title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [ChIP-Seq]

first: Aleksandra

last: Kornienko

overall_design: We performed this ChIP-seq to analyze epignetic patterns and silencing of lncRNAs in Arabidopsis thaliana. plants from many different A.thaliana natural accessions (https://1001genomes.org/accessions.html) were grown at the growth chambers of GMI, Vienna, Austria. 14 accessions were used for ChIP-sequencing with replicates corresponding to different growing batches, or in the case of not enough material - pooling samples from two-three batches. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). Mature leaves (not the oldest and not the youngest) from 2-3 individual plants were collected for each accession and snap frozen in liquid nitrogen. Leaves were collected when the plants reached 14-16-leaf stage prior to the start of bolting. Frozen tissue was ground with a Retsch machine using steel beads. Chromatin immunoprecipitation was performed with a protocol adapted from [Yelagandula R et al, Cell 2014]. Briefly, 1-2 grams of ground frozen leaf tissue was fixated with formaldehyde at 4oC for 5 min, then nuclei were isolated and lysed, and chromatin was fragmented using Covaris E220 Focused-ultrasonicator. The input sample was then taken out and frozen at -20oC and 5 antibody reactions were processed together. The antibodies used were: H1 (Agrisera) - 3 microgram per reaction, H3K4me3 (Abcam) - 3 microgram per reaction , H3K9me2 (Abcam) - 4 microgram per reaction, H3K27me3 (Millipore) - 4 microgram per reaction, H3K36me3 (Abcam) - 4 microgram per reaction. The immunoprecipitation was performed using pre-washed Dynabeads Protein A magnetic beads (Invitrogen) and ran overnight. Afterwards the samples were washed, followed by elution, overnight reverse-crosslinking, RNAse A (Fermentas) treatment for 30 min at room temperature, and DNA isolation using Qiagen PCR purification kit Qiaquick with 0.3M Sodium Acetate. Next, ChIP-seq libraries were prepared from a half of the resulting sample (due to very low amounts we did not measure the DNA concentrations) with the NEBNext Ultra II DNA kit (New England Biolabs) according to the manufacturer’s protocol and sequenced with 100bp single-end read mode on Illumina NovaSeq 6000 machine.

first: Viktoria

last: Nizhynska


title: Genome-wide H3K27me3 analysis in Arabidopsis

status: Public on Feb 28 2023

city: shanghai

first: li

last: peng

country: China

institute: PSC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To explore the bivalent histone modifications in the Arabidopsis genome, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) and histone 3 lysine-4 trimethylation (H3K4me3) in 5-day-old seedlings (Col-0) by ChIP-seq. We found that more than 1300 genes loci contain both H3K27me3 and H3K4me3.

overall_design: Nuclei were extracted from 5-day-old WT (Col-0) seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on X Ten (Illumina). Three biologically independent samples have been analyzed.

first: Yang

last: Ou

first: Yuehui

last: He


title: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq]

status: Public on Feb 15 2023

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

summary: Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.

overall_design: It is reported that the CRE variants are associated with many important agronomic traits. In this study, we unravelling the transcriptional network underlying wheat grain development by combing ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) and RNA-seq with samples from a series of time points.


title: Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders

status: Public on Feb 12 2023

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

country: USA

institute: University of Iowa

type: Expression profiling by high throughput sequencing

summary: We report two bulk transcriptomic datasets of striatum from male and female mice carrying either the 16p11.2 hemideletion of 3 genes hemideletion knockout within this region.

overall_design: We performed bulk RNA sequencing gene expression analysis obtained from mouse striatum for two paradigms in both males and females: the full 16p11.2 hemideletion of 27 genes (16pdelhet vs. 16pdelhetWT) and the 3 genes knockout (3geneKOMut vs 3geneKOWT).

