title: RNA-seq of WT, ELF4-/- CACO2 and Elf4fl/fl-Villin-Cre Livers Transcriptomes

city: beijing

first: Tongtong

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University


title: mRNA expression quantitative Analysis of MOLM-13 and THP-1 treated with I1 compared with control

status: Public on May 18 2022

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

country: China

institute: Weifang Medical University

type: Expression profiling by high throughput sequencing

summary: The goals of this study are toevaluate the mRNA expressions of genes in MOLM-13 and THP-1 cell lines treated with I13

overall_design: There are 6 samples for MOLM-13 cell line ( control and I1-treated). Another 6 samples for THP-1 cell line ( control and I1-treated).


title: RNA-sequencing in liver tissues for Wild or Ndrg3-deleted C57BL/6 mice

city: Daejeon

first: Hyun

middle: Ahm

last: Sohn

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

summary: NGS-derived liver transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: We analyzed mRNA profiles in liver of Wild or Ndrg3-deleted (exon4) in C57BL/6 mice

middle: A

first: Young

middle: I

last: Yeom

first: Dong

middle: c

last: Lee

first: Kyung

last: Park


title: Next-generation sequencing analysis of control mammary glands and ECD transgenic tumors

city: Omaha

first: Vimla

last: Band

state: Nebraska

address: 601 Saddle Creek road

department: Department of Genetics, Cell Biology & Anatomy,

country: USA

institute: University of Nebraska Medical Center

summary: Overexpression of ECD in mammary gland promotes mammary tumorigenesis. To determine the plausible mechanism of how ECD contributes the oncogenesis, we performed RNAseq analysis of three independent control mice mammary glands (6 months old) and four independent ECD transgenic mammary tumors. Out of these four tumors, T1a and T1b were adenosquamous carcinoma type, T3 was Spindle cell carcinoma type and T4 was papillary carcinoma. RNA was isolated from the respective samples and RNAseq was performed.

overall_design: Total RNA was extracted from three independent control mammary glands and four independent tumors and RNA sequencing was performed.

first: Bhopal

last: Mohapatra

first: Sameer

last: Mirza

first: Siddesh

last: Southekal

first: Sankarasubramanian

last: Jagadesan


title: RNA-seq analysis of glioblastoma stem cells where MEOX2 expression was knocked down by shRNAs

city: Roma

first: Silvia Anna

last: Ciafrè

address: Via Montpellier, 1

department: Biomedicine and Prevention

country: Italy

institute: University of Rome Tor Vergata

summary: The most widely accepted hypothesis about glioblastoma onset indicates glioblastoma stem-like cells (GSCs) as the cells of origin, also responsible for the high chemo- and radio-resistance of this tumor and of its recurrence. MEOX2 is a transcription factor overexpressed in glioblastoma, whose expression is negatively correlated to patients’ survival. Starting from our observation that MEOX2 expression is strongly enhanced in six GSC lines we tested, we performed shRNA-mediated knock-down experiments in two different GSC lines, and found that MEOX2 depletion inhibits their self-renewal and growth ability, and increases the apoptotic cell death. By a deep transcriptome analysis, we identified a core group of genes modulated in response to MEOX2 knock-down. Among these genes, the repressed ones are largely enriched in genes involved in the hypoxic response and in the glycolytic pathway, two strictly related pathways which contribute to the resistance of high grade gliomas to therapies.

overall_design: Total transcriptome results of two different human glioblastoma stem cell (GSC) lines, BT273 and BT379, transduced with lentiviral vectors expressing shRNAs targeting MEOX2. Each GSC type transduced with one specific anti-MEOX2 shRNA was assayed in two biological replicates, and the results compared to the same GSC type transduced with a negative control vector, assayed in two biological replicates.

first: Silvia

first: Carla

last: Proserpio

last: Galardi


title: Defining the skeletal myogenic lineage in human pluripotent stem cell-derived teratomas

city: Minneapolis

first: Sunny

last: Chan

institute: University of Minnesota

summary: Skeletal muscle stem cells are essential to muscle homeostasis and regeneration after injury. An attractive approach to obtain these cells is via differentiation of pluripotent stem cells (PSCs). We have recently reported that teratomas derived from mouse PSCs are a rich source of skeletal muscle stem cells. Here, we showed that the teratoma formation method is also capable of producing skeletal myogenic progenitors from human PSCs. Using single-cell transcriptomics, we discovered multiple lineages in human PSC-derived teratomas. Interestingly, we observed several distinct skeletal myogenic subpopulations. Trajectory analysis revealed that these subpopulations represented progressive stages of skeletal myogenic development. We further discovered that ERBB3 and CD82 are effective surface markers for prospective isolation of the skeletal myogenic lineage in human PSC-derived teratomas. Therefore, teratoma formation provides an accessible model for obtaining human skeletal myogenic progenitors from PSCs.

overall_design: Single-cell RNA seq of human embryonic stem cell-derived teratomas 8 weeks after injection into tibalis anterior of immunodeficient mouse

first: Matthew

middle: P

last: Pappas

first: Ning

last: Xie

first: Jacqueline

middle: S

last: Penaloza


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Elf4fl/fl-Villin-Cre Livers Transcriptomes

first: Tongtong

last: Liu

summary: Conclusion: Elf4fl/fl-Villin-Cre mice are more sensitive to alcohol induced liver steatosis

overall_design: six-week-old WT and Elf4fl/fl-Villin-Cre C57BL/6 male mice were treated with Lieber-DeCarli liquid diet containing 5% (w/v) alcohol (EtOH) or isocaloric maltose dextrin (Ctrl) for 21 days. Livers was taken out and the RNA was extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis

first: Fuping

last: You


title: LncRNA-mRNA expression pattern in invasive pituitary adenomas: A microarray analysis

city: Guangzhou

first: LI

middle: YAN

last: LI

address: Changgang East Road

institute: The Second Affiliated Hospital of Guangzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: lncRNA microarray was performed in three invasive and three noninvasive PAs

overall_design: to investigate the expression pattern of lncRNAs in both invasive and noninvasive PAs

first: Chao

last: Peng

first: Shuaikai

last: Wang

first: Yanli

last: Li

first: Yong

last: Yuan


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ELF4-/- CACO2 cells Transcriptomes

summary: Conclusion: RNA sequencing of Wild Type and ELF4-/- CACO2 cells.

overall_design: The RNA of Wild Type and ELF4-/- CACO2 cells was extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis


title: Cellular and molecular mechanisms underlying granulosa cell tumor induced by constitutively activated TGFB signaling

city: College Station

last: Ni

state: Texas

address: 400 Bizzell St

institute: Texas A&M University

summary: Mice harboring constitutively activated TGFβ signaling (TGFBR1-CA) develop ovarian GCTs that phenocopy the hormonal and several molecular characteristics of human GCTs. The goal of this study is to determine molecular alterations in the ovary upon TGFβ signaling activation. We performed Next-generation sequencing (NGS) analysis of ovaries from TGFBR1-CA mice and age-matched controls during tumor formation

overall_design: Ovarian mRNA profiles of 30-day old TGFBR1-CA mice and control mice

first: Qinglei

first: Xin

last: Fang


title: Hyperbaric oxygen therapy after mid-cervical spinal contusion injury

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Hyperbaric oxygen (HBO) therapy is frequently used to treat peripheral wounds or decompression sickness. Evidence suggests that HBO therapy can provide neuroprotection and has an anti-inflammatory impact after neurologic injury including spinal cord injury (SCI). Our primary purpose was to conduct an unbiased, genome-wide screening of mRNA expression changes in the injured spinal cord after HBO therapy. A mRNA gene array was used to evaluate samples taken from the contused region of the spinal cord following a lateralized mid-cervical contusion injury in adult female rats. HBO therapy consisted of daily, 1-hour sessions (3.0 ATA, 100% O2) initiated on the day of SCI. Gene set enrichment analyses indicated that HBO upregulated genes in pathways associated with electron transport, mitochondrial function, and oxidative phosphorylation, and downregulation genes in pathways associated with inflammation (including cytokines and NF-B) and apoptotic signaling.  In a separate cohort, spinal cord histology was performed to verify whether the HBO treatment impacted neuronal cell counts or inflammatory markers. Compared to untreated rats, there was increased NeuN positive cells in the spinal cord of HBO treated rats (p=0.007). Further, staining for anti-ionized calcium binding adaptor protein (Iba-1, a microglial marker) was reduced after HBO (p=0.028). We conclude that HBO therapy, initiated shortly after SCI and continued for 10-days, can alter the molecular signature of the lesioned spinal cord in a manner consistent with an anti-inflammatory and neuroprotective impact.

overall_design: A mRNA gene array was used to evaluate samples taken from the contused region of the spinal cord following a lateralized mid-cervical contusion injury in adult female rats. HBO therapy consisted of daily, 1-hour sessions (3.0 ATA, 100% O2) initiated on the day of SCI.  All procedures were approved by the University of Florida Institutional Animal Care and Use Committee.  Rats were housed in an Assessment and Accreditation of Laboratory Animal Care (AAALAC)-accredited facility with a 12:12 light/dark cycle with ad libitum access to rodent chow and water. Adult female Sprague-Dawley rats (200-250g, Harlan Laboratories, Indianapolis, IN, USA) were studied.  Rats (n = 4/group) were injected intraperitoneally with beuthanasia solution. After the loss of the hind-limb withdrawal reflex, cervical spinal tissues (C3-C5) were harvested, placed into RNA Later (Life Technologies, Carlsbad, CA, USA), and stored at -80°C. RNA extraction was performed using TRIzol and isolated total RNA was purified using an RNeasy Mini kit (Qiagen, Valencia, CA), according to manufacturer’s instructions. The resulting quantity and purity of total RNA was tested through absorbance spectrophotometry at 230, 260 and 280 nm. For microarray analysis, RNA samples were sent to the Boston University Medical Center Microarray Core Facility for analysis using the Affymetrix Rat Gene Array 2.0ST.  Note: the gene array work was completed on the following groups: naive (spinal intact, no prior surgery); sham (sham surgery, no spinal cord injury); cSCI (spinal contusion, no further treatment), HBOT1d (spinal cord injury followed by HBO treatment only on day 1 post-injury), HBOT10d (spinal cord injury followed by HBO treatment for 10 days).   Only the cSCI and HBOT10d groups are included in the accompanying manuscript.

