was substantially higher in patients with AAA than in healthy subjects and correlated with the size of AAA in patients. In conclusion, EPO promotes the formation of AAA in both Apoe-/- and WT mice likely via enhanced angiogenesis, inflammation, SMCs apoptosis and collagen degradation, and EPO/EPOR signaling is essential for AngII-induced and possibly human AAA.

overall_design: The entire aorta isolated from Apoe-/- mice receiving medium-dose EPO (n=3) and vehicle (n=3) treatment

first: Meng

last: Zhang

first: Yun

first: Cheng


title: ZGA-Timer: a framework for the identification of key zygotic genome activation genes from time-series RNA-seq data

city: Beijing

first: Qiu

last: Xie

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

summary: Zygotic genome activation (ZGA) is a complex process which denotes the initiation of gene expression after fertilization. Deciphering the proper timing and genes involved in ZGA program is still a fundamental challenge in early embryo development. Here, we present a new ZGA gene identification framework, named ZGA-Timer, based on the timecourse pattern from RNA-seq data. By performing ZGA-Timer and siRNA technology, we confirmed Uqcc3 as a novel ZGA gene in mice. As a unique feature of ZGA-Timer, time-series RNA-seq data are modeled by a pattern recognition method and the onset of ZGA can be estimated in multiple species. ZGA-Timer outperforms current foldchange-based approaches. Furthermore, we investigate the epigenetic modifications and find that accessible chromatin predominately contributes to the regulation of ZGA genes. Moreover, ZGA genes show significant enrichment in housekeeping genes and cancer driver genes. Together, our ZGA-Timer framework provides a new approach to further understand the ZGA process.

overall_design: We performed siRNA experiments to verify the potential role of Uqcc3 in embryonic development. We injected siRNAs targeting Uqcc3 into fertilized oocytes at 8 hpi, and performed RNA-seq to siRNA-mediated Uqcc3-depleted embryos and normal embryos as control.

first: Hao

last: Li


title: Transcriptome analysis of the microplast derived from MCF7 cells treated with macrophage conditioned medium

city: Mumbai

first: Pooja

middle: Kamal

last: Melwani

state: Maharashtra

address: Mod Lab, Trombay

department: Radiation Biology & Health Science Division

country: India

institute: Bhabha Atomic Research Centre

summary:
Purpose: Next-generation sequencing was carried out to characterize transcripts landscape of the Microplast derived from the MCF7 cells treated with macrophage conditioned medium.
Methods: To stimulate microplasts formation, MCF-7 cells were cultured in 50% macrophage conditioned medium and 50% DMEM growth medium for 48 h. Cells and microplasts were harvested and resuspended in ice cold PBS. A low-speed differential centrifugation protocol was used to isolate microplasts. Total RNA was extracted from two biological replicates of microplasts enriched samples using RNeasy mini kit (Qiagen, Hilden, Germany). RNA concentration and integrity were determined with Nanodrop 1000 (Nanodrop, Wilmington, DE,USA) spectrophotometry. Libraries were prepared using the TruSeq RNA sample prep kit V2 as per the manufacturer’s protocol (Illumina, San Diego, USA).
Conclusions: This study provide the first transcriptional profile of the microplast derived from the MCF7 cells.

overall_design: Transcriptome profiling of the Microplast was carried out in the duplicates.

first: P

middle: K

first: M

last: Padwal

first: B

last: Pandey


title: Autophagy Inhibition via Targeting of PIKfyve Potentiates Immune Checkpoint Blockade in Prostate Cancer Therapy

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: To understand the tumor microenvironment changes in terms of transcriptome upon PIKfyve inhibition by small molecule ESK981 and the immune checkpoint inhibitor anti-PD-1 in Myc-CaP syngeneic mouse model.

overall_design: Myc-CaP cells were injected into FVB male mice subcutaneously on both flanks. When tumors reached 50 mm3, mice were randomized and treated with 15 mg/kg ESK981 or vehicle at 5 days per week by oral gavage, while anti-PD-1 or isotype control were given at 200 µg per mouse 3 times per week by intraperitoneal injection. Tumors were collected after 3 weeks of treatment, and total RNA was extracted by QIAGEN RNA extraction kit, and library was prepared by RiboErase selection kit. RNA-sequencing was performed on the Illumina HiSeqTM 2500 platform.

first: Yuanyuan

last: Qiao

first: Stephanie

last: Simko

first: Josh

last: Vo

first: Andrew

middle: D

last: Delekta

first: Fengyun

last: Su

first: Rui

last: Wang

first: Xuhong

last: Cao


title: DNA methylation in osteoarthritis

city: shanghai

first: sun

middle: tong

last: xin

address: xinjunhuanlu

institute: oebiotech

summary: Illumina Infinium Epic Human DNA Methylation Beadchip V1.2.8 The Illumina Infinium Epic Human DNA Methylation Beadchip V1.2.8 is used to obtain DNA methylation profiles of about 850k CpG in osteoarthritis and normal cells to find differences, approximately 850k CpGs in osteoarthritis and normal cell

overall_design: The chip used in the project was MethylationEpic (850K) BeadChip, and 6 samples were detected and analyzed. After standardization, 2 groups of differential methylation sites were analyzed, and GO and KEGG analysis of the differential methylation sites were performed, and the copy number variation analysis was finally completed.


title: RNAseq in JARID2 siRNA-treated in vitro differentiated human primary adipocytes

city: Stockholm

first: Jurga

last: Laurencikiene

address: Hälsovägen 7

country: Sweden

institute: Karolinska Institutet

overall_design: RNAseq was performed in siJARID2 and control siRNA-treated human adipose tissue derived stem cells (hASC). The tretment of siRNA was performed by electroporation one day before induction of differentiation in vitro. The cells were lyzed and RNA was purified on day 6 (mid differentiation) and day 13 (full differentiation) from differentiation start. Three independen experiments were analyzed for both day 6 (transfections HG23, HG23_2, HG24) and day 13 (transfections TRANSF2,3,4). Samples of negative  control (non-targeting siRNA) and siJARID2 from the same experiment were anayzed as paired samples.

first: N

last: Subramanian

first: J

first: C

last: Björk


title: Functional characterization of splicing regulatory elements

city: Farmington

first: Scott

last: Adamson

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: RNA binding protein-RNA interactions mediate a variety of processes including pre-mRNA splicing, translation, decay, polyadenylation and many others. Previous high -throughput studies have characterized general sequence features associated with increased and decreased splicing of certain exons, but these studies are limited by not knowing the mechanisms underlying these associations. Here we utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins (RBPs). We identify features which make splicing events more sensitive to depletion of RBPs, as well as which RBPs act as splicing regulators sensitive tupon RBP depletion. To analyze the sequence determinants underlying RBP-RNA interactions impacting splicing, we assay tens of thousands of sequence variants in a high-throughput splicing reporter called Vex-seq and confirm a small subset in their endogenous loci using CRISPR base editors. Finally, we leverage other large transcriptomic datasets to confirm the importance of RBPs which we designed experiments around and identify additional RBPs which may act as additional splicing regulators of the exons studied.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: 8 samples are included in this experiments which include Vex-seq libraries and the associated plasmid DNA sequencing libraries. These include two amplicon DNA sequencing of a plasmid libraries, which are the primary and secondary plasmid pools, the latter of which was transfected into 3 biological replicates of K562 or HepG2 cells. These transfected cells were quantified using amplicon RT-PCR sequencing.

middle: I

first: Lijun

last: Zhan

first: Brenton

middle: R

last: Graveley