first: Jaekyoon

last: Kim

first: Zeru

last: Peterson

first: Benjamin

last: Kelvington

first: Marie

middle: E

last: Gaine

first: Thomas

last: Nickl-Jockschat

first: Ted

last: Abel


title: Identifying potential hepatic genes regulating the ovine response to gastrointestinal nematodes using RNA-Sequencing

status: Public on Feb 10 2023

city: Guelph

first: Samantha

last: Dixon

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

country: Canada

institute: University of Guelph

summary: Gastrointestinal nematode (GIN) infections are considered the most important disease of grazing sheep. Due to increasing anthelmintic resistance, chemical control alone is inadequate. Resistance to GIN infection is a heritable trait, and through natural selection many sheep breeds have higher resistance. Studying the transcriptome from GIN-exposed and GIN-unexposed sheep using RNA-Sequencing technology can provide measurements of transcript levels associated with the host response to GIN infection, and these transcripts may harbor genetic markers that can be used in selective breeding programs to enhance disease resistance. The objective of this study was to compare liver transcriptomes of sheep naturally exposed to GINs, with either high or low parasite burdens, to GIN-unexposed control sheep in order to identify key regulator genes and biological processes associated with GIN infection. Differential gene expression analysis revealed no significant differentially expressed genes (DEG) between sheep with a high or low parasite burden (P-value ≤ 0.01; False Discovery Rate (FDR) ≤ 0.05; and Fold-Change (FC) of > 2). However, when compared to the control group, low parasite burden sheep showed 159 DEG, and high parasite burden sheep showed 146 DEG (P-value ≤ 0.01; FDR ≤ 0.05; and FC of > 2). Among these two lists of significant DEG, 86 DEG were found in common between the two parasite burden groups compared to the control (GIN-unexposed sheep). Functional analysis of these significant 86 DEG found upregulated genes involved in immune response and downregulated genes involved in lipid metabolism. Results of this study offer insight into the liver transcriptome during natural GIN exposure that helps provide a better understanding of the key regulator genes involved in GIN infection in sheep.

overall_design: Compare liver transcriptomes of sheep naturally exposed to GINs, with either high (n=6) or low (n=5) parasite burdens, to GIN-unexposed control sheep (n=4).

first: Niel

middle: A

last: Karrow

first: Emma

last: Borkowski

first: Aroa

last: Suarez-Vega

first: Paula

middle: I

last: Menzies

first: Delma

last: Kennedy

first: Andrew

middle: S

last: Peregrine

first: Bonnie

last: Mallard

first: Ángela

last: Cánovas


title: Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability II

status: Public on Feb 07 2023

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

overall_design: It includes total 14 samples. pat1, pat1dhh1 (triplicates) and edc3scd6 (duplicates) were subjected to RNA-Seq. Separately, WT and dcp2 in triplicates (6 samples) were subjected to Rpb1 ChIP-seq. All strains were grown in YPD at 30ºC till the OD600 ~0.6

