title: RNA sequencing to identify fusion transcripts in late-stage relapse patients with estrogen receptor positive breast cancer

status: Public on Nov 23 2021

city: Houston

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: RNA sequencing (RNA-seq) detects estrogen receptor alpha gene (ESR1) fusion transcripts in estrogen receptor positive (ER+) breast cancer but their role in disease pathogenesis remains unclear. We performed sequencing on RNA extracted from metastatic biopsy samples from patients with ER+ breast cancer to assess the presence of fusion transcripts.

overall_design: RNA-seq of frozen metastatic biopsy samples from ER+ breast cancer patients.

first: Matthew

last: Ellis


title: BCL6 Enables Cancer Cells to Evade Genotoxic Stress

status: Public on Nov 19 2021

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

country: China

institute: East China Normal University

type: Expression profiling by high throughput sequencing

summary: Genotoxic agents remain the mainstay of cancer treatment. Unfortunately, clinical benefit is often countered by a rapid adaptive response in tumors. Here we report that the proto-oncogene BCL6 is a core component conferring tumor resistance adaption. In response to genotoxic stress, BCL6 transcription was markedly promoted in cancer cells. BCL6 upregulation was positively associated with therapy resistance and poor progression-free survival in patients. Mechanistically, we discovered that treatment of the genotoxic agent etoposide led to transcriptional reprogramming of multiple proinflammatory cytokines, among which interferon-α and interferon-γ response were significantly enriched in resistant cells. Our results further revealed that the interferon/STAT1 axis that was required for the therapeutic efficacy of etoposide directly regulated BCL6 expression. Increased BCL6 consequently activated mTOR pathway through repressing the tumor suppressor PTEN to enable cancer cell survival. Importantly, targeted inhibition of BCL6 potentiated etoposide-triggered DNA damage and apoptosis in vitro and in vivo. Collectively, our findings highlight the significance of targeting previously uncharacterized interferon-mediated BCL6 pathway to conquer tolerance of cancer cells to genotoxic stress.

overall_design: mRNA profiles of Capan2 cells (n = 3) (control, Etoposide 50 µM), H661 cells (n = 3) (control, Etoposide 40 µM), PC9 cells (n = 3) (control, Etoposide 10 µM).

first: Xiufeng

last: Pang


title: The Schistosoma mansoni nuclear receptor FTZ-F1 maintains esophageal gland function via direct transcriptional regulation of meg-8.3

status: Public on Nov 15 2021

city: Dallas

first: George

last: Wendt

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

country: USA

institute: University of Texas Southwestern Medical Center

summary: The schistosome homolog of ftz-f1 is a nuclear receptor. In order to understand the function of Smftz-f1, we performed RNAseq with samples taken on two days, Day 5 and Day 9, on either control (RNAi) or Smftz-f1 (RNAi) parasites to see the transcriptional consequences of Smftz-f1 RNAi and to find potential transcriptional targets.

overall_design: Adult male parasites were treated with either control dsRNA or Smftz-f1-targeting dsRNA and taken at two different time points (Day 5 and Day 9), then subjected to RNAseq.

first: Aracely

middle: A

last: Romero

first: David

middle: J

last: Mangelsdorf

first: James

last: Collins


title: Role of Sox9 in Yap activated hepatocytes

status: Public on Nov 17 2021

city: Boston

first: Yuchen

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

summary: Hepatocyte specific TBG promoter-driven Cre,GFP and YAP S127A expression was achieved by retro orbital injection of AAV. RNA-seq was performed for hepatocytes isolated by FACS.

overall_design: For YAP S127A overexpression groups, GFP+ control and YapS127A expressing hepatocytes were isolated by FACS 3 weeks after injection. For Mst1, Mst2, Sox9 conditional knockout; Rosa26-lsl-TdTomato groups, GFP+ control and TdTomato expressing mutant hepatocytes were isolated by FACS 4 weeks after injection.

first: Yingzi

last: Yang


title: DNA Methylation subclass Receptor Tyrosine Kinase II (RTK II) is predictive for seizure development in glioblastoma patients

status: Public on Nov 13 2021

city: Hamburg

first: Richard

last: Drexler

address: Martinistraße 52

department: Neurosurgery

country: Germany

institute: Medical Center Hamburg-Eppendorf

type: Methylation profiling by genome tiling array

summary: Background: Seizures can present at any time before or after the diagnosis of a glioma. Roughly, 25-30 % of glioblastoma (GBM) patients initially present with seizures, and an additional 30 % develop seizures during the course of the disease. Early studies failed to show an effect of general administration of anti-epileptic drugs for glioblastoma patients, since they were unable to stratify patients into high- or low- risk seizure groups.  Methods: 112 patients, who underwent surgery for a GBM, were included. Genome- wide DNA methylation profiling was performed, before methylation subclasses and copy number changes inferred from methylation data were correlated with clinical characteristics. Independently, global gene expression was analyzed in GBM methylation subclasses from TCGA datasets (n=68).  Results: Receptor tyrosine Kinase (RTK) II GBM showed a significantly higher incidence of seizures than RTK I and mesenchymal (MES) GBM (p<0.01). Accordingly, RNA expression datasets revealed an upregulation of genes involved in neurotransmitter synapses and vesicle transport in RTK II glioblastomas. In a multivariate analysis, temporal location (p=0.01, OR 6.35) and RTK II (p=0.03, OR 5.56) were most predictive for preoperative seizures. During postoperative follow-up, only RTK II remained significantly associated with the development of seizures (p<0.01, OR 8.23). Consequently, the need for antiepileptic medication and its increase due to treatment failure was highly associated with the RTK II methylation subclass (p<0.01).  Conclusion: Our study shows a strong correlation of RTK II glioblastomas with preoperative and long-term seizures. These results underline the benefit of molecular glioblastoma profiling with important implications for postoperative seizure control.

overall_design: DNA was extracted from tumors and analyzed for genome-wide DNA methylation patterns using the Illumina EPIC (850k) array from n=112 patients.


title: A chemical-induced reversible gene knockout system for studying gene function in situ [RNA-seq]

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

summary: We developed a conditional conversion allele system termed CoCo. Gene knockout is achieved through Cre-mediated transcription termination, whereas gene restoration is achieved by Flp-mediated deletion of termination signal. To tightly control the temporal expression of the recombinases, Tet-On inducible system is used to drive the expression of Cre recombinase and tamoxifen-inducible FlpO-ER fusion and therefore a dual drug-inducible conditional conversion system (DDCoCo) is developed. This system provides an efficient, rapid and flexible gene switch for studying gene function.

overall_design: 9 samples for High-throughput sequencing, including CC_Cas9_Cre-1, CC_Cas9_Cre-2, CC_Cas9_Cre-3, CC_Cas9_Flpo-1, CC_Cas9_Flpo-2, CC_Cas9_Flpo-3, CC_Cas9-1, CC_Cas9-2, CC_Cas9-3

first: Hui

last: Shi

first: Qin

last: Jin

first: Fangbing

last: Chen

first: Zhen

last: Ouyang

first: Xiaoyi

first: Lei

last: Li

first: Chengdan

last: Lai

first: Quanjun

last: Zhang

first: Yinghua

last: Ye

first: Kepin

last: Wang

first: Liangxue


title: A chemical-induced reversible gene knockout system for studying gene function in situ [AMP-seq]

type: Genome variation profiling by high throughput sequencing

overall_design: 9 samples for High-throughput sequencing, including DMD-CoCo, DMD-Cre, DMD-Flpo, TP53-CoCo, TP53-Cre, TP53-Flpo, hL-CoCo, hL-Cre and hL-Flpo

last: Liu


title: A chemical-induced reversible gene knockout system for studying gene function in situ

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

overall_design: Refer to individual Series


title: ChIPseq of the P. falciparum bromodomain proteins PfBDP7 and PfBDP1 in early and mature schizonts

status: Public on Nov 09 2021

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

institute: Univeritätsklinikum Erlangen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic regulation is recognized as a critical mechanism in controlling virulence, differentiation, and survival of the human malaria parasite P. falciparum. Bromodomain proteins contribute to this process by binding to acetylated lysine residues of histones and thereby targeting the gene regulatory machinery to gene promoters. A protein complex containing the bromodomain proteins PfBDP1 and PfBDP2 (BDP1/BDP2 core complex) was shown to play an essential role for the correct transcription of invasion related genes. Here, we performed a functional characterization of a third component of this complex, which we dubbed PfBDP7 (P. falciparum bromodomain protein 7), because structural modelling predicted a typical bromodomain fold. We confirmed that PfBDP7 is a nuclear protein that interacts with PfBDP1 at invasion gene promoters in mature schizont stage parasites and contributes to their transcription. Although partial depletion of PfBDP7 showed no significant effect on parasite viability, conditional knock down of either PfBDP7 or PfBDP1 resulted in the de-repression of variant surface antigens (VSA), which are important pathogenicity factors. This de-repression was evident both on mRNA and protein level. To understand the underlying mechanism, we mapped the genome wide binding sites of PfBDP7 by ChIPseq and showed that in early schizonts, PfBDP7 and PfBDP1 are commonly enriched in heterochromatic regions across the gene body of all VSA families, including genes coding for PfEMP1, RIFIN, Stevor, and PfMC2TM. This suggests that PfBDP7 and PfBDP1 contribute to the silencing of VSAs by associating with heterochromatin. In conclusion, we identified PfBDP7 as a chromatin binding protein that is a constitutive part of the P. falciparum BDP1/BDP2 core complex and identified PfBDP1 and PfBDP7 as novel players in the silencing of heterochromatin regulated virulence gene families of the malaria parasite P. falciparum.