first: David

last: Fuller


title: enhancer and super-enhancer landscape in ADPKD

city: Dallas

first: Ronak

last: Lakhia

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UTSW

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ChIP-Seq on 16 day old control and Pkd1 mutant kidneys using an antibody to H3K27ac to determine the enhancer and superenhancer landscape in ADPKD

overall_design: 16 day old control and Pkd1 mutant kidneys were harvested and underwent processing to perform ChIP with an antibody to H3K27ac.  4 kidneys were pooled from 2 mice for each biological replicate

first: Vishal

last: Patel


title: Transcriptome data from tomato parthenocarpic mutants lacking Aux/IAA transcription factor SlIAA9

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: We investigated the behavior of tomato mutants lacking transcription factors of SlIAA9, a key gene controlling parthenocarpy. To focus on the early stages of anthesis, ovary samples of MicroTom-J (MT-J) and the mutant at the three stages (bud, flowering, and after flowering) were collected.

overall_design: We conducted three independent hybridizations with the GeneChip® Tomato Genome Array according to the manufacturer's instructions (Affymetrix, http:// www.affymetrix.com). A single biological replicate was utilized in each hybridization. The preprocessing and normalization/summarization of all CEL files were with the Bioconductor (Gentleman et al., 2004) and a robust multi-chip average (RMA) (Bolstad et al., 2003). The quality of GeneChip data was assessed by AFFYPLM package (Bolstad et al., 2005). We used the annotation of each gene in the CSV file Tomato.na32.annot.csv (downloaded on June 2011) released by the Affymetrix. This dataset includes 2 experimental batches. Therefore, a batch adjustment for unwanted variation [e.g., ComBat (Johnson et al., 2007)] is needed for further downstream analyses.

first: Tomoko

last: Nishizawa

first: Ken

last: Kamiya

first: Miyako

last: Kusano


title: Transcriptome data from tomato parthenocarpic mutants lacking Tomato APETALA3 (TAP3)

summary: We investigated the behavior of tomato mutants lacking transcription factors of TAP3, a class B MADS-box gene controlling parthenocarpy. To focus on the early stages of anthesis, ovary samples of MicroTom-J (MT-J) and the mutant at the different stages (e.g., bud, flowering, and after flowering) were collected.

overall_design: We conducted three independent hybridizations with the GeneChip® Tomato Genome Array according to the manufacturer's instructions (Affymetrix, http:// www.affymetrix.com). A single biological replicate was utilized in each hybridization. The preprocessing and normalization/summarization of all CEL files were with the Bioconductor (Gentleman et al., 2004) and a robust multi-chip average (RMA) (Bolstad et al., 2003). The quality of GeneChip data was assessed by AFFYPLM package (Bolstad et al., 2005). We used the annotation of each gene in the CSV file Tomato.na32.annot.csv (downloaded on June 2011) released by the Affymetrix.


title: Identification of genes regulated by ID2 in Ewing sarcoma cells.

city: Iowa City

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

summary: The ID family of proteins (ID1-4), which bind to basic helix-loop-helix (bHLH) transcription factors and prevent bHLH-directed transcription, are critical regulators of the differentiation and chemoresistance of cancer cells derived from multiple cellular lineages. ID2 was previously shown to impair the in vitro differentiation of human mesenchymal stem cells. However, the functional role, if any, of ID2 in regulating differentiation, developmental pathways, and the oncogenic phenotype of Ewing sarcoma tumors is unknown. We used CRISPR/Cas9 to knockout ID2 in Ewing sarcoma cell lines and identified that the loss of ID2 significantly decreases cell growth in vitro and in vivo in a xenograft experiment. Using RNA-seq and gene set enrichment analysis with ID2-knockout and ID2-Knockout-Rescue cell lines we identified that ID2 regulates genes related to differentiation and development in Ewing sarcoma cell lines.

overall_design: We performed RNA-seq with wildtype, ID2-knockout, and ID2-Knockout-Rescue Ewing sarcoma TC71 cell lines.

middle: J


title: Transcriptome data from tomato parthenocarpic mutants lacking SlDELLA

summary: We investigated the behavior of tomato mutants lacking SlDELLA, a negative regulator of gibberellin (GA) signaling pathway. To focus on the early stages of anthesis, ovary samples of MicroTom-B (MT-B) and the mutant at the three stages (bud, flowering, and after flowering) were collected.


title: Prostate cancer urinary Extracellular Vesicles are enriched in cytoplasmic intron-free mRNAs and long noncodingRNAs with putative functional significance

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Long noncoding (lnc)RNA modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, little is known in their ability to be transferred and control adjacent cells. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and anti-tumorigenic functions by controlling the immune response. However, few studies have addressed the full RNA content of EVs in human fluids and none have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on 6 Formaldehyde-Fixed-Parafilm-Embedded (FFPE) prostate cancer (PCa) tumor tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. uEVs contain intron-free cytoplasmic transcripts, specific lnc/circular (circ)RNAs. Some uEV-circRNA were characterized as essential for prostate cell proliferation in vitro. 15 uEV-lncRNA were predicted encoding 750 unique high-affinity neoantigens. Our comparison of functional EVs-lnc/circRNAs in 3 PCa cell lines provides a fundamental resource to determine the role of uEV-lncRNA in PCa progression.

overall_design:
Here, we performed Total RNA-Sequencing on 6 Formaldehyde-Fixed-Parafilm-Embedded (FFPE) prostate cancer (PCa) tumor tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients.
Total RNA was extracted, checked for the quality and then converted into cDNA for total stranded RNA-sequencing.

first: Anna

last: Almeida

first: Marc

last: Gabriel


title: Transcriptome data from tomato parthenocarpic mutants

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

overall_design: Refer to individual Series


title: Mechanisms of Sinoatrial Node Dysfunction in Heart Failure with Preserved Ejection Fraction

city: Los Angeles

first: Thassio

last: Mesquita

state: California

address: 8700 Beverly Boulevard

department: Smidt Heart Institute

institute: Cedars-Sinai Medical Center

summary: RNA sequencing from sinoatrial node tissue was performed to identify transcriptomic changes in Dahl salt-sensitive rats fed with normal salt diet (0.4% NaCl, control group) or high-salt diet (8% NaCl, HFpEF group) for 11 weeks. Transcriptomic profiling revealed numerous changes in multiple disease-associated genes in HFpEF, which is functionally related to the observed physiological impairments and structural remodeling.

overall_design: Transcriptome changes in sinoatrial node from control and HFpEF animals

first: Eugenio

last: Cingolani


title: Epigenetic regulation of innate immune memory in microglia

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

summary: Microglia are the tissue-resident macrophages of the CNS. They originate in the yolk sac, colonize the CNS during embryonic development and form a self-sustaining population with limited turnover. A consequence of their relative slow turnover is that microglia can serve as a long-term memory for inflammatory or neurodegenerative events. We characterized the epigenomes and transcriptomes of microglia exposed to different stimuli; an endotoxin challenge (LPS) and genotoxic stress (DNA repair deficiency-induced accelerated aging). Whereas the enrichment of permissive epigenetic marks at enhancer regions explains training (hyperresponsiveness) of primed microglia to LPS challenge, the tolerized response of microglia seems to be regulated by loss of permissive epigenetic marks. Here, we identify that inflammatory stimuli and accelerated aging because of genotoxic stress activate distinct gene networks. These gene networks and associated biological processes are partially overlapping, which is likely driven by specific transcription factor networks, resulting in altered epigenetic signatures and distinct functional (desensitized vs. primed) microglia phenotypes.

overall_design: We performed RNA, ATAC, and ChIP-sequencing on acutely isolated, FACS-purified microglia from mice that were either recurrently treated with LPS with a 1-month interval, or from Ercc1Δ/ko mice that were stimulated with LPS near the end of their lifespan at 10-12 weeks of age. For the tolerance model, we analyzed four treatment groups: the controls that were treated with PBS twice (PBS-PBS), mice that were treated with LPS and after 1 month with PBS (LPS-PBS) to investigate desensitization, mice treated with PBS followed by LPS after 1 month to determine the acute response to LPS (PBS-LPS) and mice that were treated with LPS twice with a 1-month interval between challenges (LPS-LPS) to identify the tolerant response. For the microglia priming model, both the Ercc1Δ/ko mice and their control littermates (Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt) were treated with PBS (WT-PBS, KO-PBS) to identify priming effects or with LPS (WT-LPS, KO-LPS) to identify training. For RNA-seq, microglia from 3 individual mice per condition were collected. For ChIP-seq, chromatin of 5 mice per experimental group was pooled and subjected to ChIP. For ATAC-seq, microglia from 2 mice per experimental group were pooled and subjected to ATAC. RNA-seq and ATAC-seq was performed for all four experimental groups in both the tolerance and training model. ChIP-seq was performed for all four experimental group in the tolerance model, but only for PBS-treated Ercc1Δ/ko and control mice. In case of the tolerance model, we used antibodies targeting H3K4me3 and H3K27Ac to identify transcription start sites (TSSs) and enhancers of actively transcribed genes, respectively. In Ercc1Δ/ko mice, we also analyzed H3K4me3 and H3K27ac, and additionally H3K4me1 which together with H3K27ac marks active enhancers and the Polycomb-regulated H3K27me3 associated with transcriptional repression.

first: Susanne

middle: M

last: Kooistra


title: chimeric antigen receptor T cells with knockout

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University


title: Genome-wide maps of FOXK2 binding sites in ovarian cancer cell line OVCAR5 and expression profile of FOXK2 knockdown OVCAR5 cells (RNA-seq)

city: Chicago

first: Daniela

last: Matei

state: Illinois

address: 303 E Superior St

department: Ob-Gyn

institute: Northwestern University

summary: This study characterized the genome-wide binding of FOXK2 in ovarian cancer (OC) cell OVCAR-5 and investigated the expression profile of OVCAR5 cells with FOXK2 knocking-down.

overall_design: Two datasets are included: 1) Examined transcriptome of OVCAR5 cells transduced with control shRNA (shCtrl) and FOXK2-targeting shRNA (shFOXK2) in OVCAR5 cells (in biological duplicates); 2) Determined the genome-wide bindng and occupancy profile of FOXK2 in OVCAR5 cells by ChIP-seq (in biological duplicates).

first: Yaqi

last: Zhang

first: Yinu

last: Wang

first: Guangyuan

last: Zhao


title: Genome-wide maps of FOXK2 binding sites in ovarian cancer cell line OVCAR5 and expression profile of FOXK2 knockdown OVCAR5 cells (ChIP-seq)


title: Potential therapeutic effects of long-term stem cells administration: impact on the gene profile and kidney function of PKD/Mhm (Cy/+) rats

