title: A novel interplay between triglycerides and acute promyelocytic leukemia mediated by the cooperation between PPARα and PML/RARα. [RNA-Seq]

summary: Patients with newly diagnosed acute promyelocytic leukemia (APL) are often obese or overweight, accompanied by metabolic disorders, such as dyslipidemia. However, the link between dyslipidemia and leukemia development is obscure. Here, we conducted a retrospective study containing 1,412 medical records (319 APL, 393 non-APL acute myeloid leukemia (AML), and 700 non-tumor controls) and found that APL patients had higher triglyceride levels than non-APL AML and non-tumor controls. We revealed that triglyceride served as a risk factor of early death in APL patients, and there was a positive correlation between high triglyceride levels and high leukocyte counts. RNA-seq analysis on APL patients with high or normal triglyceride levels brought attention to peroxisome proliferator-activated receptor-alpha (PPARα) signaling, a crucial regulator of cell metabolism and a transcription factor involved in cancer development. We demonstrated that PPARα knockdown inhibited the proliferation of APL cells. Chromatin mapping data analysis with CUT&Tag revealed that PPARα coexisted with PML/RARα within the super-enhancer regions to maintain APL. Interventions to PPARα affected the transcription and protein level of FLT3. Moreover, in vivo results in mice having high-fat diet-induced high triglyceride levels supported the connection between high triglyceride levels and the leukemia burden, as well as the involvement of PPARα-mediated-FLT3 activation in the proliferation of APL cells. Our findings shed light on the association between APL cell proliferation and high triglyceride levels and established the contribution of an hyperlipidemia–PPARα–FLT3 axis to APL development.

overall_design:
RNA-seq of bone marrow samples isolated from 20 APL patients with normal triglyceride levels and 20 APL patients with high triglyceride levels.
Law restrictions prohibit submitters from publicly sharing raw sequencing data of patient samples, which however can be made available upon reasonable request and permission of the local ethics committee.

first: Shishuang

last: Wu

first: Kankan


title: The METTL3 RNA methyltransferase regulates gene expression in castrate resistant LNCaP:C42 prostate cancer cells

status: Public on Nov 02 2022

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

type: Expression profiling by high throughput sequencing

summary: RNA sequencing was used to determine the effect of the STM2457 METTL3 inhibitor on prostate cancer cell gene expression.

overall_design: Enzalutamide sensitive LNCaP:C42 were treated with vehicle control (DMSO) or STM2457 (10µM) for 48 hours and the effect on basal gene expression and alternative splicing determined using RNA sequencing.

first: Daisy

middle: M

last: Haigh

first: Corinne

middle: L

last: Woodcock

first: Jennifer

last: Lothion-Roy

first: Anna

middle: E

last: Harris

first: Atara

last: Ntekim

first: Jenny

last: Persson

first: Brian

middle: D

last: Robinson

first: Francesca

last: Khani

first: Kristian

middle: B

last: Laursen

first: Lorraine

middle: J

last: Gudas

first: Michael

middle: S

last: Toss

first: Emad

last: Rakha

first: Catrin

last: Rutland

first: Rupert

last: Fray

first: Jennie

middle: N

last: Jeyapalan


title: A novel interplay between triglycerides and acute promyelocytic leukemia mediated by the cooperation between PPARα and PML/RARα. [CUT&Tag]

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

country: China

institute: SHANGH RUIJIN HOSPITAL

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&Tag of PPARα and PML/RARA in NB4 cells.

first: Shishuang

last: Wu

first: Kankan

last: Wang


title: The METTL3 RNA methyltransferase regulates gene expression in castrate resistant 22Rv1 prostate cancer cells

first: Nigel

last: Mongan

overall_design: Enzalutamide-resistant 22Rv1 prostate cancer cells were treated with vehcile control (DMSO) or STM2457 (10µM) for 48 hours and basal and androgen regulated gene expression and alternative splicing determined using RNA sequencing.

first: Daisy

last: Haigh

first: Corinne

last: Woodcock


title: Impact of polyherbal formulation (PHF-KP) on transcriptome profiling of chickens

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To delineate the mechanism of action, we have evaluated the influence of PHF-KP on gene expression profiles in chicken.

overall_design: Organism : Gallus gallus, Agilent Chicken Gene Expression  4X44K Array (AMADID: 049081) designed by Genotypic Technology Private Limited, Bangalore

first: Prashanth

last: D'Souza

first: Saravana

last: Kumar


title: Simultaneous perturbation of multiple metabolic pathways by non-essential amino acid restriction is a potent cancer radio-sensitisation strategy

city: Amsterdam

first: Mattia

last: Falcone

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: NKI

summary: Cellular metabolism is an integral component of cellular adaptation to stress, consequently, metabolism plays a pivotal role in the resistance of cancer cells to a range of treatment modalities. Radiotherapy is used to treat approximately half of all cancer patients, however, most are either inherently radioresistant or acquire resistance over time. Effective radiotherapy relies on generating an overwhelming burden of DNA damage which triggers cell death. In response to radiotherapy cancer cells engage antioxidant and DNA repair mechanisms which mitigate and remove DNA damage, facilitating cancer cell survival. Given the reliance of these resistance mechanisms on amino acid metabolism we hypothesised that controlling the availability of the exogenous amino acids serine and glycine would be an effective strategy to radiosensitive cancer cells. Here we show that serine and glycine restriction sensitised a range of cancer cell lines, patient derived organoids and syngeneic mouse tumour models to radiotherapy. Comprehensive metabolomic analysis of central carbon metabolism revealed that amino acid restriction impacted not only glutathione and nucleotide synthesis but had an unexpected impact on the TCA cycle and antagonised a key cellular redox response to radiotherapy mediated by reductive carboxylation.

overall_design: RNA-Seq profile of 4T1 cells cultured with media containing either serine and glycine (+SG) or not (-SG) and subsequently irradiated with a final dose of radiations 5 Gy (IR) for 24h.

first: Oliver

last: Maddocks

first: Vasileios

last: Papalazarou


title: RUNX2 and MTA1 sequencing in non-treated  MDA-MB-231 cells

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: Runt-related-transcription factor 2 (RUNX2) is an osteogenesis related transcription and emerge as a prominent activating transcription factor in carcinogenesis. MTA1 is one of members of nucleosome remodeling and deacetylase (NuRD) complex， which exhibit important function in processes of transcription, carcinogenesis, cell cycle progression and genomic stability attributed to histone deacetylation.

overall_design: Examination of RUNX2 and MTA1 target genes in MDA-MB-231 cell line.

first: Xin

last: Yin

first: Yan


title: RUNX2 inhibits metastasis of breast cancer

summary: RNA-seq analysis was performed to identify key signaling responding to RUNX2 knockdown in MDA-MB-231

overall_design: six independent sample groups were exposed to siRUNX and controls for 48 h in MDA-MB-231 and were analyzed through RNA-seq.


title: Involvement of different plant viruses in the activation of RNA silencing-related genes and the defensive response against Plum pox virus of ‘GF305’ peach (Prunus persica) grafted with ‘Garrigues’ almond (P. dulcis)

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

type: Non-coding RNA profiling by high throughput sequencing

summary: Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. A recent study tried to identify genes responsible for this effect by studying mRNA expression through RNAseq data in peach and almond plants, before and after grafting, and before and after PPV infection. In this work, we used the same peach and almond samples, but focused the high-throughput analyses on small RNAs (sRNAs) expression. We studied massive sequencing data and found an interesting pattern of sRNAs overexpression linked to antiviral defense genes that suggested activation of these genes followed by downregulation to basal levels. We also discovered that ‘Garrigues’ almond plants were infected by different plant viruses that were transferred to peach plants. The large amounts of viral sRNAs found in grafted peaches indicated a strong RNA silencing antiviral response and led us to postulate that these plant viruses could be collaborating by cross-protection in the observed ‘Garrigues’ effect.

sample_organism:
Prunus dulcis
Prunus persica

platform_organism:
Prunus dulcis
Prunus persica

overall_design: small RNAs from seven plant samples (‘GF305’ peach (A), PPV-infected ‘GF305’ peach (B), ‘GF305’ peach grafted with ‘Garrigues’ almond (C and F), PPV-infected ‘GF305’ peach grafted with ‘Garrigues’ almond (D and G) and ‘GF305’ peach grafted with ‘Garrigues’ almond and then inoculated with PPV (E)) were sequenced with Illumina technology. No replicates were performed.

first: Bernardo

last: Rodamilans

middle: C

first: David

last: San León

first: Pedro

last: Martínez-García

last: Martínez-Gómez

middle: A

last: García

first: Manuel

last: Rubio


title: Bacterial infection disrupts established germinal center reactions through monocyte recruitment and impaired metabolic adaptation

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

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

overall_design: Refer to individual Series


title: Bacterial infection disrupts established germinal center reactions through monocyte recruitment and impaired metabolic adaptation [Single-cell RNA-seq]

summary: Consecutive exposures to different pathogens are very common and often alter host immune responses. Yet, it remains unknown how a secondary bacterial infection interferes with an ongoing adaptive immune response elicited against primary invading pathogens. Here, we demonstrate that pre-existing germinal center (GC) B cells are incapable of enduring radical metabolic changes induced by recruited Sca-1+ monocytes during Salmonella Typhimurium (STm) infection. GCs-induced by influenza, plasmodium and commensals deteriorated upon STm infection. GC collapse was independent of direct bacterial interactions with B cells, but rather, was induced through recruitment of CCR2-dependent Sca-1+ monocytes. GC collapse was dependent on non-B cell TLR-4, TNFα and IFNγ, which was essential for Sca-1+ monocyte differentiation in the bone-marrow. Monocyte recruitment and GC disruption also occurred during LPS-supplemented vaccination and Listeria monocytogenes infection. Thus, systemic activation of the innate immune response upon lethal bacterial infection is induced at the expense of antibody-mediated immunity.

overall_design: sc-RNA-seq of Peyer's patches cells after Salmonella infection

first: Adi

last: Biram


title: Bacterial infection disrupts established germinal center reactions through monocyte recruitment and impaired metabolic adaptation [Bulk RNA-seq]

overall_design: RNA-seq of GC B cells, monocytes and total tissue extract from Peyer's patches, 3 days after Salmonella infection


title: Whole genome methylation profiliing between the IMU and KRT subtypes of HPV-associated head and neck cell carcinoma (HNSCC)

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

country: USA

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: We compared the whole-genome methylation profiles between IMU and KRT samples in a 36 HNSCC cohort and identified 270,326 differentially methylated regions (DMRs; FDR < 0.05 and absolute methylation difference >= 20%) between IMU and KRT HPV(+) subtypes.

overall_design:
WGBS was performed on 36 HNSCC samples (the same cohort in GSE74956), and the differential methylated regions were identified between IMU (n=8) and KRT (n=10) HPV(+) HNSCC samples.