overall_design: ChIPseq Analysis of PfBDP7Ty and PfBDP1HA in PfBDP7Ty_GlmS or PfBDP1HA::PfBDP7BirATy  P. falciparum parasite lines at early and mature schizont stage

first: Jennifer

last: Quinn

first: Myriam

last: Jeninga

first: Michael

last: Duffy


title: Aorta intimal macrophages prevent the formation of intravascular clots in regions of turbulent flow

status: Public on Nov 08 2021

city: Los Angeles

first: Feiyang

last: Ma

state: CA

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

department: Molecular Biology Institute

institute: UCLA

summary: Vascular endothelial and hematopoietic cells hold a close relationship that is initiated during development, but that continuously broadens to include new functions aimed at maintaining homeostasis in the adult organism. Here, we report on a population of aortic intimal resident macrophages (MacAIRs) that is a permanent feature of the inner vessel wall (tunica intima) of the aorta in regions of turbulent flow and that shares the luminal surface with the endothelium. MacAIRs were found to be transcriptionally distinct from other macrophages and closely associated with the endothelium in the absence of pathology. Lineage tracing analysis indicated that adult MacAIRs were derived from definitive hematopoietic lineage precursors that migrated from the ductus arteriosus seeding the aorta immediately post-birth in areas of turbulent flow including the lesser curvature of the aortic arch and branch openings. These aortic resident macrophages expanded via direct cell renewal and continued to grow in aged aortae to also populate regions of laminar flow. Binding of MacAIRs relied heavily on expression of endothelial ICAM that interacts with CD11c on macrophages. Genetic deletion of CD11c significantly impaired anchorage of MacAIRs to the endothelium. To clarify the biological significance of this population of macrophages, we used a dual diphtheria toxin induced-depletion system that efficiently eliminated MacAIRs in adult mice. Utilizing this model, we found that absence of MacAIRs led to progressive fibrin accumulation and formation of microclots that, once dislodged, can cause blockade of vessels and organ failure. In fact, 40% of the animals with genetic-mediated depletion of MacAIRs died within 2 weeks post-depletion suggesting that these macrophages were required to clear fibrin deposits in regions of turbulent blood flow. These findings advance our knowledge of how vascular endothelial cells profit from this unique interaction with macrophages to control hemostasis, prevent intravascular clotting, and ensure vascular health.

overall_design: Single cell RNA sequencing on intimal cells from the aortic arch and the descending aorta.

first: Gloria

middle: E

last: Hernandez

first: Matteo

last: Pellegrini

first: M

middle: L

last: Iruela-Arispe


title: MicroRNA profiling and analysis of primary OPLL cell derived exosomes

status: Public on Nov 11 2021

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: In order to investigate the function and mechanism of Ossification of Posterior Longitudinal Ligament (OPLL)  primary ligament cell derived exosomes, we take advantages of high throughput sequencing technology to fully reveal the small RNA content of both OPLL and normal posterior longitudinal ligament (PLL) cell derived exosomes.

overall_design: We collect the posterior longitudinal ligament tissues of OPLL and PLL patients during surgery, PLL samples were collected from myelopathy patients who underwent ACCF operation. The collected samples were washed with PBS and subjected to primary culture immediately. The samples were  cut into small pieces and attached to culture flasks for primary culture, 10%FBS high-glucose DMEM were used as culture medium for primary ligament cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage. After 2 passages, the primary cells were ready to perform exosome collection. For exosome collection, we use 1% exosome free FBS/DMEM for culture, the medium were collected at a 3-days interval, and the collected culture medium of both OPLL and PLL primary cell were subsequently subjected to ultracentrifugation. After the ultarcentrifugation, the pellet were washed with PBS and ultarcentrifugated again before use.

first: Yang

first: Wen

last: Yuan


title: Ferric Citrate Uptake is a Virulence Factor in Uropathogenic Escherichia coli

status: Public on Nov 06 2021

city: Ann Arbor

first: Arwen

last: Frick-Cheng

state: Michigan

address: 1150 W. Medical Center Dr.

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: More than half of women will experience a urinary tract infection (UTI) with uropathogenic Escherichia coli (UPEC) causing ~80% of uncomplicated cases. Iron acquisition systems are essential for uropathogenesis, and UPEC encode functionally redundant iron acquisition systems, underlining their importance. However, a recent UPEC clinical isolate, HM7 lacks this functional redundancy and instead encodes a sole siderophore, enterobactin. To determine if E. coli HM7 possesses unidentified iron acquisition systems, we performed RNA-sequencing under iron-limiting conditions and demonstrated the ferric citrate uptake system (fecABCDE and fecIR) was highly upregulated. Importantly, there are high levels of citrate within urine, some of which is bound to iron, and the fec system is highly enriched in UPEC isolates compared to commensal or fecal strains. Therefore, we hypothesized that HM7 and other similar strains use the fec system to acquire iron in the host. Deletion of both enterobactin biosynthesis and ferric citrate uptake (ΔentB/ΔfecA) abrogates use of ferric citrate as an iron source and fecA provides an advantage in pooled human urine in absence of enterobactin. However, in a UTI mouse model, fecA is a fitness factor independent of enterobactin production, likely due to the action of host Lipocalin-2 chelating ferrienterobactin. These findings indicate that ferric citrate uptake is used as an iron source when siderophore efficacy is limited, such as in the host during UTI. Defining these novel compensatory mechanisms and understanding the nutritional hierarchy of preferred iron sources within the urinary tract are important in the search for new approaches to combat UTI.

overall_design: The differential gene expression clinical UPEC isolate HM7 under iron limited conditions  (3 biological replicates) compared to iron replete conditions (3 biological replicates).

first: A

last: Sintsova

first: S

middle: N

last: Smith

first: E

middle: S

last: Snitkin

last: Pirani

first: H

last: Mobley


title: Protective effects of ginsenoside Rh2 on doxorubicin damaged hearts from breast tumor bearing mice

status: Public on Oct 30 2021

city: Daejeon

first: Yee-Jin

last: Yun

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: The FDA approved drug Doxorubicin provokes copious irreversible cardiotoxicity and even increases the risk of heart failure. Considering the multiple and interacted molecular pathways in cancer, there is a big possibility that tumors are simultaneously sensitive to different drugs. This makes achievable to study the combinations of drug, having the virtues of less toxicity, higher efficacy and potentially antagonizing drug resistance in cancer therapy. In the present study, we addressed the synergistic effects of ginsenoside Rh2 on doxorubicin-treated breast cancer bearing mice. We showed that Rh2 significantly enhanced the antitumor effects of doxorubicin and greatly attenuated the cardiotoxicity. Transcriptomic changes can clearly distinguish the chemotherapeutic groups and non-treated control groups. Transcriptomic analysis domestrated that Rh2 protection involved in multiple vital pathways including cellular senescece, fibrosis remodeling, apoptosis and inflammation.

overall_design: Examination of pontential protection of ginsenoside Rh2 by analyzing cardiac transcriptomes changes between doxorubicin treated samples with or without ginsenoside Rh2 and vehicele samples.

first: Yeejin

first: Sunchang

last: Kim


title: Landscape of rat microRNA BodyMap across 11 organs, four ages, and two sexes

status: Public on Nov 01 2021

first: Leming

last: Shi

address: 2005 Songhu Road

institute: Fudan University

summary: The rat has been used extensively as a model system for biological studies. However, its microRNA (miRNA) transcriptome has not been well established. Here, we constructed a comprehensive rat miRNA BodyMap based on miRNA-seq of 320 samples from 11 organs of both sexes of juvenile, adolescent, adult, and aged Fischer 344 rats. We quantified the expression profiles of 993 rat miRNAs, including 268 novel miRNA candidates. A large number of miRNAs showed organ-specific, age-dependent, or sex-specific expression patterns. Particularly, brain exhibited the strongest organ-enriched expression patterns, and testis showed the most strikingly age-dependent expression patterns. Interestingly, the expression levels of two clusters of miRNAs were highly correlated with those of mRNAs and were highly age dependent. The miRNA dataset along with previously reported mRNA data from the same set of samples represents a unique resource to improve understanding of rat transcriptome and subsequently better utilize rats for biomarker discovery.

overall_design: We constructed and sequenced miRNA-seq libraries from 320 total RNA samples derived from 16 female and 16 male rats of the Fischer 344 strain, including four rats for each sex under each of the four developmental stages, namely juvenile (2-weeks old), adolescence (6-weeks old), adult (21-weeks old), and aged (104-weeks old) and ten organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testis or uterus) per rat.

first: Xintong

last: Yao

first: Shanyue

last: Sun

first: Jingcheng

last: Yang

first: Luyao

last: Ren

first: Guangchun

last: Chen

first: Wanwan

last: Hou

first: Yueqiang

last: Song

first: Jun

last: Shang

first: He

last: Jiang

first: Yi

last: Zi

first: Haiyan

last: Wang

first: Peipei

last: Zhang

first: Quan-Zhen

last: Li

first: Ying

last: Yu

first: Yuanting

last: Zheng


title: Replicative history marks transcriptional and functional disparity in the memory T cell pool

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

summary: Mice received DivisionRecorder+ or unmodified OT-I T cells and were challenged with LM-OVA. During memory phase we FACS sorted memory CD8+ OT-I T cells (and sub-sorted RFP+ and RFP-  cells in the case of DivisionRecorder+ cells) from  spleen material and performed single cell RNA sequencing.

overall_design: Spleens were collected from LM-OVA infected recipient mice, DivisionRecorder+ or unmodified OT-I T cells were isolated by FACS, after which cells were processed for scRNA-seq (10X Chromium 3' kit), and sequenced on Illumina NextSeq

first: Lianne

last: Kok

first: Ton

last: Schumacher


title: Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [Rho-Seq]

status: Public on Oct 26 2021

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

summary: Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we report that the reduction of uridine to dihydrouridine by the Dus reductase family targets tRNAs in E. coli but expands to mRNAs is yeast. The modified mRNAs are enriched for cytoskeleton related encoded protein. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridination, which affects its protein expression level. The absence of the modification onto the nda2 mRNA strongly impacts meiosis by inducing a metaphase delay or by completely preventing the formation of spindles during meiosis I and meiosis II, eventually resulting in low gamete viability. Collectively these data show that the codon specific reduction of uridine within mRNA is required for proper meiotic chromosome segregation and gamete viability.

sample_organism:
Escherichia coli
Schizosaccharomyces pombe
Homo sapiens

overall_design: Rho-seq in wild-type and strains were all genes encoding for dus enzymes are deleted in S.pombe and E.coli, in control condition (named noR or R-) or conditions where a chemical treatment makes the presence of dihydrouridine on RNA cause RT drop off during RNA-seq library preparation (a condition named R or R+).

first: Olivier

last: Finet

first: Maxime

last: Wéry

first: Antonin

last: Morillon

first: Damien

last: Hermand


title: Characterization of liver immune cell subsets of primary biliary cholangitis (PBC) mouse models using single-cell RNA sequencing

status: Public on Oct 25 2021

city: GuangZhou

first: bian

last: zhenhua

state: GuangDong

address: Panyu University Town

institute: South China University of Technology

summary: We characterized difference immune cell subsets in liver microenvironment between PBC mouse models (mainly dnTGFβRII mice) and wild type mouse by transcriptome and proteome single cell squencing, and discovered an unconventional cytotoxic CD8αα T cells increased in dnTGFβRII mice.

