title: Comparative transcriptome analysis unveiling molecular mechanisms underlying low temperature resistance in the white mangrove Laguncularia racemosa

first: Yuchen

last: Yang

address: Xingangxi Road 135

country: China

summary: Temperature is an important factor that affects the growth and reproduction of mangrove plants. Laguncularia racemosa (L.) C.F. Gaertn is a controversial species in China, in terms of being a pioneer species for mangrove restoration and a putative invasive species occupying the natural habitats. One of its advantages is the strong resistance to low temperature, which makes L. racemose more adaptive to extreme climate change than local mangrove species. However, little is known about the regulatory mechanisms underlying the cold-stress tolerance in L. racemose, which restricted our understanding on its biological features and invasion potential. In this study, In the current study, we investigated the physiological and molecular mechanisms involved in chilling-stress adaptation in L. racemose. Freezing temperature caused damage to cell membrane system and reduced photosynthesis efficiency in L. racemose. To combat the adverse impacts, plasma membrane biosynthesis and antioxidant processes were substantially enhanced. Furthermore, we showed that there was a difference between the responses to freeze-thaw injury in L. racemose from different locations. It may provide new clues to the different genetic background between varieties of L. racemose. These novel findings could provide biochemical and genetic basis for the cultivation and restoration of L. racemose.

overall_design: To investigate the molecular mechanisms underlying cold-stress resistance in L. racemose, we treated the seedlings of L. racemose with freezing temperature (0℃) for 0h, 3h, 12h and 12h with 24h recovery, and then conducted comparative transcriptome analysis between the treated and untreated plants.

first: Shijie

last: Zhang

first: Ying


title: Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice

status: Public on May 09 2023

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: NAL1 (NARROW LEAF 1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, but the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure whose formation is mediated by ATP-containing positively charged pocket at the N-terminal region. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signaling pathways, eventually achieving its pleiotropic physiological function. An elite allele NAL1A originated from wild rice could increase grain yield. Furthermore, the NAL1 homologs in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.

overall_design: Seedlings of wild type (ZH11) and NAL1-Knockout line at 4-leaf stage were harvested for ChIP-seq,  in two replicates, using Illumina Hiseq X Ten.

first: Wenjing

last: Li

first: Lizhong

last: Xiong


title: Effect of GSK3368715 on GBM patient samples, kept in a novel perfusion device for 8-days

city: Hull

first: Pedro

last: Beltran-Alvarez

address: University of Hull, Cottingham Road

department: HYMS Centre for Biomedicine

country: United Kingdom

institute: University of Hull

type: Expression profiling by high throughput sequencing

summary: Glioblastoma patient samples were microdissected into ~20mg pieces and put onto a novel perfusion device, within an hour of resection. Samples were left for 8 days, at a flow rate of 3ul/min, with a media change at day 4. Treatment was with 1uM GSK3368715. Please refer to Barry et al. Lab-on-chip 2023 for details.

overall_design: Four patient GBM samples were treated with 1 uM GSK3368715, or DMSO control via the media supplying the microfluidics system. Samples were numbered 4 to 7, which correspond to patients D31 to D34. Please refer to Barry et al. Lab-on-chip 2023 for details.

first: Antonia

last: Barry


title: A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

country: USA

institute: National Heart, Lung, and Blood Institute

summary: Proteins containing DZF (domain associated with zinc fingers) modules play important roles throughout gene expression, from transcription to translation. Derived from nucleotidyltransferases but lacking catalytic residues, DZF domains serve as heterodimerization surfaces between DZF protein pairs. Three DZF proteins are widely expressed in mammalian tissues, ILF2, ILF3, and ZFR, which form mutually exclusive ILF2-ILF3 and ILF2-ZFR heterodimers. Using eCLIP-Seq, we find that ZFR binds across broad intronic regions to regulate the alternative splicing of cassette and mutually exclusive exons. ZFR preferentially binds dsRNA in vitro and is enriched on introns containing conserved dsRNA elements in cells. Many splicing events are similarly altered upon depletion of any of the three DZF proteins; however, we also identify independent and opposing roles for ZFR and ILF3 in alternative splicing regulation. Along with widespread involvement in cassette exon splicing, the DZF proteins control the fidelity and regulation of over a dozen highly validated mutually exclusive splicing events. Our findings indicate that the DZF protein complexes form a complex regulatory network that leverages dsRNA binding by ILF3 and ZFR to modulate splicing regulation and fidelity.

overall_design: Paired-end high-throughput RNA sequencing of total RNA from triplicate biological replicate treatments of HEK-293 cells.

first: Nazmul

last: Haque

first: J

middle: R


title: A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

overall_design: RNA Bind-n-Seq of 6X-His tagged ZFRDZF/ILF2, ZFRlong/ILF2, and PTBP1

first: Alexander

last: Will

first: Atlanta

middle: G

last: Cook


title: A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

overall_design: eCLIP analysis of FLAG-ZFR binding in HEK-293 Flp-In TREx cell lines, with size-matched input control.


title: A network of DZF proteins controls alternative splicing regulation and fidelity.

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE206058: Paired-end total RNA-seq of triplicate biological replicate treatments of HEK-293 cells with negative control siRNAs or siRNAs targeting ZFR, ILF2, or ILF3.
GSE206059: eCLIP analysis of FLAG-ZFR binding in HEK-293 Flp-In TREx cell lines, with size-matched input control.
GSE206060: RNA Bind-n-Seq of recombinantly expressed and purified ZFR-ILF2 complexes, with PTBP1 as a positive control for successful library generation.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Please refer to individual series for information about experimental design and data processing.


title: Time course transcriptional profiles of the Arabidopsis thaliana response to in planta expression of the Pseudomonas syringae effector AvrRpt2 for all combinatorial genotypes of the alleles dde2-2, ein2-1, pad4-1, and sid2-2

city: Saint Paul

first: You

last: Lu

state: MN

address: 1500 Gortner Avenue

department: Department of Plant and Microbial Biology

institute: University of Minnesota, Twin Cities

summary: Plant immunity protects plants from numerous potentially pathogenic microbes. The biological network that controls plant inducible immunity must function effectively even when network components are targeted and disabled by pathogen effectors. Network buffering could confer this resilience by allowing different parts of the network to compensate for loss of each other’s functions. Networks rich in buffering rely on interactions within the network, but these mechanisms are difficult to study by simple genetic means. Through a network reconstitution strategy, where we disassemble and stepwise reassemble the plant immune network that mediates Effector-Triggered-Immunity, we have resolved systems-level regulatory mechanisms underlying the Arabidopsis transcriptome response to the ETI-eliciting Pseudomonas syringae effector AvrRpt2. To isolate ETI response from any other effects of the pathogen, AvrRpt2 was transgenically expressed in Arabidopsis cells under the control of the estradiol-inducible promoter system. The signaling sectors (subnetworks) interrogated for their roles and interactions in ETI through the network reconstitution were the jasmonate (JA), ethylene (ET), phytoalexin-deficient 4 (PAD4), and salicylate (SA) signaling sectors.

overall_design: We profiled the Arabidopsis thaliana response to AvrRpt2 expression in the genetic backgrounds of the wild type (Col-0), as well as 4 single-gene mutants, 6 double-gene mutants, 4 triple-gene mutants, a quadruple-gene mutant for the null-mutant alleles dde2-2, ein2-1, pad4-1, and sid2-2, as well as a control genotype, rps2/rpm1, which has null mutations in the ETI receptors for AvrRpt2 (RPS2 is the major receptor while RPM1 is a minor receptor). The mutations dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively. In these lines AvrRpt2 expression can be induced by estradiol (Ed) treatment (pER-AvrRpt2). We included another control line, in which an arbitrary reporter gene GUS (beta-glucuronidase) is induced upon estradiol treatment (pER-GUS) in the wild-type (Col-0) background. Profiles were collected through a time course 0, 1, 2, 3, 4, 5, and 6 hours after infiltration of 50µM estradiol in three biological replicates. Since most Arabidopsis cells undergo hypersensitive cell death (a typical ETI response) about 9 hours after estradiol-induction of AvrRpt2 expression, the time course of the transcriptome response was taken up to 6 hours after estradiol treatment. In addition, profiles from these 18 genotypes were collected through a time course 0, 2, and 5 hours after infiltration of water (mock) as a control treatment with three biological replicates. In each of these experiments, 3 leaves, leaf stages 7-9, of 31-32 days old plants were infiltrated with 50µM Ed or water and collected at the indicated timepoint. Thus each biological replicate contained the tissue of 4*3 = 12 leaves. These experiments resulted in 18 genotypes * 7 time points * 3 replicates = 378 libraries with Ed-treated tissues and 18 genotypes * 3 time points * 3 = 162 libraries with mock-treated tissues (total 540 libraries). These mRNA-Tag-Seq libraries were generated according to Rallapalli G, Kemen EM, Robert-Seilaniantz A, Segonzac C, Etherington GJ, Sohn KH, et al. EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. 2014, BMC Genomics 15, 341. Internal barcodes—the first 4-8 bases of the sequence—were used to multiplex stranded mRNA Tag-Seq libraries for sets of 16 samples each (in most cases) into a single lane of an Illumina HiSeq 2000.

first: R

middle: A

last: Hillmer

first: D

last: Igarashi

first: Y

first: F

last: Katagiri


title: Molecular basis of non-canonical stop codon recognition by mtRF1 in human mitochondria

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

summary: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial translation, however, exhibits deviations from the standard genetic code including reassigning of two arginine codons to stop codons. Translation termination at these non-canonical stop codons requires a protein factor to release the newly synthesized polypeptide chain. Currently it is not known how, and by which release factor, these stop codons are recognized. Here, we used biochemical experiments on knockout mutants in human cells in combination with cryo-electron microscopy to establish that the unusual mitochondrial release factor 1 (mtRF1) detects the non-canonical stop codons. We show that loss of this factor leads to stalling of mitochondrial ribosomes on non-canonical stop codons. As a result, reduced levels of cytochrome C oxidase subunit 1 of the oxidative phosphorylation complex IV are synthesized leading to a defect in mitochondrial respiration. We further show that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual distortion in the mRNA conformation and that the ribosomal RNA importantly participates in the specific recognition of the non-canonical stop codons.