The file IDmapping.csv, available at the foot of this record, provides the titles of the corresponding samples between GSE74956 and this series.

first: Tingting

last: Qin

first: Raymond

last: Cavalcante


title: Transcriptome analysis of gene expression divergence in BBX11 mutation in red light

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: phytochrome B (phyB) acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4 (PIF4) through a direct physical interaction, which in turn changes the expression of a large number of genes. phyB-PIF4 module regulates a variety of biological and developmental processes in plants. In this study, we demonstrate that B-BOX PROTEIN 11 (BBX11) physically interacts with both phyB and PIF4. BBX11 negatively regulates PIF4 accumulation as well as its biochemical activity, consequently leading to the repression of PIF4-controlled genes' expression and promotion of photomorphogenesis in the prolonged red light. This study reveals a regulatory mechanism that mediates red light signal transduction and sheds a light on phyB-PIF4 module in promoting red light-dependent photomorphognenesis.

overall_design: Col-0, bbx11-1 and pif4-2 mutant seedlings were grown in constant red (94 μmol/m2/s) light for 4 d. The samples were harvested and used to isolate total RNA with an RNeasy Plant Mini Kit (Qiagen).

first: Dongqing

last: Xu


title: Blockade of Wnt secretion by LGK974 after ischemia reperfusion injury

city: Heidelberg

first: Sören

last: Meyer

address: Im Neuenheimer Feld 669

country: Germany

institute: University Hospital Heidelberg

summary: The LAD of C57BL6 mice were temporally occluded to induce ischemia-reperfusion injury of the heart. Mice received a daily dose of the porcupine inhibitor LGK974 starting directly after the surgery to prevent Wnt protein secretion. Control animals received a DMSO vehicle control. Hearts were extracted 48h after induction of ischemia-reperfusion injury. The infarcted area was identified and processed for RNAseq analysis.

overall_design: In this study, three animals received the Porcupine inhibitor LGK974. Three animals received a DMSO vehicle control.

first: I

first: Xue

last: Li

first: Carina

first: Hugo

last: Katus

first: Norbert

last: Frey

first: Florian

last: Leuschner


title: Postnatal Conditional Knockout of Bcl11b in Striatal Projection Neurons Mimics the Transcriptional Signature of Huntington’s Disease

city: Novato

first: Lisa

last: Ellerby

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Dysregulation of the striatum is linked to multiple diseases including Huntington’s (HD), Parkinson’s, X-linked dystonia-parkinsonism (XDP), addiction, autism, and schizophrenia. Striatal medium spiny neurons (MSNs) make up 90% of the neuronal cell type in the striatum and are critical to motor control. The transcription factor Bcl11b (also known as CTIP2) is known to regulate of MSN differentiation, striatal striosome (patch) development and the architecture of the striatum during development. However, the function of Bcl11b adult striatal neurons in vivo has not been investigated. Therefore, we conditionally knocked out Bcl11b specifically in MSNs using D9-cre under the control of a regulatory elements of the mouse Ppp1r1b gene encoding DARPP-32 resulting in knockout around 5-6 weeks of age. Transcriptomic and behavioral analysis were performed on these mice.

overall_design: RNA-Seq analysis of the mouse straitum of 4 D9-Cre-Bcl11b tm1.1 Lead mice and Cre- mice have reduced expression of Bcl11b in the straitum at 4 months of age.

first: Sean

last: Mooney

first: Michelle

last: Ehrlich

first: Sicheng

last: Song

first: Jordi

last: Muncunill

first: Carlos

middle: G

last: Aguirre

first: Kizito-Tshitoko

last: Tshilenge


title: Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea infection

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

summary: Next generation sequencing (NGS) was performed to identify genes changed in ginseng upon Botrytis cinerea infection. The goal of the work is to find interesting genes involved in medical plant in response to fungi infection. The object is to reveal the molecular mechanism of medical plant defense.

overall_design: mRNA profiling of ginseng plants in response to Botrytis cinerea infection.


title: Comparative genomic analysis focused on early and intermediate phases of cellular reprogramming

city: Daejeon

first: Jeongmin

last: Ha

address: 125, Gwahak-ro, Yuseong-gu

department: Stem Cell Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Mechanistic interpretation of the reprogramming process is still remained elusive. Thus, we compared two reprogramming processes, pluripotent cell-specific factor-mediated direct reprogramming (PDR) and induced pluripotent stem cells reprogramming (iPSCR), to figure out how and when these processes are bifurcated from each other during the reprogramming. Until day 6, all samples showed a similar pattern of gene expression, but the pattern has changed dramatically after day 6 regardless of dox-induction or specific cues for cell fate determination. These suggest that the process of PDR also can be divided into two stages, early and late. We assume that around day 6 is intermediate stage which is not clearly defined but to be epigenetically flexible as in iPSCR. When we focused on the increased genes during early phase of reprogramming, we found these genes could be divided into five distinct groups by the expression pattern during whole reprogramming process.  Interestingly, one of the groups showed exclusively up-regulated pattern on day 4 or 6 but down-regulated afterwards in all analyzed samples. Thus, we assumed that this group of genes are highly related to the cells in intermediate stage (IC). Gene Ontology analysis shows that these IC-genes are majorly involved in epidermis development and retinoic acid metabolism. We expect that study on the roles of these genes provides mechanistic understanding of the early and intermediate stages of cellular reprogramming.

overall_design: Time series design with samples during iPSCR and PDR of 2'MEF and 4F2A MEF

first: Beomseok

last: Kim

first: Byungkuk

last: Min

first: Juhyeon

last: Nam

first: Jae-Geun

last: Lee

first: Minhyung

first: Byoung-Ha

last: Yoon

first: Ilkyun

last: Im

first: Jung

last: Park

first: Hyosun

last: Choi

first: Areum

last: Baek

first: Sang

last: Cho

first: Mi-Ok

first: Ki-Hoan

first: Ji

middle: Y

last: Mun

first: Mirang

first: Mi

last: Son

first: Yong-Kook

last: Kang

first: Jeong-Soo

first: Jong

middle: K

first: Janghwan


title: Pioneering function of Yap and Taz in promoting osteogenesis of neural crest cells by preventing chondrogenesis

city: Houston

first: Jun

last: Wang

state: TX

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: Neural crest cells (NCCs) are multipotent stem cells with a remarkable ability to differentiate into multiple cell lineages, including osteoblasts and chondrocytes. NCCs contribute to the majority of craniofacial skeleton, yet the molecular mechanisms regulating NCCs diversification into osteoblasts or chondrocytes remain poorly understood. We found that Yap and Taz function redundantly as key determinants of the osteogenesis versus chondrogenesis fate decision and differentiation in NCCs in vitro, ex vivo and in vivo, and Yap/Taz-deficiency in NCCs resulted in a switch from osteogenesis to chondrogenesis. Comprehensive analysis of unbiased datasets including CUT&RUN-seq and RNA-seq indicated that Yap/Taz directly regulate key genes that govern osteogenesis and chondrogenesis. During NCC-derived osteogenesis, Yap/Taz promote expression of osteogenic genes such as Runx2 and Sp7 but repress expression of chondrogenic genes such as Sox9 and Col2a1. Further, we found Yap/Taz directly interact with β-catenin in NCCs to coordinately promote osteoblast differentiation and repress chondrogenesis. Together our data indicate that Yap/Taz promote osteogenesis in NCCs by preventing chondrogenesis, partly through interactions with the Wnt-β-catenin pathway.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design:
1. We performed CUT&RUN in O9-1 neural crest cells using Yap, IGG and H3K27me3 antibodies, followed by sequencing.

2. O9-1 cells were cultured under conditioned basal medium. Then the cells were seperated into 2 group: one group used for Yap/Taz dKD and the other group used as control. For the siRNA-mediated KD of Yap and Taz, O9-1 cells were plated at 50% confluency in the conditioned basal media and transfected with siRNA SMART pools of Yap (Dharmacon, L-046247-01-0005), Taz (Dharmacon, L-041057-01), and nontargeting siRNA (Dharmacon, D-001810-04-05) for 48 h according to the guidelines of the RNAiMAX transfection procedure (Life Technologies, 13778075) and cultured to 80% confluency. Then the cells were harvested and used for CUT&Tag experiment.

first: Xiaolei

last: Zhao

first: Li

last: Tang


title: Transcriptome profile of Escherichia coli K12 MG1655 under Rtc-inducing conditions

city: London

first: Ioly

last: Kotta-Loizou

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

sample_organism: Escherichia coli str. K-12 substr. MG1655


title: Transcriptome profile of Escherichia coli K12 MG1655 Hpx- cells

summary: The aim of the study was to compare the transcriptome of E. coli K12 MG1655 cells lacking hydroperoxidase (Hpx-) and therefore unable to detoxify hydrogen peroxide, to wild-type cells; both when the Rtc RNA repair system is active and when it is inhibited; at 8 and 24 hpi. A very large number of genes (up to 1/3) were found to be differentially expressed in Hpx- as compared to wild-type. Inhibition of the Rtc system had dramatic effects on Hpx- but not on wild-type.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli K12 MG1655 HPX versus wild-type; active versus inactive Rtc RNA repair system; 8 and 24 hpi.


title: Transcriptome profile of Escherichia coli K12 MG1655 cells lacking selected genes

summary: The aim of the study was to compare the transcriptome of E. coli K12 MG1655 cells lacking genes known to induce the Rtc RNA repair system, such as gor, mazF and srmB, to wild-type cells. In all cases, less than 1% of the genes were found to be differentially expressed.

overall_design: E. coli K12 MG1655 mutants versus wild-type.


title: Polysome profiling and RNA-seq of adult mouse neural stem cells (NSCs) treated with 1.5uM, 10uM and 80uM folic acid for 4 days

city: Blacksburg

first: Xiguang

last: Xu

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

summary: We performed polysome profilinga and RNA-seq of adult mouse NSCs treated with 1.5uM, 10uM and 80uM folic acid for 4 days.

overall_design: Polysome profiling and RNA-seq of adult mouse NSCs treated with different concentration of folic acid for 4 days, in biological duplicates.

first: Hehuang

last: Xie


title: RNA bisulfite sequencing of total and polysome RNA from adult mouse neural stem cells (NSCs) treated with 1.5uM, 10uM and 80uM folic acid for 4 days

summary: We performed RNA methylation profiling for adult mouse NSCs treated with 1.5uM, 10uM and 80uM folic acid for 4 days.

overall_design: RNA bisulfite sequencing of total and polysome RNA from adult mouse NSCs treated with 1.5uM, 10uM and 80uM folic acid for 4 days, in biological duplicates.