overall_design: CD45+ immune cells sorted from liver of wild type mice and PBC mouse models, including dnTGFβRII mice, IFN-γ ARE-Del-/- mice and P40-/-IL-2Ra-/- mice.

first: Zhen-Hua

last: Bian

first: Yi-Chen

last: Han


title: Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs

status: Public on Oct 31 2021

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

country: Canada

institute: University of British Columbia

summary: Lifelong production of the many types of mature blood cells from less differentiated progenitors is a hierarchically ordered process that spans multiple cell divisions. The nature and timing of the molecular events required to integrate the environmental signals, transcription factor activity, epigenetic modifications, and changes in gene expression involved are thus complex and still poorly understood. We now show that the more primitive types of human cells in this system display a unique repressive H3K27me3 signature that is retained by mature lymphoid cells but is lost in terminally differentiated monocytes and erythroblasts. Additional intervention data implicate that control of this chromatin state change is a requisite part of the process, whereby normal human hematopoietic progenitor cells make lymphoid and myeloid fate decisions.

overall_design: Examination of H3K27me3 in EZH2i (EPZ-6438) treated HL60 and BMI1-KO HL60.

first: Alireza

last: Lorzadeh

first: Colin

last: Hammond

first: Fandwu

first: David

last: Knapp

first: Jasper

last: Wong

first: Alice

last: Zhu

first: Qi

last: Cao

last: Heravi-Moussavi

first: Annaick

last: Carles

first: Marcus

first: Zohreh

last: Sharafian

first: Jonathan

last: Steif

first: Michelle

last: Moksa

first: Misha

last: Bilenky

first: Pascal

last: Lavoie

first: Connie

last: Eaves


title: Real-time quantitative PCR analysis of mouse skin samples

status: Public on Oct 21 2021

city: PARIS

first: VIVIANE

last: AGBOGAN

state: Île-de-France

address: 160 RUE DE VAUGIRARD

country: France

institute: INEM

summary: Development of chronic Graft Versus Host Disease (cGVHD) represents a major impediment in allogeneic hematopoietic stem cell transplantation (HSCT). This disorder has been shown to be associated with severe impairment of B-cell homeostasis, regulatory B-cell function and distribution. Conversely, the presence of bone marrow and circulating hematogones has been correlated with reduced GVHD risks. We herein raised the question whether B-cell progenitors that upon activation with the TLR-9 agonist CpG (CpG-proBs) provide protection in various models of autoimmune diseases, could as well reduce disease in a sclerodermatous model of cGVHD. We found that CpG-proBs, adoptively transferred during the initial phase of disease, reduced the diarrhea score and mostly prevented cutaneous fibrosis. Donor cells migrated to the draining lymph nodes and to the skin where they mainly differentiated into follicular B cells. CpG activation and IFN- expression were required for the protective effect, which resulted in reduced CD4+ T-cell-derived production of cytokines critically involved in cGVHD, such as TGF-, IL-13, IL-21. Adoptive transfer increased the ratio of follicular regulatory to helper T cells (TFh), which generated less IL-21 but more IL-10. Moreover, CpG-proBs privileged the accumulation of IL-10-expressing CD8+ T-cells, B-cells and dendritic cells in the skin. Collectively, these data support the notion that adoptively transferred CpG-proBs provide an efficient strategy for preventing sclerodermatous cGVHD either per se or as beneficial adjunct to the HSC graft.

overall_design: 3 samples were analysed for each group (GVHD control, CpG proBs recipient).

first: Pauline

last: Gastineau

first: Viviane

last: Agbogan


title: Single-cell RNA-sequencing Analysis Reveals the Dynamic Immune Cell Landscape and Cellular Immune Responses in Bony Fish

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

summary: We used 10X scRNA-Seq to investigate gene expression dynamics and cell type changes in four turbot immuno-organs (gill, head kidney, posterior intestine and spleen) during infection. In total, 103,055 high quality leukocytes were characterized. Our results not only provide a useful resource for the study of fish immune system, but also uncover the origins of adaptive immunity throughout vertebrate evolution.

overall_design: Single-cell transcriptome dynamics of turbots during Edwardsilella piscicida EIB202 infection.

first: Weijie

last: Chen

first: Jianchang

last: Huang

first: Wei

last: Wang

first: Ying

first: Qiyao

first: Yuanxing

last: Zhang

first: Dahai

first: Qin

last: Liu


title: Gene expression profiling of Jun -/- and Jun +/+ facial motor neurons

first: Matthew

last: Mason

address: Meibergdreef 47

department: Neuroregeneration

institute: Netherlands Institute for Neuroscience

summary:
To determine target genes, biological functions of Jun and mechanisms of gene regulation by Jun in regenerating neurons, gene expression profiling was carried out of axotomized and uninjured facial motor neurons in floxed c-Jun mice crossed with nestin-cre mice.
Nestin-promoter-driven Cre ensures deletion of Jun in the central nervous system including facial motor neurons. KO animals were Jun Flox/Fox Cre+, while WT animals were Jun Flox/Flox, Cre-.

overall_design:
At 1 day, 4 days and 14 days after facial nerve injury and in uninjured animals, gene expression profiles of facial nuclei were determined in KO and WT mice.
US12302316_251486819468_S01_GE2-v5_95_Feb07_1_4.txt

middle: R

first: Susan

last: van Erp

first: Kim

last: Wolzak

first: Axel

last: Behrens

first: Gena

last: Raivich

first: Joost

last: Verhaagen


title: Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation.

first: Carlo

last: Yague-Sanz

platform_organism:
Escherichia coli
Schizosaccharomyces pombe
Homo sapiens


title: Next Generation Sequencing Facilitates Quantitative Analysis of MED23-knockdown and Control HUVEC Cells Transcriptomes

first: Gang

address: 2005 Songhu Rd

department: School of life sciences

institute: Fudan university

summary: Purpose: RNA-seq analysis to evaluate the impact of MED23 knockdown on the transcriptome of HUVEC cells.Methods: Total RNA was isolated with TRIzol from Med23 knockdown HUVECs (n = 3) or control cells (n = 3). cDNA sequencing libraries were prepared with an NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The RNA-Seq FASTQ raw data were trimmed to remove low-quality reads and adapters using Trimmomatic. The trimmed reads were aligned to the mouse reference genome UCSC GRCh37/hg19 with HISAT2. Gene and transcript quantification was performed using Cutdiff. The results of the mapping of the RNA-seq reads, transcript assembly and abundance estimation were reported as fragments per kilobase of exon per million fragments mapped (FPKM).

overall_design: mRNA profiles of  MED23-knockdown HUVEC cells (n = 3) or control cells (n = 3).

first: Yenan

first: Qi

last: Xiao

first: Jingwen

last: Yin

first: Chonghui

last: Li


title: A single-cell epigenetic atlas of human IDH-mutant glioma

status: Public on Oct 20 2021

city: San Francisco

first: Aaron

last: Diaz

department: Neurological Surgery

institute: University of California, San Francisco

summary: Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. To reconcile these findings, we profiled 22 human IDH-mutant gliomas via single-cell assay for transposase-accessible chromatin (scATAC-seq). We determined the cell-type specific differences in transcription-factor expression and associated regulatory grammars between IDH-mutant glioma subtypes. We find that while IDH-mutant gliomas do share a common distribution of cell types, there are significant differences in the expression and targeting of transcription factors that regulate glial identity and cytokine elaboration. We knocked out the chromatin-remodeler ATRX, which suffers loss-of-function alterations in most IDH-mutant astrocytomas, in an IDH-mutant immunocompetent intracranial murine model. We find that both human ATRX-mutant gliomas and murine ATRX-knockout gliomas are more heavily infiltrated by immunosuppressive monocytic-lineage cells derived from circulation than ATRX-intact gliomas, in an IDH-mutant background. ATRX knockout in murine glioma recapitulates gene expression and open-chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. ATRX knockout in murine glioma recapitulates gene expression and open chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. Through single-cell cleavage under targets and tagmentation assays and meta-analysis of public data, we show that ATRX loss leads to a global depletion in CCCTC-binding factor association with DNA, gene dysregulation along associated chromatin loops, and protection from therapy-induced senescence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We profiled specimens from 22 grade-II/III IDH-mutant untreated human gliomas via single-cell assay for transposase-accessible chromatin (scATAC-seq). We profiled murine IDH1R132H+/ATRX-KO and IDH1R132H/ATRX-intact gliomas via scATAC-seq, snRNA-seq, and anti-CTCF snCUT&Tag.
*** Raw data not available due to privacy concerns.

first: Husam

last: Babikir

first: Lin

first: Karin

last: Shamardani

first: Francisca

last: Catalan

first: Sweta

last: Sudhir

first: Manish

middle: K

last: Aghi

first: David

last: Raleigh

first: Joanna

last: Phillips


title: Screening for potential target genes of hsa-mir-199a-1 and hsa-mir-4423 using Clariom D arrays

status: Public on Oct 15 2021

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary: We screened for target genes of hsa-mir-199a-1 and hsa-mir-4423 by transcriptome profiling. The miRNAs were overexpressed in HeLa cells by transient transfection of precursor miRNA expression plasmids. High-density Clariom D arrays for human were used for the gene expression analysis. This GEO entry provides the microarray data preprocessed according to the gene level workflow.

overall_design: HeLa cells were transiently transfected with non-viral precursor miRNA expression plasmids from GeneCopoeia (HmiR0296-MR04 and HmiR1083-MR04, respectively). As negative control, a plasmid with scrambled sequence (CmiR0001-MR04, GeneCopoeia) was used. Total RNA was isolated 24 h (n=2 replicates) and 48 h (n=4 replicates) following transfection. For all 18 RNA samples, transcript levels were measured with Clariom D arrays.

first: Dirk

last: Koczan

first: Nina

last: Boxberger

first: Uwe

last: Zettl


title: PBMCs from metastatic breast cancer patients

status: Public on Oct 18 2021

city: Albuquerque

first: DARIO

last: MARCHETTI

state: NM

address: 915 Camino de Salud

department: Internal Medicine

institute: UNM Health Sciences Center

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

overall_design: Refer to individual Series


title: Analysis of PBMCs from metastatic breast cancer patients

summary: The goal of this study is to analyze the blood from patients with metastatic breast cancer to examine the genome of circulating tumor cells that initiate metastatic tumors.

overall_design: RNA-Seq and single cell RNA sequencing of PBMCs from metastatic breast cancer patients

first: Dario

last: Marchetti

first: Kathryn

last: Brayer

first: Christine

last: Pauken

first: S

last: Kenney


title: Bulk RNAseq Analysis of PBMCs from metastatic breast cancer patients

summary: The goal of this study is to analyze the blood from patients with metastatic breast cancer to examine the genome of circulating tumor cells that initate metastatic tumors.


title: Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [sorted_BM_PB_THY]

city: Rochester

first: Stephan

last: Emmrich

state: NY

address: 213 Hutchison Hall, River Campus

institute: University of Rochester

summary: Naked mole-rats are a mammalian model organism of exceptional longevity. We mapped the hematopoietic hierarchy and used functional characterizations to define a purified stem and progenitor cell (HSPC) compartment similar to mouse LIN-/Sca-1+/Kit+ HSPCs or human LIN-/CD34+/CD38lo HSPCs.

overall_design:
Naked mole-rat cells were sorted according to functionally characterized immunophenotypes as described in the manuscript, in parallel FACS-antibodies were conjugated to oligo-ADT tags to quantify surface marker binding as described for CITE-Seq. The mRNA libraries were aligned to either the FRAMA bone marrow transcriptome assembly from our publication or a mouse genome reference.