first: Anil

middle: K

last: Vijjamarri

first: Xiao

last: Niu

first: Matthew

middle: D

last: Vandermeulen

first: Chisom

last: Onu

first: Fan

last: Zhang

first: Hongfang

last: Qui

first: Neha

last: Gupta

first: Swati

last: Gaikwad

first: Miriam

middle: L

last: Greenberg

first: Paul

middle: J

last: Cullen

first: Zhenguo

last: Lin


title: Interleukin-27-dependent transcriptome signatures regulation of the transcriptome  during neonatal sepsis [ATAC-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Human newborns exhibit increased vulnerability and risk of mortality from infection. Increased susceptibility to infection during the neonatal period reflects key differences in the innate and adaptive immune responses relative to those in adult cells. We have previously shown an increase in the pleiotropic immune suppressive cytokine, IL-27, in macrophages derived from human umbilical cord blood compared with those obtained from adult peripheral blood. Similar findings exist in the neonatal murine system, as well as elevated splenic transcripts and serum levels. Recently, we established a murine model of neonatal sepsis to explore the impact of early life IL-27 levels on the host response to infection. In this model, neonatal mice deficient in IL-27 signaling exhibit reduced mortality, increased weight gain, and better control of the bacterial burden with reduced systemic inflammation. These results suggest that there is a reprogramming of the host response in the presence of IL-27 signaling. To explore this hypothesis, we profiled the neonatal transcriptome of the spleen in the presence or absence of Escherichia coli-induced sepsis in wild-type (WT) and IL-27Rα-deficient mice.  The spleen, a known site of infection, exhibits increased IL-27 expression and bacterial burdens in WT pups that were significantly lower in IL-27Rα KO pups during infection. We identified 549 genes that were differentially expressed in WT neonates in response to E. coli infection. The upregulated genes were associated with inflammation, cytokine signaling, and G protein coupled receptor ligand binding and signaling. The expression level of these genes generally failed to increase in IL-27Rα KO mice upon the E. coli infection. We observed similar changes in gene expression, aligned with changes in chromatin accessibility, for macrophages isolated from the spleens of control and infected neonates with or without IL-27Rα KO, supporting macrophages as an innate myeloid population contributing to the inflammatory profile in septic WT pups.  Collectively, our findings highlight a less inflammatory environment in KO pups that is not expected given the anti-inflammatory/suppressive activity of IL-27. However, it is consistent with a lower bacterial burden. This suggests that improved bacterial clearance in the absence of IL-27 signaling does not require a heightened inflammatory state, and instead, there is a direct relationship between IL-27 signaling and bacterial killing. An improved response to infection that is not reliant upon heightened levels of inflammation offers new promise to the potential of antagonizing IL-27 as a host-directed therapy for neonates without concern for driving inflammatory responses that are pathological to host tissues.

overall_design: Four-day old C57BL/6 pups were sorted into four groups based on IL27RA status (KO or wild type) and based on infection status with Escherichia coli strain O1:K1:H7 infection (with or without infection; 24 hours). For each of the four group, PolyA RNA-seq were performed for spleen tissue and for myeloid cells enriched from the spleen. Additional ATAC-seq assay to measure chromatin accessibility was performed for myeloid cells from each group.

first: Jessica

middle: M

last: Povroznik

first: Halima

last: Akhter

first: Jordan

last: Vance

first: Madhavi

last: Annamanedi

first: Sebastian

last: Dziadowicz

first: Lei

last: Wang

first: Ashley

last: Divens

first: Cory

last: Robinson


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues [spatial CUT&Tag]

status: Public on Jan 29 2023

city: New Haven

first: Di

address: 55 Prospect St

institute: Yale University

summary: We present spatially resolved high-spatial-resolution genome-wide co-mapping of epigenome and transcriptome by simultaneously profiling of chromatin accessibility and gene expression (spatial-ATAC-RNA-seq), as well as histone modification and gene expression (spatial-CUT&Tag-RNA-seq) on the same tissue section at cellular level by combining the microfluidic deterministic barcoding strategy in DBiT-seq and the chemistry used in ATAC-seq/CUT&Tag.

overall_design: Spatially resolved co-sequencing of epigenome and transcriptome in mouse brains.

first: Rong

last: Fan


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues [Human RNA-Seq]

last: Zhang

state: CT

department: Biomedical Engineering

overall_design:
Spatially resolved co-sequencing of epigenome and transcriptome in Human hippocampus

*** Submitter declares that the raw data have not been submitted due to patient privacy concerns ***


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues [RNA-Seq]

overall_design: Spatially resolved co-sequencing of epigenome and transcriptome in mouse embryos and mouse brains.