overall_design: Comparative ribosome footprint of RIBO-seq data of human WT cells and mtRF1 mutants (mtRF1-AAQ)

first: Martin

last: Saurer

first: Marc

last: Leibundgut

first: Hima

middle: P

last: Nadimpalli

first: René

first: Alain

last: Scaiola

first: Tanja

last: Schönhut

first: Richard

last: Lee

first: Oliver

last: Rackham

first: David

last: Gatfield

first: Aleksandra

last: Filipovska

first: Nenad

last: Ban


title: Next-generation sequencing reveals IL11 drives preeclampsia by disrupting trophoblast differentiation and activating the placental inflammasome

city: Parkville

first: Guannan

last: Yang

address: Grattan Street

country: Australia

institute: University of Melbourne

summary: Preeclampsia is a life-threatening disorder of pregnancy unique to humans. Interleukin (IL)11 is elevated in serum from pregnancies that subsequently develop early-onset preeclampsia and pharmacological elevation of IL11 in pregnant mice causes the development of preeclampsia-like features (hypertension and proteinuria), however, the mechanism by which IL11 drives preeclampsia-like features is unknown. Using Next-generation sequencing we demonstrate that treatment with PEGylated IL11 (PEGIL11) inhibited placental expression of markers of spongiotrophoblast and syncytiotrophoblast linages and increased placental cathepsin production in wild-type and Asc-/- mice. Function studies showed that IL11 acts via Asc inflammasomes to induce tissue fibrosis and preeclampsia in mice. This study has far-reaching implications on our understanding of the underlying etiology of preeclampsia and the mechanism by which IL11 causes inflammation and fibrosis in many tissues and disease states.

overall_design: mRNA profiles of embryonic day 13 placenta following PEGylated (PEG) interleukin (IL)11 treatment in wild-type and Asc-/- (Pycard-/-) mice.

first: Ellen

middle: M

last: Menkhorst

first: Leilanie

middle: L

last: Santos

first: Wei

last: Zhou

first: Kim-Anh

last: Lê Cao

first: Evdokia

last: Dimitriadis


title: Gene expression profiles of MDA-MB-231 breast cancer cell line treated with DMSO, 10 μM DAC, 1 μM DEX, or DAC+DEX for 6 days.

city: Hsinchu

first: Yi-Chen

last: Huang

state: Hsinchu

address: No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu City 300044 , Taiwan (R.O.C.)

department: college of life science

country: Taiwan

institute: National Tsing Hua University

summary: We observed gene expression difference between different groups after MDA-MB-231 treated with DMSO, 10 μM DAC, 1 μM DEX, or DAC+DEX. Data obtained from high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. Gene expression of each groups are listed in raw data files. Some different expression genes between two groups are further validated with qRT-PCR.

overall_design: Examination of gene expression difference of MDA-MB-231 cells treated with DMSO, 10 μM DAC, 1 μM DEX, or DAC+DEX for 6 days


title: Longitudinal Mult-omics Study of Palbociclib Resistance in Hormone Receptor (HR) Positive/Human Epidermal Growth Factor Receptor (HER) 2 Negative Metastatic Breast Cancer (MBC)

city: Seoul

first: Yeon Hee

last: Park

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: A comprehensive genomic and transcriptomic analysis of pre-treatment and post-treatment tumors from Asian metastatic breast cancer patients treated with palbociclib plus endocrine therapy identified novel markers associated with poor prognosis.

overall_design:
whole transcriptome sequencing of pre-treatment (Baseline) and post-treatment (PD) tumors from 67 breast cancer patients treated with palbociclib plus endocrine therapy by Illumina Hiseq 2500
Raw data files are submitted to EGA with the accession number EGAS00001005736

first: Yeon

middle: H

first: Kyunghee


title: A versatile nuclei extraction protocol for single nucleus sequencing in non-model species - optimization in various Atlantic salmon tissues

status: Public on May 08 2023

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

institute: The University of Edinburgh

summary: The use of single cell sequencing technologies has exploded in non-model organisms, including fish and invertebrates in an aquaculture setting. One of the most expanding areas is the use sequencing nucleus from frozen tissues allowing being able to sample and sequence at different sites. Here we present a tested nucleus isolation protocol that outperforms the most reliable methods to extract nuclei (chopping in salt tween buffer) and improves its performance in non-model organisms.

overall_design: A versatile nuclei extraction protocol for single nucleus sequencing in fish species – optimization in various Atlantic salmon tissues. dx.doi.org/10.17504/protocols.io.261genwm7g47/v2

first: Rose

last: Ruiz Daniels

last: Taylor

first: Ross

last: Dobie

first: Sarah

last: Salisbury

first: Emily

last: Clark

first: Dan

last: Macqueen

first: Diego

last: Robledo


title: Nf1 Deficiency Increases Mammary Collagen Deposition and Restricts Adipocyte Differentiation Before Tumor Formation

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

summary: BACKGROUND: The NF1 tumor suppressor gene is the main negative regulator of the RAS pathway and is frequently mutated in various cancers. Women with Neurofibromatosis Type I (NF1) – a tumor predisposition syndrome caused by a germline NF1 mutation – have an increased risk of developing aggressive breast cancer with poorer prognosis. The mechanisms by which NF1 mutation leads to breast cancer tumorigenesis are not well understood. Therefore, the objective of this work was to identify stromal alterations before tumor formation that result in the increased risk and poorer outcome seen among NF1 patients with breast cancer.  METHODS: To accurately model the germline monoallelic NF1 mutations in NF1 patients, we utilized an Nf1-deficient rat model with accelerated mammary development and develops highly penetrant breast cancer.  RESULTS: We identified increased collagen content in Nf1-deficient rat mammary glands before tumor formation that correlated with age of tumor onset. Additionally, gene expression analysis revealed that Nf1-deficient rat mammary mature adipocytes have increased collagen expression and shifted to a fibroblast and preadipocyte expression profile. This alteration in lineage commitment was also observed with in vitro differentiation but flow cytometry analysis did not show a change mammary adipose-derived mesenchymal stem cell abundance. CONCLUSION: Collectively, these studies uncovered the previously undescribed role of Nf1 in mammary collagen deposition and regulating adipocyte differentiation. In addition to unraveling the mechanism of tumor formation, further investigation of adipocytes and collagen modifications in preneoplastic mammary gland will create a foundation for developing early detection strategies of breast cancer among NF1 patients.

overall_design: Transcriptome profiling of 80 samples from Rattus norvegicus. Samples include primary tumor from three Nf1-mutated rat lines and flow sorted normal tissue types from these same lines and wildtype rats. Normal tissues include whole mammary pad, adipocytes, fibroblasts, and mammary epithelial cells.

first: Menusha

last: Arumugam

first: Carrie

last: Graveel

first: Matt

last: Steensma


title: Sex-specific transcriptomic profiling of reward and sensory brain areas in perinatal fentanyl exposed juvenile mice+G4

city: Baltimore

first: Mahashweta

last: Basu

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

summary: Using bulk RNAseq, we explored transcriptomic landscape of three reward areas - PrL, NAc, VTA and two sensory areas -S1, VBT in perinatal fentanyl exposed juvenile mice

overall_design: Pregnant C57BL/6 dams were administered 10µg/ml fentanyl in drinking water from embryonic day 0 through weaning. At juvenile ages, tissue punches from 5 brain areas were obtained and sequenced.

first: Jimmy

last: Olusakin

first: Gautam

last: Kumar

first: Cali

last: Calarco

first: Megan

middle: E

last: Fox

first: Jason

middle: B

last: Alipio

first: Catherine

last: Haga

first: Makeda

middle: D

last: Turner

first: Asaf

last: Keller

first: Seth

last: Ament

first: Mary

middle: K

last: Lobo


title: ARID1A plays an important role in skin inflammation.

city: San Diego

first: George

last: Sen

state: California

address: 9452 Medical Ctr Dr, La Jolla, CA 92037

department: Department of Dermatology

institute: University of California San Diego

summary: Loss of ARID1A reduced the inflammatory gene expression of human keratinocytes treated with POLY IC

overall_design: ARID1A knockdown RNA-Seq in polyIC induced  primary human  keratinocytes.

first: Uyanga

last: Batzorig


title: Laser capture microdissection-based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in Ponkan (Citrus reticulate)

first: Liqing

last: Lu

address: No.1 of Shizishan street, Hongshan District

summary: Seed abortion is one of the important reasons for the formation of seedless characters in citrus. However, the molecular mechanism of seed abortion in citrus is still unclear. We identified several genes that may play an important role in seed abortion of 'Huagan 4', such as CrWRKY74. The downstream regulatory network of CrWRKY74 was identified based on DAP seq analysis to gain insight into the molecular mechanism related to seed abortion.

overall_design: The young citrus fruits (Citrus reticulate, Ponkan) were used for nucleic acid extraction and vector construction, and two replicates are set for each sample

first: Juxun

last: Wu

first: Hualin

last: Yi


title: Targeting TIP60 inhibits tumorigenesis in non-small cell lung cancer

city: Boston

first: Daisuke

middle: Jefferson

last: Shibahara

state: Massachusetts

address: 330 Brookline Avenue, E/CLS-0417

department: Oncology

institute: Beth Israel Deaconess Medical Center

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

overall_design: Refer to individual Series


title: RNA-seq of Talaromyces marneffei under mycelium and yeast conditions

city: Beijing

first: Xueyan

last: Hu

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: Peking University Health Science Center

summary: Although many studies have focused on dimorphic switching, noncoding RNAs in Talaromyces marneffei have been neglected until now. rRNA depletion RNA-seq with or without RNase R treatment were performed in mycelium and yeast conditions of Talaromyces marneffei by  to unveil the functions of circRNAs in dimorphic switching.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PM1 strains and its KD and OE strains in triplicates in Illumina platform and PM1 strains only in Nanopore platform in duplicates.

first: Minghao

last: Du

first: Changyu

last: Tao

first: Juan

last: Wang

first: Yun

last: Zhang

first: Yueqi

last: Jin

first: Ence

last: Yang


title: Trem2 Promotes Foamy Macrophage Lipid Uptake and Survival in Atherosclerosis

city: Minneapolis

first: Jesse

middle: W

last: Williams

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

institute: University of Minnesota

summary: To investigate the function of Trem2 on foamy macrophage gene regulation, we generated Trem2 deficientBV2 cells using CRISPR and comparedgene expression to Trem2 sufficientcontrols in the presence or absence of cholesterol loading.