Note: Raw data represents only gene expresion (GEX). Raw data for ADT not included.


title: Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [unfractionated BM]

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design:
Naked mole-rat or Mouse bone marrow was extracted, RBC-lysed and submitted to scRNA-Seq as unfractionated BM, in parallel FACS-antibodies were conjugated to oligo-ADT tags to quantify surface marker binding as described for CITE-Seq. The mRNA libraries were aligned to either the FRAMA bone marrow transcriptome assembly from our publication or a mouse genome reference.

Note: Raw data represents only gene expresion (GEX). Raw data for ADT not included.


title: Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [Xeno]

overall_design:
Naked mole-rat cells were sorted according to functionally characterized immunophenotypes (CP1 or LTC) which correspond to hematopoietic stem and progenitor subsets. Live cells were transplanted into 2.5Gy irradiated NSGS immunodeficient hosts, marrow from hindlimbs was extracted 4 weeks post xenotranplantation. FACS-purification was used to enrich the graft within the mouse host marrow, in parallel FACS-antibodies were conjugated to oligo-ADT tags to quantify surface marker binding as described for CITE-Seq. The mRNA libraries were aligned to both a mouse genome reference and the FRAMA bone marrow transcriptome assembly from our publication to exclude any host cells.

Note: Raw data represents only gene expresion (GEX). Raw data for ADT not included.


title: Transcriptome-wide N6-methyladenine profiling in low input multiplex samples by a kit-free multi-barcode method

status: Public on Oct 14 2021

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

summary: N6-methyladnine, which is the most abundant post-transcriptional RNA modification in eukaryotic mRNA, has been proved to be essential in various biological processes and related to numerous diseases. Transcriptome-wide m6A profiling by next generation sequencing is widely used to explore the distributions as well as quantity of m6A modifications. As traditional m6A-seq demands large amount of starting RNA which limited its application to clinical samples, we present a strategy of low input multi-barcode m6A-seq (SLIM-m6A-seq) to realize simplified m6A profiling of mixed clinical samples. This method maintains the advantages of preferable detection limit, low cost and simplified experiment procedures. Sequencing data of clinical blood samples from patients with diabetic myocardial infarction suggest that this method is practical in clinical application and m6A may play a critical role in the progression of diabetic cardiovascular complications.

overall_design: 91 samples are analysed (cell line data is mainly used to verify the reliability of the method, human peripheral blood samples and murine heart tissue are mainly used to apply the method to disease studies)

last: Qin

first: K

last: Yang

last: Han

first: Y

last: Yuan

first: J

last: Mo

first: M

last: Xiao

last: Wang

first: X

last: Fang

last: Liu

last: Weng

last: Zhou


title: Innate immunity-driven cell recruitment in rat autoimmune diabetes

status: Public on Oct 04 2021

city: Worcester

first: Alan

middle: G

last: Derr

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: Comparative analysis of the response of wild-type (WT) and Ifnar1 knockout LEW.1WR1 rats to infection with Kilham rat virus (KRV) using the Seq-Well single-cell RNA-Seq method. KRV induces the equivalent of human type I diabetes (T1D) in WT rats.

overall_design: Seq-Well single-cell RNA-Seq analysis of wild-type and Ifnar1 knockout LEW.1WR1 rats infected with Kilham rat virus.

first: Natasha

last: Qaisar

first: Adediwura

last: Arowosegbe

first: Alper

last: Kucukural

first: Melanie

middle: I

last: Trombly

first: Basanthi

last: Satish

first: Riccardo

last: Racicot

first: Zhiru

last: Guo

first: Jennifer

middle: P


title: Single-cell RNA analyses of cattle ruminal epithelial cells

status: Public on Oct 01 2021

city: Beltsville

first: Yahui

last: Gao

state: Maryland

address: 10300 Baltimore Ave Bldg 306

institute: ARS, USDA

summary: Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. Here we present an initial effort of single-cell transcriptomic analyses of cattle ruminal epithelial cells during the rumen development. We obtained 5064 and 1372 cells from Holstein ruminal epithelial cells before and after weaning, respectively. We reported 6 cell types across their temporal and spatial distributions, which were partially correlated with rumen epithelium layer’s structures and functions. We also reported a distinct sets of cell markers for these cell types, for example, CRA1, HMMR, MKI67, and EZH2 for the dividing epithelial cells and the TGFB pathway and the keratin gene family for keratinized epithelial cells. Our proposed a cell lineage model may contribute to the understanding of cattle rumen epithelial proliferation and development.

overall_design: Two samples from cattle rumen

first: Lingzhao

first: Ransom

last: Baldwin

first: Erin

last: Connor

first: John

middle: B

last: Cole

first: Curtis

last: Van Tassell

first: Li

last: Ma

first: Cong-jun

last: Li

first: George


title: WSB1 regulates c-Myc expression through β-Catenin signalling and forms a feedforward circuit.

city: Hangzhou

first: Xiaomeng

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: The dysregulation of transcription factors is widely associated with tumourigenesis. As the most well-defined transcription factor in multiple types of cancer, c-Myc can transform cells by transactivating various downstream genes. Given that there is no effective way to directly inhibit c-Myc, c-Myc targeting strategies hold great potential for cancer therapy. In this study, we found that WSB1, which has a highly positive correlation with c-Myc in 10 cancer cell lines and clinical samples, is a direct target gene of c-Myc, and can positively regulate c-Myc expression, which forms a feedforward circuit promoting cancer development. RNA sequencing results from Bel-7402 cells confirmed that WSB1 promoted c-Myc expression through the β-Catenin pathway. Mechanistically, WSB1 affected β-Catenin destruction complex-PPP2CA assembly and E3 ubiquitin ligase adaptor β-TRCP recruitment, which inhibited the ubiquitination of β-Catenin and transactivated c-Myc. Of interest, the effect of WSB1 on c-Myc was independent of its E3 ligase activity. Moreover, overexpressing WSB1 in the Bel-7402 xenograft model could further strengthen the tumour-driven effect of c-Myc overexpression. Thus, our findings revealed a novel mechanism involved in tumourigenesis in which the WSB1/c-Myc feedforward circuit played an essential role, highlighting a potential c-Myc intervention strategy in cancer treatment.

overall_design: Bel-7402 cells stably overexpressing pCDH, pCDH-WSB1 and pCDH-ΔSOCS by lentivirus transfection were harvested and washed for 3 times with pre-cold PBS. Total RNA of the cells was extracted by TRIzol reagent and sent to Bohao Biotechnology (Shanghai, China) for RNA expression profiling.

first: Ji

last: Cao

first: Jieqiong

last: You

first: Yanling

last: Gong

first: Meng

last: Yuan

first: Haiying

last: Zhu

first: Liang

last: Fang

first: Hong

first: Meidan

last: Ying

first: Qiaojun

last: He

first: Bo

last: Yang


title: RNAseq time course for P7 neonatal cardiomyocytes induced to proliferate with 4 cell cycle factors

status: Public on Sep 24 2021

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

summary: we conducted temporal bulk RNAseq on P7 neonatal cardiomyocytes infected with either LacZ (control) or CDK1, CDK4, CCNB, CCND (4F) adenovirus for 24, 48 or 72 h.

overall_design: bulk RNA-seq

first: Riham

last: Abouleisa


title: CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals

city: Bonn

first: Daniele

last: Bano

address: Sigmund-Freud-Strasse 27

institute: DZNE


title: CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals (ChIP-Seq)

summary: ChIP-Seq of H3.3 loading on promoters of genes in short-lived and long-lived mitochondrial mutant nematodes identifies genes which could potentially regulate longevity

overall_design: ChIP-Seq of wild-type, gas-1(fc21) and nuo-6(qm200) mutant Caenorhabditis elegans

first: Antonia

last: Piazzesi

first: Yiru

last: Wang

first: Viktoria

last: Zeisler-Diehl

first: Joshua

last: Jackson

first: Nils-Thorben

last: Hoffmann

first: Pablo

last: Gómez Martín

first: Fabio

last: Bertan

first: Chester

last: Wrobel

first: Dan

last: Ehninger

first: Frank

middle: C

last: Schroeder

first: Kristian

last: Händler

first: Joachim

last: Schultze

first: Lukas

last: Schreiber

first: Gerhild

last: van Echten-Deckert

first: Pierluigi

last: Nicotera


title: Gene expression analysis of spleens from virus-infected rats

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

summary: Comparison of gene expression between wildtype (WT) and Ifnar1 ko rats following Kilham rat virus (KRV) challenge

overall_design: Uninfected WT or Ifnar1 ko rat spleens (n=2 each group), KRV-infected WT or Ifnar1 ko rat spleens (n=4 each group)

first: Natasha

last: Qaisar

first: Jennifer

first: Riccardo

last: Racicot

first: Basanthi

last: Satish


title: CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals (RNA-Seq)

first: Daniele

last: Bano

summary: Intestine-specific transcriptome of wild-type. gas-1(fc21) and gas-1(fc21); cest-2.2 OE Caenorhaditis elegans in order to gain insight into how cest-2.2 overexpression ameliorates Complex I deficiency

overall_design: RNA-Seq of intestines from 5-day old wild-type. gas-1(fc21) and gas-1(fc21); cest-2.2 OE Caenorhaditis elegans

first: Antonia

last: Piazzesi

first: Yiru

last: Wang

first: Viktoria

last: Zeisler-Diehl

first: Joshua


title: Next Generation Sequencing Facilitates Quantitative Analysis of Zinc treated Wild-Type or CmtR-deleted strains of Mycobacterium bovis BCG Transcriptomes

status: Public on Sep 22 2021

city: Wuhan

first: Liu

last: Chen

state: Hubei

address: No.1 Shizishan Street, Hongshan District, Wuhan, Hubei Province, China

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: The goal of this study aims to quantitatively compare the gene expression difference in wild-type or cmtR-deleted strains of Mycobacterium bovis BCG with and without excess zinc treatment at the transcriptome level and find the underlying mechanism how could excess zinc inhibit mycobacterial growth and its relation with  transcription factor CmtR.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: Four samples in triplicate are analyzed. The control sample is the wild-type or cmtR-deleted strains of Mycobacterium bovis BCG without zinc treatment.