first: Yanxiang

last: Deng


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues [ATAC-Seq]


title: A virus-borne DNA damage signaling pathway controls the lysogeny-induction switch of a group of temperate pleolipoviruses

status: Public on Feb 11 2023

city: wuhan

first: chen

last: zhao

state: huibei

address: luojiashan

department: college of life sciences

institute: wuhan university

summary: To determine the difference in gene expression of SNJ2 genes with and without MMC treatment, Natrinema sp. J7-1 was incubated to middle exponential phase (OD600=0.6-0.8) in Halo-2 medium and treated with MMC

overall_design: Cell samples were then collected at 0, 1, 4 and 9h after MMC treatment. RNA extraction and RNAseq was performed

first: Zhao

last: Chen

first: Ying

last: Liu

first: Shishen

last: Du

first: Xiangdong


title: Individualized mRNA Neoantigen Vaccines provoke substantial T cell immunity in Pancreatic Cancer

status: Public on Feb 01 2023

city: New York

first: Zachary

last: Sethna

state: NY

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Phase 1 trial of individualized mRNA vaccine for Pancreatic Cancer. We used scRNA-seq to characterize the phenotype of vaccine associated T cells.

overall_design: 5 samples, TCR and GEX

first: Luis

last: Rojas

first: Kevin

middle: C

last: Soares

first: Cristina

last: Olcese

last: Pang

first: Erin

last: Patterson

first: Jayon

last: Lihm

first: Nicholas

last: Ceglia

first: Alexander

last: Chu

first: Rebecca

last: Yu

first: Adrienne

last: Chandra

first: Theresa

last: Waters

first: Jennifer

last: Ruan

first: Masataka

last: Amisaki

first: Pablo

last: Guasp

first: Abderezak

last: Zebboudi

first: Zagaa

last: Odgerel

first: Evelyna

last: Derhovanessian

first: Felicitas

last: Müller

first: Ina

last: Rhee

first: Mahesh

last: Yadav

first: Anton

last: Dobrin

first: Michel

last: Sadelain

first: Marta

last: Luksza

first: Noah

last: Cohen

first: Laura

last: Tang

first: Olca

last: Basturk

first: Mithat

last: Gönen

first: Seth

last: Katz

first: Richard

last: Do

first: Andrew

last: Epstein

first: Parisa

last: Momtaz

first: Wungki

last: Park

first: Ryan

last: Sugarman

first: Anna

last: Varghese

first: Elizabeth

last: Won

first: Avni

last: Desai

first: Alice

last: Wei

first: Michael

last: D'Angelica

first: T

middle: P

last: Kingham

first: Ira

last: Mellman

first: Taha


title: Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [RNAseq_Riboseq]

status: Public on Feb 09 2023

city: Tel Aviv

first: Shir

last: Mandelboum

address: chaim levanon

department: Sagol School of Neuroscience

country: Israel

institute: Tel Aviv University

summary:
We optimized a standard polysome profiling protocol considering the unique morphology and ribosomal distribution of astrocytes.
This ‘astrocyte-optimized’ protocol was then used to study primary astrocytes treated with proinflammatory cytokines,
enabeling Ribo-seq analysis for measurment of the transcriptome, translatome, and translation efficiency with a coverage of over 12,000 genes.
We found several regulation strategies of gene expression executed as part of an extensive inflamatory response.
Enhanced translation efficiency was one of these strategies, used specifically for genes related to oxidative phosphorylation, and ribosomal proteins.

overall_design:
Three biological repetitions of primary astrocytes were treated or not with 20ng/ml TNFα and 0.25ng/ml IL-1β  for 24 hr or 48 hr.
A portion of each sample was treated with RNase-I to generate ribosome footprints used for Ribo-seq analysis, while an undigested portion was used for RNA-seq.