overall_design: WT or Trem2-/- BV2 cells were cultured overnight with 20 ug/mL soluble cholesterol to differentiate into cholesterol-loaded foamy macrophages or treated with media alone (nonfoamy, nf) then we performed RNA sequencing.

first: Yingzheng

last: Xu

first: Michael

last: Patterson


title: Targeting TIP60 inhibits tumorigenesis in non-small cell lung cancer [RNA-seq]

summary: Histone modifications play crucial roles in transcriptional activation, and aberrant epigenetic changes are associated with oncogenesis. Lysine (K) acetyltransferases 5 (TIP60, also known as KAT5) is reportedly implicated in cancer development, although its function in lung cancer remains unclear. Here we demonstrate that TIP60 knockdown in non-small cell lung cancer cells decreased tumor cell progression. Furthermore, analysis of a mouse lung cancer model with lung-specific conditional Tip60 knockout revealed suppressed tumor formation relative to controls, but no apparent effects on normal lung homeostasis. RNA-seq and ChIP-seq analyses of inducible TIP60 knockdown H1975 cells relative to controls revealed transglutaminase enzyme (TGM5) as downstream of TIP60. In addition, a candidate TIP60 inhibitor suppressed tumor growth in cell culture and in vivo. Taken together, suppression of TIP60 activity shows tumor-specific efficacy against lung cancer, with no overt effect on normal tissues. Our work suggests that targeting TIP60 could be a promising approach in treating lung cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H1975 control cells and its KD derivatives {shTIP60-1 (sh-B) and shTIP60-2 (sh-C)}.

first: Susumu

last: Kobayashi

first: Naoki

last: Akanuma

first: Gilbert

last: Pan


title: Small RNA-seq for alfalfa roots under alkaline stress

first: Lin

last: Chen

state: Haidian

address: Beijing, Haidian, West Road 2 yuanmingyuan.

institute: Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Abstract: In order to understand the expression patterns of miRNAs in alfalfa under alkali stress, small RNA sequencing was performed on alfalfa roots at different time points under alkali stress, and miRNAs were identified and analyzed.

overall_design: Small RNA-seq for 14 days-old alfalfa roots under alkaline stress (50 mmol/L NaHCO3)


title: Alfalfa roots under alkaline stress


title: RNA-seq datasets from differentiating iHA-Foxk1 and Foxk1 KO mESCs in mesodermal conditions

first: Daniel

last: Garry

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

summary: D3, D5 and D10 EBs from iHA-Foxk1 and Foxk1 KO cells were harvested for RNA and submitted for sequencing to understand the transcriptional profile of these cells during differentiation in the presence and absence of FOXK1

overall_design: iHA-Foxk1 and Foxk1 KO mESCs were differentiated using mesodermal conditions to form embryoid boddies and harvested at D3, D5 and D10 for RNAseq

first: Javier

last: Sierra-Pagan


title: Seq datasets from differentiating iHA-Foxk1 and Foxk1 KO mESCs in mesodermal conditions


title: Expression data of human induced pluripotent stem cells (hiPSCs), human embryonic stem cells (hESCs) and those differentiated cells.

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

type:
Expression profiling by array
Third-party reanalysis

summary:
We examined hiPSCs, hESCs and those differentiated cells to identify pluripotent signature genes, differentiation marker genes and relationship between expression and phenotypes.
Additionally, we performed microarray experiments to examine gene expression in human tissues. This data was used for comparison with hESCs, hiPSCs and those differentiated cells.
A total of 22 tissues (bone marrow, cerebellum, colon, cortex, fetal brain, heart, kidney, liver, lung, pancreas, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea and uterus) were examined.

overall_design:
The hiPSCs, hESCs and those differentiated cells were cultured, and their cDNAs were used for microarray analysis.
Total RNA isolated from cultivated cells and human tissues were labeled and hybridized to the GeneChip Human Genome U133 Plus 2.0 Array according to the manufacturer's protocol.

first: Yohei

last: Okada

first: Masato

last: Koike

first: Shuta

last: Tomisato

first: Tomoko

last: Tokura

first: Yasuharu

last: Ishihara

first: Daisuke

last: Shimojo

last: Kanematsu

first: Yonehiro

last: Kanemura

first: Kazuhisa

last: Kohda

first: Gen

last: Sobue

first: Shinya

last: Yamanaka

first: Michisuke

last: Yuzaki

first: Yasuo

last: Uchiyama

first: Eiji

last: Ikeda

first: Tatsuhiko

last: Tsunoda

first: Hideyuki

last: Okano


title: ATAC-seq datasets from differentiating iHA-Foxk1 and Foxk1 KO mESCs in mesodermal conditions

first: Daniel

last: Garry

summary: 50k cells from D3, D5 and D10 EBs from iHA-Foxk1 and Foxk1 KO cells were harvested for ATAC-seq and submitted for sequencing to understand the chromatin dynamics of these cells during differentiation in the presence and absence of FOXK1

overall_design: iHA-Foxk1 and Foxk1 KO mESCs were differentiated using mesodermal conditions to form embryoid boddies and harvested at D3, D5 and D10 for ATACseq

first: Javier

last: Sierra-Pagan

first: Nikita

last: Dsouza


title: Targeting TIP60 inhibits tumorigenesis in non-small cell lung cancer [ChIP-seq]

last: Shibahara

overall_design: Comparative H4ac modification profiles of ChIP-seq data for H1975 control cells and its KD derivatives {shTIP60-1 (sh-B) and shTIP60-2 (sh-C)}.

first: Susumu

last: Kobayashi

first: Naoki

last: Akanuma

first: Hideo

last: Watanabe

first: Gilbert

last: Pan

first: Feng

last: Jiang


title: Gene expression profile at single cell level of immune cells from gastric cancer

city: Hangzhou

first: Jian

last: Chen

address: Jiefang Road

department: Department of Gastrointestinal Surgery of the Second Affiliated Hospital

institute: Zhejiang University School of Medicine

summary: Immune cells within gastric cancer microenvironment greatly influence disease outcome. We used single cell RNA sequencing (scRNA-seq) to analyze the immune heterogeneity of gastric cancer.

overall_design: Tumor infiltrating immune cells of gastric cancer patients were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Lie

last: Wang

first: Han

last: Liang

first: Jing

first: Kuai

last: Liu

first: Yikai

last: Luo


title: Context dependent role of Pho binding sites in Polycomb complex recruitment in Drosophila

first: J.

middle: Lesley

last: Brown

address: 9000 Rockville Pike

department: NICHD

institute: NIH

summary: Polycomb group (PcG) proteins maintain the silenced state of key developmental genes, but how these proteins are recruited to specific regions of the genome is still not completely understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) comprised of a flexible array of sites for sequence-specific DNA binding proteins, “PcG recruiters”, including Pho, Spps, Cg, GAF and many others.  Pho is thought to play a central role in PcG recruitment. Early data showed that mutation of Pho binding sites in PREs in transgenes abrogated the ability of those PREs to repress gene expression.  In contrast, genome-wide experiments in pho mutants or by Pho knockdown showed that PcG proteins can bind to PREs in the absence of Pho.  Here we directly addressed the importance of Pho binding sites in two engrailed (en) PREs at the endogenous locus and in transgenes.  Our results show that Pho binding sites are required for PRE activity in transgenes with a single PRE. In a transgene, two PREs together lead to stronger, more stable repression and confer some resistance to the loss of Pho binding sites. Making the same mutation in Pho binding sites has little effect on PcG-protein binding at the endogenous en gene.  Overall, our data support the model that Pho is important for PcG binding but emphasize how multiple PREs and chromatin environment increase the ability of PREs to function in the absence of Pho.

overall_design: Genome-wide binding of different PcG recruiters or PcG proteins (Pho, Spps, Ph, Ez, Sfmbt) in Crispr generated lines in an en△1.5 background. 1.5kb fragments carrying either wild-type PRE1 and PRE2 of the engrailed gene or MutPRE2 (WT PRE1 and Pho site mutations in PRE2) or Mut PRE1+2 (Pho site mutations in both PRE1 and PRE2). These lines were generated specifically to look at PcG recruitment to the engrailed PREs.  H3K27me3 ChIP seq was carried out on transgenic lines with the split mini-white transgene constuct (inserted at 2L:9437482 (Dm version 6)) with either no insert (control), a WT line carrying WT enPRE1+2, PhoKO PRE1+2) or MutallGAGA PRE1+2. These experiments were carried out to look at the levels of H3K27me3 recruited over the reporter genes and genes neighboring the insertion site to see the impact of H3K27me3 in the absence of Pho binding sites or GAGA binding sites.

first: J

first: Joshua

last: Price

first: Maksim

last: Erokhin

first: Judith

last: Kassis


title: Single cell RNA sequencing of adult mouse Acta2+ lung cells

first: Pushpinder

last: Bawa

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: Smooth muscle cells exist in many different locations within the body, including blood vessels and airways. The heterogeneity of smooth muscle cells has been related to their embryological origins and could have implications in many diseases, including atherosclerosis, pulmonary hypertension, and asthma. Here we aimed to study the heterogeneity of Acta2+ cells in the mouse lung and to identify specific markers for Acta2+ sub-populations. We used a mouse line containing an Acta2hrGFP/Cspg4dsRed reporter and performed single cell RNA sequencing of Acta2+ cells isolated from adult mouse lungs. We identified 3 main distinct clusters, corresponding to airway smooth muscle (ASM), vascular smooth muscle (VSM) and mesenchymal alveolar niche cells (MANCs), and extracted specific gene signatures for each of these cell types. Our dataset and gene signatures help address the heterogeneity of Acta2+ lineages in the lung and will be of use for future studies focusing on smooth muscle cells in the lung and in other organs.

overall_design: Global transcriptomic profiling of freshly isolated Acta2-hrGFP+ lung cells from an Acta2hrGFP/Cspg4-dsRed reporter mouse (Paez-Cortez et al,  Plos One 2013) by single cell RNA sequencing.

first: George

last: Kwong

first: Carlos

last: Villacorta-Martin

first: Andrea

last: Alber

first: Darrell

middle: N

last: Kotton


title: Identifying key events from Per- and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA-sequencing analysis of perfluorohexane-1-sulfonate (PFHxS)