title: Transcriptomic network of Tulipa gesneriana during petal senescence

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary:
Purpose: We aimed to dissect transcriptomic responses of Tulipa gesneriana during petal senescence and characterize function of senescence related genes.
Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis between each two different stages was performed using the DESeq R package (1.18.0).
Results:In total, 15 samples with three biological replicates per stage combination were used for RNA sequencing analysis. At least 6 G clean bases were generated for each sample. Comparative analysis identified genes involved in flower development and/or fllower senescence.

overall_design: In this study, five stages of a flower including buds, partial blooming, full blooming, early senescence and late senescence are collected individually. The whole flowers with different developmental stages were then used in RNA sequencing.

first: Yanping


title: Differential expression from healthy skin derived melanocyte-keratinocyte co-culture from familial melanoma patients vs controls

city: Barcelona

first: Miriam

last: Potrony

address: Villarroel 170

institute: Hospital Clinic of Barcelona

summary:
Background: Familial melanoma accounts for 10% of cases, withCDKN2A being the main high-risk gene. However, the mechanisms underlying melanomagenesis in individuals at high risk of developing melanoma remain poorly understood.
Objective: To analyze the transcriptome of melanocyte/keratinocyte co-cultures derived from healthy skin from familial melanoma patients vs. controls, to comprehend melanoma development.
Methods: Primary melanocyte-keratinocyte co-cultures were established from healthy skin biopsies from 16 unrelated familial melanoma patients (8 CDKN2A mutant, 8 CDKN2A wild-type) and from 7 healthy controls. Whole transcriptome was captured using the SurePrint G3 Human Microarray. Transcriptome analyses included: differential gene expression, functional enrichment, and protein-protein interaction (PPI) networks.
Results: We identified a gene profile associated with familial melanoma independently of CDKN2A germline status. Functional enrichment analysis of this profile showed a downregulation of pathways related to DNA repair and immune response in familial melanoma (P < 0.05). In addition, the PPI network analysis revealed a network that consisted of double stranded DNA repair genes (including BRCA1, BRCA2, BRIP1, and FANCA), immune response genes and regulation of chromosome segregation. The hub gene was BRCA1.
Conclusion: The constitutive deregulation of BRCA1 pathway genes and immune response in healthy skin could be a mechanism related with melanoma risk.

first: Tariq

last: Haddad

first: Gemma

last: Tell-Martí

first: Pol

last: Gimenez-Xavier

first: Judit

last: Mateu

first: Carlos

last: Leon

first: Marta

last: Pevida

first: Celia

last: Badenas

first: Cristina

last: Carrera

first: Josep

last: Malvehy

first: Paula

last: Aguilera

first: Sara

last: Llames

first: Maria

last: Escamez

first: Joan

last: Puig-Butillé

first: Marcela

last: del Río

first: Susana

last: Puig


title: Next generation sequencing to determine changes in Drosophila Atg6 mutant larval transcriptome

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

summary: Next generation sequencing was performed on third instar Drosophila larvae to determine changes in the transcriptomes of Atg6 heterozygous and Atg6 homozygous animals compared to wild type animals

overall_design: RNA was isolated from Drosophila third instar larvae of the genotypes w118, w118;;Atg6-/+, and w118;;Atg6-/- using Qiagen Rneasy kit. Paired-end next generation RNA sequencing (20 milliion reads at 2 x 75bp PE)  was performed in triplicate for each sample using illumina

first: Johnna

last: Doherty


title: Limited depth in bone defect-combining computational fluid dynamics and genes sequence analysis due to osteogenic effect under negative pressure wound therapy

status: Public on Nov 01 2022

city: Guangzhou

first: Ziling

last: Lin

state: Guangdong

address: No.12 Jichang Road

institute: Guangzhou University of Chinese Medicine

summary: To Validate the effect of different scales of NP on gene expression in BMSCs. The role of NPWT within bone tissue was determined by combining CFD results and gene expression.

overall_design: Comparison of gene expression profiling of RNA-seq data from NP-treated mouse BMSCs with applied pressures of -80 mmHg, -120 mmHg, -160 mmHg and -200 mmHg, respectively.

first: Shaohong

last: Huang

first: Xiuhong

first: Liqin

last: Zheng


title: An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation downstream of TSC2 loss

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

state: MD

address: 1550 ORLEANS

institute: JOHNS HOPKINS MEDICINE

summary: The mechanistic target of rapamycin complex 1 (mTORC1) integrates inputs from growth factors and nutrients, but how mTORC1 autoregulates its activity remains unclear. The MiT/TFE transcription factors are phosphorylated and inactivated by mTORC1 following lysosomal recruitment by RagC/D GTPases in response to amino acid stimulation. We find that starvation-induced lysosomal localization of the RagC/D GAP complex, FLCN:FNIP2, is markedly impaired in a mTORC1-sensitive manner in cells with TSC2 loss, resulting in unexpected TFEB hypophosphorylation and activation upon feeding. TFEB phosphorylation in TSC2-null cells is partially restored by destabilization of the lysosomal folliculin complex (LFC) induced by FLCN mutants and is fully rescued by forced lysosomal localization of the FLCN:FNIP2 dimer. Our data indicate that a negative feedback loop constrains amino acid-induced, FLCN:FNIP2-mediated RagC activity in cells with constitutive mTORC1 signaling, and the resulting MiT/TFE hyperactivation may drive oncogenesis with loss of the TSC2 tumor suppressor.

overall_design: RNAseq profiling of human xenografts with TSC2 KO, TSC2/TFE3 KO, TSC2/TFEB KO, TSC2/TFE3/TFEB KO, and HEK293T WT genotypes. RNAseq of CRISPR-Cas9 TSC1/2 KO and WT HEK293T cells.

first: Kaushal

last: Asrani

first: Juhyung

last: Woo

first: Adrianna

last: Mendes

first: Ethan

last: Schaffer

first: Thiago

last: Vidotto

first: Clarence

middle: R

last: Villanueva

first: Kewen

last: Feng

first: Lia

last: Oliveira

first: Sanjana

last: Murali

first: Hans

last: Liu

first: Daniela

last: Salles

first: Brandon

last: Lam

first: Pedram

last: Argani

first: Tamara

last: Lotan


title: Stress triggers expression of bovine herpesvirus 1 infected cell protein 4 (bICP4) RNA during early stages of reactivation from latency in pharyngeal tonsil

city: Stillwater

first: Clinton

middle: R.

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

summary: Bovine herpesvirus 1 (BoHV-1), an important pathogen of cattle, establishes lifelong latency in sensory neurons within trigeminal ganglia (TG) after acute infection.  The BoHV-1 latency-reactivation cycle, like other -herpesvirinae subfamily members, is essential for viral persistence and transmission.  Notably, cells within pharyngeal tonsil (PT) also support a quiescent or latent BoHV-1 infection.  The synthetic corticosteroid dexamethasone, which mimics the effects of stress, consistently induces BoHV-1 reactivation from latency allowing early stages of viral reactivation to be examined in the natural host.  Based on previous studies, we hypothesized that stress-induced cellular factors trigger expression of key viral transcriptional regulatory genes.  To explore this hypothesis, RNA-sequencing studies compared viral gene expression in PT during early stages of dexamethasone-induced reactivation from latency.  Strikingly, RNA encoding infected cell protein 4 (bICP4), which is translated into an essential viral transcriptional regulatory protein, was detected 30 minutes after dexamethasone treatment.  Ninety minutes after dexamethasone treatment bICP4 and to a lesser extent bICP0 RNA were detected in PT.  All lytic cycle viral transcripts were detected within three hours after dexamethasone treatment.  Surprisingly, the latency related (LR) gene, the only viral gene abundantly expressed in latently infected TG neurons, was not detected in PT during latency.  In TG neurons, bICP0 and the viral tegument protein VP16 are expressed before bICP4 during reactivation suggesting distinct viral regulatory genes mediate reactivation from latency in PT versus TG neurons.  Finally, these studies confirm PT is a biologically relevant site for BoHV-1 latency, reactivation from latency, and virus transmission.

overall_design: We performed RNA-sequencing studies and compared viral gene expression in bovine pharyngeal tonsils (PT) using BoHV-1 latently infected (controls) and BoHV-1  genes in PT reactivated from latency during early timepoints (0-min 30-min, 90-min, 180-min) following dexamethasone treatment (Three biological replicates for each timepoint).  We analyzed simultaneous expression of Bos taurus cellular genes.

first: Gabriela

last: Toomer

first: Aspen

last: Workman

first: Kelly

last: Harrison

first: Erin

last: Stayton

first: Peter

last: Hoyt


title: Fetuin A is an immunomodulator and therapeutic target for Heterotopic ossification and associated bone loss

city: Hefei

first: Chen

last: Kan

address: Meishan Road 81

institute: Anhui Medical University

summary: Heterotopic ossification (HO), the pathologic growth of extra-skeletal bone, occurs as a common complication of trauma or in genetic disorders and can be disabling and lethal.We report that mice harboring injury-induced HO exhibit bone loss similar to the presentation of HO patients. Esepecially, Fetuin A dysregulation promotes immunosupression in HO lesion to link HO and bone loss.

overall_design: Total mRNA profiles of injured tibial muscle from WT and NSE-BMP4 mice at different time points(i.e., at day 1 ,3,7 after muscle injury via cardiotoxin)

first: Jiazhao

last: Yang


title: SnRNA-seq analysis of hippocampus in TAFE3 and TAFE4 mice

city: St. Louis

first: Jason

last: Ulrich

state: MO

address: 660 S Euclid

department: Neurology

institute: Washington University

summary: Tau-mediated neurodegeneration (TN) is a hallmark of Alzheimer's disease. Primary tauopathies are characterized by pathological tau accumulation and neuronal and synaptic loss. Studies have shown that ApoE-mediated neuroinflammation is involved in progression of TN and emerging evidence suggests that the gut microbiota regulates neuroinflammation in an APOE-genotype dependent manner. However, there is no evidence showing a causal link of the microbiota to TN. Therefore, we have characterized a genetically engineered mouse model of tauopathy expressing human ApoE isoforms, reared under germ-free conditions or after perturbation of their gut microbiota with antibiotics. Both these manipulations produced a striking reduction of gliosis, taupathology, and neurodegeneration in a sex- and ApoE isoform-dependent manner. The findings reveal mechanistic and translationally relevant interrelationships between the microbiota, neuroinflammation, and TN."

overall_design: Droplet-based 3? end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5? Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.

first: David

middle: M

last: Holtzman

first: Dong-oh

last: Seo


title: UTX Loss Alters Therapeutic Responses in KMT2A-rearranged Acute Myeloid Leukemia [RNA-seq]