first: Melisa

last: Herrero Boco

first: Andrea

last: Atzmon

first: Orna

last: Elroy-Stein


title: Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [Heavy_complex_RNAseq]

summary:
We optimized a polysome profiling protocol considering the unique morphology and ribosomal distribution of astrocytes.
This ‘astrocyte-optimized’ protocol was then used to study primary astrocytes treated with proinflammatory cytokines,
enabeling Riboseq analysis for measurment of the transcriptome, translatome, and translation efficiency with a coverage of over 12,000 genes.
We found several regulation strategies of gene expression in astrocytes executed as part of an extensive inflamatory response.
Enhanced translation efficiency was one of these strategies, used specifically for genes related to oxidative phosphorylation, and ribosomal proteins.

overall_design:
Three biological repetitions containing qual number of primary astrocytes were lysed using the ‘standard’ or ‘optimized’ extraction method
followed by pelleting the heavy complexes from each lysate through 1M sucrose cushion. Equal emount of mRNA from each pellet was sequenced by RNA-seq,
representing the population of transcripts that was in association with heavy  complexes (RNPs) whithin the cells.

last: Herrero


title: miRNA profiles of EVs released from menstrual blood-derived stem cells

status: Public on Jan 24 2023

city: Xinxiang

first: JIE

last: LIAN

state: Henan

address: Jinsui Road

department: Henan Joint International Research Laboratory of Stem Cell Medicine

institute: Xinxiang Medical University

summary: To identify specific miRNAs carried by MenSC-EVs, and explore their crucial roles in MenSC-EV-based improvement of inflammatory diseases.

overall_design: miRNAs expression in MenSC-EVs derived from two different donors (25-35 years old, female). EVs were isolated from the cell-free conditioned medium of MenSCs culture over 48 hr by differential ultracentrifugation.

first: Juntang

last: Lin

first: Jie

last: Lian

first: Xinxing

last: Zhu

first: Rui

last: Guo


title: Single Cell Cortical Bone Transcriptomics from Sost-Cre

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Single cell cortical bone transcriptomics from Sost-Cre enriched cell population.

overall_design: Long bone pieces were digested and the Sost-cre cell population was enriched to obtain osteoblast and osteocytes.

first: Rafiou

last: Agoro

first: Kenneth

last: White


title: Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes

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

overall_design: Refer to individual Series


title: Interleukin-27-dependent transcriptome signatures regulation of the transcriptome during neonatal sepsis

first: Gangqing

last: Hu


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues [Human ATAC-Seq]

first: Di

last: Zhang

overall_design:
Spatially resolved co-sequencing of epigenome and transcriptome in  Human hippocampus

*** Submitter declares that the raw data have not been submitted due to patient privacy concerns ***

first: Rong

last: Fan


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues [CUT&TAG]


title: Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability

first: Alan

last: Hinnebusch

overall_design: This study includes total 24 samples, 6 for ribosome profiling and 6 for RNA-Seq derived from duplicates of WT, dcp2D and dcp2-EE. Separately, total RNA of WT, dcp2, and xrn1 in duplicates,  were subjected to CAGE-Seq (6 samples) and total RNA-Seq (6 samples). All strains were grown in YPD at 30ºC till the OD600 ~0.6

first: Anil

last: Kumar Vijjamarri

first: Xiao

last: Niu

first: Matthew

last: Vandermeulen

first: Chisom

last: Onu

first: Fan

first: Hongfang

last: Qui

first: Neha

last: Gupta

first: Swati

last: Gaikwad

first: Miriam

last: Greenberg

first: Paul

last: Cullen

first: Zhenguo


title: Interleukin-27-dependent transcriptome signatures regulation of the transcriptome  during neonatal sepsis [RNA-seq]

overall_design: Four-day old C57BL/6 pups were sorted into four groups based on IL27RA status (KO or wild type) and infection status with Escherichia coli strain O1:K1:H7 infection (with or without infection; 24 hours). For each of the four group, PolyA RNA-seq were performed for spleen tissue and for myeloid cells enriched from the spleen. Additional ATAC-seq assay to measure chromatin accessibility was performed for myeloid cells from each group.