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

summary: Gene expression data from short-term in vivo studies shows efficacy in quantifying concentration-dependent effects that inform toxicity outcomes, particularly for chemicals with limited toxicity data such as Per- and Polyfluoroalkyl Substances (PFAS). Automated behavioral assessments, at non-teratogenic concentrations reveal perfluorohexane-1-sulfonate (PFHxS) exposure causes hyperactivity in larval zebrafish (6 days post fertilization (dpf)) during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide (DMSO) vehicle control. To identify key events that drive this abnormal behavior, zebrafish embryos were exposed to 7.87-25.1 μM PFHxS or 0.4% DMSO, and RNA was isolated from pooled head tissue collected at 4 and 5 dpf, before the onset of hyperactivity, for RNA-sequencing (NextSeq 500). Differentially expressed genes (DEGs) were identified using Gene Specific Analysis (Partek Flow, St. Louis, MO) and mapped to human orthologs for pathway analyses to inform modes of action.

overall_design: At 0 dpf, zebrafish embryos were bleached as previously described (Tal et al. 2017). A single embryo at the dome-to-epiboly stages (Kimmel et al. 1995) was placed into each individual well of a 96-well plate containing a 40-μm nylon mesh filter (Millipore, Catalog No. MANMN4010) with 400μL of 10% Hanks’ balanced salt solution (HBSS) per well. Filter inserts containing zebrafish embryos were transferred to 96-well culture trays (Millipore, Catalog No. MAMCS9610) containing 250μL of 10% HBSS (Westerfield 2007) and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily, from 1–4 or 1-5 dpf, plates underwent 100% media changes to refresh chemical dosing solutions by blotting (Brandel; Catalog No. FPXLR-196) and transferring mesh inserts containing zebrafish to new bottom plates (Millipore; Catalog No. MAMCS9610). To minimize evaporation, plates were sealed (Biorad; Catalog No. MSA5001) and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0°C and scored daily for death, malformations, hatching, and swim bladder inflation. Zebrafish embryos were exposed to 7.87-25.1 μM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.

first: Xia-meng

last: Howey

first: Carmen

last: Wood

first: Sheza

last: Gaballah

first: Tamara

last: Tal


title: circRNA Microarray Service for 16 human samples

first: Rui

last: Chen

address: No.10 Xitoutiao, You An Men

institute: Capital medical university

summary:
We have completed the Arraystar Human circRNA Array analysis of the 24 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

overall_design: Examination of circRNA expression of COPD patients experienced exacerbation upon PM2.5 exposure

first: Xiaobo

last: Li


title: Transcriptome profiling for seed abortion in Ponkan (Citrus reticulata)

city: Wuhan

first: Liqing

last: Lu

institute: Huazhong Agricultural University

summary: Seed developmental arrest is one of the early phenotypes of seed abortion. However, the molecular mechanism underlying seed developmental arrest of citrus is still unclear. In this study, laser capture microdissection (LCM) was used to accurately divide the seeds of seedless Ponkan ‘Huagan No.4’ (Citrus reticulata) (HG) and seeded Ponkan ‘Egan No.1’ (Citrus reticulata) (EG) into nucellus and integument/seed coat tissues. The captured tissues were used for subsequent RNA-seq. Moreover, single-molecule real-time (SMRT) sequencing was used to generate full-length transcripts of EG, which were used as reference transcripts for RNA-seq. These data can be utilized to analyse the causes of citrus seedlessness formation and the molecular regulatory network in the process of seed abortion.

overall_design: Twelve samples of three key developmental stages and two tissues in HG and EG were collected. Three biological replicates were set for each sample.

first: Juxun

last: Wu

first: Hualin

last: Yi


title: Identifying key events from Per- and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA-sequencing analysis of perfluorooctane sulfonic acid (PFOS)

summary: Gene expression data from short-term in vivo studies shows efficacy in quantifying concentration-dependent effects that inform toxicity outcomes, particularly for chemicals with limited toxicity data such as Per- and Polyfluoroalkyl Substances (PFAS). Automated behavioral assessments, at non-teratogenic concentrations reveal perfluorooctane sulfonic acid (PFOS) exposure causes hyperactivity in larval zebrafish (6 days post fertilization (dpf)) during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide (DMSO) vehicle control. To identify key events that drive this abnormal behavior, zebrafish embryos were exposed to 0.88-2.8 μM PFOS or 0.4% DMSO, and RNA was isolated from pooled head tissue collected at 4 and 5 dpf, before the onset of hyperactivity, for RNA-sequencing (NextSeq 500). Differentially expressed genes (DEGs) were identified using Gene Specific Analysis (Partek Flow, St. Louis, MO) and mapped to human orthologs for pathway analyses to inform mode of action.

overall_design: RNA-seq of zebrafish head after exposure to  perfluorooctane sulfonic acid at various concentrations or DMSO.


title: PTBP2 knock-down RNA-seq from human iPSC-neurons

city: Philadelphia

first: Jennine

last: Dawicki-McKenna

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

summary: To determine targets of PTBP2-dependent alternative splicing, we depleted PTBP2 in human neurons derived from induced-pluripotent stem cells (iPSC-neurons) using an LNA gapmer and performed RNA-seq on untreated, negative control-treated, and knock-down samples.

overall_design: We performed differential gene expression and splicing analysis of RNA-seq data from untreated, negative control LNA gapmer-treated, and PTBP2 LNA gapmer-treated human iPSC-neurons.

first: Alex

middle: J

last: Felix

first: Elisa

last: Waxman

first: Congsheng

last: Cheng

first: Defne

last: Amado

first: Paul

last: Ranum

first: Alexey

last: Bogush

first: Lea

last: Dungan

first: Elizabeth

last: Heller

first: Deborah

last: French

first: Beverly

last: Davidson

first: Benjamin

last: Prosser


title: Cap analysis gene analysis (CAGE) of  Ba/F3 cells harbouring FLT3-ITD mutations (mouse)

first: Kotoko

last: Yamatani

address: Building A 6F, Hongo Bunkyo-ku 2-1-1

institute: Juntendo University

summary: The purpose of the experiment is to investigate transcriptome signatures of FLT3-ITD and TKD double mutations in AML and the underlying molecular mechanism of mutation-driven acquired resistance. We identify 1945 upregulated and 1470 downregulated promoters in FLT3-ITD/D835 mutant Ba/F4 cells  compared to cells with FLT3-ITD (FDR<0.05).

overall_design: Examination of differentially expressed promoters beween FLT3-ITD Ba/F3 cells expressing  FLT3-ITD and Ba/F3 cells expressing  FLT3-ITD/D835

first: Yoko

last: Tabe


title: Cap analysis gene analysis (CAGE) of  primary AML samples harbouring FLT3-ITD mutation (human)

summary: The purpose of the experiment is to investigate transcriptome signatures of FLT3-ITD and TKD double mutations in AML and the underlying molecular mechanism of mutation-driven acquired resistance. We identify that  310 upregulated and 22 downregulated promoters in FLT3-ITD/D835 mutant AML cells  compared to cells with FLT3-ITD (FDR<0.05).

overall_design: Examination of differentially expressed promoters beween FLT3-ITD AML cells and FLT3-ITD/D835 AML cells


title: Regional transcriptomics and proteomics of DMPK genes in human intestine

city: Kobe

first: Hijiri

last: Fujioka

address: 6-7-5, Minatojimaminamimachi, Chuouku,

institute: NBI

summary: The intestine is an organ responsible for absorption and metabolism of orally administered drugs. It is necessary to examine the human intestinal expression profiles of the genes related to drug absorption, distribution, metabolism, and excretion (ADME), for accurate prediction of pharmacokinetics in the intestine. However, previous studies had issues such as the evaluation limited to specific molecules and regions, and relatively small sample sizes. In this study, to obtain more accurate expression profiles of mRNA and protein in various regions of human intestine, biopsy samples were collected from 38 patients with various regions, duodenum, jejunum, ileum, colon and rectum, and RNA-seq analysis and quantitative proteomics analysis were performed. We performed the expression analysis of drug-metabolizing enzymes (cytochromes P450 (CYP ) and non–CYP enzymes), apical and basolateral drug transporters, and nuclear receptors. Overall, mRNA expression levels of these ADME-related molecules were highly correlated with the protein expression levels. The characteristics of the expression of ADME-related genes in human small and large intestines differed significantly, such as higher or lower expression levels of CYP enzymes in the small or large intestines, respectively. Most CYPs were expressed dominantly in the small intestine. Non-CYPs were expressed in the large intestine, but their expression levels were lower than those in the small intestine. The expression levels of ADME-related genes differed even between the proximal and distal small intestine. The expression of transporters showed their highest abundance in the ileum. The data in the present study contributes to an improved understanding of intestinal ADME of drug candidates, and would be useful for drug discovery research.

overall_design: RNA expression profiles of Intestinal biopsies

first: Michika

last: Murata

first: Jumpei

last: Yokota

first: Kentaro

last: Okada

first: Tomoki

last: Yamashita

first: Daisuke

last: Hirayama

last: Kawakami

first: Gaku

last: Morinaga

first: Asami

last: Saito

first: Hiroshi

last: Nakase

first: Wataru

last: Kishimoto

first: Hiroyuki

last: Mizuguchi


title: HSV-2 Triggers Upregulation of MALAT1 in CD4+ T cells and Promotes HIV Latency Reversal

status: Public on May 07 2023

city: New Haven

first: Holly

last: Steach

state: Connecticut

address: 300 Cedar St.

department: School of Genetics

institute: Yale University

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

overall_design: Refer to individual Series


title: HSV-2 Triggers Upregulation of MALAT1 in CD4+ T cells and Promotes HIV Latency Reversal (Bulk RNA-Seq)

summary: HSV-2 coinfection is associated with increased HIV-1 viral loads and expanded tissue reservoirs, but the mechanisms are not well-defined. HSV-2 recurrences result in an influx of activated CD4+ T cells to sites of viral replication and an increase in activated CD4+ T cells in peripheral blood. We hypothesized that HSV-2 induces changes in these cells that facilitate HIV-1 reactivation and replication and tested this hypothesis in human CD4+ T cells and 2D10 cells, a model of HIV-1 latency. HSV-2 promoted latency reversal in HSV-2 infected and bystander 2D10 cells. Bulk and single-cell RNA sequencing studies of activated primary human CD4+ T cells identified decreased expression of HIV-1 restriction factors and increased expression of transcripts including MALAT1 that could drive HIV replication in both the HSV-2-infected and bystander cells. Transfection of 2D10 cells with VP16, an HSV-2 protein that regulates transcription, significantly upregulated MALAT1 expression, decreased trimethylation of lysine 27 on histone H3 protein, and triggered HIV latency reversal. Knockout of MALAT1 from 2D10 cells abrogated the response to VP16 and reduced the response to HSV-2 infection. These results demonstrate that HSV-2 contributes to HIV-1 reactivation through diverse mechanisms including upregulation of MALAT1 to release epigenetic silencing.