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

summary: Acute myeloid leukemias (AML) patients bearing chromosomal rearrangements of KMT2A or MLL gene (KMT2A -r) have poor overall survival. Recently, compounds targeting the KMT2A fusion protein complex, such as DOT1L and Menin inhibitors, have shown promising pre-clinical efficacy. Yet, molecular regulators of the anti-tumor activities of these agents remain poorly studied. UTX is a histone H3K27 demethylase with recurrent loss-of-function mutations in human cancers including leukemia. UTX-null leukemia shows greater resistance to chemotherapy agents. However, the impact of UTX on drug resistance of KMT2A -r AML has not been explored. Through a epigenetic compound screen, we identified a unique role of UTX in the regulation of DOT1L and Menin therapies in KMT2A-r AML. Loss of UTX confers resistance to DOT1L and Menin inhibition in an MLL target gene-independent manner. Mechanistically, We show that UTX is required for activation of myeloid differentiation programs induced by DOT1L inhibition. We also revealed BCL2A1 as a target of UTX. Depletion of UTX increased vulnerability to BCL2 inhibitor venetoclax in vitro and in vivo, and combinational treatment of venetoclax could overcome the therapeutic resistance to DOT1L inhibition caused by UTX loss. Our study provides new insights into the role of UTX in therapeutic responses in KMT2A-r AML.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for UTX wildtype and UTX knockout in OCI-AML2 cells treated with DMSO or SGC0946.

first: Xinyue

last: Zhou

first: Rui

last: Lu


title: UTX Loss Alters Therapeutic Responses in KMT2A-rearranged Acute Myeloid Leukemia

overall_design: Refer to individual Series


title: Modulation of RNA cytosine-5 methylation by folate in neural stem cells

first: Xiguang

last: Xu

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


title: RNA‐seq of comprehensively examine variations in MHCC-97H cells treated with various doses of lenvatinib at the transcriptomic level.

city: Nantong

first: Cheng

last: Gao

address: 20 Xisi Road

institute: Affiliated Hospital of Nantong University

summary: To determine the drug target of lenvatinib, RNAseq was used to evaluate the transcriptome differences between lenvatinib-treated MHCC-97H cells and their parental counterparts.Results show that  SERPINE1 may be direct target of lenvatinib, and AKR1C1 have potential prognostic significance in the prediction of LR(lenvatinib-resistant) in HCC. AKR1C1 could be a promising therapeutic target for patients with LR-type liver cancer.

overall_design: MHCC-97H cells treated with 40, 60, 80, and 100 μM lenvatinib,  and RNAseq was used to evaluate the transcriptome differences between lenvatinib-treated MHCC-97H cells and their parental counterparts.For more information, please consult 1065152807@qq.com

first: Zhong

last: Chen

first: Tianxin

first: Changliang


title: Bi-allelic SNAPC4 variants lead to altered global splicing and a neurodevelopmental disorder

city: Rockville

first: May Christine

middle: V

last: Malicdan

address: 5625 Fisher's Ln

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: To investigate the transcriptomic effects of deleterious SNAPC4 variants, patient-derived cells and SNAPC4-deficient HeLa cells were used to generate RNA-Seq data.

overall_design:
Four comparisons were made: 1) PolyA-selected data from patient-derived fibroblasts against control fibroblasts,  2) PolyA-selected data from a parental HeLa-Cas9 line against SNAPC4-deficient HeLa cells,
3) small RNA-selected data from patient-derived fibroblasts against control fibroblasts, and  4) small RNA-selected data from a parental HeLa-Cas9 line against SNAPC4-deficient HeLa cells

first: Graeme

last: Frost

first: Marie

last: Morimoto


title: DNA dioxygenases Tet2/3 control epithelial differentiation

city: Boston

first: Andrey

last: Sharov

state: Massachusetts

address: 609 Albany Street

department: Dermatology

institute: Boston University School of Medicine

summary: Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes catalyzing 5-methylcytosine oxidation in DNA. Here, by using Keratin 14-Cre-driven ablation of Tet genes in skin epithelial cells, we demonstrate that ablation of Tet2/Tet3 result in marked alterations of hair shape and length followed by hair loss. We show that through DNA demethylation, Tet2/Tet3 control chromatin accessibility, Dlx3 binding and promoter activity of the Krt25 and Krt28 genes regulating hair shape, as well as regulate interactions between the Krt28 gene promoter and distal enhancer. Moreover, Tet2/Tet3 also control three-dimensional chromatin topology in Keratin type I/II gene loci via DNA methylation-independent mechanisms. These data demonstrate the essential roles for Tet2/3 in establishment of lineage-specific gene expression program and control of Dlx3/Krt25/Krt28 axis in hair follicle epithelial cells and implicate modulation of DNA methylation as a novel approach for hair growth control.

overall_design: Hi-C kit is purchased from Arima and procedure is followed with the manual. 1.3 M sorted cells are fixed with formaldehyde in a final concentration to 2% at room temperature for 10 minutes for DNA crosslinking and quenched with glycine in a final concentration to 300 mM, then suspended in 20 μl of Lysis buffer. Cross-linked DNA of the cells is digested with Arima RE cocktail. The ends of DNA fragments are repaired, then labeled with biotin and re-ligated again. Biotin-labeled DNA is sheared to 300 - 500 bp, and enriched with enrichment beads.

first: Guodong

first: Iqra

last: Fatima

first: Qin

first: Michael

last: Fessing

first: Andrei

last: Mardaryev

first: Elena

last: Rozhkova

first: Guoliang

first: Vladimir

last: Botchkarev


title: Zac1 target genes during mouse tongue and cartilage development

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary:
Here we analyze transcriptome profiles between wild type tongues and tongues harboring Zac biallelic expression.
Here we analyse transcriptome profiles between wild type (Zac1MOI) and Zac1 biallelic expression (Zac1LOM) primary costal chondrocytes.

overall_design:
Transcriptome (RNA-Seq) from E13.5, P0 and P20 tongues, comparison between wild type tongues and Zac1 biallelic expression tongues.
Transcriptome (mRNA-Seq) from E18.5 primary costal chondrocytes, comparison between wild type and Zac1 biallelic expression.

first: Salah

last: Azzi

first: Florence

last: Naillat

first: Sebastien

last: Smallwood

first: Gavin

last: Kelsey


title: The m6A Reader IGF2BP2 Regulates Glutamine Metabolism and Represents a Therapeutic Target in Acute Myeloid Leukemia

first: Hengyou

last: Weng

address: Room 304, Building D, 190 Kaiyuan Ave,

institute: Guangzhou Laboratory


title: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features

city: Chapel Hill

first: Marielle

last: Bond

state: North Carolina

address: 104 Manning Drive Thurston Building Room 4012

department: Genetics Curriculum

institute: UNC Chapel Hill


title: IRX5 promotes DNA damage repair and activation of hair follicle stem cells [NHEK RNA-Seq]

city: Irvine

first: Jefferson

last: Chen

address: UC Irvine

institute: UC Irvine

summary: Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice display delayed onset of first postnatal anagen, with increased DNA damage and diminished HFSC proliferation. Through transcriptomic and epigenetic analysis, we discover the formation of open chromatin regions near key cell cycle progression- and DNA damage repair genes in Irx5-/- HFSC. We also identify DNA damage repair factors BRCA1 and BARD1 as IRX5 downstream targets. Inhibition of FGF18 kinase signaling partially rescues the anagen delay in Irx5-/- mice, indicating that the Irx5-/- HFSC quiescent phenotype is in part due to failure to suppress Fgf18 expression. Our findings identify IRX5 as a required promoter of DNA damage repair in HFSC activation and hair cycle initiation.

overall_design: Normal Human Epidermal Keratinocytes (NHEK) were obtained from donor neonatal foreskin and grown in Keratinocyte Serum Free Media supplemented with Epidermal Growth Factor and Bovine Pituitary Extract (Life Technologies). Individual Dharmacon on-TARGETplus siRNAs [negative control (4390843), IRX2 (s45799, s45801), IRX3 (s35710, s35712), IRX4 (s55542, s27096), IRX5 (s20056, s20054)] were validated and siRNAs with at least 70% knockdown efficiency were pooled. 30nM pooled siRNAs were transfected into semi-confluent monolayers with Lipofectamine RNAi Max (Life Technologies) in OptiMEM medium. Twelve hours after transfection, 1.8mM Ca2+ was added into the growth medium to induce differentiation. RNA lysate was collected 72 hours after transfection.

first: Chen

last: Jefferson

first: Andersen

last: Bogi


title: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features [dataset 2]

summary: 3D chromatin structure is thought to play a critical role in regulating gene transcription during cellular transitions. While our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising 4 biological replicates and 6 billion reads per time point. Statistical analysis revealed 1,503 differential loops. Gained loops were enriched for AP-1 occupancy and correlated with increased expression of genes at their anchors. Lost loops were characterized by increases in expression of genes within the loop boundaries. Linear modeling revealed that changes in histone H3K27 acetylation, chromatin accessibility, and JUN binding in between the loop anchors were often just as predictive of changes in loop strength as changes to CTCF and/or cohesin occupancy at loop anchors. Finally, we built linear models and found that incorporating the dynamics of enhancer acetylation and loop strength increased accuracy of gene expression predictions. Together, our well-powered study has added to our understanding of the mechanisms that regulate looping, and the relationship of looping with gene expression.

overall_design: RNA-seq of K562 cells treated with PMA to differenitate into a megakaryocyte-like state after 0, 0.5, 1.5, 3, 6, 24, 48, or 72h

middle: L

first: I

last: Quiroga

middle: I

last: Love

first: Hyejung

last: Won

first: Douglas

middle: H

last: Phanstiel


title: UTX Loss Alters Therapeutic Responses in KMT2A-rearranged Acute Myeloid Leukemia [ChIP-seq]

first: xinyue

last: zhou

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for UTX and H3K27ac in UTX wildtype and UTX knockout OCI-AML2 cells.