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg


title: Differential DNA Methylation Associated with Sexual Partner Preferences in Rams

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

type: Methylation profiling by high throughput sequencing

summary: The present study evaluated the genome-wide methylation level of the medial basal hypothalamus using reduced representation bisulfite sequencing (RRBS) in female- and male-oriented rams.

overall_design: RRBS of 5 male oriented rams (MORs) and 4 female oriented rams (FORs.

first: Rebecka

last: Amodei

first: Surajit

last: Bhattacharya

first: Eric

last: Vilain

first: Charles

middle: E

last: Roselli


title: Microarray analysis of gene expression in human bronchial epithelial cells exposed to arsenic, BaP alone or arsenic plus BaP

city: Lexington

first: Zhishan

state: Kentucky

address: Toxicology, 256 HSRB, 1095 Veterans Drive

department: Toxicology and Cancer Biology

institute: University Of Kentucky

summary: Human bronchial epithelial cell BEAS-2B cells were continuously exposed to a vehicel control (DMSO), arsenic (NaAsO2, 1 uM), BaP (2.5 um) alone or arsenic plus BaP for 30 weeks. At the end of exposure, cells were collected and total RNA was extracted for microarray analysis.


title: RNAseq of a cohort series of 18 pediatric MBs in Taiwan

city: Taipei

first: Kuo-Sheng

last: Wu

address: No.250, Wuxing St., Xinyi Dist.

country: Taiwan

institute: Taipei Medical University

summary: Background: Since 2016, a project for molecular diagnosis of childhood medulloblastoma (MB) was initiated in Taiwan. We aimed to integrate molecular classification, molecular and clinical risk factors, somatic mutations, and phenotypic traits for up to date adaptive care. Method: 18 MBs in children with frozen tumor tissue were assembled. Clinical data were retrieved. RNA-Seq and DNA methylation array data were generated. Molecular subgrouping and molecular-clinical correlation were performed.  Subgroup-based risk stratification included an adjusted Heidelberg risk stratification scheme were defined and evaluated. We selected 51 genes for somatic variant calling using RNA-Seq. Relevant phenotypic traits were defined for the linkage of genetic predisposition. Results: Four core molecular subgroups (WNT, SHH, Group 3, and Group 4) were identified. Genetic backgrounds of metastasis at diagnosis and extent of tumor resection were observed. The overall survivals of the adjusted Heidelberg scheme matched with the definition of each risk subgroups. Somatic mutations in DNA damage response were detected. Conclusion: The findings of this study provide valuable information for adaptive risk stratified treatment and personalized care of childhood MBs in our cohort series and in Taiwan.

overall_design: mRNA profiles of a cohort series of 18 pediatric MBs in Taiwan were generated by RNAseq, using Illumina Nextseq 500.

first: Tai-Tong

last: Wong


title: Potential therapeutic effects of long-term stem cells administration: impact on the gene profile and kidney function of PKD/Mhm (Cy/+) rats [PKD_Jan19]

summary: Cystic kidney disease (CKD) is a heterogeneous group of genetic disorders and one of the most common causes of end-stage renal disease. Here, we investigate the potential effects of long-term human stem cells treatment on kidney function and the gene expression profile of PKD/Mhm (Cy/+) rats.  Human adipose derived stromal cells (ASC) and human skin-derived ABCB5+ stromal cells (2x106) were monthly, over a period of 6 months, infused intravenously or injected intraperitoneally. Additionally, ASC and ABCB5+ derived conditioned media were administrated intraperitoneally. Gene expression profile results showed a significant reprogramming of metabolism related pathways along with the down-regulation of cAMP, NF-B and apoptosis pathways. During the experimental period, the principal renal parameters as well as renal function using an innovative non-invasive transcutaneous device were measured. All together, these analyses show a moderate amelioration of the renal function in ABCB5+ and ASC treated groups. Additionally, ABCB5+ and ASC derived conditioned media treatments lead to milder, but still promising improvements. Cell-based therapy may constitute a novel therapeutic approach in CKD.

overall_design: Human adipose derived stromal cells (ASC) and ABCB5+ cells (2x106) were infused intravenously and injected intraperitoneally. Additionally, ASC and ABCB5+ derived conditioned media were administrated intraperitoneally. Gene expression profile results showed a significant reprogramming of metabolism related pathways along with the down-regulation of cAMP, NF-kB and apoptosis pathways. During the experimental period, the principal renal parameters as well as renal function using an innovative non-invasive transcutaneous device were measured. All together, these analyses show a moderate amelioration of the renal function in ABCB5+ and ASC treated groups. Additionally, ABCB5+ and ASC derived conditioned media treatments lead to milder, but still promising improvements. Cell-based therapy may constitute a novel therapeutic approach in CKD.

last: Nardozi

first: Stefania

last: Palumbo

first: Arif

last: ul Maula Khan

first: Karen

last: Bieback

first: Samar

last: Sadeghi

first: Mark

last: Kluth

first: Micheal

last: Keese

first: Norbert

last: Gretz


title: Potential therapeutic effects of long-term stem cells administration: impact on the gene profile and kidney function of PKD/Mhm (Cy/+) rats [PKD_Dez19]

first: Daniela


title: RNAseq of a cohort series of 52 pediatric MBs in Taiwan

summary: Background: Since 2016, a project for molecular diagnosis of childhood medulloblastoma (MB) was initiated in Taiwan. We aimed to integrate molecular classification, molecular and clinical risk factors, somatic mutations, and phenotypic traits for up to date adaptive care. Method: Fifty-two MBs in children with frozen tumor tissue were assembled. Clinical data were retrieved. RNA-Seq and DNA methylation array data were generated. Molecular subgrouping and molecular-clinical correlation were performed.  Subgroup-based risk stratification included an adjusted Heidelberg risk stratification scheme were defined and evaluated. We selected 51 genes for somatic variant calling using RNA-Seq. Relevant phenotypic traits were defined for the linkage of genetic predisposition. Results: Four core molecular subgroups (WNT, SHH, Group 3, and Group 4) were identified. Genetic backgrounds of metastasis at diagnosis and extent of tumor resection were observed. The overall survivals of the adjusted Heidelberg scheme matched with the definition of each risk subgroups. Somatic mutations in DNA damage response were detected. Five patients with SHH MB presented potential genetic predisposition and three patients had related germline mutations. Conclusion: The findings of this study provide valuable information for adaptive risk stratified treatment and personalized care of childhood MBs in our cohort series and in Taiwan.

overall_design: mRNA profiles of a cohort series of 52 pediatric MBs in Taiwan were generated by RNAseq, using Illumina Nextseq 500.


title: Genome-wide maps of FOXK2 binding sites in ovarian cancer cell line OVCAR5 and expression profile of FOXK2 knockdown OVCAR5 cells

last: Matei


title: Platelet miRNA expression from patients of PDAC and healthy donors

status: Public on May 17 2022

city: Mexico City

first: Jorge

middle: Yassen

last: Blancas

state: CDMX

address: Periferico Sur 4809

department: Research

country: Mexico

institute: INMEGEN

summary:
Platelets can change their expression of mRNA and miRNAs when educated by tumors. In this assay we assesed the diferential expression of miRNA between healthy individuals and patients suffering pancreatic cancer (PDAC)
Platelets form 4 healthy donors, 4 PDAC patient blood and 4 PDAC patient pancreatic drainage were collected to asses differential expression

overall_design: Platelets were collected from blood of healthy donors and PDAC patients before surgery. Platelets derived from pancreatic drainage were collected 1-2 days after surgery. RNA was extracted by TriZol according to manufacturer instructions. We used the Affymetrix GeneChip™ miRNA 4.0 Array to map miRNA transcriptome profiles.

first: J

last: Diaz-Blancas

first: V

last: Maldonado-Lagunas

last: Melendez-Zajgla


title: The role of GABPA,GPD1L and BRD9 in renal cancer progression and metasasis

city: Ji'nan

first: Ning

last: Zhang

state: Shandong

address: 107, West wenhua Xi road

institute: Qilu hospital of Shandong Universit

summary: RNAseq was performed on the cells with GABPA knockdown, the cells with GPD1L knockdown, the cells with BRD9 knockdown and the control cells.

overall_design: 3 replicates for each conditions

first: Zhiqing

last: Fang

first: Dawei

last: Xu


title: Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

summary:
Purpose: Transcriptome analysis of pancreatic ductal adenocarcinoma (PDAC) has been useful to identify gene expression changes that sustain malignant phenotypes. Yet, most studies examined only tumor tissues and focused on protein-coding genes, leaving long non-coding RNAs (lncRNAs) largely underexplored.

Methods: We generated total RNA-Seq data from patient-matched tumor and nonmalignant pancreatic tissues and implemented a computational pipeline to survey known and novel lncRNAs. siRNA-mediated knockdown in tumor cell lines was performed to assess the contribution of PDAC-associated lncRNAs to malignant phenotypes. Gene co-expression network and functional enrichment analyses were used to assign deregulated lncRNAs to biological processes and molecular pathways.

Results: We detected 9,032 GENCODE lncRNAs as well as 523 unannotated lncRNAs, including transcripts significantly associated with patient outcome. Aberrant expression of a subset of novel and known lncRNAs was confirmed in patient samples and cell lines. siRNA-mediated knockdown of a subset of these lncRNAs (LINC01559, LINC01133, CCAT1, LINC00920 and UCA1) reduced cell proliferation, migration and invasion. Gene co-expression network analysis associated PDAC-deregulated lncRNAs with diverse biological processes, such as cell adhesion, protein glycosylation and DNA repair. Furthermore, UCA1 knockdown was shown to specifically deregulate co-expressed genes involved in DNA repair and to negatively impact DNA repair following damage induced by ionizing radiation.