overall_design: CD4 T cells from 5 healthy donor leukopaks were stimulated with ImmunoCultTM Human CD3/CD28 T Cell Activator (Cat. 10971, STEMCELL Technologies) for 72 h. Stimulated cells were mock infected or infected with HSV-2(333 ZAG) at MOI = 10 as described above. 24 hours post-infection cells were sorted on GFP by FACS, and RNA was isolated using the miRNeasy Micro Kit (Qiagen Cat. no. 217084) per manufacturer’s instructions.

first: Carl

last: Pierce

first: Lip

last: Loh

middle: R

first: Natalia

last: Cheshenko

first: Paula

last: Preston-Hurlburt

first: Fengrui

last: Zhang

first: Stephanie

last: Stransky

first: Leah

last: Kravets

first: Simone

last: Sidoli

first: William

last: Philbrick

first: Michel

last: Nassar

first: Smita

last: Krishnaswamy

first: Kevan

middle: C

last: Herold

first: Betsy


title: Cap analysis gene analysis (CAGE) of  AML cells harbouring FLT3-ITD mutations

first: Kotoko

last: Yamatani

summary:
This SuperSeries is composed of the SubSeries listed below.
The purpose of the experiment is to investigate transcriptome signatures of FLT3-ITD and TKD double mutations in AML cells (primary samples and Ba/F3 cell) and the underlying molecular mechanism of mutation-driven acquired resistance. We identify 310 upregulated and 22 downregulated promoters in FLT3-ITD/D835 mutant AML cells  compared to cells with FLT3-ITD (FDR<0.05), and 1945 upregulated and 1470 downregulated promoters in FLT3-ITD/D835 mutant Ba/F3 cells  compared to cells with FLT3-ITD.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We examined differentially expressed promoters of FLT3-ITD AML cells expressing  FLT3-ITD and AML cells expressing  FLT3-ITD/D835


title: HSV-2 Triggers Upregulation of MALAT1 in CD4+ T cells and Promotes HIV Latency Reversal (scRNA-Seq)

overall_design: CD4+ T cells were isolated by immunomagnetic negative selection, activated by anti-CD3/CD28 beads for 72 hours,  infected with HSV-2(SD90), and isolated at 0 (mock), 6 and 24 hours for scRNAseq analysis.

middle: A


title: Evaluating ER-alpha and PR interactions with chromatin in Esr1-wildtype and mutant mammary luminal cells

city: South San Francisco

first: Jackson

last: Liang

state: CA

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

summary: To understand the interactions between ER-alpha and PR interactions with chromatin in Esr1-wildtype versus mutant mammary cells, ChIP-seq was performed against both transcription factors. Animals were treated for four days with E2 and P4, then harvested for analysis.

overall_design: 12 samples are included in total between a previous submission and this one, 2 biological replicates per condition. No references were used. Important note: in our original submission, we included 8 samples; in this submission, we include an additional 4 samples which were generated at the same time but excluded from the original submission as we did not feel these data were relevant at the time. At the request of a manuscript reviewer, we are now also including four samples associated with the 'D542G' mutation, in addition to the 8 previous samples associated with 'WT' and "Y541S" mutation.

first: Marc

last: Hafner

first: Ciara

last: Metcalfe


title: RNA seq analysis of Cere-120 (AAV2-NRTN) pretreatment in irradiated SMGs compared to AAV2-GFP pretreatment and Non-IR controls.

city: Bethesda

first: Matthew

middle: P

last: Hoffman

address: 30 Convent Dr MSC4370

institute: NIDCR

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular and molecular pathways. The goals of this study are to compare NGS-derived Cere-120 treated SMG transcriptome profile (RNA-seq) to the AAV2-GFP and Non-IR SMGs

overall_design: Methods: SMG mRNA profiles of  Non-IR, IR-GFP and Cere-120 treated  mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays

first: Isabelle

last: Lombaert

first: Vaishali

last: Patel

first: Christina

last: Jones

first: Derrick

last: Villier

first: Ashley

last: Canada

last: Moore

first: Elsa

last: Berenstein

first: Changyu

last: Zheng

first: Corinne

last: Goldsmith

first: Jay

last: Chorini

first: Daniel

last: Martin

first: Lee

last: Zourelias

first: Mark

last: Trombetta

first: Kathleen

last: Meyer

first: Dale

last: Ando

first: Michael

last: Passineau


title: Evaluating hormone responses in Esr1-wildtype and mutant mammary luminal cells [RNA-seq]

first: Jackson

last: Liang

summary: To examine the effects of hormone stimulation on Esr1-wildtype and Esr1-mutant mammary glands, we will ovariectomize both wildtype and ER-mutant mice. Following ovariectomy (OVX), animals will be implanted with hormone pellets (either placebo, estrogen, and/or progesterone). Then, we perform RNA-seq on FACS-sorted mature luminal cells (ML) from mammary glands of treated mice. This analysis will allow for separation of ER mutant-intrinsic effects on gene expression vs. combinatorial effects from exposure to either estrogen or progesterone.

overall_design: 37 samples are included, 3 biological replicates per condition (except for the 'WT + P4' condition, which has 4 biological replicates). 'WT + placebo' condition is used as a reference.

first: Marc

last: Hafner

first: Ciara

last: Metcalfe


title: Methadone alters transcriptional programs associated with synapse formation in human cortical organoids

status: Public on May 06 2023

city: La Jolla

first: Gabriel

last: Haddad

department: Pediatrics

institute: University of California, San Diego

summary: Opioid use disorder (OUD) among pregnant women has become an epidemic in the United States. Pharmacological interventions for OUD involve methadone, a synthetic opioid analgesic that attenuates withdrawal symptoms and behaviors linked with maternal drug abuse. However, methadone’s ability to readily  accumulate in neural tissue, and cause long-term neurocognitive sequelae, has led to concerns regarding its effect on prenatal brain development. We took advantage of  human cortical organoid (hCO) technology to probe how this drug impacts the earliest mechanisms giving rise to the cerebral cortex. To this end, we conducted bulk mRNA sequencing of 2-month-old hCOs derived from two cell lines that were chronically treated with a clinically relevant dose of 1μM methadone for 50 days. Differential expression and gene ontology analyses revealed a robust transcriptional response to methadone associated with functional components of the synapse, the underlying extracellular matrix (ECM), and cilia. Further unsupervised co-expression network and predictive protein-protein interaction analyses demonstrated that these changes occurred in concert, centered around a regulatory axis consisting of growth factors, developmental signaling pathways, and matricellular proteins. Our results demonstrate that exposure to methadone during early cortico-genesis fundamentally alters transcriptional programs associated with synapse formation, and that these changes arise by modulating extra-synaptic molecular mechanisms in the ECM and cilia. These findings provide novel insight into methadone’s putative effect on cognitive and behavioral development and a basis for improving interventions for maternal opioid addiction.

overall_design: RNA-sequencing data from 2-month-old human cortical organoids derived from two iPSC cell lines chronically treated with a therapeutically relevant dose of 1μM methadone or a vehicle of nuclease-free water for 50 days.

first: Ila

last: Dwivedi

first: Andrew

last: Caldwell

first: Dan

last: Zhou

first: Shankar

last: Subramaniam

middle: G


title: Xmal-RRBS on breast carcinoma samples taken before and after neoadjuvant chemotherapy

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

type: Methylation profiling by high throughput sequencing

summary: Determination of genes demonstrating differential methylation of CpG islands in tumor samples before and after treatment for revealing main metabolic, regulatory and biological processes

overall_design: Reduced representation bisulfite sequencing by XmaI-RRBS (Tanas et al., 2017)

middle: I

first: Alexander

middle: S

last: Tanas

first: Vladimir

middle: V

last: Strelnikov


title: Effects of 4-nitrophenol on testicular somatic cells [TM4]

city: nantong

first: Yonghui

last: Zhang

address: 19 Qixiu Road

institute: nantong university

summary: These data suggested that TM3 and TM4 cells showed different responses to PNP, which might mediate different toxic mechanisms.

overall_design: Here we utilized two testicular somatic cell lines (TM3 and TM4) to explore the possible toxic effects of PNP on male reproductive system. TM3 and TM4 cells were exposed to 10 μM PNP for 24 h. After the exposure experiment, Agilent mouse mRNA Array was used to identify gene expression changes in the control and PNP treated TM3 and TM4 cells.

first: Fulu

last: Dong


title: Effects of transcription factor POX04513 on the transcription of cellulase genes and xylanase genes in Penicillium oxalicum

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: To investigate the effect of the transcription factor POX04513 in Penicillium oxalicum on the expression levels of cellulase and xylanase genes in solid and liquid fermentation

first: Zhao

last: Shuai

first: Ning

last: Yuanni


title: Effects of 4-nitrophenol on testicular somatic cells


title: Single-nucleus spatial transcriptomic RNA-seq in the  dlPFC of macaque

city: Chongqing

first: Peng

last: Xie

address: 1st, Youyi Street

institute: The first affiliated hospital of Chongqing medical university

summary: We performed high-throughput snRNA-seq and spatial transcriptomic RNA-seq on dorsolateral prefrontal cortex (BA9) tissue in Macaca fascicularis to identify cell-type specific differentially expressed genes. The macaques include depressive-like, healthy control and resilient individuals.