first: Xinyue

last: Zhou

first: Rui

last: Lu


title: Single -Cell RNA Sequencing of the Normal Human Ascending Aortic Tissues from Donors of Different Ages Reveals Significant Age-dependent Changes in the Cellular Composition, Cellular Phenotypes, and Cell-Cell Communication

first: Bin

last: Zhang

address: 107 Yanjiang West Road

department: Department of Cardiovascular Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: The ascending aorta is a common site for age-related aortic diseases. Therefore, age-related changes in the cellular composition and development in the normal human ascending aorta tissue is associated with the pathogenesis of aortic diseases. In this study, we performed single-cell transcriptome sequencing of the normal ascending aorta tissues from 6 organ donors of different ages, namely, the young group (3 months, 1 year, 3 years, and 12 years) and the old group (57 years and 58 years), and evaluated the changes in the composition of the cell types, cellular phenotypes, and the cell-cell communication. The single-cell sequencing data analysis of 65,470 cells from the 6 donor aortic wall specimens identified ten cell types (27 high-resolution subtypes of cells), including endothelial cells, smooth muscle cells, fibroblasts, mesenchymal cells, mesenchymal-fibroblast cells, macrophages, Schwann cells, T cells, natural killer cells, and B cells. In comparison with the young group, the aortic wall tissue of the old group showed significant reduction in the proportion of endothelial cells (young vs. old, 22.47% vs. 10.37%),  smooth muscle cells (20.40% vs. 18.50%), fibroblasts (30.21% vs. 13.29%), and mesenchymal cells (5.12% vs 1.55%) and significant increase in the proportion of  macrophages (10.94% vs. 17.02%) and T cells (3.80% vs. 26.01%). Functional enrichment analysis of the ligand-receptor pairs between the macrophages and the T cells demonstrated enrichment of pathways related to inflammation and endocrine resistance in the elderly group. Immunohistochemical analysis of the aortic tissue from the 58-year-old donor showed  higher expression of the M2 macrophage marker, CD163, in comparison with the aortic tissue of the 12-year-old donor. This confirmed the results of the single-cell sequencing analysis. In summary, single-cell sequencing analysis of the normal ascending aorta tissues from multiple donors of different ages demonstrated significant age-related changes in the proportions of multiple cell types, cellular phenotypes, and cell-cell communications. These age-related changes are likely involved in the pathogenesis of age-related aortic diseases.

overall_design: We performed scRNA sequencing to understand age-related changes in the proportions of multiple cell types, cellular phenotypes, and cell-cell communications. These age-related changes are likely involved in the pathogenesis of age-related aortic diseases.

first: Kuan

last: Zeng

first: Ruicong

last: Guan

first: Yanqi

last: Yang


title: IRX5 promotes DNA damage repair and activation of hair follicle stem cells [ms_epidermis]

overall_design: Whole epidermis from postnatal (P) day 20 Irx5-/- (n=2) and Irx5+/+ (n=2) mice was mechanically and enzymatically dissociated into single cell suspension for bulk RNA sequencing


title: Comprehensive screens and a universal zinc finger model enable transcription factor reprogramming  2 factor reprogrammingComprehensive screens and a universal zinc finger model enable transcription factor reprogramming

city: New York

first: Marcus

last: Noyes

state: NY

address: 435 East 30th Street

department: Department of Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Programmable regulation of gene expression promises to be a powerful therapeutic venue for diseases caused by the misexpression of genes, haploinsufficiencies, or gain of function mutations. While dCas9-effector domain fusions have been used to alter expression levels, their in vivo application is limited by size and immunogenicity. Conversely, the Cys2His2 Zinc Finger domain offers ideal characteristics for in vivo use. However, their intricate engagement with the DNA has made the design of Zinc Finger arrays challenging. We here describe the screening of 49 billion protein-DNA interactions and development of the first deep learning model that solves Zinc Finger design for any genomic target. We demonstrate the versatility of designed Zinc Fingers as nucleases and as activators or repressors by seamlessly reprogramming human transcription factors.

overall_design: Samples are synthetic zinc fingers fused to either an effector domain. Two replicates are included per sample and the input DNA was sequenced for each sample. As a positive control/reference, the YY1 zinc finger protein was used.

first: David

last: Ichikawa

first: Osama

last: Abdin

first: Nader

last: Alerasool

first: Manjunatha

last: Kogenaru

first: April

last: Mueller

first: Han

last: Wen

last: Giganti

first: Gregory

last: Goldberg

first: Samantha

last: Adams

first: Jeffrey

last: Spencer

first: Rozita

last: Razavi

first: Satra

last: Nim

first: Hong

last: Zheng

first: Courtney

last: Gianco

first: Finnegan

last: Clark

first: Alexey

last: Strokach

first: Timothy

last: Hughes

last: Lionnet

first: Mikko

last: Taipale

first: Philip

last: Kim


title: IRX5 promotes DNA damage repair and activation of hair follicle stem cells [ATAC-Seq]

first: Jefferson

last: Chen

overall_design: HFSC (Ly-6A/E- CD34+ CD45f+) were FACS sorted and lysed.  Nuclei were incubated in 50uL of Tn5 transposition buffer for 30mins at 37C. DNA isolation was preformed with Qiagen MinElute Cleanup kit. Library preparation with Illumina TrueSeq library preparation kit and paired end Illumina HiSeq 2500 sequencing (80million reads per sample) was performed at the University of California, Irvine High Throughput Genomics Facility.

first: Chen

last: Jefferson

first: Andersen

last: Bogi


title: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features [dataset 3]

first: Marielle

last: Bond

first: I

last: Quiroga

first: Michael

last: Love

first: Hyejung

last: Won

first: Douglas

last: Phanstiel


title: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features [dataset 1]

overall_design: ATAC-seq of K562 cells treated with PMA to differenitate into a megakaryocyte-like state after 0, 6, or 72h


title: DNA dioxygenases Tet2/3 control epithelial differentiation (bisulfite-seq)

first: Andrey

last: Sharov

overall_design: Genomic DNA is isolated from 400K sorted native or formaldehyde fixed cells with Lysis Buffer (100 mM Tris-HCl pH 8.8, 5 mM EDTA, 200 mM NaCl, 0.2% SDS and 0.4 mg/ml Proteinase K) at 55 °C for 4 hours, sheared to the length of 300 – 500 bp and eluted in 20 µl of ddH2O. DNA methylation conversion is performed with EZ DNA Methylation-Gold kit (Zymo, #5005). Briefly, 20 µl of sheared genomic DNA is converted with 130 μl of the CT Conversion Reagent. The converted genomic DNA binds to Zymo-Spin™ IC Column and is proceeded for desulphonation with 200 μl of M-Desulphonation Buffer, and is eluted in 17 μl of Low EDTA TE Buffer. Bisulfite sequencing DNA libraries are prepared by using ACCEL-NGS® Methyl-seq DNA Library kit (Swift Biosciences, #30024 and #x6024) with 7 - 9 cycles’ PCR amplification as the manual described. Paired-end sequencing is performed in the Illumina NovaSeq 6000 system (2 × 150 bp) for WGBS.

first: Guodong

first: Iqra

last: Fatima

first: Qin

last: Xu

last: Fessing

first: Andrei

last: Mardaryev

first: Elena

last: Rozhkova

first: Guoliang

first: Vladimir

last: Botchkarev


title: Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation

city: Bunkyo-Ku

first: Yoshibumi

last: Ueda

state: Tokyo

address: 7-3-1 Hongo

department: Chemistry

country: Japan

institute: The University of Tokyo

summary: Hyperactivation of phosphatidylinositol-3 kinase (PI3K) signaling is a prominent feature in cancer cells. However, the mechanism underlying malignant behaviors in the state remains unknown. Here, we describe a mechanism of cancer drug resistance through protein synthesis pathway, downstream of PI3K signaling. An optogenetic tool (named PPAP2) controlling the PI3K signaling was developed. Melanoma cells stably expressing PPAP2 (A375-PPAP2) acquired resistance to a cancer drug in the hyperactivation state. Proteome analyses revealed that expression of the antiapoptotic factor tumor necrosis factor alpha–induced protein 8 (TNFAIP8) was upregulated. The TNFAIP8 upregulation was mediated by protein translation from pre-existing mRNA. These results suggest that cancer cells escape death via upregulation of TNFAIP8 expression from pre-existing mRNA even though alkylating cancer drugs damage DNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of A375-PPAP2.2 cells with or without PI3K signaling hyperactivation.

first: Yuri

last: Miura

first: Takeaki

last: Ozawa


title: Rb family proteins and Activator E2F family transcription factors are master regulators of the molecular signatures instructing the quiescent and activated adult neural stem cell state

city: Ottawa

first: Ruth

last: Slack

state: ON

address: 451 Smyth Rd

department: Brain and Mind Research Institute

country: Canada

institute: University of Ottawa


title: transcriptional profiling of neutrophils in Behcet's Disease (BD).

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

summary: Behçet’s Disease (BD) is a chronic and systemic vasculitis with unknown etiology. Although BD is considered a condition linking both autoimmunity and autoinflammation, aberrant innate immunity has emerged in its significant pathogenetic role, among which neutrophils directly drive inflammation in BD. To investigate neutrophil aberrance in BD, we performed bulk RNA-sequencing on isolated peripheral neutrophils from 10 pairs of BD and sex- and age-matched healthy control (HCs).

overall_design: Transcriptional profiling of peripheral neutrophils from 20 samples (10 healthy controls and 10 BD patients).

first: Xin

last: Yu

first: Lu

last: Li

first: Menghao

last: Zhang

first: Jinjing

last: Liu

first: Hua

last: Chen


title: The m6A Reader IGF2BP2 Regulates Glutamine Metabolism and Represents a Therapeutic Target in Acute Myeloid Leukemia [Ribo-seq]

first: Hengyou

last: Weng

summary: We report that m6A reader IGF2BP2 participates in the regulation of glutamine metabolism in AML. To further clarify whether IGF2BP2 knockdown (KD) leads to translational inhibition, we perform Ribo-seq in control and IGF2BP2 KD cells.

overall_design: MM6 cells infected with shNS or shIGF2BP2 (including shBP2B and shBP2D) were employed for ribo-seq.

first: Huilin

last: Huang

first: Jianjun


title: Elongating bovine embryos display genes involved in metabolism and growth factor signaling, suggesting a dietary effect on elongation

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: We report the transcriptome of bovine embryos collected on day 15 of pregnancy, whose mothers were fed with an omega-3 or an omega-6 rich diet.

overall_design: Examination of diet effects on day 15 bovine embryos.