first: Jessica

last: Povroznik

first: Halima

last: Akhter

first: Jordan

last: Vance

first: Madhavi

last: Annamanedi

first: Sebastian

last: Dziadowicz

first: Lei

last: Wang

first: Ashley

last: Divens

first: Cory

last: Robinson


title: Single cell RNA-seq of human cornea organoids identifies cell fates of a developing immature cornea

status: Public on Jan 25 2023

first: Shukti

last: Chakravarti

address: 435 E 30th Street

department: Department of Ophthalmology and Pathology, Department of Ophthalmology

institute: NYU Grossman School of Medicine

summary: The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly.  Here we elucidated the transcriptomic cell fate map of 4-month-old human cornea organoids and human donor corneas. The organoids harbor cell clusters that resemble cells of the corneal epithelium, stroma and endothelium with sub-populations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids contain large proportions of epithelial and endothelial-like cells. These corneal organoids offer a three-dimensional model to study corneal diseases and integrated responses of different cell types.

overall_design: scRNAseq profiling of human cornea organoids and human donor corneas.

first: George

last: Maiti

first: Maithê

last: Rocha Monteiro de Barros

last: Hu

first: Igor

last: Dolgalev

first: Mona

last: Roshan

first: James

middle: W

last: Foster

first: Aristotelis

last: Tsirigos

first: Karl

last: Wahlin


title: Spatial epigenome-transcriptome co-profiling of mammalian tissues

first: Di

last: Zhang

first: Rong

last: Fan


title: Pharmacological intervention of PRMT5 links the E2F pathway with tumor associated antigens derived from the non-coding genome

status: Public on Jan 26 2023

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

summary: E2F activity impacts on an extensive gene network mediated in part by PRMT5-dependent arginine methylation which widens its functional role in gene expression control. We show here that the PRMT5-E2F1 axis has an additional and unexpected level of control through facilitating expression of the non-coding genome where long non-coding (lnc) genes are direct targets for PRMT5 and E2F1. The expression of some lncRNAs results in their translation into small proteins, which then give rise to peptides which populate the MHC class I antigen presentation machinery.  Pharmacological inhibition of PRMT5 alters the expression of lncRNA genes and thereby the repertoire lncRNA-derived peptides presented as MHC bound peptides. Delayed tumor growth upon PRMT5 inhibition reflects an influx of lncRNA peptide-specific cytotoxic CD8 T cells. When presented to the immune system as a stand-alone therapeutic vaccine, lncRNA-derived MHC-bound peptides are immunogenic and drive a potent anti-tumor T cell response with a significant delay in tumor growth. Our results show that the PRMT5 through its control of the E2F pathway influences expression of the non-coding genome and derived peptides presented to the immune system, which can subsequently be harnessed to deliver an effective stand-alone cancer vaccine. These results have important implications for deploying pharmacological intervention to manipulate gene expression and antigen presentation to the immune system and deploying new types of cancer vaccine. They also indicate that cell cycle control through the E2F pathway is intimately connected with immune recognition.

overall_design: Examination of expression profile of murine (CT26) colorectal cancer cells treated with DMSO (Control) or PRMT5 inhibitor (T1-44). In the experiment, the impact of PRMT5 inhibition on gene expression profiles was monitored.  The experiment had 2 samples (CT26 + DMSO, CT26 + T1-44) and was performed in biological triplicate.  CT26 + DMSO samples were used as the reference sample to which all others were compared.  An analysis was also performed on RNA extracted from tumor samples (Colon26 cells grown in situ in Balb/c mice, treated with DMSO or T1-44).  Again the experiment had two treatment conditions (DMSO and T1-44) and was performed in biological triplicate.  Tumor samples treated with DMSO were used as the reference sample to which all others were compared.