overall_design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from dlpfc of the post-mortem brain tissue of 7 depressive-like (DL), 5 mild depressive-like in low rank (resilient, RES) and 7 healthy (HC) female cynomolgus macaque (Macaca fascicularis). 10X Genomics Visium Spatial transcriptomic was performed on tissue slices from dlpfc of the post-mortem brain of 2 depressive-like (DL), 3 mild depressive-like in low rank (resilient, RES) and 3 healthy (HC) female cynomolgus macaque. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3’ Reagent Kits v2. Paired-end sequencing was performed on theIllumina NovaSeq 6000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count.

first: Jing

last: Wu


title: Investigation of diurnal polyadenylation site usage reveals differential regulation in the transcription of gene isoforms

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

summary: Gene isoforms are mRNAs produced from the same locus, but that differ in their transcription start sites, protein coding DNA sequences, and/or untranslated regions. Consequently, different isoforms of the same gene can have altered gene function or even serve different biological functions. Conventional RNA-Seq strategies cannot accurately distinguish expression levels between distinct isoforms, and differences in gene expression studies almost always report total gene expression. However, increasing evidence indicates that differences in isoform usage may be important for the regulation of biological functions and for development of diseases such as cancer. Here, we aimed to define whether gene isoforms are subjected to differential regulation and expression by characterizing 24-hour rhythms in polyadenylation site (PAS) usage over the course of the day in the mouse liver. Conventional RNA-Seq experiments have shown that 15-30% of genes in the mouse liver are rhythmically expressed, and it is assumed that the comprising isoforms are expressed in a similar pattern. By performing 3‟-end mRNA-Seq and using stringent criteria for defining differential rhythmic expression, we show that 15% of the genes with more than one PAS exhibit differential rhythmic expression. In particular, many genes known to be rhythmic in the mouse liver harbor at least one constitutively expressed isoform, while several hundred genes characterized as arrhythmically expressed also exhibit a rhythmic isoform. Analysis of PAS usage in nuclear mRNA and single-cell data reveals that the vast majority of isoform-specific regulation does not involve post-transcriptional regulation (e.g., miRNA targeting, RNA half-life) or cell subtype-specific differences in expression. Finally, characterization of PAS usage in Bmal1-/- mice revealed that co-transcriptional regulation plays a large role in the expression of specific gene isoforms. Taken together, our results indicate that gene isoforms can be differentially regulated, and imply that gene isoforms can behave as distinct transcriptional units. Furthermore, our data suggest that conventional RNA-Seq strategies are not the most appropriate choice for detecting changes in gene isoform expression.

overall_design: 3' mRNA sequencing on WT total, nuclear, and polysomal RNA and Bmal1-/- total RNA from ad libitum-fed mice livers at 6 timepoints in sextuplicate

first: Ben

last: Greenwell


title: Effects of 4-nitrophenol on testicular somatic cells [TM3]


title: Periostin+ stromal cells guide lymphovascular invasion by cancer cells [DSP]

status: Public on May 05 2023

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Cancer cell dissemination to sentinel lymph nodes associates with poor patient outcomes, particularly in breast cancer. The process by which cancer cells egress from the primary tumor upon interfacing with the lymphatic vasculature is complex and driven by dynamic interactions between cancer cells and stromal cells, including cancer associated fibroblasts (CAFs). The matricellular protein periostin can distinguish CAF subtypes in breast cancer and is associated with increased desmoplasia and disease recurrence in patients. However, since periostin is secreted, periostin-expressing CAFs are difficult to characterize in situ, limiting our understanding of their specific contribution to cancer progression. Here, we used in vivo genetic labeling and ablation to lineage trace periostin+ cells and characterize their functions during tumor growth and metastasis. Periostin-expressing CAFs were spatially found at periductal and perivascular margins, were enriched at lymphatic vessel peripheries, and were differentially activated by highly-metastatic cancer cells versus poorly-metastatic counterparts. Surprisingly, genetically depleting periostin+ CAFs slightly accelerated primary tumor growth but impaired intratumoral collagen organization and inhibited lymphatic, but not lung, metastases. Periostin ablation in CAFs impaired their ability to deposit aligned collagen matrices and inhibited cancer cell invasion through collagen and across lymphatic endothelial cell monolayers. Thus, highly-metastatic cancer cells mobilize periostin-expressing CAFs in the primary tumor site that promote collagen remodeling and collective cell invasion within lymphatic vessels and ultimately to sentinel lymph nodes.

overall_design: We used digital spatial profiling (DSP) technology to quantitate transcript in spatially distinct populations of periostin-expressing cells located proximal to lymphatic vessels and near blood vessels and ducts in the naive mammary gland of periostin lineage tracing mice. To quantitate gene expression, we used GeoMx mouse Whole Transcriptome Atlas (WTA) panel from NanoString with fluorescence labelled morphology markers; green fluorescent protein (ZSGreen) for periostin-expressing cells, PDPN for lymphatic vessel marker and SMA for ducts and blood vessels to visualize morphology of tissues on GeoMx DSP platform.

last: Dudley

first: Jamie

middle: L

first: Patcharin

last: Pramoonjago


title: Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics (additional files)

city: Montreal

first: Valerie

last: Mongrain

state: QC

address: 333 rue Saint-Antoine Est

department: Research center

country: Canada

institute: CRCHUM

summary: Here, we investigated the effects of Rhynchophylline (RHY) on the mouse brain spatial transcriptome. More precisely, we injected male and female mice intraperitoneally with either saline (NaCl) or RHY, either at Zeitgeber time (ZT referring to time in hour after light onset) 0 or ZT0 and ZT11. Brains were sampled at ZT4 or ZT14, respectively, and immediately frozen embedded in OCT. Brains were treated and libraries were prepared according to 10x Genomics protocols for Visium Spatial Gene Expression. Sequencing was conducted by Genome Quebec (Montreal, Quebec, Canada). Findings reveal molecular routes by which RHY acts on the brain in a sleep-relevant context. Please cite the original paper when using these data (Ballester Roig et al., Biol Direct, 2023) and see also the submission GSE217058.

overall_design: Brain transcriptome measured 3 to 4 hours after one or two intraperitoneal injection of Rhynchophylline (RHY, 100 mg/kg) conducted at two different times of the day (ZT0 or ZT0 and ZT11) in male and female C57BL/6J mice that were kept under a 12 h light:12 h dark cycle. The same measurements were conducted in mice receiving saline (acting as controls). The total number of samples for this project is thus 8 (one female receiving RHY at ZT0, one female receiving saline at ZT0, one female receiving RHY at ZT0 and ZT11, one female receiving saline at ZT0 and ZT11, one male receiving RHY at ZT0, one male receiving saline at ZT0, one male receiving RHY at ZT0 and ZT11, one male receiving saline at ZT0 and ZT11). The brain transcriptome was quantified with the Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics). Original fastq files and processed files were uploaded at GSE217058. However, raw fastq files for two samples were damaged during file storage and are missing (i.e., female receiving RHY at ZT0 and female receiving saline at ZT0 and ZT11). Here we provide the BAM files of these two samples (ZT4_F_RHY and ZT14_F_Saline) which were created with the pipeline ''spaceranger count'' with the original uncorrupted fastq files. These BAM files can be used to reconstitute the corresponding fastq files using the bamtofastq tool.

first: Maria Neus

last: Ballester Roig

first: Julien

last: Dufort-Gervais


title: T-CAST: An optimized CAST-Seq pipeline for TALEN reveals superior safety and efficacy of obligate-heterodimeric scaffolds

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Transcription activator-like effector nucleases (TALENs) are programmable nucleases that have entered the clinical stage. Each subunit of the dimer consists of a DNA-binding domain composed of an array of TALE repeats fused to the catalytically active  portion of the FokI endonuclease. Upon DNA-binding of both TALEN arms in close proximity, the FokI domains dimerize and induce a staggered-end DNA double strand break. In this present study, we describe the implementation and validation of TALEN-specific  CAST-Seq (T-CAST), a pipeline based on CAST-Seq that identifies TALEN-mediated off-target effects, nominates off-target sites with high fidelity, and predicts the TALEN pairing conformation leading to off-target cleavage. We validated T-CAST by assessing  off-target effects of two promiscuous TALENs designed to target the CCR5 and TRAC loci. Expression of these TALENs caused high levels of translocations between the target sites and various off-target sites in primary T cells. Introduction of amino acid  substitutions to the FokI domains, which render TALENs obligate-heterodimeric (OH-TALEN), mitigated the aforementioned off-target effects without loss of on-target activity. Our findings highlight the significance of T-CAST to assess off-target effects of  TALEN designer nucleases and to evaluate mitigation strategies, and advocate the use of obligate-heterodimeric TALEN scaffolds for therapeutic genome editing.

overall_design: T cells expanded from PBMCs were treated with either wild type or obligate heterodimeric TALE nucleases targeting the clinically relevant loci TRAC and CCR . In total 16 paired-end samples were processed, including 12 samples treated with nulceases. The cells were harvested approximately one week after TALEN transfer and CAST-Seq was performed to assess the formation of stable translocations between the on-target site and various newly detected off-target sites.

first: Manuel

last: Rhiel

first: Tatjana

last: Cornu

first: Melanie

last: Boerries

first: Toni

last: Cathomen


title: Knockdown of the transcription regulators Spt5 and dom in Drosophila photoreceptors results in premature retinal degeneration and transcriptional signature similar to old flies

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

summary: Aging is associated with a decline in visual function and increased prevalence of ocular disease, correlating with changes in the transcriptome and epigenome of cells in the eye. Here, we sought to test if age-associated changes in gene expression patterns in the eye directly contribute to the increased risk of retinal degeneration. To do this, we performed a targeted photoreceptor specific RNAi screen in Drosophila to identify gene regulatory factors that result in premature, age-dependent retinal degeneration. From an initial set of 155 RNAi lines each targeting a unique gene and spanning a diverse set of gene regulatory factors, we identified 18 high confidence target genes whose decreased expression in adult photoreceptors leads to premature and progressive retinal degeneration. The 18 target genes were enriched for factors involved in the regulation of transcription initiation, pausing, and elongation, suggesting that these processes are essential for maintaining the health of aging photoreceptors. To identify the genes regulated by these factors, we profiled the photoreceptor transcriptome in a subset of lines. Strikingly, two of the 18 target genes, Spt5 and domino, show substantially similar changes in gene expression to those observed with advanced age. Together, our data suggests that dysregulation of the mechanisms involved in transcription initiation and elongation plays a key role in shaping the transcriptome of aging photoreceptors. Further, our findings indicate that the age-dependent changes in gene expression not only correlate, but might also contribute to increased risk of retinal degeneration.