Conclusions: Our study expands the repertoire of lncRNAs deregulated in PDAC, thereby revealing novel candidate biomarkers for patient risk stratification. It also provides a roadmap for functional assays aimed to characterize novel mechanisms of action of lncRNAs in pancreatic cancer, which could be explored for therapeutic development.

overall_design: Strand-oriented total RNA-seq libraries from 15 paired samples (tumor and non-tumor adjacent pancreatic tissue) were sequenced using Illumina HiSeq 1500/2500 platform

first: Omar

last: Sosa


title: DNA methylation-based machine learning classification distinguishes pleural mesothelioma from chronic pleuritis, pleural carcinosis, and pleomorphic lung carcinomas

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

type: Methylation profiling by genome tiling array

summary:
Objectives
Our goal was to evaluate the diagnostic value of DNA methylation analysis in combination with machine learning to differentiate pleural mesothelioma (PM) from important histopathological mimics.
Material and methods
DNA methylation data of PM, lung adenocarcinomas, lung squamous cell carcinomas and chronic pleuritis was used to train a random forest as well as a support vector machine. These classifiers were validated using an independent validation cohort including pleural carcinosis and pleomorphic variants of lung adeno- and squamous cell carcinomas. Furthermore, we used a deconvolution method to estimate the composition of the tumor microenvironment.
Results
T-distributed stochastic neighbor embedding clearly separated PM from lung adenocarcinomas and squamous cell carcinomas, but there was a considerable overlap between chronic pleuritis specimens and PM with low tumor cell content. While both machine learning algorithms achieved comparable accuracies in a nested cross validation on the training cohort (random forest: 94.9%; support vector machine: 95.5%), the support vector machine outperformed the random forest in distinguishing PM from chronic pleuritis. Differential methylation analysis revealed promoter hypermethylation in PM specimens, including the tumor suppressor genes BCL11B, EBF1, FOXA1, and WNK2. Furthermore, we observed comparable accuracies for the support vector machine on the validation cohort (97.1%) while the random forest performed considerably worse (89.9%). Deconvolution of the stromal and immune cell composition revealed higher rates of regulatory T-cells and endothelial cells in tumor specimens and a heterogenous inflammation including macrophages, B-cells and natural killer cells in chronic pleuritis.
Conclusion
DNA methylation in combination with machine learning is a promising tool to reliably differentiate PM from chronic pleuritis and lung cancer, including pleomorphic carcinomas. Furthermore, our study highlights new candidate genes for PM carcinogenesis and shows that deconvolution of DNA methylation data can provide reasonable insights into the composition of the tumor microenvironment.

overall_design: 76 specimens were analyzed using the Illumina Infinium MethylationEPIC BeadChip


title: Silk scaffolding drives self-assembly of functional and mature human brain organoids [RNA-seq]

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich

summary: Human pluripotent stem cells (hPSCs) are intrinsically able to self-organize into cerebral organoids that mimic features of developing human brain tissue. These three-dimensional (3D) structures provide a unique opportunity to generate cytoarchitecture and cell-cell interactions reminiscent of human brain complexity in a dish. However, current in vitro brain organoid methodologies often result in intra-organoid variability, limiting their use in recapitulating later developmental stages as well as in disease modeling and drug discovery. In addition, cell stress and hypoxia resulting from long-term culture lead to incomplete maturation and cell death within the inner core. Here, we used a recombinant silk microfiber network as a scaffold to drive human PSCs to self-arrange into engineered cerebral organoids. Silk scaffolding promoted neuroectoderm formation and reduced heterogeneity of cellular organization within individual organoids. Bulk and single cell transcriptomics confirmed that silk cerebral organoids display more homogeneous and functionally mature neuronal properties than organoids grown in the absence of silk fibers. Furthermore, oxygen sensing analysis showed that silk scaffolds create more favorable growth and differentiation conditions by facilitating the delivery of oxygen and nutrients. Silk-engineering platform appears to reduce intra-organoid variability and enhances functional maturation during spontaneous self-patterning in human brain organoid differentiation.

overall_design:
RNA-seq of silk and non-silk organoids; 3 biological replicates per condition.

**Submitter declares that the raw data cannot be provided due to privacy concerns**

first: Petter

last: Storm

first: Alessandro

last: Fiorenzano

first: Malin

last: Parmar


title: Effects of nitrate-induced promotion of de novo NAD synthesis in Arabidopsis thaliana

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

institute: The University of Tokyo

summary: In higher plants, NAD synthesis starts with the oxidation of aspartate. This oxidation is catalyzed by aspartate oxidase (AO) encoded by a nitrate-inducible gene. To assess the effects of this upregulation of AO gene in response to a nitrate supply, a transgenic line was generated by introduction of AO gene under the control of a mutated AO promoter into the ao knockout mutant. Since, unlike the wild-type AO promoter, this mutated AO promoter was not activated by a nitrate supply, gene expression in this transgenic line was compared with that in another transgenic line that was generated by introduction of AO gene under the regulation of the wild-type AO promoter into the ao knockout mutant. Changes in gene expression in response to a nitrate supply were analyzed in these transgenic lines.

overall_design: Effects of nitrate-inducibility of AO gene on gene expression in Arabidopsis thaliana was assessed using transgenic lines expressing AO gene from the wild-type or nitrate-non-inducible mutated AO promoter. Hydroponically-grown transgenic plants (0d) were subjected to 3-day nitrogen-starvation treatment (Nstarvation3d) and then grown with 10 mM nitrate-containing solution for 24 hours (resupply).

first: Moriaki

last: Saito

first: Mineko

last: Konishi


title: Transcriptomic Characterization of wilms tumor

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

summary: Wilms tumor (WT) is the most common renal malignancy in children. So we aim to investigate the transcriptomic map of Wilms tumor.

overall_design: The mRNA profiles of five primary tumors and their matched paratumor tissue from five patients with wilms tumor were generated by illumina plartform.

first: Rui

first: Kuiran

first: Yong

last: Zhan


title: The m6A Methylated mRNA Pattern and the Activation of the Wnt Signaling Pathway under Hyper-m6A modifying condition in the keloid [RIP-seq]

city: guangzhou

first: rong

middle: ke

last: xiang

state: china

address: shipai

institute: xiangkerong

summary: Purpose: The present study was carried out to investigate the global m6A modified RNA pattern and possible mechanisms underlying the pathogenesis of keloid.     Method: 14 normal skin and 14 keloid tissue were firstly collected on clinic. Then 3 samples from each group were randomly selected to be verified with the Western Blot to determine the level of methyltransferase and demethylase. The total RNA of all samples in each group was isolated and subjected to the analysis of MeRIP-sequencing and RNA-sequencing. With the software of MeTDiff and htseq-count, the m6A peaks and differentially expressed genes (DEGs) were determined within the fold change > 2 and p -value < 0.05. The top 10 pathways of m6A modified genes in each group and the differentially-expressed genes were enriched by the Kyoto Encyclopedia of Genes and Genomes signaling pathways. Finally, the closely associated pathway was determined with the Western Blot and immunofluorescence staining.     Results: There was a higher protein level of WTAP and Mettl3 in the keloid than in the normal tissue. 21,020 unique m6A peaks with 6573 unique m6A-associated genetic transcripts appeared in the keloid samples. In the normal tissue, 4028 unique m6A peaks with 779-associated modified genes appeared in the keloid. In the RNA-sequencing, there were 847 genes significantly changed between these groups, transcriptionally. The genes with m6A methylated modification and the upregulated differentially expressed genes between two tissues were both mainly related to the Wnt signaling pathway. Moreover, the hyper-m6A modified Wnt / β-catenin pathway in keloid was verified with western blotting. From immunofluorescence staining results, we found that the accumulated fibroblasts were under a hyper-m6A condition in the keloid and the Wnt/β-catenin signaling pathway was mainly activated in the fibroblasts.     Conclusion: The fibroblasts in the keloid were under a cellular hyper-m6A methylated condition, and the hyper-m6A modified highly-expressed Wnt / β-catenin pathway in the dermal fibroblasts might promote the pathogenesis of keloid.

overall_design: Patients And Samples  This study was approved by the Ethics Committee of the First Affiliated Hospital of Jinan University, and informed consent was obtained from all patients and unaffected individuals.  14 keloid samples were collected from 14 patients at the Department of plastic surgery at the First Affiliated Hospital of Jinan University (Table 1). In addition, 14 individuals without a personal or family history of keloid were recruited from the Department of thoracic surgery and general surgery at the First Affiliated Hospital of Jinan University. Normal skin samples were obtained from these volunteers (Table 1). After being isolated, the samples were divided into two parts: One was immediately frozen and preserved in liquid nitrogen for the molecular analysis of MeRIP-Seq, RNA-Seq, and western blotting test. The other part was stored in the 4% formalin for the pathological change analysis of immunofluorescence staining.

first: Can-Xiang

last: Lin

first: Zhi-Jing

last: Chen

first: Qi-Lin

last: Peng

first: Ke-Rong

last: Xiang

first: Ruo-Xi

first: Tai-Xing

last: Cui

first: Yue-Sheng

last: Huang

first: Hong-Wei

last: Liu


title: The m6A Methylated mRNA Pattern and the Activation of the Wnt Signaling Pathway under Hyper-m6A modifying condition in the keloid

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


title: The m6A Methylated mRNA Pattern and the Activation of the Wnt Signaling Pathway under Hyper-m6A modifying condition in the keloid [RNA-seq]


title: Ligand diversity guarantees full activation of the jasmonate pathway in Marchantia polymorpha (array)

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: In plants, jasmonate signalling regulates a wide range of processes from growth and develop-ment to defence responses and thermotolerance. Bioactive jasmonates, such as JA, JA-Ile, OPDA and dn-OPDA, are derived from C18- and C16- fatty acids (FAs), which are found ubiquitously in the plant kingdom. Bryophytes also contain long chain C20- and C22- FAs (LCFAs), which are absent in most vascular plants but are found in organisms of other king-doms, including mammals. The existence of bioactive jasmonates derived from LCFAs is cur-rently unknown. Here, we describe the identification of an OPDA-like molecule derived from a C20-FA in Marchantia polymorpha, which we term C20-OPDA. This molecule accumulates upon wounding, and when applied exogenously can activate known COI1-dependent and -independent jasmonate responses. Furthermore, we identify a dn-OPDA-like molecule (Δ4-dn-OPDA) deriving from C20-OPDA and demonstrate it to be a ligand of the jasmonate co-receptor (MpCOI1-MpJAZ) in Marchantia. By analysing mutants involved in the production of LCFAs, we elucidate the major biosynthetic pathway of C20-OPDA and Δ4-dn-OPDA. Moreover, using a double mutant compromised in the production of both Δ4-dn-OPDA and dn-OPDA, we demonstrate the additive nature of these molecules in the activation of jasmonate responses. Taken together, our data identify LCFAs as a source of bioactive jasmonates that are essential to plant plasticity and resilience.