first: Zhengguo

last: He


title: An organoid screening framework to engineer intestinal epithelial composition

status: Public on Sep 16 2021

city: Cambridge

first: Benjamin

last: Mead

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

summary: Barrier epithelia are essential to organismal homeostasis, and changes in their cellular composition are observed in human diseases. Within the small intestine, adult stem cells establish tissue cellularity, and may provide a means to control the abundance and quality of specialized epithelial cells. Nevertheless, we lack suitable approaches to identify biological targets and small molecules to modulate them. Here, we develop an extendable framework utilizing a physiologically-inspired organoid model to identify unknown, druggable regulators of intestinal stem cell differentiation that translate to intended manipulations in vivo. Specifically, we miniaturize and adapt an organoid model of Paneth cell differentiation to enable multiplexed phenotypic screening on the scale of thousands of samples, and employ longitudinal single-cell RNA-sequencing to understand hit biology. Strikingly, we identify that inhibitors of the nuclear exporter XPO1 modulate stem cell fate commitment, significantly increasing the abundance of Paneth cells independent of known differentiation cues. Our framework elucidates small molecules which modulate tissue stem cell biology and their underlying targets without the need for a priori knowledge of in vivo pathway biology.

overall_design: Single-cell RNA-sequencing experiments on Seq-Well S^3 platform of differentiating intestinal organoids (ENR+CD +/- KPT-330). We performed a longitudinal comparison between untreated and KPT-330-treated or-ganoids over a 6-day differentiation. We collected 17 samples at following timepoints: 6 hours (0.25 days),  and 1, 2, 3, 4, or 6 days. Each sample consists of single cells from >1,000 organoids from pre-differentiation ENR+CV organoids and both ENR+CD and ENR+CD + KPT-330 (160 nM) conditions. For time points beyond 2 days, media was refreshed every other day. The resulting dataset consists of 19,877 cells. Unique molecular identifier (UMI), percent mitochondrial, and detected gene distributions are similar across samples, within acceptable quality bounds (genes > 500, UMI < 30,000, percent mitochondrial < 35). ENR+CV, ENR+CD media formulations and organoid culture protocols are per Mead, et al. BMC Biology 2018.

first: Alex

last: Shalek


title: Binge Alcohol Disrupts Skeletal Muscle Core Molecular Clock Independent of Glucocorticoids

status: Public on Sep 10 2021

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: Circadian rhythms are central to optimal physiological functioning and their interruption contributes to the development of several chronic diseases. Alcohol (EtOH) intoxication disrupts circadian rhythms within liver, brain, and intestines, but it is unknown whether alcohol also disrupts components of the core clock in skeletal muscle. Female C57BL/6Hsd mice were randomized to receive either saline (control) or alcohol (EtOH) (5g/kg) via intraperitoneal injection at the start of the dark cycle (ZT12), and gastrocnemius was collected every 4hr from Control and EtOH treated mice for the next 48hr following isoflurane anesthetization. In addition, metyrapone was administered prior to alcohol intoxication in separate mice to determine whether the alcohol-induced increase in serum corticosterone contributed to circadian gene regulation. Finally, synchronized C2C12 myotubes were treated with alcohol (100mM) to assess the influence of centrally or peripherally mediated effects of alcohol on the muscle clock. Alcohol significantly disrupted the mRNA expression of Bmal1, Per1/2, and Cry1/2 in addition to perturbing the clock-controlled genes, Myod1, Dbp, Tef, and Bhlhe40 (p<0.05). Alcohol increased serum corticosterone levels and glucocorticoid target genes, Redd1 and Klf15, in muscle.  Metyrapone decreased serum corticosterone in EtOH mice but did not normalize the mRNA expression of Per1, Cry1 and Cry2 and Myod1 which were altered by EtOH. Alcohol did not alter core clock gene expression (Bmal, Per1/2, Cry1/2) at 4, 8, and 12hrs post treatment in synchronized C2C12 myotubes. Therefore, binge alcohol disrupted genes of the core molecular clock independently of elevated serum corticosterone.

overall_design: Gastrocnemius and plantaris muscle mRNA from adult male ethanol treated or control C57BL/6 mice was analyzed by RNA sequencing of 5 biological replicates per group on and Illumina NovaSeq 6000.

last: Steiner

first: Abigail

last: Tice

first: Joseph

last: Laudato

first: Michael

last: Rossetti

first: Christopher

last: Wolff

first: Karyn

last: Esser

first: Choogon

last: Lee

first: Charles

middle: H

last: Lang

first: Bradley

last: Gordon


title: Tumor Microenvironment Profiling Identifies Prognostic Signatures and Suggests Immunotherapeutic Benefits in Neuroblastoma

first: Feng

last: Chenzhao

address: No.1095 Jiefang Road

institute: Huazhong University of Science and Technology

summary: Here, we profiled the TME landscape of 498 NB patients on a self-curated gene list and identified 3 prognostic TMEsubgroups. Differentially expressed genes (DEGs) among 3 TMEsubgroups constructed a genetic background of the TME landscape and characterized 3 GeneSubgroups. We further created a 48-gene signature, the TMEscore, to infer prognosis and validated in 3 independent NB cohorts and a pan-cancer cohort of 9460 patients. We did RNA-seq on 16 samples and verified that TMEscore was higher in stage 3/4 patients.

overall_design: RNA-seq of 10 stage 1/2 and 6 stage 3/4 neuroblastoma samples

first: Xiaojuan

last: Wu

first: Xiang

last: Zhao

first: Jiexiong

last: Feng


title: State-Transition Analysis of Time-Sequential microRNA Expression Predicts Development of Acute Myeloid Leukemia

status: Public on Sep 08 2021

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

summary: We show that the microRNA transcriptome undergoes a global state transition during the initiation and progression of acute myeloid leukemia, and accurately predicts time to disease development.

overall_design: We conducted a longitudinal study in a mouse AML model induced by the Cbfb-MYH11 (CM) oncogene to observe the temporal evolution of the transcriptome from healthy state to leukemia state. In the conditional CM knock-in mouse model (Cbfb+/56MMx1Cre), expression of CM in the adult bone marrow alters normal hematopoietic differentiation creating aberrant pre-leukemic progenitor cells which acquire additional genetic and epigenetic alterations needed for malignant transformation and AML development. We used two independent cohorts of mice as training and validation cohorts. For the training cohort, we collected PBMC from the CM-induced mice (n = 7) and the similarly treated littermate controls (n = 7) before induction (t = 0) and monthly after induction up to 10 months (t = 1-10) or when the mouse developed leukemia and became moribund, whichever event occurred first. Similarly, for the validation cohort, we collected PBMC from CM mice (n=9) or control (n=7) before induction and monthly thereafter up to 6 months. Total RNA was isolated from PBMC using AllPrep DNA/RNA Kit (Qiagen) and subjected to micro RNA-sequencing.

first: D

last: Frankhouser

last: O’Meally

first: S

last: Branciamore

first: L

last: Uechi

last: Zhang

first: Y

last: Chen

first: M

last: Li

first: X

first: N

last: Carlesso

first: G

last: Marcucci

first: R

last: Rockne

last: Kuo


title: Inflammatory response in HSPC of PTPN11-mutated JMML

status: Public on Sep 06 2021

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

institute: APHP Hôpital Robert Debré

summary: Activating mutations in PTPN11 gene are the most frequent in JMML patients. Here we explore the transcriptome of HSPC (hematopoietic stem and progenitor cells) sorted from sporadic JMML patients with PTPN11 mutation and from healthy age matched donnors. Bulk transcriptome of sorted HSPC reveals an inflammatory gene expression signature which may represent a future target for JMML therapy.

overall_design: RNAseq data

last: Cavé

first: Florian

last: Piques

first: Marion

last: Strullu

first: Chloé

last: Arfeuille

first: Aurélie

last: Caye


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and non-antibiotic pharmaceuticals stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes

status: Public on Sep 03 2021

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

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

sample_organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

overall_design: Refer to individual Series


title: equinox RNAi gene expression profiling

status: Public on Sep 04 2021

first: Peter

middle: W

last: Reddien

address: 9 Cambridge Center

department: MIT Biology

institute: Whitehead Institute for Biomedical Research

summary: Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. Following equinox inhibition, animals failed to form blastemas, reset positional information, and upregulate stem cell (neoblast) proliferation at wounds. Associated with these defects was an inability to maintain wound-induced gene expression. We propose that activation of equinox in the wound epidermis initiates planarian regeneration.

overall_design: Polyadenylated RNA was isolated from post-pharyngeal fragments at 0, 3, 6, 16, 24, and 48 hours post-amputation (hpa) from planarians following RNAi of a control gene (C.elegans unc-22; 4-5 replicates) and equinox (5 replicates). Worms were fed eight times over four weeks, and cut 7 days after 4th feeding.

first: Jennifer

last: Cloutier

first: Lucila

last: Scimone

first: Chloe

last: Maybrun


title: equinox is a planarian wound epidermis gene required for the initiation of regeneration


title: CircMAN1A2 is upregulated by Helicobacter pylori and promotes development of gastric cancer

status: Public on Sep 09 2021

city: Jinan

first: Xixi

last: Cui

address: 44 Wenhua Xilu

institute: Shandong University

summary: In this study, we treated the gastric cancer cell line AGS with PBS and Helicobacter pylori to perform RNA-seq analysis. A total of 18,308 different circRNA candidates were obtained in the experiment.Compared with the control, 101 significantly differentially expressed circRNAs were identified in the AGS cells infected with H. pylori, including 84 upregulated circRNAs and 17 downregulated circRNAs.Then, circMAN1A2 with the most significant expression difference was selected according to the sequencing results to study the epigenetic mechanism of H. pylori-induced gastric carcinogenesis.