overall_design: RNA-seq

first: Spencer

last: Escobedo

first: Vikki

last: Weake


title: Epigenome analysis of a paraganglioma sample carrying the DLST-p.Y422C mutation [methylation array]

city: Madrid

first: Alberto

last: Cascón

address: Melchor Fernández Almagro 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Genome wide DNA methylation profiling of a paraganglioma sample carrying the DLST-p.Y422C mutation. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2 was used to obtain a DNA methylation profile across approximately 850,000 CpGs. The main goal of this project was to find specific methylation profiles associated to the presence of mutations in the DLST gene of pheochromocytomas/paragangliomas.

overall_design: Bisulphite converted DNA from the tumor sample was hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Mellid

last: Sara

first: Robledo

last: Mercedes

first: Cascon

last: Alberto


title: Gene expression analysis of a paraganglioma sample carrying the DLST-p.Y422C mutation

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of a paraganglioma sample carrying the DLST-p.Y422C mutation. The main goal of this project was to find specific gene expression profiles associated to the presence of mutations in the DLST gene of pheochromocytomas/paragangliomas.

overall_design: Gene expression profiling of RNA-seq data from a paraganglioma sample carrying the DLST-p.Y422C mutation

first: Cascón


title: Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics

summary: Here, we investigated the effects of Rhynchophylline (RHY) on the mouse brain spatial transcriptome. More precisely, we injected male and female mice intraperitoneally with either saline (NaCl) or RHY, either at Zeitgeber time (ZT referring to time in hour after light onset) 0 or at ZT0 and ZT11. Brains were sampled at ZT4 or ZT14, respectively, and immediately frozen embedded in OCT. Brains were treated and libraries were prepared according to 10x Genomics protocols for Visium Spatial Gene Expression. Sequencing was conducted by Genome Quebec (Montreal, Quebec, Canada). Findings reveal molecular routes by which RHY acts on the brain in a sleep-relevant context. Please cite the original paper when using these data (Ballester Roig et al., Biol Direct, 2023).

overall_design:
Brain transcriptiome measured 3 to 4 hours after one or two intraperitoneal injection of Rhynchophylline (RHY, 100 mg/kg) conducted at two different times of the day (ZT0 or ZT0 and ZT11) in male and female C57BL/6J mice that were kept under a 12 h light:12 h dark cycle. The same measurements were conducted in mice receiving saline (acting as controls). The total number of samples for this project is thus 8 (one female receiving RHY at ZT0, one female receiving saline at ZT0, one female receiving RHY at ZT0 and ZT11, one female receiving saline at ZT0 and ZT11, one male receiving RHY at ZT0, one male receiving saline at ZT0, one male receiving RHY at ZT0 and ZT11, one male receiving saline at ZT0 and ZT11). The brain transcriptome was quantified with the Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics).
***Please note that raw fastq files for two samples have been damaged during file storage and thus are not provided (female receiving RHY at ZT0 and female receiving saline at ZT0 and ZT11). BAM files of these two samples are provided in GSE218537.***


title: Analysis of a paraganglioma sample carrying the DLST-p.Y422C mutation

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

overall_design: Refer to individual Series


title: Transcriptomic changes of sleep and genotype dependent states in 5xFAD mouse model of amyloidosis.

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Our aim was to investigate whether and how changes in sleep influences microglial function in the brain. We chronically sleep deprived mice expressing humanized TREM2 common variant, and mice without TREM2 expression in the presence or absence of amyloid plaques (Aβ).

overall_design: Hippocampal mRNA profiles of 4 months old 5xFAD and wild-type mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.

first: Samira

last: Parhizka

first: David

middle: M

last: Holtzman


title: Shrimp transcriptome analysis after exposure to recombinant Vibrio parahaemolyticus PirA and PirB toxins

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Vibrio parahaemolyticus is a Gram-negative bacterium commonly found in marine and estuarine environments. Acute hepatopancreatic necrosis disease (AHPND) caused by this bacterium is an ongoing problem among shrimp farming industries. V. parahaemolyticus proteins PirA and PirB have been determined to be major virulence factors that induce AHPND. In this study, Pacific white shrimp (Litopenaeus vannamei) were challenged with recombinant PirA and PirB by a reverse gavage method and then at 30 m, 1, 2, 4, and 6 h time points, the hepatopancreas of five individual shrimp were removed and placed into RNA later. We conducted RNA sequencing of the hepatopancreas samples from a no PirA/B control (n = 5) and PirA/B-treated shrimp at the different time intervals (n=5). We evaluated the different gene expression patterns between the time groups to the control with a focus on identifying differences in innate immune function.

overall_design: Total 60 samples from shrimp exposed to pirAB toxins at timepoints 0.5h, 1h, 2h, 4h, and 6h compared against control condition (buffer-only at 0.5h), 5 replicates from each condition.

first: Anna

last: Rawles

first: Miles

middle: D

last: Lange

first: Craig

last: Shoemaker

first: Dunhua

last: Zhang

first: Troy

last: Bader

first: Benjamin

middle: H

last: Beck


title: Translational fidelity screens reveal eIF3 as a key regulator of start codon selectivity [RNA-seq]

city: Cambridge

first: Richard

last: She

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

summary: To investigate the function eIF3D, eIF1A, eIF4G2, and ZNF324 in near-cognate start codon usage, we established K562, HeLa, and Jurkat cell lines in which each target gene has been knocked down by CRISPRi sgRNAs.

overall_design: We then performed RNA-seq in K562 cells depleted of all target genes and RNA-seq in HeLa and Jurkat cells depleted for eIF3D.

first: Jonathan

last: Weissman


title: Transcriptome analysis of the transgenic and non-transgenic fleshy roots

status: Public on May 04 2023

city: Nanjing

first: Bo

last: mianWang

address: 1 weigang road, Nanjing, China.

department: College of Horticulture

institute: Nanjing Agricultural University

summary: Effect of betanin synthesis on the metabolism of transgenic carrot. Betalain is a natural pigment with important nutritional value and broad application prospects. Previously, we produced betanin biosynthesis transgenic carrots via expressing optimized genes CYP76AD1S, cDOPA5GTS and DODA1S. Betanin can accumulate throughout the whole transgenic carrots. But the effects of betanin accumulation on the metabolism of transgenic plants and whether it produces unexpected effects are still unclear.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of the transgenic and non-transgenic fleshy roots. In our previous study, stably transformed carrot lines containing CYP76AD1S, cDOPA5GTS and DODA1S genes can synthesize and accumulate betanin in the whole plant. In addition, metabolic changes were analyzed by transcriptome between betanin-transgenic carrots (BC) and non-transgenic carrots (WT) in this study.

last: Wang


title: The transcription factor Foxp1 regulates aerobic glycolysis in adipocytes and myocytes

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

summary: The goal of this study was to apply Next Generation Sequencing analyses to identify genes and pathways regulated by the Foxp1 transcription factor in 3T3-L1 adipocytes. We found, that series of genes involved in metabolism, glycolysis, signal transduction, as well as nervous system development are regulated in response to overexpression and knock down of this transcription factor, thereby providing important insight into biological role of Foxp1 for cells survival and metabolism.

overall_design: Next Generation Sequencing analyses of 3T3-L1 adipocytes with overexpression and downregulation of Foxp1

first: Sven

last: Enerback

first: Haixia

last: Ma

first: Valentina

last: Sukonina

first: Wei

first: Chandrasekhar

last: Kanduri


title: Expression of miR-381-3p is elevated in the retina of OIR mice, but the role in the retinal neovascularization is elusive，and its mechanism of action was investigated by vitreous injection of miR-381-3p antagomir

city: Shen Yang

first: Tian

middle: Qi

last: Cheng

state: Liao ning

address: Qiuyuehu Street, Shenbei New District

institute: Chinese Medical University

summary: To investigate the mechanism of miR-381-3p  in the OIR mice retinal tissues  OIR mice.

overall_design: At P12, OIR mice were intravitreal injected with 1 nmol miR-381-3p antagomir (n=3) or 1 nmol antagomir nc (n=3). Mice were euthanized at P17, the total RNA of OIR mice retina was extracted with TRNzol kit. Subsequently, the RNA-seq library was prepared and sequenced in Novagene company.

first: QiCheng

last: Tian


title: Single-nucleus atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

city: Saint Louis

first: Sanjay

last: Jain

state: MO

address: 660 S. Euclid Ave.

department: Division of Nephrology

institute: Washington University in Saint Louis

summary: Kidney stone disease causes significant morbidity and increases health care utilization. In this dataset, we applied a single-nucleus assay to renal papila samples in order to charachterize the cellular and molecular niches in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.

overall_design: Nuclei from papilla were isolated from Kidney and analyzed using snRNAseq.

first: Madhurima

last: Kaushal

first: Ricardo

last: Melo Ferreira

first: Blue

middle: B

last: Lake

first: Michael

last: Eadon

first: Tarek

last: El-Ashcar


title: Effect of meiosis specific cohesin subunit SMC1 on chromatin architecture in primary murine spermatocytes [RNA-Seq 2]

city: Dresden

first: Rolf

last: Jessberger

state: Saxony

address: Fetscherstraße 74

department: Institut für Physiologische Chemie

institute: Technische Universität Dresden

summary: To investigate the function of meiosis-specific SMC1beta on chromatin architecture near the telomeric end in primary murine spermatocytes we used a SMC1beta knockout mouse model.

overall_design: Further to study seperation of function of universal cohesin subunit SMC1alpha and meiosis specific SMC1beta, we compared open chromatin between SMC1b knockout spermatocytes and SMC1alpha overexpressed in a SMC1beta knockout mouse model.