first: Wojciech

last: Barczak

first: Simon

last: Carr

first: Geng

last: Liu

first: Shonagh

last: Munro

first: Annalisa

last: Nicastri

first: Lian-Ni

last: Lee

first: Nicola

last: Ternette

first: Paul

last: Klenerman

first: Anastasia

last: Samsonova

first: Nicholas

middle: B

last: La Thangue


title: Adult nucleus accumbens single-nucleus RNA-seq dataset for "Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine"

status: Public on Jan 15 2023

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to repeated cocaine injections (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to repeated cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out with FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after the final (7th) daily treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

last: Phillps

first: Corey

last: Duke

first: Jennifer

last: Tuscher

first: Morgan

last: Zipperly

first: Lara

last: Ianov


title: Single molecule-level metabolic responsive landscape of human liver transcriptome

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Short-term fasting releases the hematopoietic brake to promote bone marrow erythropoiesis

status: Public on Jan 02 2023

city: Suzhou

first: Jiawei

last: Qian

state: Jiangsu

address: Renai Road, No. 199 Suzhou University

institute: Cyrus Tang Medical Institute

summary: How our body adapts erythropoiesis to fluctuating nutrient availability is an unanswered question in hematopoietic development. Here, we demonstrate that short-term fasting triggers a sustained increase in red blood cell (RBC) production by remodeling the developmental trajectory of bone marrow megakaryocyte-erythroid progenitors (MEPs).

overall_design: We sorted megakaryocyte–erythroid progenitor cell from bone marrow of 6h fasted mice and control mice for bulk RNA-seq to investigate the molecular influence which fasting poses on erythropoiesis.

first: Wen

last: Wei

first: Xueqin

last: Gao

first: Li

last: Xu

first: Yixuan

last: Fang

last: Yuan

first: Jianrong

last: Wang


title: Specification of human germ cell fate with enhanced progression capability

status: Public on Jan 07 2023

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Human primordial germ cells (hPGCs) are the embryonic precursors of sperm and eggs. While the exact temporal window of hPGC specification and the cellular identity of their precursors remains unclear, few studies on ex vivo and in vitro cultured human embryos reported plausible hPGCs on embryonic day (E) 12−13, and in a E16−17 gastrulating embryo. In vitro, hPGC-like cells (hPGCLCs) can be specified from intermediary pluripotent stage or peri-gastrulation precursors. Nevertheless, it remains unclear the extent of the spectrum of precursors for hPGCLC specification and how these different cellular identities impact hPGCLC development. Here we show that capacitating and resetting precursors respond to BMP and induce resetting hPGCLCs (rhPGCLCs). Strikingly, rhPGCLC in the human hindgut organoid co-cultures show progression at a pace reminiscent of in vivo timing, demonstrating their higher potential for progression compared to those derived from peri-gastrulation precursors. Notably, EOMES and TBXT act synergistically during rhPGCLC specification, while only EOMES is necessary for peri-gastrulation hPGCLC specification. Our results emphasize the notion that the function of a cell identity can be largely influenced by features of their precursors rather than their convergent identity. Importantly, our study provides the foundation for refined and efficient in vitro models of human gametogenesis, which may contribute to design new therapeutic approaches for human infertility.

overall_design: RNA-seq of hESC-derived cell types (2-4 biological replicates for each cell type)

first: João

last: Alves-Lopes

first: Wolfram

middle: H

last: Gruhn


first: Di

last: Zhang


title: Spatiotemporal local and abscopal cell death and immune responses to histotripsy focused ultrasound tumor ablation

status: Public on Jan 12 2023

city: Ann Arbor

first: Clifford

last: Cho

address: 2215 Fuller Road

institute: University of Michigan Ann Arbor

summary: Histotripsy is a novel focused ultrasound tumor ablation modality with potent immunostimulatory effects. To measure the spatiotemporal kinetics of local and abscopal responses to histotripsy, C57BL/6 mice bearing bilateral flank B16 melanoma or Hepa1-6 hepatocellular carcinoma tumors were treated with unilateral sham or partial histotripsy. Treated and Controltralateral untreated (abscopal) tumors were analyzed using multicolor immunofluorescence, digital spatial profiling, RNA sequencing (RNASeq), and flow cytometry.