overall_design: After Hp26695-infected AGS cells were infected at a multiplicity of infection (MOI)  = 100:1 for 12 h,  gastric cancer cells were sequenced. The control group used PBS for the same amount of time.

first: Wenjuan

first: Ruiting

first: Xue


title: Microarray-predicted marker genes indicating handling stress in maraena whitefish (Coregonus maraena)

status: Public on Sep 01 2021

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

summary: Stress represents a major factor negatively affecting fish welfare in aquaculture. The head kidney is the effective centre for neuro-immune interactions in teleost as it is the main secretory organ of stress hormones and gathers major leukocyte populations. The present study investigated the influence of acute and long-term (chronic) handling stress in maraena whitefish. The aim was to define stress-related physiological changes in maraena whitefish using traditionally used and newly identified parameters. We determined the levels of the well-established biomarkers included triglycerides, lactate and cholesterol in blood plasma. In addition, the transcriptome of the head kidney of differently treated whitefish was recorded to identify new potential biomarkers and to investigate the relationship between immune functions and stress responses.

overall_design:
For the acute stress approaches, the fish were first acclimatised in pairs in a tank, then the control fish was removed, killed and sampled. The remaining fish was subjected to a one-minute handling stress: The fish was captured with previously moistened nets and lifted out of the tank, placed in a bucket and then transferred back into the tank. This was done in parallel, with both fish transferred to another tank after stress, where they were kept until sampled after 3h or 24h. For the chronic stress approaches, two animals from the same treatment group (control or stress) were kept in each tank and different tanks were used for each replicate. A one minute handling stress was applied daily for 10 d.
After 3 h, 24 h and 10 d, respectively, the fish were killed, measured and sampled.

first: Joan

last: Martorell Ribera

first: Dirk

last: Koczan

first: Marzia

last: Tindara Venuto

first: Torsten

last: Viergutz

first: Ronald

last: Brunner

first: Tom

last: Goldammer

first: Ulrike

last: Gimsa


title: Transcriptome changes induced by bitter melon (Momordica charantia)- intake in a high-fat diet induced obesity model

city: Aurora

first: Rajesh

last: Agarwal

state: Colorado

address: 12850 E Montview Blvd

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary:
Metabolic effects of lyophilized bitter melon juice (BMJ) extract (oral gavage 200mg/kg/body weight-daily for 40 days) intake were evaluated in diet-induced obese C57BL/6J male mice [fed-high fat diet (HFD), 60 kcal% fat]. Changes in gene expression in the hepatic transcriptome (microarray analysis using Affymetrix Mouse Exon 1.0 ST arrays)
Expression estimates for individual genes were estimated using Affymetrix Power Tools and the RMA-sketch algorithm.  Probe sets were grouped into gene clusters using Ensembl gene annotation (version GRCm38).  A probe set was included in a gene cluster if all of its associated probes aligned to a region completely contained within the exonic region of the gene.

overall_design: Total of 7 samples from mice randomized into two groups: a) Control-DIO group (n = 3 per group) and b) BMJ+DIO group (n = 4 per group)

first: Dominique

last: Reed

first: Dileep

last: Kumar

first: Sushil

first: Komal

last: Raina

first: Reenu

last: Punia

first: Rama

last: Kant

first: Laura

last: Saba

first: Charmion

last: Cruickshank-Quinn

first: Boris

last: Tabakoff

first: Nichole

last: Reisdorph

first: Michael

last: Edwards

last: Wempe

first: Chapla


title: The global transcriptomic profile in the spermidine-stressed E. coli

city: Chandigarh

first: Dipak

last: Dutta

email: dutta@imtech.res.in, ddutta25@gmail.com

state: Chandigarh

address: Sector 39-A

department: Molecular Biochemistry

country: India

institute: CSIR IMTECH

summary: To achieve extreme spermidine stress we used DspeG E. coli strain. We identified the pathways that are altered under spermidine stress. Among many changes spermidine altered the iron-sulfur cluster metabolism and redox balance in the cells. Therefore, we have shown that superoxide quencher, NAC and ascorbate mitigates spermidine stress. Overall our data explains the importaance of tight spermidine homeostasisin the cell.

overall_design: Organism : Escherichia coli , Agilent custom E.coli Gene Expression  8x15k Array (AMADID: 068043) designed by Genotypic Technology Private

first: Vineet

last: Mishra

first: Amit

last: Arora


title: Gene expression data of micro RNA from skeletal muscle sample of F2 population based German Landrace (DL) and Pietrain (Pi) pig breeds

status: Public on Aug 31 2021

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: Gene expression data of micro RNA from skeletal muscle samples of F2 population based DL and Pi F2 63 days post conception (dpc).

overall_design: miRNAs of skeletal muscle from Pietrain F2 at 63 dpc were hybridized to Affymetrix GeneChip miRNA arrays.

first: Klaus

last: Wimmers


title: Different hot spot mutations in the TP53 genes exerts different biology and outcome

city: DVIRA

first: Ori

last: Hassin

state: HADAROM (SOUTHERN)

address: DVIRA 91

department: MCB

country: Israel

institute: Weizmann

summary: We report that R273 mutation in the TP53 gene in Colorectal cancer promotes transcriptional signature affecting cytoskeleton dynamics and increasing cell migration. This signature is not a general transcriptional output of mutantp53 as other known hot spot such as R175H mutation could not exerts this signature.

overall_design: Examination of two different hot spot mutations in the TP53 gene compared to p53 null cells

first: Moshe

last: Oren


title: Gene expression data of mRNA from longissimus muscle sample of F2 population based German Landrace (DL) and Pietrain (Pi) pig breeds

summary: 47,845 probe-sets were screened, in the first part of this study pig embryos at 63 days post conception (dpc)

overall_design: RNAs of longissimus muscle from  F2 at 63 dpc were hybridized to Affymetrix Porcine Snowball Array.


title: bmp4 RNAi gene expression profiling

first: Peter

last: Reddien

overall_design: Polyadenylated RNA was isolated from post-pharyngeal fragments at 0, 3, 6, 16, 24, and 48 hours post-amputation (hpa) from planarians following RNAi of a control gene (C.elegans unc-22; 5 replicates) and bmp4 (5 replicates). Worms were fed four times over two weeks, and cut 7 days after 4th feeding.

first: Jennifer

last: Cloutier

first: Lucila

last: Scimone

first: Chloe

last: Maybrun


title: Immunel Landscape of Spinal Cord after Injury in Mice Using Single-Cell RNA-Seq

status: Public on Aug 28 2021

first: Jingyu

last: Wang

state: Zhejiang

address: No.688 Yuhangtang road

institute: Zhejiang University

summary: Single-cell RNA sequencing of immune cells of mouse spinal cord using Drop-Seq

overall_design: Drop-Seq was performed for spinal cord immnue cells dissociated from ambisextrous C57BL/6J mice after spinal cord injury at 0, 3, and 14 day-post injury (dpi). Single-cell suspensions derived from heathy spinal cords were generated using the ActD-based protocol or standard dissociation protocol. Single-cell suspensions dissociated from injured spinal cords were generated only using the ActD-based protocol. Drop-Seq was used to produce single-cell cDNA libraries attached to microbeads. cDNAs were amplified by PCR and prepared for sequencing.

first: Lintao

last: Xu

first: Lin-lin

first: Yongjian

last: Zhu


title: Single cell gene expression profiling using 10x v3

overall_design: FACS sorted cells were isolated from post-pharyngeal wound fragments at 0, 6, and 18 hours post-amputation (hpa) from planarians. One condition was fed control RNAi four times over two weeks prior to the sort. Only x-insensitives were collected. All conditions except for the 6 hour were sorted based on hoeschst high, propidium iodide low. The 6 hour time point was sorted on hoechst high, calcein medium to hight to allow for more damaged cells to be captured.


title: Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.

overall_design: Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

first: A

last: Marieke Oudelaar

first: Abrar

last: Aljahani

first: Peng

last: Hua

first: James

middle: O

last: Davies


title: Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability

status: Public on Aug 25 2021

city: LA

first: Zhiheng

last: Liu

state: CA

address: 610 Charles E Young Dr S

institute: UCLA


title: Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability [single-cell RNA-seq]

summary: Most non-coding regions of the human genome do not harbour any annotated element and are even not marked with any epigenomic or protein binding signal. However, an overlooked aspect of their possible role in stabilizing 3D chromatin organization has not been extensively studied. To illuminate their structural importance, we started with the non-coding regions forming many 3D contacts (referred to as hubs) and performed a CRISPR library screening to identify dozens of hubs essential for cell viability. Hi-C and single cell transcriptomic analyses showed that their deletion could significantly alter chromatin organization and impact the distal genes expression. This study revealed the 3D structural importance of non-coding loci that are not associated with any functional element, providing a new mechanistic understanding of disease-associated genetic variations (GVs), and we focused on single nucleotide variations. Furthermore, our analyses also suggest a powerful approach to develop "one-drug-multiple-targets" therapeutics targeting disease-specific non-coding regions.

overall_design: Examination of gene expression profile of K562 hub_22_7 deletion cells at single cell level

first: Ying

last: Zhao

first: Peiyao

last: Wu

first: Bo

last: Ding

first: Lina

last: Zheng


title: scRNAseq of innate lymphoid cells generated in vitro from umbilical cord blood derived CD34+ hematopoietic progenitors.