first: Katrin

last: Giller

first: Paula

last: Papa

first: Corina

last: Schanzenbach

first: Jochen

last: Bick

first: G

last: Geisslinger

first: M

last: Schmicke

first: H

last: Kienberger

first: Barbara

last: Drews

first: Susanne

last: Ulbrich


title: Next generation gene sequencing facilitates transcriptome analysis of liver tissue in dexmedetomidine-treated liver resection model mice

city: Shanghai

first: Liqun

last: Yang

address: No 160, Pujian road

institute: Shanghai Jiaotong University School of Medicine

summary:
Purpose: Liver tissue regeneration is vital in the restoration of liver function after hepatectomy and liver transplantation. Dexmedetomidine is a highly selective alpha2-adrenergic receptor (A2R) agonist, whichis  regarded as a sedative and analgesic medication that is frequently used intra- and postoperatively in hepatic surgery. Owing to its critical role in the protection of multiple organs, the purpose of this study is to investigate the effects of dexmedetomidine on liver regeneration.
Methods:Dexmedetomidine 25 μg.kg-1 was injected intraperitoneally 30 minutes before a 70% hepatectomy performed in mice. Blood and liver samples were obtained for analysis after 48 hours. Mouse primary hepatocytes (MPHMPHs) were incubated with 10 μM dexmedetomidine for 24 hours, then analyzed for cell proliferation from mRNA and protein levels. Transcriptome sequencing revealed the potential mechanism of dexmedetomidine promoting liver regeneration, verified by western blot analysis. Loss of function analysis was performed using the selective corresponding antagonist of Dexmedetomidine .
Results:25 μg.kg-1 Ddexmedetomidine significantly promoted mouse liver regeneration in vivo. The liver/body weight ratio was elevated following dexmedetomidine preconditiontreatment. ImmunohistochemistryProliferative markers of Ki67, PCNA and cyclin-D1 suggested more hepatocytes enter a state of proliferatimore cell proliferationon in dexmedetomidine group via immunohistochemistry. These effects were also phenocopied in vitro Incubating withwhere 10 µM dexmedetomidine increased MPH proliferation in vitro, detected by Edu and Ki67 immunofluorescence staining. The expression of cyclins, PCNA mRNA, protein expression levels of cyclins and PCNA were higher with dexmedetomidine treatment in vivo and in vitro. The p-AKT, p-GSK3beta and beta-catenin expression levels were elevated by dexmedetomidine. The effect of dexmedetomidine on MPH proliferation and p-AKT, p-GSK3beta and beta-catenin expressionse phenomenon  was blocked by atipamezole (ATI, alpha2 adrenoceptor antagonist) pretreatment.
Conclusion:Dexmedetomidine activates AKT/GSK3beta/beta-catenin pathway to promote enhance liver regeneration via binding the alpha-2 adrenoreceptor, which would shed light on a potential therapeutic clinical role to protect liver function in a broad of hepatic surgery.

overall_design: 70% partial hepatectomy (PHx) as previously reported was used to study liver regeneration. The saline and DEX groups received saline and dexmedetomidine 25 μg.kg-1 (Yangtze River Pharmaceutical, China) respectively via intraperitoneal injection 30 minutes before PHx. Liver samples were obtained for RNA-suquecing after 48 hours.

first: Dongdong

last: Lv

first: Wenming


title: RNA-Seq analysis of SK-N-BE(2) neuroblastoma cells after ARID1A and ARID1B silencing for BAF complex disruption

city: Barcelona

first: Carlos

last: Jimenez

state: Barcelona

address: Pg. Vall dHebron 119-129, Edificio Collserola, lab 207

department: Pediatric Oncology

institute: Vall d'Hebron Institut de Recerca

summary: In order to determine the transcriptomic network under the control of BAF chromatin remodeling complex in neuroblastoma cells, we performed RNA-Seq analysis on a neuroblastoma cell lines to detect those transcriptionally modulated genes after the disruption of this complex through silencing of its key structural subunits ARID1A and ARID1B.

overall_design: SK-N-BE(2) cells were transduced with lentiviral particles carrying shRNA for ARID1A and ARID1B silencing and 72 h later RNA was extracted in biological triplicates for RNA-Seq analysis.

last: Jiménez

first: Miguel

middle: F

last: Segura


title: Chromatin accessibility changes after BAF complex disruption in neuroblastoma cells by ATAC-Seq

summary: In order to study the genomic regions undergoing chromatin accessibility changes when BAF chromatin remodelling complex is inhibited, ATAC-Seq of SK-N-BE(2) neuroblastoma cells was performed after silencing of BAF structural subunits ARID1A and ARID1B.

overall_design: SK-N-BE(2) cells were transduced with lentiviral particles carrying shRNA for ARID1A and ARID1B silencing  in biological triplicates and 72 h later ATAC-Seq was performed as previously described (Buenrostro et al. Nat Methods. 2013).

first: Mariona

last: Nadal-Ribelles

first: Pablo

last: Latorre

first: Carme

last: Solé

first: Francesc

last: Posas

first: Eulàlia

last: de Nadal


title: IRX5 promotes DNA damage repair and activation of hair follicle stem cells [nhek_d]

first: Jefferson

last: Chen

first: Bogi

last: Andersen


title: A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells [PAR-CLIP]

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

summary: PIWIL4 is a RNA binding enzyme required for the resolution of R-loops in AML cells. We examine the RNA associated with PIWIL4 protein in AML cell line THP-1

overall_design: Examination of PIWIL4 protein associated RNA in THP-1 cell line using PAR-CLIP

first: Christian

last: Buske

first: Vijay

last: Rawat

first: Shiva

last: Bamezai


title: Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors [bulk RNA-Seq]

city: Salt Lake City

first: Ying

last: Li

state: UT

address: 15 North 2030 East, Eccles Institute of Human Genetics

department: NUIP

institute: University of Utah

summary: Cancers of the gastrointestinal tract including esophageal adenocarcinomas, colorectal cancers, and cancers of the gastric cardia are common comorbidities of obesity. Excessive delivery of macronutrients to the cells lining the gut can increase one’s risk for these cancer by inducing imbalances in the rate of intestinal stem cell proliferation vs. differentiation, which can produce polyps and other aberrant growths. We demonstrate that serine palmitoyltransferase (SPT), which diverts dietary fatty and amino acids into the sphingolipid biosynthesis pathway, is a critical modulator of intestinal stem cell homeostasis. SPT and other enzymes in the biosynthetic pathway are upregulated in  human colon tumors. These enzymes produce sphingolipids that serve as pro-stemness signals that stimulate peroxisome-proliferator activated receptor alpha (PPARa)-mediated induction of  fatty acid binding protein-1. This increases fatty acid uptake and oxidation and enhances the stemness program.  Serine palmitoyltransferase thus serves as a critical link between dietary macronutrients, epithelial regeneration, and cancer risk.

overall_design: Examination of 2 different treatments in intestinal organoids.

first: Bhagirath

last: Chaurasia


title: The m6A Reader IGF2BP2 Regulates Glutamine Metabolism and Represents a Therapeutic Target in Acute Myeloid Leukemia [RNA-seq]

city: Guangzhou

first: Hengyou

last: Weng

summary: We report that m6A reader IGF2BP2 participates in the regulation of glutamine metabolism in AML. Targeting IGF2BP2 with our developed inhibitor CWI1-2 shows promising therapeutic efficacy in AML.To explore the mechanism of the inhibitor, we performed RNA-seq in AML cells upon treatment with CWI1-2 or DMSO. On the other hand, to distinguish the mechanism between IGF2BP2 and YTHDF2, we compare RNA-seq data of IGF2BP2 KD with YTHDF2 KD.

overall_design: Total RNA from MonoMac6 cells with different treatments (i.e., CWI1-2 vs DMSO, YTHDF2 KD vs shNS) was isolated using the TRIzol reagent (Thermo fisher Scientific). Library construction of 1 µg RNA per sample was made using the NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's instructions. The library preparations were sequenced on an Illumina NovaSeq platform and 150 bp paired-end reads were generated.

first: Huilin

last: Huang

first: Jianjun


title: Disruption of the gut microbiota attenuates epithelial ovarian cancer sensitivity to cisplatin therapy

city: Cleveland

first: Peter

last: Bazeley

state: OH

address: 9500 Euclid Avenue

department: Lerner Research Institute

institute: Cleveland Clinic

summary: Epithelial Ovarian Cancer (EOC) is the leading cause of gynecologic cancer death. Despite many patients achieving remission with first-line therapy, up to 80% of patients will recur and require additional treatment. Retrospective clinical analysis of OC patients indicates antibiotic use during chemotherapy treatment is associated with poor overall survival. We assessed whether antibiotic (ABX) therapy would impact growth of EOC and sensitivity to cisplatin in murine models. Immune competent or compromised mice were given control or ABX containing water (metronidazole, ampicillin, vancomycin, and neomycin) before being intraperitoneally injected with murine EOC cells. Stool was collected to confirm microbiome disruption and tumors were monitored, and cisplatin therapy was administered weekly until endpoint. EOC tumor-bearing mice demonstrate accelerated tumor growth and resistance to cisplatin therapy in ABX treated compared with nonABX treatment. Stool analysis indicated most gut microbial species were disrupted by ABX treatment except for ABX resistant bacteria. To test for role of the gut microbiome, cecal microbiome transplants (CMTs) of microbiota derived from ABX or nonABX treated mice were used to recolonize the microbiome of ABX treated mice. nonABX cecal microbiome was sufficient to ameliorate the chemoresistance and survival of ABX treated mice indicative of a gut derived tumor suppressor. Mechanistically, tumors from ABX treated compared to nonABX treated mice contained a high frequency of cancer stem cells that were augmented by cisplatin. These studies indicate an intact microbiome provides a gut derived tumor suppressor and maintains chemosensitivity that is disrupted by ABX treatment.

overall_design: 13 mice (4 ABX-Cisplatin, 2 ABX-Placebo, 4 H2O-Cisplatin, 3 H20-Placebo)

first: Laura

last: Chambers

first: Emily

last: Esakov

first: Chad

last: Braley

first: Lexie

last: Trestan

first: Zahraa

last: Alali

first: Defne

last: Bayik

first: Justin

middle: D

last: Lathia

first: Naseer

last: Sangwan

middle: S

first: Amy

last: Joehlin-Price

first: Mohammed

last: Dwidar

first: Adeline

last: Hajjar

first: Philip

middle: P

last: Ahern

first: Jan

last: Claesen

last: Rose

first: Roberto

last: Vargas

first: J

last: Brown

last: Michener

first: Ofer

last: Reizes


title: RNA-sequencing analysis of transcriptoms in Wild Type (WT) and Trdn-as knockout (KO) hearts.

city: Augusta

first: Hongyan

last: Xu

state: GA

department: Population Health Sciences

institute: Augusta University

summary: The goal of this study is to examine differential gene expression between WT and Trdn-as KO heart using RNA-sequencing (RNA-seq). Total RNA was extracted from mouse hearts and subjected for RNA-seq. The conclusion of the study is that deletion of Trdn-as affects expression levels of a group of genes.

overall_design: RNA_seq profiling hearts from adult WT and Trdn-as KO mice.

first: Kunhua

last: Song


title: Quantitative Analysis of Transcriptomes of small molecules generated Neural Precursor Cesll (smNPCs)  and smNPCs-derived neurons by next generation sequencing

city: Hannover

first: shuyong

last: zhu

state: Lower Saxony

address: OE 5230, Carl-Neuberg-Str. 1, 30625

department: Institute of Virology

institute: Hannover Medical School

summary: The aim of this next generation sequencing is to analyze the difference between smNPC and smNPC derived neurons by RNA-sequencing. In this study, the smNPCs were generated from inducible pluripotent stem cells (iPSCs) derived from human cord blood cells. The obtained smNPCs were further differentiated into neurons using a protocol that stems from Stuart M Chambers et al (2012, Nature Biotech), which described a system to differentiate human embryonic stem cells into nociceptive sensory neurons and Peter Reinhardt et al (2013, Plos one), which developed a protocol to generate human peripheral neurons from smNPC. Briefly, a peripheral sensory lineage was induced from smNPCs by activating WNT signaling, while inhibiting NOTCH and FGF prior to BMP4 treatment. Neuronal differentiation was further enhanced by treatment with dbcAMP and other growth factors until 60 days post differentiation (dpd). The neurons at 60 dpd are termed hiNeurons. In this study, the transcriptomes of hiNeurons and smNPCs were quantitatively analyzed by RNA-seq.

overall_design: Investigate the differential gene expression before (smNPCs) and after (hiNeurons) differentiation

first: Shuyong

last: Zhu

first: Abel

last: Viejo-Borbolla

first: Michael

last: Spohn

first: Adam

last: Grundhoff


title: Expression data from mouse embryonic fibroblasts

summary: We use microarray to measure the global gene expresson of mouse embryonic fibroblasts cells

overall_design:
Mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5. RNA was extracted from different time points post infection and hybridized to the Affymetrix Mouse Gene 1.0 ST array.