first: Uddipta

last: Biswas

first: Tanaya

last: Mallik

first: Johannes

last: Pschirer

first: Mathias

last: Lesche

first: Katrin

last: Sameith


title: Effect of meiosis specific cohesin subunit SMC1 on chromatin architecture in primary murine spermatocytes [RNA-Seq 1]


title: Effect of meiosis specific cohesin subunit SMC1 on chromatin architecture in primary murine spermatocytes [ATAC-Seq]


title: Cytokinopathy with aberrant cytotoxic lymphocytes and profibrotic myeloid response in SARS-CoV-2 mRNA vaccine-associated myocarditis

city: New Haven

first: Anis

last: Barmada

state: CT

address: 300 Cedar Street

department: Department of Immunobiology

institute: Yale University

summary: Rare immune-mediated cardiac tissue inflammation can occur after vaccination, including after SARS-CoV-2 mRNA vaccines, yet the underlying immune cellular and molecular mechanisms driving this pathology remain poorly understood. Here, we investigated the systemic immunopathological landscape underlying such rare cases of myopericarditis occurring after SARS-CoV-2 LNP-mRNA vaccination using peripheral blood single-cell transcriptome and repertoire sequencing, among other multimodal approaches.

overall_design: For single-cell sequencing, PBMCs were analyzed from a cohort of patients during acute myocarditis/pericarditis shortly after SARS-CoV-2 LNP-mRNA vaccination (n = 4), in comparison to recovered patients more than six months after vaccination (n = 3) as well as healthy vaccinated controls (n = 4).


title: Epiploic Adipose Tissue (EPAT) in Obese Individuals Promotes Colonic Tumorigenesis: A Novel Model for EPAT-Dependent Colorectal Cancer Progression

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1430 Tulane Ave

department: Pathology & Laboratory Medicine

institute: Tulane University

summary: The obesity epidemic is associated with increased colorectal cancer (CRC) risk and progression, the mechanisms of which remain unclear. In obese individuals, hypertrophic epiploic adipose tissue (EPAT), attached to the colon, has unique characteristics compared to other fats. We hypothesized that this understudied fat could serve as a tumor-promoting tissue and developed a novel microphysiological system (MPS) for human EPAT-dependent colorectal cancer (CRC-MPS). In CRC-MPS, obese EPAT, unlike lean EPAT, considerably attracted colon cancer HT29-GFP cells and enhanced their growth. Conditioned media (CM) from the obese CRC-MPS significantly increased the growth and migration of HT29 and HCT116 cells (p< 0.001). In HT29 cells, CM stimulated differential gene expression (hOEC867) linked to cancer, tumor morphology, and metabolism similar to those in the colon of high-fat-diet obese mice. The hOEC867signature represented pathways found in human colon cancer. In unsupervised clustering, hOEC867separated transcriptomes of colon cancer samples from normal with high significance (PCA,p =9.6 × 10−11). These genes, validated in CM-treated HT29 cells (p< 0.05), regulate the cell cycle, cancer stem cells, methylation, and metastasis, and are similarly altered in human colon cancer (TCGA). These findings highlight a tumor-promoting role of EPAT in CRC facilitated with obesity and establishes a platform to explore critical mechanisms and develop effective treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT29 cells  treated with conditioned media from ESC-only MPS and obese EPAT MPS

first: Rida

last: Iftikhar

first: Patricia

last: Snarski

first: Angelle

middle: N

last: King

first: Jenisha

last: Ghimire

first: Emmanuelle

last: Ruiz

first: Frank

last: Lau


title: Effect of meiosis specific cohesin subunit SMC1 on chromatin architecture in primary murine spermatocytes


title: Cell State Dependent Alteration of Melanoma Plasticity and Immunity by the Circadian Transcription Factor Bmal1 [ChIP-Seq II]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The circadian transcription factor Bmal1 accelerates melanoma tumorigenesis through initial cell state dependent mechanisms in which Hif1??, Sox9 or Myh9, MRTF-SRF, AP-1 are involved and modulate tumor microenvironment to favor tumor growth

overall_design: CHIP-seq of H3K27ac in cells of different Bmal1 and H3K27ac and H3K4me3 of different Myh9 status

first: Chi

last: Dang

first: Xue

last: Zhang


title: Transcriptome analysis of aging mouse heart compared with adult heart

city: Zhengzhou

first: zhenglong

last: guo

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: To identify the gene regulatory network during heart aging, we used the RNA-seq to analyze the gene expression profile difference between adult mouse heart and aging mouse heart.

overall_design: 6-8 week adult C57BL6 mouse heart ventricle and 24-26 month aged C57BL6 mouse heart ventricle were collected, mRNA profiles were generated by deep sequencing, in triplicate, using BGIseq500 platform.

first: Zhenglong

last: Guo

first: Bingtao

last: Hao


title: Cell fusion with type 2 macrophage induce heterogeneity of melanoma cells that potentiate immunological escape from cytotoxic T lymphocytes

city: Sapporo

first: Tomoyuki

last: Minowa

state: Hokkaido

address: west 17, south 1, Chuo-ku

department: Pathology

institute: Sapporo medical university school of medicine

summary: Evasion from immunity is a major obstacle for achievement of successful cancer immunotherapy. Hybrids derived from cell-cell fusion is a theory associated with tumor heterogeneity and progression by conferring novel properties to tumor cells, such as drug resistance or metastatic capacity; however, its impact on immune evasion remains still unknown. Here, we investigated the potency of hybrids in immune evasion using tumor-macrophage hybrids. Hybrids were established by co-culture of a melanoma cell line, A375 and type 2 macrophages. The hybrids showed higher migration ability and higher tumorigenicity than those of the parental melanoma cells. We found that the hybrids were less sensitive to T cell receptor (TCR) specific for NY-ESO-1 transduced T cells (TCR-T cells) than parental melanoma cells, although hybrids and parental melanoma cells showed equivalent NY-ESO-1 expression. An in vitro tumor heterogeneity model revealed that TCR-T cells preferentially killed parental cells than hybrids and the survival rate of hybrids were higher than that in parental cells indicating hybrids evade from killing by TCR-T cells efficiently. A single cell analysis data set revealed that a few macrophage cells expressed melanoma differentiation antigens including gp100, MART-1 and tyrosinase, indicating hybrids exist in primary melanoma, and number of potential hybrids were corelated with poorer response to immune checkpoint blockade. These results provide evidence that melanoma-macrophage fusion has a role in tumor heterogeneity and immune evasion.

overall_design: Comparative gene expression profiling analysis of CAGE-seq data for A375 cell line and its hybrid clone fused with  peripheral monocyte derived macrophages.

first: Yoshihiko

last: Hirohashi

first: Kenji

last: Murata

first: Kenta

last: Sasaki

first: Toshiya

last: Handa

first: Munehide

last: Nakatsugawa

first: Yuka

last: Mizue

first: Aiko

last: Murai

first: Terufumi

last: Kubo

first: Takayuki

last: Kanaseki

first: Tomohide

last: Tsukahara

first: Sadahiro

last: Iwabushi

first: Shinichi

last: Hashimoto

first: Akemi

last: Ishida-Yamamoto

first: Hisashi

last: Uhara

first: Toshihiko

last: Torigoe


title: Single-Nucleus Chromatin Accessibility Identifies a Critical Role for TWIST1 in IPF Myofibroblast Activity

city: Pittsburgh

first: Tracy

last: Tabib

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Multiomic single-cell analyses on human IPF lungs identify a global opening of TWIST1 and other E-box motifs in IPF myofibroblasts, with in vivo murine models confirming a critical regulatory function for TWIST1 in IPF myofibroblast activity.

overall_design:
We performed single-nucleus ATAC sequencing (snATAC-seq) on explanted lungs from patients with IPF (n=3) and donor controls (n=2) and integrated this with a larger scRNA-seq dataset (n=10 IPF, 8 control) to identify differentially accessible chromatin regions and enriched TF motifs within lung cell populations.  We performed RNA-sequencing on pulmonary fibroblasts of bleomycin-injured Twist1-overexpressing Col1a2 Cre-ER mice to examine alterations in fibrosis-relevant pathways following Twist1 overexpression in collagen producing cells.

This Series includes human samples.

first: Eleanor

last: Valenzi

first: Harinath

last: Bahudhanapati

first: Jiangning

last: Tan

first: Daniel

last: Sullivan

first: Mehdi

last: Nouraie

first: John

last: Sembrat

first: Li

last: Fan

first: Kong

last: Chen

first: Mauricio

last: Rojas

first: Audrey

last: Lafargue

first: Dean

middle: W

last: Felsher

first: Phuoc

middle: T

last: Tran

last: Kass

first: Robert

last: Lafyatis


title: A hPSC system for characterizing MUC5B-expressing airway epithelia

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: scRNA-seq of air-liquid interface airway epithelial cultures derived from a human fluorescent reporter hPSC line labeling MUC5B-expressing cells

overall_design: A biallelic MUC5B-tdTomato reporter hPSC line was generated from an individual with progressive fibrotic interstitial lung disease and homozygous for the MUC5B rs35705950 risk allele.  Derived airway-ALI cultures were differentiated from this line and sequenced 21 days following air-phase transition.

first: Sheng

last: Si

first: Darrell

last: Kotton


title: Cell State Dependent Alteration of Melanoma Plasticity and Immunity by the Circadian Transcription Factor Bmal1 [ChIP-Seq]

first: Priyankara

last: Wickramasinghe

overall_design: CHIP-seq of H3K4me3 and H3K27me3 in cells of different Bmal1 status

first: Chi

last: Dang

first: Xue

last: Zhang


title: Cell State Dependent Alteration of Melanoma Plasticity and Immunity by the Circadian Transcription Factor Bmal1 [scRNA-Seq]

overall_design: RNA-seq of different Bmal1 status


title: Cell State Dependent Alteration of Melanoma Plasticity and Immunity by the Circadian Transcription Factor Bmal1

overall_design: Refer to individual Series


title: Genome-wide characterization of the Caenorhabditis elegans intestine GATA transcription factor ELT-2

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

summary: ELT-2 is the major transcription factor required for Caenorhabditis elegans intestinal development. It initiates in embryos to promote development then persists after hatching through larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are described, a major missing piece has been the lack of an intestine-specific transcriptome profile over developmental time. We generated this dataset by Fluorescence Activated Cell Sorting (FACS) intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate ELT-2’s role in directing the intestinal regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional transcription factors promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2’s direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Indeed, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20 – 50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that our current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.

overall_design: mRNA-seq transcriptome profilng performed on FACS sorted C. elegans cells at three developmental stages: mixed embryo, L1 larval stage, and L3 larval stage. FACS enrichme elt-2promoter::GFP marker strain; GFP minus FACS sorted cells and the sum of GFP+ and GFP- cells are included as controls; un-sorted, dissociated cells are included as controls

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