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Innate lymphoid cells (ILCs) were generated in vitro from CD34+ hematopoietic progenitors derived from umbilical cord blood, and RNA sequencing was performed on CD45+ LineageLD- cells  to assess transcriptional identities of lineages generated

overall_design: ILCs were generated through in vitro culture from CD34+ HPCs as described in the manuscript, from 2 independent donors. Cells from conditions OP9+IL-15, DL1+IL-15 and DL1 were FACS-sorted as CD45p cells which were Lineage (CD14, CD123, FcERa, Viability dye) negative, combined with the following CITE-Seq 34 anitbodies: CD117, CD304(Neuropilin-1), CD254 (RANKL), CD336 (NKp44), CD196(CCR6), CD34, CD7, CD127(IL-7Rα), CD1a, CD5, CD3(SK7), CD4, CD8a, TCRα/β, TCRγ/δ, CD183(CXCR3), CD94, NKp80, CD335(NKp46), CD294(CRTH2), CD278(ICOS), HLA-DR, integrinβ7, CD49d (a4), CD19, CD161, CD2, KLRG1, CD56, CD16, Siglec-7, KIR2DL1, KIR2DL2, KIR3DL1. Cells were individually hashtaged per donor and per condition.

first: Daniela

last: Hernandez

first: Kerstin

last: Juelke

first: Müller

last: Nils

first: Bilge

last: Ugursu

first: Mir-Farzin

last: Mashreghi

first: Timo

last: Rückert

first: Chiara

last: Romagnani


title: Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability [HiC]

overall_design: Our above analysis suggested that hubs can be critical for maintaining the chromatin structure. Deletion of a hub may have a global impact that can propagate through the 3D genome to alter chromatin organization and thus gene expression in the distal genomic regions. One hub loci in K-562 cell line was deleted with CRISPR/Cas9. And their overall chromatin organization in distal genomic regions were compared with non-modified parental cells.

first: Zhao

last: Chen


title: Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability [bulk RNA-seq]

summary: In this study, we performed network analysis on Hi-C data and identified a group of non-coding regions forming many 3D contacts (referred to as hubs). Through a high-throughput CRISPR-Cas9 library screening by targeted deletion, we discovered that some hubs without any epigenetic marks were essential for cell growth and survival. Hi-C and single cell transcriptomic analyses showed that their deletion could significantly alter chromatin organization and impact the distal genes expression. This study revealed the 3D structural importance of non-coding loci that are not associated with any functional element, providing a new mechanistic understanding of disease-associated genetic variations. Furthermore, our analyses also suggest a powerful approach to develop "one-drug-multiple-targets" therapeutics targeting disease-specific non-coding regions.

overall_design: Examination of the mRNA profiles of K562 cells infected with pgRNA targeting AAVS1 locus


title: Memory-like natural killer cells facilitate effector functions of daratumumab in multiple myeloma

status: Public on Aug 01 2021

city: Seoul

first: Kyung Hwan

last: Kim

address: 50-1 Yonsei-ro

institute: Yonsei University College of Medicine

summary: Natural killer (NK) cells support the anti-myeloma activity of daratumumab via antibody-dependent cellular cytotoxicity (ADCC) in multiple myeloma (MM). However, the different roles of heterogeneous NK cell subpopulations have not been elucidated in MM. Here, we delineate memory-like NK cells in the bone marrow (BM) of newly diagnosed MM (NDMM) patients using single-cell RNA sequencing, and further characterize their distinct immunophenotypic features and functions by multicolor flow cytometry. Memory-like NK cells exert robust daratumumab-mediated effector functions ex vivo, including cytokine production and degranulation, compared to conventional NK cells. The composition of memory-like NK cells in BM determines the daratumumab-mediated ex vivo functional activity of BM NK cells in NDMM patients. Unlike conventional NK cells, sorted memory-like NK cells from the BM of NDMM patients exert substantial cytotoxic activity against myeloma cells in the presence of daratumumab. Our findings indicate that memory-like NK cells are an important mediator of daratumumab-dependent effector functions in MM and support direct future efforts to better predict and improve the clinical efficacy of therapeutic antibodies by selectively employing memory-like NK cells.

overall_design: NK cells sorted from 3 MM patients' bone marrow, no replicates

first: Hyunsoo

last: Cho

first: Kyung

first: Eui-Cheol

last: Shin

first: Jin


title: Human Apoe3 and Apoe4 alleles have differential effects on mouse olfactory epithelium

status: Public on Jul 30 2021

city: Lexington

first: Timothy

last: McClintock

state: Kentucky

address: 800 Rose street

department: Department of Physiology

institute: University of Kentucky

summary: Alzheimer’s Disease (AD) is a progressive age-dependent disorder whose risk is determined in large part by genetic factors. We investigated the effects of human APOE3 and APOE4 alleles on the mouse olfactory epithelium.

overall_design: Six biological replicates of Apoe4 and four biological replicates of Apoe3 were analyzed at six months aged mice

first: Naazneen

last: Khan


title: Transcriptomic data of downregulated chaperone-mediated autophagy in glioma stem cell activity.

status: Public on Aug 11 2021

city: Donostia

first: Jaione

last: Auzmendi

address: Paseo Dr. Beguiristain s/n

country: Spain

institute: IIS Biodonostia

summary: We studied the transcriptomic changes induced by downregulating LAMP2A, key mediator of chaperone-mediated autophagy, in patient-derived glioma stem cells. Overall, 1299 transcripts were significantly downregulated, whereas 1673 appeared to be upregulated. KEGG pathway analysis highlighted PI3K-AKT and p53 signaling and pathways associated with ECM interactions, actin cytoskeleton and focal adhesion as the main altered pathways.

overall_design: Examination of transcriptomic changes induced by chaperone-mediated autophagy downregulation in patient-derived glioma stem cells.

first: A

last: Matheu

first: J

last: Auzmendi-Iriarte


title: RNA-Seq of innate lymphoid cells generated in vitro from umbilical cord blood derived CD34+ hematopoietic progenitors.

first: Pawel

last: Durek

summary: Innate lymphoid cells (ILCs) were generated in vitro from CD34+ hematopoietic progenitors derived from umbilical cord blood, and RNA sequencing was performed on the ILC subsets generated to assess global phenotype and compare lineage signatures with each other and to those from ex vivo isolated ILCs.

overall_design: ILCs were generated and cultured in vitro for 30 days, as described in the manuscript, prior to sorting based on surface factors and RNA isolation. CD94+ NK/ILC1 and ILC3 were isolated from the condition of OP9+IL-15, CD94+ NK/ILC1 and CD94- NK/ILC1 were isolated from the condition DL1+IL-15, and CD5- and CD5+ ILC2 were isolated from the condition DL1. A CD161- CD5+ population from the condition DL1 was isolated as an internal, non-ILC, control. From 4 independent donors, 7 populations were sequenced. From 1 independent donor 4 populations were sequenced. Total of 32 samples.

first: Daniela

first: Kerstin

first: Nils

last: Müller


title: RNA seq of the retina and optic nerve from goats 1 day after pre-chiasmatic optic nerve crush injury

status: Public on Aug 19 2021

city: Wenzhou City

first: Yu

last: Zhonghao

state: Zhejiang Province, China

address: 270 Xueyuan West Road

institute: The Eye Hospital, School of Ophthalmology & Optometry

summary: Transcriptomic changes in the pre-chiasmatic optic nerve, retrobulbar optic nerve and retina of goats 1 day after optic nerve crush injury

overall_design: optic nerve and retinal mRNA profiles of injured and uninjured site

first: Zhonghao

last: Yu

first: Lanfang

last: Sun

first: Yikui

last: Zhang

first: Tian

last: Xia

first: Shengjian

last: Lu

first: Mengyun

last: Li


title: Functional and Structural Segregation of Overlapping Helices in HIV-1

status: Public on Jul 15 2021

city: San Francisco

first: Jason

last: Fernandes

address: 600 16th Street, Genentech Hall, Room S574, MC 2280

institute: UCSF

summary: We report deep mutational scanning data for the Env protein's LLP-2 domain in the  NL4-3 strain HIV-1 Env.  Processed Data repersents counts for each amino acid pre and post spread

overall_design: Each fastq file represents either a pre or post-selection virus in which a single codon of the Env LLP-2 has been randomized to NNN.  Pre-selection (Inputs) are roughly randomly spread out amongst all 64 codons, while post selection viruses represent only amino acids that are viable in a spreading assay.

middle: D


title: Resitant populations to photodynamic therapy (PDT) of squamous cell carcinoma cells (SCC-13)

status: Public on Jul 21 2021

city: Madrid

first: Marta

last: Mascaraque-Checa

state: Madrid (ES)

address: C/Darwin nº2

institute: Universidad Autónoma de Madrid

summary: aCGH of control cells not subjected to PDT (Parental), cells subjected to 10 sequential PDT treatments (10G) and 10G cells inoculated in immunosuppressed mice; the induced tumors were subcultured by explants to obtain a cell resistant population called 10GT

overall_design: Three-condition experiment, cultures of SCC-13 cells not subjected to PDT (Parental) vs 10G generations and 10GT generation of resistant cells.

first: Juarranz

last: Ángeles

first: Gilaberte

last: Yolanda


title: STAMPScreen: An Integrated Pipeline for Mammalian Genetic Screening

status: Public on Aug 14 2021

city: BOSTON

first: George

last: Church

address: CLS, 528/7A, 3 Blackfan Cir.

institute: Harvard Medical School

summary: With the recent advancements in genome editing, next generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop novel algorithms for target identi fication and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for Sequencing-based Target Ascertainment and Modular Perturbation Screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.

overall_design: 4 independent biological samples are analyzed. GFP or ZGLP1 was induced via docycyline in female hiPSCs in biological duplicates. GFP is used as a control for ZGLP1 induction.

first: Christian

last: Kramme

first: Alexandru

last: Plesa

first: Helen

last: Wang

first: Bennett

last: Wolf

first: Merrick

last: Smela

first: Xiaoge

last: Guo

first: Richie

middle: E

last: Kohman

first: Pranam

last: Chatterjee


title: Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disease that impacts nearly 400 million people worldwide. The accumulation of Amyloid beta (Aβ) in the brain has historically been associated with AD, and recent evidence suggests that neuroinflammation plays a central role in its origin and progression. The combination of these observations has led to the proposal of Aβ as the main trigger to induce the proinflammatory activation of immune brain cells that culminates in neuronal damage and cognitive decline. In order to test this hypothesis, many in vitro systems have been established to study Aβ-mediated activation of innate immune cells. Nevertheless, the resemblance of these models to the AD brain has never been comprehensively studied on a genome-wide scale. To address this, we used bulk RNA-seq to assess the transcriptional differences between in vitro cell types used to model AD and its similarities to primary brain immune cells. We then analysed the transcriptional response of different innate immune cells to synthetic Aβ.  We found that human induced pluripotent stem cell (hIPSC)-derived microglia (IMGL) is the in vitro cell model that best resembles primary microglia, but surprisingly, synthetic Aβ does not trigger a robust transcriptional response in any of the cellular models analysed, even when different formulations and concentrations of Aβ were employed. Finally we found that the alternative use of bacterial LPS and INF𝛄 to activate the inflammasome in microglia, induces the transcription of genes that are also elevated in disease associated microglia present in the AD brain suggesting the suitability of this model to study AD-related neuroinflammation.

overall_design: This study features seven different cell types that were treated with various combinations of PBS (control for each treatment), Aβ (in various forms and concentrations), and a combination of LPS and IFN-gamma, with or without 10% FBS, prior to RNA extraction. There are 74 samples in total (37 unique conditions, 2 biological replicates each). Experiments were conducted across 10 days (experiment number).