>>>Submitter states that the raw data are unavailable since the experiment was performed in 2013 and the raw data files were not kept <<<


title: Rb family proteins are master regulators of the molecular signatures instructing the quiescent and activated adult neural stem cell state

first: Ruth

last: Slack

summary: The long-term maintenance of the adult neurogenic niche and neurogenesis is dependent on the proper regulation of entry and exit from quiescence. The dynamic transition from quiescence to activation is a complex process requiring not only precise cell cycle control, but also a co-ordinated phenotypic transition involving transcriptional and morphological changes. Presently, the mechanisms by which such a complex repertoire of factors interact and co-ordinate with the core cell cycle machinery to mediate these critical NSC fate transitions remains unknown. Here we show that the Rb/E2F axis functions as an on-off switch for NSC quiescence and activation, by linking the cell cycle machinery to pivotal regulators of NSC fate. Compound deletion of Rb family proteins results in massive activation and expansion of NSCs, and induces a global transcriptomic transition towards NSC activation followed by niche depletion. Deletion of their target activator E2Fs1/3 results in the failure of NSCs to become activated and the acquisition of a global transcriptome associated with intractable NSC quiescence and the cessation of adult neurogenesis. We further show that the Rb/E2F axis orchestrates these fate transitions through the direct regulation of factors essential to NSC function, including REST and ASCL1. This places the Rb/E2F axis as a master regulator of NSC fate, coordinating cell cycle control with NSC activation and quiescence fate transitions.

overall_design: Six samples total; three biological replicates were analyzed for each of two conditions (two genotypes; three replicates per genotype)

first: Bensun

middle: C

last: Fong


title: Activator E2F family transcription factors are master regulators of the molecular signatures instructing the quiescent and activated adult neural stem cell state


title: CircRNA as Predictive Biomarker of Penumbra in Acute Ischemic Stroke

first: Dan

last: Lu

address: No.601, West Huangpu Avenue

department: Neurology and Stroke center

institute: Jinan University

summary: Acute ischemic stroke (AIS) is a leading cause of disability and mortality worldwide. By high-throughput sequencing of infarct and ischemic penumbra tissue from middle cerebral artery embolization (MCAO) mice, we identified the CircRNA expression was dramatically and selectively regulated in the penumbra tissues.

overall_design: The permanent middle cerebral artery occlusion mice were established by intraluminal filament 3 h after MCAO. The RNA sequencing analysis was performed on the infarction core (core close to frontal lobe and occipital lobe, respectively) and penumbra cortex tissues obtained from six 3h-MCAO mice. The RNA extracted from tissues of six mice was mixed before library construction, separately.


title: Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs [RNA-Seq]

city: La Jolla

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

summary: As we age, structural changes contribute to progressive decline in organ function, which in the heart acts through poorly characterized mechanisms. Utilizing the rapidly aging fruit fly model with its significant homology to the human cardiac proteome, we found that cardiomyocytes exhibit progressive loss of Lamin C (mammalian Lamin A/C homologue) with age. Unlike other tissues and laminopathies, we observe decreasing nuclear size, while nuclear stiffness increases. Premature genetic reduction of Lamin C phenocopies aging’s effects on the nucleus, and subsequently decreases heart contractility and sarcomere organization. Surprisingly, Lamin C reduction downregulates myogenic transcription factors and cytoskeletal regulators, possibly via reduced chromatin accessibility. Subsequently, we find an adult-specific role for cardiac transcription factors and show that maintenance of Lamin C sustains their expression and prevents age-dependent cardiac decline. Our findings are conserved in aged non-human primates and mice, demonstrating age-dependent nuclear remodeling is a major mechanism contributing to cardiac dysfunction.

overall_design: Bulk RNA-Sequencing of Drosophila melanogaster isolated hearts, conducted for two control fly strains at 1 week of age (w1118, n = 4; attp2, n = 5) and 5 weeks of age (w1118, n = 4; attp2, n = 5) , and flies expressing Lamin C RNAi from the heart specific, Hand promoter at 1 week of age (n = 5). The purpose of sequencing was, 1) To Identify differentially expressed genes upon aging that may contribute to age-dependent nuclear remodeling in w1118 flies; 2) Show conserved age-dependent changes in gene expression across wildtype control strains (w1118 and attp2); and 3) Identify overlapping co-regulated genes upon aging (attp2 1- and 5-week aged flies) and Lamin C RNAi expressing flies.

middle: J

first: Natalie

last: Kirkland


title: HDAC1 over-expression in SH-SY5Y cells

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

summary: HDAC1 gene is over-expressed in SH-SY5Y cells to find the differentially expressed genes

overall_design: mRNA profiles of 2 HDAC1 over-expressed samples and 2 control samples

first: Zhenzhen

last: Zhao


title: Longitudinal Immune Profiling Highlights CD4+ T cell Exhaustion Correlated with Liver Fibrosis in Schistosoma japonicum Infection

city: Tianjin,China

first: Zhuo

last: Yue

address: Qixiangtai Road

institute: Tianjin medical university

summary: Schistosoma japonicum causes severe disease or even death and liver fibrosis is the major damage, which is caused by immunopathological injury. However, a comprehensive understanding of the immune cell changes during S. japonicum infection is lacking. Here, we performed single-cell RNA-sequencing and T/B cell receptor sequencing (scRNA-seq/scTCR-seq/scBCR-seq) of the total mouse splenocytes after cercaria infection.The changes of immune cells with advancing disease stages were analyzed and the relationship with liver fibrosis was investigated.

overall_design: BALB/c mice were percutaneously infected with cercariae of S. japonicum. The splenocytes were isolate for single-cell RNA-sequencing and T/B cell receptor sequencing on week 0, 4, 6, 12, 16 after infection.

first: Dongming

last: Zhou

first: Yue

last: Zhuo

first: Jiling

last: Ren

first: Furong

last: He


title: Gene expression in activated WT or PDK4 -/- CD4+ T cells

city: Daegu

first: Hoyul

last: Lee

address: 807, Hoguk-ro, Buk-gu

department: Bio-medical Research Institute

institute: Kyungpook Nationatl University Hospital

summary: Activation of CD4+ T cells requires metabolic reprograming to sustain demands of cellular building blocks and ATP. Pyruvate dehydrogenase kinase (PDK) is an enzyme regulating pyruvate dehydrogenase complex subunit alpha 1 (PDHE1-alpha), which converts pyruvate to acetyl-CoA. Gene expression analysis of TCR-stimulated CD4+ T cells with PDK4 deletion exhibited the reduced calcium signaling and aerobic glycolysis pathway.

overall_design: Comparing gene expression of WT and PDK4 deficient CD4+ T cells

first: Eun

last: Kim

first: In-Kyu


title: RNA-Seq analysis of the spongy tissue disorder in Mangifera indica Cv. Alphonso.

city: pune

first: vineet

last: jha

state: Maharashtra

address: 9 A/12 Pingale Aryabhatta Persistent Tower,

department: LABS

institute: Persistent systems

summary: Transcriptome analysis of the spongy tissue disorder in Mangifera indica Cv. Alphonso was carried out individually at two stages of ripening (Table green and mid ripe) in the healthy and the spongy mesocarp. Sequencing was carried out using Illumina technique. Total number of raw reads generated from each stage of tissue ranged from 5-7 Gb. Importantly, 30,582 transcripts were annotated and 1,218 enzyme commission number were assigned from oxidoreductase, transferase, hydrolase, ligase, lyase and isomerase classes. Various differential transcripts (p < 0.05) were highlighted within the healthy and the spongy tissue during ripening. These were involved in biological pathways related to metabolism of fatty acids, sugars, amino acids etc. The altered expression pattern of these transcripts indicated the change in primary as well as secondary metabolism of fruit under the spongy tissue condition. Interestingly, several stress related transcripts were differentially expressed in both the stages of the spongy mesocarp which has advocated the role of abiotic stress in the spongy tissue disorder.

overall_design: Transcriptome analysis of two ripening stages (table green (5DAH) and mid ripe (10DAH)) of Alphonso mango under the healthy and the spongy tissue disorder condition.

first: Vidya

last: Gupta

first: Pranjali

last: Oak

first: Vineet

last: Jha

first: Kishanpal

last: Anamika

first: Ashok

last: Giri


title: Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors [single cell RNA-Seq]

first: Ying

last: Li


title: Transcriptomic response of bermudagrass to 7 days of drought, salt, heat and submergence

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary:
Purpose: We aimed to dissect response of bermudagrass to drought, salt, submergence and heat stresses and identify stress responsive genes inbermudagrass.
Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.Paired-end clean reads were aligned to the reference genome of TAIR10 and rice protein sequence from MSU (version_7.0) using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated . Differential expression analysis of abiotic stress versus control condition was performed using the DESeq R package (1.18.0).
Results:In total, 12 samples with two biological replicates per treatment were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified genes modulated by different abiotic stress treatments.

overall_design: In this study, 3-week-old bermudagras seedlings were withheld water, treated with 400mM NaCl, submerged under water, 42oC temperature for 7days, respectively. The leaves of control and stress treated bermudagrass plants were then collected for RAN isolation.


title: The origin and contribution of the tumor stroma in colorectal carcinogenesis