overall_design: 4 replicates for mock and wound-treated samples

first: Sophie

last: Kneeshaw

first: Gonzalo

last: Soriano

first: Isabel

last: Monte

first: Mats

last: Hamberg

first: Angel

last: Zamarreño

first: Jose

last: García-Mina

first: Nobuki

last: Kato

first: Minoru

last: Ueda

first: M

last: Rey-Stolle

first: Andrea

last: Chini

first: Coral

last: Barbas

first: Santiago

last: Michavila

first: Selena

last: Gimenez-Ibanez

first: Guillermo

middle: H

last: Jimenez-Alemán

first: Roberto

last: Solano


title: Ligand diversity guarantees full activation of the jasmonate pathway in Marchantia polymorpha (RNA-Seq)

overall_design: 3 replicates for mock and wound-treated samples


title: TN/SCM pre-selection generates CAR T-cell products driving superior anti-tumor responses while curtailing severe CRS

city: Milan

first: Monica

last: Casucci

address: Via Olgettina, 58

department: Division of immunology, transplantation and infectious diseases

institute: IRCCS San Raffaele Scientific Institute

summary: Chimeric antigen receptor (CAR) T-cell expansion and persistence represent key factors to achieve complete responses and prevent relapses. These features are typical of early memory T cells, which can be highly enriched through optimized manufacturing protocols. Here, we investigated the efficacy and safety profiles of CAR T-cell products generated from pre-selected naive/stem memory T cells (TN/SCM), as compared to unselected T cells (TBULK). Notwithstanding their reduced effector signature in vitro, limiting CAR TN/SCM doses showed superior antitumor activity and the unique ability to counteract leukemia re-challenge in hematopoietic stem/precursor cell-humanized mice, featuring increased expansion rates and persistence, together with an ameliorated exhaustion and memory phenotype. Most relevantly, CAR TN/SCM proved to be intrinsically less prone to induce severe cytokine release syndrome, independently of the costimulatory endodomain employed. This safer profile was associated with milder T-cell activation, which translated in reduced monocyte activation and cytokine release. These data suggest that CAR TN/SCM are endowed with a wider therapeutic index compared to CAR TBULK.

overall_design: Examination of monocytes transcriptomic differences  when in the presence of pre-selected naive/stem memory T cells (TN/SCM) compared to unselected T cells (TBULK).

first: Camilla

last: Bove


title: Overexpression of human estrogen biosynthetic enzyme Hydroxysteroid (17beta) dehydrogenase type 1 which induces adenomyosis-like phenotype in transgenic mice

city: Turku

first: Michael

last: Gabriel

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

summary: We report uterine mRNA transcriptome sequencing of mice over-expressing human estrogen biosynthetic enzyme HSD17B1 (HSD17B1TG mice) present with adenomyosis phenotype.

overall_design: Total RNA was extracted, and mRNA transcriptome sequenced from the uterus of 5 HSD17B1TG mice at the age of 4 months and compared to 5 wild-type controls.

first: Taija

last: Heinosalo

first: Kalle

middle: T

last: Rytkönen

first: Matti

last: Poutanen


city: Dallas

first: Ronak

last: Lakhia

address: 5323 Harry Hines

institute: UTSW

summary: Enhancer and super-enhancer landscape in ADPKD. 2 biological replicates of Pkd1RC/- cells are analyzed via H3K27ac ChIP-Seq

first: Vishal

last: Patel


title: mRNA-seq of iXist-ChrXDom mESCs

city: Oxford

first: Joseph

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: X chromosome inactivation (XCI) is mediated by the non-coding RNA Xist which directs chromatin modification and gene silencing in cis. The RNA binding protein SPEN and associated corepressors have a central role in Xist-mediated gene silencing. Other silencing factors, notably the Polycomb system, have been reported to function downstream of SPEN. Making use of a SPEN separation-of-function mutation we show that SPEN and Polycomb pathways in fact function in parallel to establish gene silencing. Additionally, we find that differentiation-dependent recruitment of the chromosomal protein SmcHD1 is required for silencing many X-linked genes.

overall_design: This series contains messenger RNA-seq (mRNA-seq) in uninduced iXist-ChrX-Dom cells, in which Xist on the M.m.Domesticus allele of female (XX) mESCs  is under doxycyline-inducible control. These datasets were used to calculate and rank genes by initial gene expression levels (Transcripts per Million; TPM) prior to Xist induction.

first: Tatyana

middle: B

last: Nesterova

first: Guifeng

last: Wei

first: Neil

last: Brockdorff


title: ChrRNA-seq of mESC to NPC timecourses for WT and SmcHD1 KO clones

overall_design: This series contains datasets of Chromatin RNA-seq experiments conducted in both iXist-ChrX-Dom and iXist-ChrX-Cast model cell lines, in which Xist is dox-inducible on the M.m.Domesticus or M.m.Castaneous allele of female (XX) mESCs. Here we compare WT cell lines over timecourses of ES to NPC differentiation (under constant Xist induction), with SmcHD1 KO clones cultured in parallel. We analyze XCI by isolation of chromatin-associated RNA (ChrRNA) for next-generation sequencing, followed by allelic assignment of reads to Xi or Xa chromosomes, and thus calculation of  allelic ratio (Xi/(Xi+Xa)) as a quantitative measure of X-linked silencing on a gene-by-gene basis. In later timepoints, SmcHD1 KO clones fail to complete gene silencing for a subset of genes, demonstrating a role for SmcHD1 in the establishment phase of XCI.


title: ChrRNA-seq of SPEN-SPOC and Polycomb mutant lines

overall_design: This series contains datasets of Chromatin RNA-seq experiments conducted in the iXist-ChrX-Dom model cell line in which Xist on the M.m.Domesticus allele of female (XX) mESCs  is under doxycyline-inducible control. Here we compare cell lines with engineered mutations to the SPEN SPOC domain or to components of the Polycomb system recruited by Xist (PCGF3/5 degron or deletion of Xist B/C-repeat), both individually and in combination. We analyze XCI by isolation of chromatin-associated RNA (ChrRNA) for next-generation sequencing, followed by allelic assignment of reads to Xi or Xa chromosomes, and thus calculation of  allelic ratio (Xi/(Xi+Xa)) as a quantitative measure of X-linked silencing on a gene-by-gene basis.


title: Xist-mediated silencing requires additive functions of SPEN and Polycomb together with differentiation-dependent recruitment of SmcHD1

overall_design: Refer to individual Series


title: PABPN1 effect on translation efficiency.

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: The effect of PABPN1 on translation efficiency was assessed using RNA sequencing of polysomal fractions from muscle cells: parental vs. cells with stable PABPN1 down-regulation (shPAB). The library was constructed after rRNA depletion, allowing to investigate the abundance of different RNA biotypes.

overall_design: The comparision is between parental vs. shPAB, and across fractions (F1-F5).

first: Vered

last: Raz

first: Jasper

last: Boom


title: Chromatin remodeling governs postnatal maturation in dermal fibroblasts [scRNA-Seq]

city: Seoul

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

institute: Seoul National University College of Medicine

summary: Tissue stem cells preserve a certain level of potency to maintain intact tissue integrity after various injury. Postnatal dermal fibroblasts lose differentiation potential for regenerative healing that recreates normal tissue including functional hair follicles (HFs), however, their intrinsic cellular changes are not understood yet. Here, we uncover a postnatal maturation process in papillary fibroblasts (PFs) mediated by Twist2-driven chromatin and transcriptional remodeling. Within 4 days after birth, dermal PFs lost WNT transcription factors (TFs) and target gene expressions accompanied by loss of H3K27ac expression. Through single-cell transcriptomics, ATAC-seq and ChIP-seq profiling, we define a postnatal maturation trajectory of PFs, in addition to loss of regenerative trajectory, triggered by decrease of H3K27ac and chromatic accessibility. In vivo inhibition of histone deacetylation delays the postnatal chromatin remodeling and maintains developmental signaling and differentiation potential in PFs. TF motif analysis on the chromatin regions losing accessibility identifies TWIST as a potential regulator specifying these regions. Using Twist2 conditional knock-out mouse model, we unearth a postnatal role of Twist2 TF as governing the postnatal maturation process resulting in switch-off of developmental pathways after birth. Together, our findings expose a comprehensive intracellular mechanism driving postnatal maturation in dermal fibroblasts with profound implications for regenerative medicine.

overall_design: To define the intrinsic temporal changes in total skin cells after birth, mouse back skin was harvested and dissociated into dermal and epidermal single-cell suspension at postnatal day 0, 2 and 4 (PD0, PD2, PD4), or postnatal day 4 after intraperitoneal TSA treatment for 4 days (TPD4, 5μg/g body weight). For scRNA-seq, dermal and epidermal single-cell suspension were mixed with 1:1 ratio for each sample. All samples were processed according to Chromium Single Cell 3' Reagent Kits v3 Chemistry (10X Genomics) as per the manufacturer’s protocol. Library was sequenced using Illumina HiSeq X Ten platform (Illumina). Transcripts were mapped to the mm10 reference genome using CellRanger v4.0.0 with default reference package (10X Genomics).

first: Minji

last: Park

first: Seong Jin

last: Jo

first: Ohsang

last: Kwon


title: Study on the Mechanism of Codonopsis pilosula Enhancing Immune Function of Aging Mice Based on lncRNA-mRNA Network

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

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

summary: Objective: To explore the molecular mechanism of Codonopsis pilosula in enhancing the immune function of aging mice, the expression profile of long-chain non-coding RNA (lncRNA), mRNA in spleen of mice was detected. Methods: An aging mouse model was established, the aging mice were treated with low, middle and high doses of Codonopsis pilosula, and the aging related indexes, spleen pathology and cellular ultrastructure were detected and analyzed. Then microarray analysis and bioinformatics methods were used to analyze the lncRNA and mRNA expression profile. GO enrichment analysis and KEGG pathway analysis were performed to analyze the differential genes between groups using KOBAS. Finally, the common lncRNAs and mRNAs in high-dose Codonopsis pilosula treatment group compared with the model group and the model group compared with the control group were selected for lncRNA-mRNA co-expression network construction, and real-time quantitative polymerase chain reaction (qRT-PCR) was used to verify the genes in the network. Results: The aging mouse model was successfully established. Codonopsis pilosula can improve the pathology and cellular ultrastructure of spleen in aging mice. Microarray analysis showed that 96 lncRNAs and 65 mRNAs changed significantly after aging, 623 lncRNAs and 435 mRNAs expressed abnormally after high-dose Codonopsis pilosula treatment. KEGG pathways involved in aging and high-dose Codonopsis pilosula treatment are mainly related to immunity, including allograft rejection, graft-versus-host disease, autoimmune thyroid disease, antigen processing and presentation and so on. The three mRNAs (Enpp6, Cped1, and Galnt15) in lncRNA-mRNA co-expression network may be related to Codonopsis pilosula improving the immunity of aging mice, which were verified by qRT-PCR. Conclusion: Codonopsis pilosula has a certain protective effect on the spleen of aging mice and the lncRNA-mRNA network may play an important role in enhancing the immunity of aging mice.