first: Yoseli

last: Quiroga

first: Eden

last: Cruikshank

first: Marielle

last: Bond

first: Baggio

last: Evangelista

first: Jui-Heng

last: Tseng

first: Rick

last: Meeker

first: Joey

last: Ragusa

first: Sarah

last: Cohen

first: Todd

first: Douglas

last: Phanstiel


title: The RNA m6A binding protein YTHDF2 promotes the B cell to plasma cell transition

status: Public on Jul 13 2021

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

type: Methylation profiling by high throughput sequencing

summary: The B cell to plasma cell transition relies on the coordinated remodelling of the gene expression program. We performed a CRISPR/Cas9 knockout screen of RNA binding proteins to identify post-transcriptional regulation of gene expression during the B cell terminal differentiation. The m6A binding protein YTHDF2 was identified as promoting B cell terminal differentiation. In the absence of YTHDF2 the germinal centre reaction is broadly intact, however, plasma cells fail to accumulate. YTHDF2 has previously been shown to mediate RNA decay through the recruitment of the CCR4-NOT deadenylase machinery. Furthermore, our genetic screen in B cells identified that other CCR4-NOT recruitment factors inhibit rather than promote differentiation. Thus, the CCR4-NOT complex coordinates competing regulatory pathways of B cell differentiation at the post-transcriptional level.

overall_design: m6A-eCLIP libraries were generated from two biological replicates in B cells after 8 days of iGB culture. Libraries from the input RNA were also generated for each of the replicates. For CRISPR screens, an sgRNA library targeting RNA binding proteins was transduced at day 3 in iGB culture. Screens were performed to assess proliferation/survival (guide representation at day 8 compared with day 4 in bulk B cells, 1 biological replicate each), and differentiation (guide representation in CD138+ compared with CD138- cells at day 8, 2 biological replicates each).

first: David

middle: J

last: Turner

first: Martin


title: Targeting the N-terminus of the androgen receptor for prostate cancer therapy

status: Public on Jul 01 2021

city: Boston

first: Irene

last: Lee

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: All current clinically approved androgen deprivation therapies for prostate cancer (PCa) target the C-terminal ligand-binding domain (LBD) of the androgen receptor (AR), although the N-terminal domain (NTD) is the main regulator of AR activity. Targeting the AR NTD directly is a challenge because of its intrinsic disordered nature and the lack of secondary structure and clefts for drugs to bind. Here, we make use of the cochaperone BAG1L that functions through the NTD to develop alternative AR inhibitors. We show that BAG1L binds to a short alpha-helical region of the AR NTD and regulates AR dynamics and the expression of AR target genes. We further show that disruption of the BAG1L-AR NTD action by a small molecule 2-(4-fluorophenyl)-5-(trifluoromethyl)-1,3-benzothiazole (A4B17) downregulates AR target gene expression and blocks proliferation of AR-positive PCa cells. Targeting a cochaperone as a surrogate to the AR NTD is therefore key to developing novel AR antagonists.

overall_design: LNCaP cells treated with either Vehicle Control, DHT, A4B17, or A4B17+DHT.

first: Valeria

last: Solozobova

first: Nane

last: Kuznik

first: Myles

last: Brown

first: Andrew

last: Cato


title: Transcriptomic analysis of in vitro induced germinal centre-like B cells and plasmablast differentiation

status: Public on Jul 12 2021

summary: To elucidate molecular mechanisms that regulate the terminal differentiation of B cells into plasmablasts, we analysed how the B cell transcriptome changes during an in vitro culture system that mimics the germinal centre response (known as iGB culture). By culturing B cells on feeder cells expressing CD40L and B-cell activating factor BAFF in the presence of interleukin 4 and interleukin 21, this system allows class switch recombination to IgG1-producing cells and formation of CD138+ TACI+ B220low CD19int/low plasmablasts.

overall_design: B220high CD138- and B220low CD138+ cells were FACS sorted from splenic mouse B cells that were cultured for 8 days in iGB conditions (n= 3 biological replicates)

first: Fiamma

last: Salerno

middle: S


title: ChIP sequencing for Endothelial cells and Magnesium-based alloy treated Endothelial cells

status: Public on Jul 08 2021

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: ChIP-seq analysis identifies that YAP directly binds to the promoter of inflammatory genes, inflammation-related transcription factors and co-transcription factors to induce their high expression in ECs.

overall_design: Examination of YAP transcriptonal function

first: Hongchi

first: Rifang

last: Luo


title: Microarray expression profiling of circular RNAs in human esophageal carcinoma

city: Guangzhou

first: Xiaohua

last: Chen

state: Guangdong

address: Fuyudong Road 8，Qiaonan street，Panyu

institute: Panyu Central Hospital

summary: Using the highly sensitive microarray, 102 circRNAs and 67 circRNAs significantly upregulated and downregulated, respectively, were distinguished by Arraystar platform, in esophageal carcinoma (EC) tumors relative to adjacent normal tissue. Hsa_circRNA_401955 showed the most connection, thus regarded as the hub gene. Hsa_circRNA_100375 and its four connected MREs axis played a key role in the cancer related pathway of EC. CircRNA dysregulation may be involved in the tumorigenesis of EC and certain circRNAs may become new biomarker and therapeutic target for EC.

overall_design: To characterize different expressed of circRNA in esophageal carcinoma, ten samples including five tumor tissues and five matched normal adjacent tissues from patients were detected by microarray.

first: Xiao

first: Si

middle: N

last: Cai


title: Transcriptome sequencing wide functional analysis of human hepatocellular carcinoma in response to BRD4 inhibition

status: Public on Jun 09 2021

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

summary: We investigated that differentially expressed genes (DEG) targeted by BET inhibitors, JQ1 and OTX-015 in HCC cells using RNA sequencing. These DEGs are involved in HCC cells migration, of which SMARCA4 inhibition is effective in suppressing HCC cell migration.

overall_design: The gene expression profile was performed with control HepG2 (Con), JQ1-treated HepG2 (JQ1), OTX-015-treated HepG2 (OTX). Samples were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Chai

last: Young Gyu


title: Differences in renal cortex transcriptional profiling of wild-type and novel type B cystinuria model rats

status: Public on Jun 26 2021

city: Shanghai

first: zihan

last: zhang

address: No. 1665, Kongjiang Road

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

summary: Cystinuria is a genetic disorder of cystine transport that accounts for 1–2% of all cases of renal lithiasis. It is characterized by hyperexcretion of cystine in urine and recurrent cystine lithiasis. Defective transport of cystine into epithelial cells of renal tubules occurs because of mutations of the transport heterodimer, including protein b0,+AT (encoded by SLC7A9) and rBAT (encoded by SLC3A1) linked through a covalent disulfide bond. Study generated a novel type B cystinuria rat model by artificially deleting 7bp of Slc7a9 gene exon 3 using the CRISPR-Cas9 system, and those Slc7a9-deficient rats were proved to be similar with cystinuria in terms of genome, transcriptome, translation, and biologic phenotypes and typical secondary changes as medullary fibrosis. Study then established the first transcription database of type B cystinuria based on this novel cystinuria rat model. In accordance with the functional annotation of DEGs, the potential role of glutathione metabolism processes in kidney of cystinuria rat model was proposed, and KEGG analysis results showed that knock-out of Slc7a9 gene triggered more biological changes which has not been study. This rat model and its transcriptional database that mimics the pathogenesis and clinical consequences of human type B cystinuria was generated for a better understanding of pathophysiological mechanism underlying in cystinuria that can be used to provide references when looking for new target and strategies for reducing kidney damage of cystinuria patients.

overall_design: 6 samples of renal cortex tisue were divided into two groups: Slc7a9 deficient group (KO) and control group (SD), with 3 replicates in each group.

first: Zihan

last: Zhang

first: Rui

last: Zheng

first: Zhoutong

first: Xia

last: Zhan

first: Xiaoliang

last: Fang

first: Meizhen

last: Liu

first: Yongmei

last: Li

first: Dali

first: Yonghu

last: Xu

first: Hongquan

last: Geng

first: Xiaohui

first: Guofeng


title: The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [MNase-seq]

status: Public on Jun 08 2021

first: Jianing

last: Wang

address: Dongchuan Road

institute: Shanghai JiaoTong University

summary: Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. To investigate the relationship of stably high methylation sites with gene expression, we cultured the ARPE-19 for lasting 10 generations and performed reduced representation bisulfite sequencing (RRBS) to obtain the highly methylated sites. Then we analyzed the characters of highly methylated sites and detected the transcription level of the cells. After filtered the low methylated CpG island (CGI), we found that highly methylated CpG sites had a preference for CGI boundary. In the promoter CGI, only in the condition as the gene expression is inhibited and the promoter CGI is at a high methylation level, a significant enrichment of the highly methylated sites is observed in the promoter CGI boundary. Our results showed that the enrichment of high methylation sites at the boundary of the CGI in the promoter region would have a significant inhibitory effect on the gene expression. In summary, we provide new insights into the regulatory mechanisms of DNA methylation.

overall_design: MNase-seq was used to detect the nucleosome occupancy.

first: Yulan

last: Qin

first: Yani

last: Kang

first: Daniel

last: Czajkowsky

first: Hua

first: Zhifeng

last: Shao


title: Transcriptional responses of Tanreqing treated Staphylococcus aureus cells

status: Public on Jun 07 2021

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Analysis of Staphylococcus aureus  treated by Tanreqing. Staphylococcus aureus cells are evaluated with RNA-seq to understand the genes affected by this antibacterial agent. Our results provide new vision on the mode of action by Tanreqing.

overall_design: We used three Staphylococcus aureus replicates and three Tanreqing (TRQ)-treated Staphylococcus aureus replicates to compare the differential gene expression.

first: Yi


title: RNA profiling of IRF7 knockout acute myeloid leukemia (AML) cells

status: Public on Jun 30 2021

city: Tianjin

first: Hao

state: Tianjin

address: 288 nanjing Road

institute: institute of blood

summary: Acute myeloid leukemia (AML) is an aggressive hematopoietic malignant. In our study, we found that knockout of IRF7 in AML cells accelerates the  AML progression and shorten the mice survival, which is medicated by LSC level. The goals of this study aim to reveal the mechanism mediated by IRF7 knockout, we performed the RNAseq profiling of WT c-kit-, WT c-kit+ and IRF7-/- c-kit+ AML cells

overall_design: c-kit+ cells were isolated from AML-WT  and AML-IRF7-/- mice. c-kit- cells were isolated from AML-WT mice. mRNA profiles of these cells were generated by RNA sequencing.

first: GuoGuang

first: DongYue

first: Yibo

last: Dai