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

summary: Background and aims  Cancer-associated fibroblasts (CAFs) play a critical role in colorectal cancer (CRC) progression. However, the precise cellular origins of the tumor stroma remain unknown, making it challenging to therapeutically target the tumor mesenchyme. Here, we aimed to identify key cellular contributors to and components of the CRC mesenchyme associated with poor prognosis.  Methods  We used a mouse model of inflammation-associated CRC in 5 different genetic fate-mapping transgenic mouse lines to characterize the origins of the CRC stroma. To identify a potential therapeutic target expressed by the CRC stroma, RNA-sequencing of fluorescence-activated cell sorting (FACS)-purified CRC stromal cells was performed. CRC patient RNA-sequencing data (n=621) and tissue microarray (n=101) were used to examine the prognostic significance of marker expression.  Results   We found that approximately half of the CRC CAFs marked by α-smooth muscle actin (αSMA) in a mouse model of CRC emerge through proliferation. Lineage tracing experiments revealed that intestinal leptin receptor (Lepr)-lineage stromal cells expanded and contributed to 75% of the αSMA+ proliferating CAFs. Notably, no αSMA+ CAFs arose from Krt19-lineage epithelial cells or bone marrow-derived cells. Moreover, RNA-sequencing of FACS-purified CRC mesenchymal cells identified MCAM as a CRC stroma-specific marker, which is expressed by Lepr-lineage cells. Analysis of human CRC samples showed that high MCAM expression driven, in part, by TGF-β was independently prognostic of poor overall survival.   Conclusion  Our data identify intestinal Lepr-lineage cells as a major source of the tumor stroma in CRC and suggest that targeting MCAM+ cells may serve as an attractive therapeutic approach to restrain CRC progression.

overall_design: Four 8-week-old adult mice (2 males and 2 females), four postnatal day 14 mice (2 males and 2 females), and four AOM/DSS-treated mice (2 males and 2 females) were used to isolate colonic cells. Stromal cells were selected by FACS-sorting of CD45- immune cells, EPCAM- epithelial cells, CD31- endothelial cells on FACSAria Fusion (BD Bioscience). Differential gene expression analyses were performed between prenatal vs normal and AOM/DSS tumor vs normal.

first: Hiroki

last: Kobayashi

first: Krystyna

middle: A

last: Gieniec

first: Tamsin

last: Lannagan

first: Tongtong

last: Wang

first: Siddhartha

last: Mukherjee

first: Masahide

last: Takahashi

first: Timothy

first: Atsushi

last: Enomoto

first: Daniel

last: Worthley


title: Next Generation Sequencing confirmed exon alternative splicing and lineage switching in one patient

city: Tianjin

first: 傅

last: 雪航

state: Tianjin

address: heping

institute: CAMS & PUMC

summary:
Purpose: To analyze the expression of two different CD19 isoforms during BiTE treatment, and to further determine cell lineage specific molecules before and after BiTE treatment
Methods: For transcriptome sequencing, we isolated patient's bone marrow samples, quality of total RNA was evaluated by Agilent 2100. RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB,USA). RNA sequencing process and the data acquisition were finished on Novogene Experimental Department according to the manufacturer’s protocol. Reads were aligned to hg38 reference genome. Relative abundance of CD19 and other gene transcripts were mapped and estimated at both gene and transcript level (FPKM) by feature Counts.
Results: The expression of CD19 isoform with exon 2 deletion was found at diagnosis before BiTE therapy. The patient did not achieve remission after BiTE treatment, and the expression of CD19 antigen turned negative by flow cytometry detection. But the expression ratio of exon 2 deleted CD19 was not increased, and the flow cytometry phenotype and transcriptome sequencing confirmed that no linage switching occurred, which suggested the expression of CD19 isoform caused by exon alternative splicing and lineage switching was not the driving mechanism of CD19 epitope loss in this patient. Immune escape could not be prevented by targeting alternative exons. This patient achieved complete remission by sequential infusions of our own developed CD22 CAR-T and CD19 CAR-T after disease progression
Conclusions: transcriptome sequencing confirmed that no linage switching occurred in this patient, which suggested the expression of CD19 isoform caused by exon alternative splicing and lineage switching was not the driving mechanism of CD19 epitope loss in this patient.

overall_design: bone marrow samples mRNA profiles before and after therapy were generated by deep sequencing


title: Analysis of LPS stimulation on F480Low CD11b High Macrophages from WT and PI3KδE1020K-B KI mice

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: Single cell suspensions from WT or PI3KδE1020K-B KImice were stimulated with LPS for 2 hours after which macrophages were sorted

overall_design: 3 WT mice and 4 PI3KδE1020K-B KI mice

first: J

first: O

last: Suchanek

first: M

last: Clatworthy


title: Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors.

first: Ying

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

overall_design: Refer to individual Series


title: Analysis of LPS stimulation on F480low CD11b High Macrophages from WT and muMT KO mice

summary: Single cell suspensions from WT or muMT KO mice were stimulated with LPS for 2 hours after which macrophages were sorted

overall_design: 3 WT mice and 4 muMT KO mice


title: Analysis of LPS stimulation on F480Hi CD11blo Macrophages from WT and muMT KO mice

overall_design: 3 WT mice and 3 muMT KO mice


title: Analysis of UTI on WT and PI3KδE1020K-B KI mice

summary: Either WT or PI3KδE1020K-B KI mice were infected with UPEC trans urethrealy twice 1 hour apart and culled 12 hours later. Kidneys were subsequently perfused, RNA extracted and analysed via RNASeq

overall_design: 2 WT mice and 3 PI3KδE1020K-B KI mice


title: Analysis of UTI on WT and muMT KO mice

summary: Either WT or muMT KO mice were infected with UPEC trans urethrealy twice 1 hour apart and culled 6 hours later. Kidneys were subsequently perfused, RNA extracted and analysed via RNASeq

overall_design: 4 WT mice and 4 muMT KO mice


title: Loss of Phf6 prevents aging associated transcriptomic profile changes in LT-HSCs

city: New York

first: Stuart

middle: Aidan

last: Quinn

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

summary: Loss of Phf6 prevents the functional decline and immunophenotypic changes associated with age-related, long-term repopulating hematopoietic stem cell (LT-HSC) exhaustion. To identify the underlying molecular mechanisms that account for these differences, we performed RNA-seq profiling of LT-HSCs isolated from the bone marrow of Phf6 wild-type and knock-out, young (16-week-old) and aged (24-month-old) C57BL/6 mice. Our analysis revealed that LT-HSCs isolated from 24-month-old, Phf6 knockout mice retained the molecular signatures associated with young LT-HSCs whereas LT-HSCs isolated from aged, Phf6 wild-type mice acquired signatures consistent with HSC exhaustion. Mechanistically, these data revealed important roles for key metabolic pathways including glutathione metabolism and sterol biosynthesis, as well as cell-cell interaction and signaling pathways such as the interferon and TGF-beta responses.

overall_design: RNA-seq of LT-HSCs isolated from young and old, Phf6 wild-type and knock-out mice.

first: Aidan

first: Agnieszka

last: Wendorff

first: Adolfo

last: Ferrando


title: Next-generation sequencing facilitates quantitative analysis of wild type and diabetic db/db mice islets transcriptomes

first: Li

last: Xiong

state: Guangdong

address: 58 Zhongshan Road 2

department: Department of Endocrinology

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Long non-coding RNAs (LncRNAs) constitute an extensive fraction of the mammalian transcriptome. In this study, lncRNAs dysregulated in the islets of diabetic db/db mice were identified by high-throughput RNA sequencing. More than 1600 lncRNAs were detected using RNA sequencing, indicating that lncRNAs were abundant in islets. Among them, we found that lncRNA-Malat1 was significantly reduced in diabetic mouse islets. Further experiments suggested an involvement of lncRNA-Malat1 in lipotoxicity-induced β-cell dysfunction.

overall_design: Islet lncRNAs and mRNA profiling in db/db and db/m control mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.

first: Liting

last: Wu


title: Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs

first: Adam

last: Engler


title: RNA-seq of sEV derived from primary cortical neurons under hypoxic or normoxic conditon

status: Public on Oct 31 2022

first: Yousheng

address: 601 Huangpu Avenue West

institute: the First Affiliated Hospital of Jinan University

summary: Few studies have investigated the properties and function of small extracellular vesicles (sEV) derived from neurons under hypoxic conditions; these sEV represent potential new strategies for neuroprotection or neuroregeneration after ischemic stroke. We then performed gene expression profiling analysis using data obtained from RNA-seq of sEV derived from neurons under hypoxic conditions (HypEV) and those derived from neurons under normoxic conditions (NorEV).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sEV derived from neurons under hypoxic conditions (HypEV) and those derived from neurons under normoxic conditions (NorEV).

first: Xiaoxiong

last: Huang

first: Zefeng

last: Tan

first: Jiankun

last: Zang

first: Min

last: Peng

first: Niu

last: He

first: Tao

last: Zhang

first: Dan

last: Lu

first: Anding

last: Xu


title: Circulating Y-RNAs, a predicted function mainly in controlling the Immune System, Cell Signaling, and DNA Replication in Pediatric Patients with Pilocytic and Diffuse Astrocytoma

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary: Y-RNAs are small noncoding RNAs firstly identified in patients suffering the Sjögren’s syndrome and lupus erythematosus, having different predicted cellular functions. Y-RNAs are very abundant ncRNAs present in serum and only a few is known respect their molecular roles. The aim of the study was to determine the circulating Y-RNAs expression from blood serum of pediatric patients with pilocytic or diffuse astrocytoma. Y-RNAs expression was determined by means of the HTA 2.0 arrays. In addition, a bioinformatic approximation of the possible biological functions of Y-RNAs was determined with the “Random Forest” (RF) and “Vector Support Machine” (VSM) algorithms. Results. Data showed a differential expression of RNY-3, RNY-4, and RNY-5 in pediatric patients with astrocytoma, relative to the control. Meanwhile, RNY-1 was shown to be upregulated in the Diffuse condition versus the Pilocytic. The bioinformatic analysis showed that RNY-4 and RNY-5 had the highest scores of interaction with Claudin, Toll-like receptors, and Hyaluronidase-1. In addition, the Y-RNAs loop domain by itself had the highest score of interaction with B cell receptor CD22 (RNY-3) and Toll-like receptor 7 and 3 (RNY-4). Conclusions. Our results showed, for the first time  a differential expression of circulating Y-RNAs in pediatric astrocytoma, allowing to distinguish pediatric subjects without cancer from patients with pediatric diffuse or pilocytic astrocytoma and their potential involvement in regulating diverse biological processes, such as immune activation-suppression, cell signaling, selective transcription, and cell proliferation through activation of DNA replication.