overall_design: Total RNA was extracted from spleen tissues in the control group, the model group and high dose Codonopsis pilosula treatment group (n=3 mice).

first: Jiajia

last: Liu

first: Jie

last: Meng

first: Jiachao

last: Kang

first: Yongqiang

last: Duan

first: Jing

last: Wang


title: Chromatin remodeling governs postnatal maturation in dermal fibroblasts


title: Calibrated native ChIP-seq for H2AK119ub1 and H3K27me3 in FKBP12-PCGF3/5 mESCs

first: Joseph

last: Bowness

overall_design: This series contains datasets of calibrated native ChIP-seq for the Polycomb modifications H2AK119ub1 and H3K27me3. We performed two replicate experiments for untreated, 24h Dox, and 36h dTAG-13 + 24h Dox FKBP12-PCGF3/5 mESCs. mESCs were mixed with 20% Drosophila spike-in (Sg4 cells), native chromatin was extracted, and ChIP was performed with H2AK119ub1 and H3K27me3 antibodies. Calibration of ChIP-seq datasets shows that 36h PCGF3/5 degradation results in a ~30% reduction of genome-wide H2AK119ub1 with little effect of genome-wide H3K27me3. Allelic analysis of ChrX shows widespread deposition of both Polycomb modifications over Xi after 24h of Xist induction. This is abolished by degradation of PCGF3/5 (12h dTAG-13 treatment prior to Xist induction), demonstrating that PCGF3/5-PRC1 complexes are required for all Xist-mediated Polycomb deposition over Xi.


title: Glioblastoma stem cells RNAseq profiling

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

summary: RNAseq-profile of independent glioblastoma stem cells lines was determined

overall_design: Glioma stem cells were derived from glioma specimens obtained after informed consent from patients with a median age of 62 years (range 48-79). Tumor samples were obtained during surgery from patients of the Neurosurgery Department, San Martino Hospital (Genova, Italy). All patients underwent surgery for the first time and never received chemotherapy or radiotherapy. Tumor samples, classified as gliomas grade IV based on World Health Organization criteria, were immediately processed for isolation of single cells by mechanical dissociation and plated at the concentration of 10e5 cells/ml in Matrigel-coated culture flasks.

first: Antonio

last: Daga

first: Stefano

last: Indraccolo

first: Davide

last: Ceresa


title: Chromatin remodeling governs postnatal maturation in dermal fibroblasts [ATAC and ChIP]

overall_design: To define the temporal changes in chromatin accessibility and H3K27ac modification of freshly FACS-sorted CD140a+CD26+ papillary fibroblasts after birth, mouse back skin was harvested and the dermis was dissociated into single-cell suspension at postnatal day 0, 2 and 4 (PD0, PD2, PD4), or postnatal day 4 after intraperitoneal TSA treatment for 4 days (TPD4, 5μg/g body weight). ATAC-seq library and H3K27ac and input control ChIP-seq library were prepared. Library was sequenced using Illumina HiSeq 2500 platform using a paired-end setting. Transcripts were mapped to the mm10 reference genome (UCSC).


title: Single cell 3' RNA sequencing of  WM239A melanoma cell line and its highly metastatic subclones

first: YOON-SEOB

last: KIM

state: Korea (the Republic of)

address: Banpodaero 222

institute: The Catholic University of Korea

summary: The molecular mechanism of melanoma metastasis is poorly understood. The aim of our study was to delineate expression kinetics during the acquisition of metastatic potential, and thereby to characterize subclone of primary cell line responsible for metastasis. We performed single-cell RNA sequencing of poorly metastatic melanoma cell line (WM239A), its subclones with high potential of lung (113/6-4L) and brain metastasis (131/4-5B1 and 131/4-5B2).

overall_design: Single-cell RNA sequencing libraries were generated using Chromium Single-cell 3' Reagent Kits v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol.

first: Yeun-Jun

last: Chung


title: Intrahepatic microbes govern liver immunity by programming NKT cells

city: New York

first: Joshua

middle: Caleb

last: Leinwand

state: NY

address: 177 Fort Washington Ave, 7th Floor

department: Surgery

institute: Columbia University Irving Medical Center

summary: The gut microbiome shapes local and systemic immunity. The liver is presumed to be a protected sterile site. As such, a hepatic microbiome has not been examined. Here, we show that the liver hosts a robust microbiome in mice and humans that is distinct from the gut and is enriched in Proteobacteria. It undergoes dynamic alterations with age and is influenced by the environment and host physiology. Fecal microbial transfer experiments revealed that the liver microbiome is populated from the gut in a highly selective manner. Hepatic immunity is dependent on the microbiome, specifically Bacteroidetes species. Targeting Bacteroidetes with oral antibiotics reduced the hepatic immune cell infiltrate by ~90%, prevented APC maturation, and mitigated adaptive immunity. Mechanistically, presentation of Bacteroidetes-derived glycosphingolipids to NKT cells promotes CCL5 signaling, which drives hepatic leukocyte expansion and maturation. Collectively, we reveal a microbial – glycosphingolipid – NKT – CCL5 axis that underlies hepatic immunity.

overall_design: CD45+ leukocytes were FACS-sorted from mouse livers after 1 week of treatment with oral antibiotics or vehicle.

middle: C


title: Annexin 10 promotes invasion in QBC-939 cell

city: jinan

first: qi

middle: rong

last: sun

state: shandong

address: wenhuxi road 107

institute: qilu hospitai

summary: Annexin family is the largest category of eukaryotic calcium and phospholipid-binding proteins and plays important roles in various physiological processes, including cell differentiation and proliferation. More than 160 Annexin proteins are classified into 65 different speciesAs a new member of Annexin family, the role of ANXA10 in cancer progression is rarely investigated, and its expression and function in CCA need more experiments to reveal.

overall_design: 6 human cholangiocarcinoma cell samples, including 3 control and 3 ANXA10-knockdown

first: Rongqi

last: Sun

first: Yunfei

last: Xu


title: The gene expressional profiles between U87MG glioma cells and the derived TMZ-resistance cells

city: Tainan

first: Kwang-Yu

last: Chang

address: 367 Sheng-Li Road

institute: National Institute of Cancer Research, National Health Research Institutes

summary: We want to investigate whether there is an aquired resistance in glioma cells after TMZ treatment.

overall_design: We use the parental U87MG cells and the resistant U87MG clone cells selected by TMZ to examine the gene levels.

first: Jian-Ying

last: Chuang


title: scRNA-seq to study features of CD4conv and Treg cells in spleen and bone marrow of mice

status: Public on May 16 2022

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

summary: The aim of the study was to compare gene experession between Treg cells in the bone marrow and the spleen

overall_design: 2 male Foxp3-DTR-GFP were used for the study. Single cells suspension from BM and spleen were prepared, then enriched for CD4 by magneic beads and sorted by gating on CD4+TCRb+.  GFP was used to differentiate between Tregs and CD4conv. CD4conv or Tregs cells from the same tissue were pooled from the two mice and hashtagged (total of 4 groups: Tregs BM/Tregs spleen/CD4 conv BM/CD4 conv spleen). The mice were not treated by DT.

first: S

last: Elias

first: M

first: A

middle: Y

last: Rudensky


title: Effect of cardiomyocyte-specific deletion of glucocorticoid receptor on gene expression of cultured neonatal cardiomyocytes

city: Bologna

first: Gabriele

last: D'Uva

address: via Massarenti 9

institute: University of Bologna

summary: To investigate the role of the glucocorticoid receptor (GR) in the regulation of cardiomyocyte maturation and proliferation, we established a cardiomyocyte-specific GR knock-out (GR-cKO) mouse model by Cre-Lox technology. We thus performed gene expression profiling analysis using data obtained from RNA-seq of cardiomyocytes isolated from GR-cKO and control mouse models at neonatal stage and cultured in vitro. Our analyses unveiled a role for GR in regulating gene networks related to the energetic metabolism, which in turn may impact on cardiomyocyte proliferative and regenerative ability.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of cardiomyocytes isolated from GR-cKO and control mouse models at postnatal-day-1 (P1) and cultured in vitro


title: Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043) [Immune]

city: Waltham

first: Uma

last: Saxena

state: MA

address: 1000 Winter Street

institute: Glaxosmithkline

summary:
Autologous T cells transduced to express a high affinity T-cell receptor specific to NY-ESO-1 (letetresgene autoleucel, lete-cel) show promise in the treatment of metastatic synovial sarcoma, with 50% overall response rate. Biomarkers predictive of response and resistance remain to be better defined. In 45 synovial sarcoma patients, we analyzed the association of response to lete-cel (NCT01343043) with tumor gene expression.
Analysis of tumor samples post-treatment illustrated lete-cel infiltration and decreased expression of macrophage genes, suggesting remodeling of the tumor microenvironment.

overall_design:
This dataset consists of 23 tumor samples collected from synovial sarcoma patients pre or post treatment with NY-ESO-1 TCR T cells in trial NCT01343043. There are 13 pre-infusion samples from 10 patients; 3 patients had two samples tested in replicate, results were averaged for downstream analysis. There are 5 at-progression samples. Five samples were excluded from downstream analysis due to time of collection and focus of analysis (see Sample notes for more details). For each sample, five 4-µm unstained slides were used for macrodissection and subsequent RNA extraction. RNA extract was quantified (including assessment of RNA purity) using the Quant-iT RiboGreen RNA Reagent and Kit, and RNA quality was assessed using Agilent RNA Pico chip analysis. RNA was analyzed using the NanoString nCounter® system, with 2 sets of NanoString assays (nCounter® PanCancer Immune Profiling Panel and nCounter® PanCancer Pathway Panel) run on the same extract. The normalization for raw nCounter counts of expressed genes was separately done for QC-passed samples in PanCancer immune and PanCancer pathway panel using the R-package “NanoStringNorm” (R version 4.0.3) with a set of parameters; CodeCount = ‘geo.mean’, Background = ‘mean.2sd’, SampleContent = ‘housekeeping.geo.mean’, round.values = TRUE, take.log = TRUE.
nCounter® PanCancer Immune Profiling Panel
*** Submitter declares that individual raw reads are not provided in order to protect patient privacy. ***

first: Alexandra

last: Gyurdieva

first: Ya-Fang

first: E

middle: A

last: Houseman

first: Jaegil

last: Kim

first: Kishan

last: Dhusia

first: Ioanna

last: Eleftheriadou


title: Gene expression of blood cells in a patient with GATA2 deficiency.

city: Maebashi

first: Akira

last: Shimizu

state: Gunma

address: 3-39-11 showamachi, Maebashi

department: Dermatology

institute: Gunma university

summary:
To determine the difference of GATA2 related gene expression in blood cells.
Gene expression of GATA2 deficiency comparing to a healthy person.

overall_design: One GATA2 patient and 1 normal control.

first: Yuko

last: Kuriyama


title: A prominent activation role of CtBP on HOX gene expression along PcG/trxG pathways

city: Nangjing

first: Ming

last: Fang

state: jiangsu

address: 2 Sipailou Road

institute: Southeast University

summary: Purpose: The goals of this study are to find out CtBP and PcG coregulated targets through transcriptome profiling (RNA-seq). Methods: Kc cell mRNA profiles of 7-day Ctrl and CtBP and ph-p+E(z) RNAi were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: hyper-geometric test and the Benjamini Hochberg FDR correction method and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the drosophila genome (build dm6) and identified 11,282 transcripts in the 9 samples, among which 381 PcG targets were selected for further analysis. Hierarchical clustering of differentially expressed genes divided these targets into three groups named CtBP co-activated genes,CtBP unaffected genes and CtBP co-repressed genes respectivly. RNA-seq data confirmed CtBP co-activated genes contain 22 known homeobox genes, and 4 of these were validated with qRT–PCR. These results suggest that CtBP is selectively required for the activation of PcG-repressed genes, especially the homeobox transcription factors including Hox genes.Conclusions: Our study represents the first detailed analysis of CtBP and PcG coregulated targets.

overall_design: Drosophila Kc cell mRNA of 7-day Control and CtBP and ph-p+E(z) RNAi treated samples were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.

first: Hao

last: Xie

first: Caili

last: Bi


title: Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043)

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


title: Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043) [Pathway]

overall_design:
This dataset consists of 22 tumor samples collected from synovial sarcoma patients pre or post treatment with NY-ESO-1 TCR T cells in trial NCT01343043. There are 11 pre-infusion samples from 10 patients; 1 patients had two samples tested in replicate, results were averaged for downstream analysis. There are 5 at-progression samples. Six samples were excluded from downstream analysis due to time of collection and focus of analysis (see Sample notes for more details). For each sample, five 4-µm unstained slides were used for macrodissection and subsequent RNA extraction. RNA extract was quantified (including assessment of RNA purity) using the Quant-iT RiboGreen RNA Reagent and Kit, and RNA quality was assessed using Agilent RNA Pico chip analysis. RNA was analyzed using the NanoString nCounter® system, with 2 sets of NanoString assays (nCounter® PanCancer Immune Profiling Panel and nCounter® PanCancer Pathway Panel) run on the same extract. The normalization for raw nCounter counts of expressed genes was separately done for QC-passed samples in PanCancer immune and PanCancer pathway panel using the R-package “NanoStringNorm” (R version 4.0.3) with a set of parameters; CodeCount = ‘geo.mean’, Background = ‘mean.2sd’, SampleContent = ‘housekeeping.geo.mean’, round.values = TRUE, take.log = TRUE.
nCounter® PanCancer Pathway Panel
*** Submitter declares that individual raw reads are not provided in order to protect patient privacy. ***

last: Chang


title: DNA methylation analysis of glioblastomas harboring FGFR3-TACC3 fusions identifies a methylation subclass with better patient survival.

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

summary: Genomewide DNA methylation array profiling of 244 gliobastoma and ganglioglioma samples to study FGFR3-TACC3 gene fusions and resolved into a new entity, glioblastoma IDH-wildtype, FGFR3-TACC3 fusion postive methylation outlier group (GBM-F3T3-O). GBM-F3T3-O showed a unique methylation profile and better survival than other glioblastoma patients. The methylation idat profiles were provided here.

overall_design:
Bisulfite converted genomic DNA extracted from tumor samples was hybridized to Illumina Infinium EPIC Human DNA Methylation Beadchips
Please note that the processed data files contains total 276 data columns, including 32 samples (columns) whose the raw data was provided by authors of paper PMID: 33168106.

first: Kenneth

last: Aldape


title: Plants grow in lunar regolith

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: The extent to which plants can enhance human life support on other worlds depends on the ability of plants to thrive in extraterrestrial environments using in situ resources. Using samples from Apollo 11, 12 and 17, we show that the terrestrial plant Arabidopsis thaliana germinates and grows in diverse lunar regoliths. However, our results show that growth is challenging; the lunar regolith plants were slow to develop, expressed genes indicative of ionic stresses, and many showed severe stress morphologies. Therefore, although in situ lunar regolith can be useful for plant production in lunar habitats, they are not benign substrates. The interaction between plants and lunar regolith will need to be further elucidated, and likely mitigated, to enable efficient use of lunar regolith for life support.

overall_design: Arabidopsis thaliana (Col-0) was grown in lunar regolith from three different mission sites: Apollo 11, Apollo 12 and Apollo 17. The plants were grown completely within the regolith as a growth substrate and compared to plants grown in an identical fashion in a lunar simulant (JSC-1A) as the control. Comparisons between and among lunar regoliths, and the simulant controls, included morphology and development, and transcriptomic responses.

first: Anna-Lisa

last: Paul

first: Stephen

last: Elardo


title: Effect of cardiomyocyte-specific deletion of glucocorticoid receptor on gene expression of the cardiac tissue during early postnatal development

first: Gabriele

last: D'Uva

summary: To investigate the role of the glucocorticoid receptor (GR) in the regulation of cardiomyocyte maturation and proliferation, we established a cardiomyocyte-specific GR knock-out (GR-cKO) mouse model by Cre-Lox technology. We thus performed gene expression profiling analysis using data obtained from RNA-seq of the cardiac tissue of GR-cKO and control mouse models extracted during the early postnatal development. Our analyses unveiled a role for GR in regulating gene networks related to the energetic metabolism, which in turn may impact on cardiomyocyte proliferative and regenerative ability.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of cardiac tissue lysates from GR-cKO and control mouse models at postnatal-day-7 (P7).


title: Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling

city: Toronto

first: Alexander

middle: F

last: Palazzo

state: ON

address: 661 University Ave.

country: Canada

institute: University of Toronto

summary: In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we ask whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we identified the glycolytic enzyme Pyruvate Kinase M (PKM) as a cytosolic (i.e., ER-excluded) polyribosome interactor and investigate how it influences mRNA translation. We discovered that the PKM-polysome interaction is directly regulated by ADP levels–providing a link between carbohydrate metabolism and mRNA translation. By performing enhanced crosslinking immunoprecipitation-sequencing (eCLIP-seq), we found that PKM crosslinks to mRNA sequences that are immediately downstream of regions that encode for lysine and glutamate enriched tracts. Additionally, PKM binding to ribosomes causes translational stalling near these lysine and glutamate encoding sequences. Lastly, we find that PKM recruitment to polysomes is dependent on poly-ADP ribosylation. Overall, our study uncovers a novel role for PKM in posttranscriptional gene regulation, linking cellular metabolism and mRNA translation, and provides the first reported evidence of nascent chains being co-translationally modified with poly-ADP ribose.

overall_design: Ribosome profiling analysis of HEK293T depleted of PKM by RNAi

first: Nevraj

middle: S

last: Kejiou

first: Lena

last: Ilan

first: Stefan

last: Aigner

first: Enching

last: Luo

first: Tori

last: Tonn

first: Hakan

last: Ozadam

first: Muyoung

last: Lee

first: Ines

last: Rabano

first: Nishani

last: Rajakulendran

first: Hamed

last: Najafabadi

first: Stephane

last: Angers

first: Gene

middle: W

last: Yeo

first: Can

last: Cenik


title: GPR174 signals via Gαs to control a CD86-containing gene expression program in B cells [GNAS KO]

city: San Francisco

first: Lihui

last: Duan

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

summary: GPR174 is abundantly expressed in B and T lymphocytes and has a role in restraining T cell responses, but the function of GPR174 in B cells is less clear. Here we report that upon in vitro culture B cells undergo a spontaneous GPR174-dependent activation process that is associated with marked changes in gene expression, including upregulation of Cd86, Nr4a1, Ccr7 and phosphodiesterases. B cells lacking Gas show a block in induction of the GPR174-dependent program. Spontaneous upregulation of CD86 in cultured B cells is dependent on protein kinase A. Both GPR174- and Gas-deficient B cells show enhanced survival in culture. In vivo, GPR174 contributes to NUR77 expression in follicular B cells and is needed for establishing a marginal zone compartment of normal size. Treatment of mice with lysophosphatidylserine (lysoPS), a GPR174 ligand, is sufficient to promote CD86 upregulation by follicular B cells. These findings demonstrate that GPR174 can signal via Gas to modulate B cell gene expression and show this can occur in vivo in response to lysoPS. Additionally, the findings illuminate a pathway that might be targeted to improve systems for the in vitro study of B cell responses.

overall_design: Follicular B cells were isolated from adult mice (N=3 per genotype) for RNA-seq either immediately post-sort or following 1 or 4 hours of culture in complete RPMI 1640 (containing 10% FBS, 10 mM HEPES, 55 µM 2-mercaptoethanol, 2 mM glutamine and 50 IU penicillin/streptomycin)

first: Elise

last: Wolf

first: Zachary

last: Howard

first: Hanson

last: Tam

first: Ying

last: Xu

first: Jason

middle: G

last: Cyster


title: GPR174 signals via Gαs to control a CD86-containing gene expression program in B cells [0h and 4h culture]


title: Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in Saccharomyces cerevisiae

city: Boston

first: Fred

last: Winston

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

institute: Harvard Medical School

summary: Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans. Several studies have shown that Spn1 functions as a histone chaperone to control transcription, RNA splicing, genome stability, and histone modifications as an integral member of the RNA polymerase II elongation complex. However, the precise role of Spn1 is not understood, and there is little understanding of why it is essential for viability. To address these issues, we have isolated eight suppressor mutations that bypass the essential requirement for Spn1 in Saccharomyces cerevisiae. Unexpectedly, the suppressors identify several functionally distinct complexes and activities, including the histone chaperone FACT, the histone methyltransferase Set2, the Rpd3S histone deacetylase complex, the histone acetyltransferase Rtt109, the nucleosome remodeler Chd1, and a member of the SAGA co-activator complex, Sgf73. The identification of these distinct groups and their analysis suggests that there are multiple mechanisms by which Spn1 bypass can occur, including changes in histone acetylation and alterations of other histone chaperones. Thus, Spn1 may participate in multiple functions during transcription. Our results suggest that bypass of a subset of these functions allows viability in the absence of Spn1.

overall_design: ChIP-seq of histone H4 and histone H4 acetylation, in Spn1-depletion yeast strains with wild-type and Set2 deletion backgrounds.

first: Francheska

last: López-Rivera

first: James

last: Chuang

first: Dan

last: Spatt

first: Rajaraman

last: Gopalakrishnan


title: GPR174 signals via Gαs to control a CD86-containing gene expression program in B cells [1 hour culture]

overall_design: Follicular B cells were isolated from adult mice (N=3 per genotype) for RNA-seq following 1 hour of culture in complete RPMI 1640 (containing 10% FBS, 10 mM HEPES, 55 µM 2-mercaptoethanol, 2 mM glutamine and 50 IU penicillin/streptomycin)


title: GPR174 signals via Gαs to control a CD86-containing gene expression program in B cells

overall_design: Refer to individual Series


title: Gene expression profile in SOD1-G85R transgenic mice, a mouse model of amyotrophic lateral schelosis

city: Vancouver

first: Honglin

last: Luo

state: British Columbia

address: Room 166, 1081 Burrard Street

institute: University of British Columbia

summary: Profilling of neuroinflammatory-related genes signatures that contributes to the progression of ALS in SOD1-G85R mice model.

overall_design: In the study presented here, whole brain from day-10 WT or SOD1-G85R transgenic mice was used to acquire expression profiles of a total of 770 unique genes


title: Quantitative analysis of sugar-induced gene expression in Drosophila larvae

city: Kurume

first: Hiroko

last: Sano

state: Fukuoka

address: 67 Asahi-machi

institute: Kurume University

summary: In order to clarify the role of the polyol pathway on gene expression,  metabolites produced by the polyol pathway were administered to starved wild-type and sorbitol dehydrogenase (sodh1, sodh2) mutant larvae, and gene expression in these larvae was examined using next-generation sequencing.

overall_design: Third-instar larvae were starved for 18 hours then refed with different sugars for 6 hours. PolyA-selected RNA from whole larvae was used to generate libralies for sequencing.


title: DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells [END-seq]

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs must be repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 mammalian cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in cycling cells at the G1 or G2 phase cells was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, and has important implications for DNA DSB repair in quiescent cells.

overall_design: We used a combinatorial approach of END-seq and RPA SSDS to characterize DNA-PK's role in DNA End Resection at DNA Double Strand Breaks in G0 cells

first: Faith

last: Fowler

first: Bo-Ruei

last: Chen

first: Nicholas

last: Zolnerowich

first: Raphael

last: Pavani

first: Jacob

last: Paiano

first: Chelsea

last: Peart

first: Andre

last: Nussenzweig

first: Barry

last: Sleckman

first: Jessica

last: Tyler


title: DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells

institute: Center for Excellence in Molecular Cell Science


title: DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells [ChIP-Seq]


title: Lef1 Ablation Alleviates Cartilage Mineralization during Post-traumatic Osteoarthritis

city: jerusalem

first: lital

last: zecharyahu

address: Campus Ein Kerem

country: Israel

institute: hebrew university

summary: Cartilage mineralization is a tightly controlled process, imperative for skeletal growth and fracture repair. However, in osteoarthritis (OA), cartilage mineralization may impact the joint range of motion, inflict pain and may increase chances for joint effusion. Here we attempt to understand the link between inflammation and cartilage mineralization by targeting SIRT1 and LEF1, both reported to have contrasting effects on cartilage.

overall_design: mRNA was extracted from ribcage E17 chondrocytes bearing a Lef1 fl/fl and ATCLef1 fl/fl genotype

first: Mona

last: Dvir-Ginzberg

first: Jinan

last: Elayyan

first: Lital


title: mRNA-seq analysis of mouse hepatocellular carcinoma cell lines

city: Miaoli County

first: Li-Rung

last: Huang

address: No.35, Keyan rd. Zhunan town

institute: National Health Research Institutes

summary: There are few well-characterized syngeneic murine models for hepatocellular carcinoma (HCC), which limits immunological studies and the development of immunotherapies for HCC. We previously established an oncogene-induced spontaneous HCC mouse model based on transposon-mediated oncogene (AKT and NRASG12V) insertion into the genome of hepatocytes to induce tumorigenesis. Here is the result of transcriptomic analysis of two pool cell clones (pool #1 and pool #8) and three single cell clones (NHRI-1-F1, NHRI-8-A4 and NHRI-8-C4) from Akt/N-Ras-induced HCC mouse model, also including a commercial murine hepatocellular carcinoma cell line (Hepa 1-6) as control.

overall_design: Before cells reaching confluence, total RNA was extracted from each cell clone by using RNeasy mini kit (QIAGEN, Hilden, Germany). The quality of RNA was validated by a Bioanalyzer (Agilent, Santa Clara, CA, USA) and subjected to Welgene Biotech Co., Ltd. for RNA-sequencing. Clean reads of each sample provided by the sequencing Labs were used for downstream bioinformatic analysis.

first: Ying-Chieh

last: Ko

first: Yun-Hsing

last: Cheng


title: Expression analysis of primary mouse mebryonic fibroblasts lacking the POLE4 and P53 tumour suppressors genes

city: London

first: Roberto

last: Bellelli

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Mouse embryonic fibroblasts lacking the POLE4 subunit of Pol Epsilon show signs of replication stress and DNA damage. Strikingly this phenotype is lost upon deletion of the Trp53 gene. In order to reveal the mechanism responsible for this phenotype we carried oud bulk RNA sequencing from primary mouse embryonic fibroblast WT or KO for POLE4, in a p53 knock-out genetic background or in the presence of one of 2 copies of the wt allele

overall_design: Passage 1 primary mouse embryonic fibroblasts from POLE4 wt or ko (null) embryos, wt, heterozygous (het) or knock-out (null) for Trp53 were cultived in low oxygen concentration. Cell were lysed and total RNA was extracted,  according to standard procedures.

first: Valerie

last: Borel

first: Stefan

last: Boeing

first: Simon

last: Boulton


title: Multi-omics analyses reveal the molecular pathogenesis toolkit of Lasiodiplodia hormozganensis, a cross-kingdom pathogen

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: The transcriptome of L. hormozganensis CBS339.90 grown at 25 °C and 37 °C was sequenced by Illumina TruSeq. The aim of this study was to understand the effect that temperatures have on the biology of L. hormozganensis strain CBS339.90, specifically on the molecular effectors of pathogenesis.

overall_design: L. hormozganensis was  grown in PBD medium at 25 ºC and 37 ºC. The transcriptome of CBS339.90 was sequenced by Illumina TruSeq to characterise the differential expression at both temperatures.

first: Carina

last: Félix

first: Rodrigo

last: Meneses

first: Micael

last: Gonçalves

first: Ana

last: Duarte

first: Jesus

middle: V

last: Jorrín-Novo

first: Yves

last: Peer

first: Dieter

last: Deforce

first: Filip

last: Nieuwerburgh

first: Artur

last: Alves

last: Esteves


title: ChIP sequencing of ETV6-NCOA2 H3K27Ac profile in T/M mixed-phenotype acute leukemia

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

institute: Weizmann Institute of Science

summary: H3K27Ac ChIP-sequencing of CD34 positive cord blood cells expressing either ETV6-NCOA2 or empty-vector in-vitro and ETV6-NCOA2 patient derived xenograft.

overall_design: Expression of ETV6-NCOA2 or empty vector in CD34+ cells in-vitro (for each biological replicate, at least three different cord blood samples were mixed). Sample of ETV6-NCOA2 patient-derived xenograft.

first: Shai

last: Izraeli

first: Hila

last: Fishman


title: ChrRNA-seq after 10 days of Xist induction in mESCs

city: Oxford

first: Joseph

last: Bowness

address: South Parks Road

institute: University of Oxford

summary: X chromosome inactivation (XCI) is mediated by the non-coding RNA Xist which directs chromatin modification and gene silencing in cis. The RNA binding protein SPEN and associated corepressors have a central role in Xist-mediated gene silencing. Other silencing factors, notably the Polycomb system, have been reported to function downstream of SPEN. Making use of a SPEN separation-of-function mutation we show that SPEN and Polycomb pathways in fact function in parallel to establish gene silencing. Additionally, we find that differentiation-dependent recruitment of the chromosomal protein SmcHD1 is required for silencing many X-linked genes.

overall_design: This series contains datasets of Chromatin RNA-seq experiments conducted in both iXist-ChrX-Dom and iXist-ChrX-Cast model cell lines, in which Xist is dox-inducible on the M.m.Domesticus or M.m.Castaneous allele of female (XX) mESCs. Here we investigate silencing in mESCs after continuous Dox-induced Xist expression for 10 days. We analyze XCI by isolation of chromatin-associated RNA (ChrRNA) for next-generation sequencing, followed by allelic assignment of reads to Xi or Xa chromosomes, and thus calculation of  allelic ratio (Xi/(Xi+Xa)) as a quantitative measure of X-linked silencing on a gene-by-gene basis. Silencing does reach completion in mESCs, demonstrating that differentiation-dependent mechanisms are required to complete XCI.

first: Tatyana

last: Nesterova

first: Guifeng

last: Wei

first: Neil

last: Brockdorff


title: ETV6-NCOA2 expression in CD34 positive cord blood cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Role of B cells in generating anti-melanoma immunity in response to anti-PD-L1 antibody therapy

status: Public on May 15 2022

city: Houston

first: manisha

last: singh

state: TX

address: 1901,East road

institute: MDACC

summary:
B cells potentially play a role in the immune response to melanoma, including during treatment with immune modulators. We profiled (transcriptome analysis) effects of anti-PD-L1 antibody therapy on gene expression in B16 melanoma tumors of B cells depleted and WT syngeneic mice.
After 7 days of B16 tumors implantation, mice were treated or untreated with anti-PD-L1 antibody (every three days).

overall_design: Tumors from 4 mice in each group (B cells depleted treated with anti-PD-L1, WT treated with anti-PD-L1, B cells depleted untreated,WT untreated) were harvested 3 days after 3rd anti-PD-L1 treatment intratumoral injection of 3M-052 or control.

first: Shubhra

last: Singh

first: Jason

last: Roszik

first: Richard

middle: E

last: Davis

first: Willem

last: Overwijk

first: Manisha