overall_design: Flow-sorted CD45+ and CD45- cells were lysed and RNA was extracted per manufacturer instructions using the Qiagen RNeasy Mini Kit.  RNA was  submitted to the University of Michigan Advanced Genomics Core for library preparation and QuantSeq analysis.  Pooled libraries were subjected to 101 bp single-end sequencing with Illumina NovaSeq following manufacturer protocols .  Bcl2fastq2 Controlversion Software (Illumina) was used to generate de-multiplexed Fastq files.  Reads were trimmed using Trim Galore (v0.5.0) using default settings.  Reads were aligned using STAR (v 2.6.0) using default settings .  Unique molecular identifiers were collapsed using Lexogen Quantseq (v2.3.6). Reads were mapped to the mouse genome GRCm38 from the Ensembl genome database.  Reads were counted using BioControlductor R package Rsubread and featureCounts function .  RNASeq data analysis and visualizations were performed using BioJupies.

first: Ashley

last: Pepple

first: Joe

last: Guy

first: Reliza

last: McGinnis

first: Amy

last: Felsted

first: Brian

last: Song

first: Ryan

last: Hubbard

first: Tejaswi

last: Worlikar

first: Hannah

last: Garavaglia

first: Joseph

last: Dib

last: Chao

first: Nicoleen

last: Boyle

first: Michal

last: Olszewski

first: Zhen

first: Anutosh

last: Ganguly


title: Methylation Analysis of ALK-positive pediatric Anaplastic Large Cell Lymphom

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Anaplastic large cell lymphoma (ALCL) is a peripheral T-cell lymphoma that accounts for 10–15% of all childhood lymphomas. Despite the observation that more than 90% of the cases show ALK-rearrangement resulting in aberrant ALK kinase expression, there is significant clinical, morphologic, and biological heterogeneity. To gain insight into the molecular heterogeneity within ALK-positive ALCL, we analyzed 46 ALK-positive ALCL samples by whole-exome sequencing, RNA-sequencing, and DNA methylation array analysis. Gene expression and methylation profiling consistently subclassified ALK-positive ALCL cases into two groups differentiated by ALK expression level. The ALK-low group showed enrichment pathways of the immune response and cytokine signaling and were more heavily hypermethylated than the ALK high group, which was characterized by enriched pathways of cell growth, proliferation, metabolic pathways, and large copy number change. Taken together, these findings suggest that there is molecular heterogeneity within pediatric ALK+ALCL, predicting distinct biological mechanisms that may be utilized as prognostic markers.

overall_design: Methylation Analysis of 41 primary samples ALK-positive pediatric ALCL

first: Vasiliki

last: Leventaki


title: Whole-organism C. elegans L2 GRH-1 ChIP-seq

status: Public on Dec 31 2022

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)


title: Whole-organism C. elegans L2 GRH-1 ChIP-seq (experiment 1 of 2)

state: Basel-Stadt

department: Multicellular Systems

institute: Friedrich Miescher Institute for Biomedical Research

summary: We performed ChIP-seq to determine chromatin regions binding Transcription Factor GRH-1, and thereby potential binding motifs and sites thereof, in C. elegans (larval stage 2) whole organisms.

overall_design: One sample was used as "input", ie non-specific pulldown. 3 GRH-1-specific samples were generated, using 3 different salt concentrations for protocol optimisation and potential replication. Samples were collected at two time points to broadly cover the L2 stage, before pooling.

first: Chiara

last: Azzi

first: Kathrin

last: Braun

first: A

last: Smith

first: Dimosthenis

last: Gaidatzis

first: Milou

last: Meeuse


title: Early-Stage Lung adenocarcinoma MDM2 genomic heterogeneity predicts clinical outcome and response to targeted therapy

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Invasive subtypes of lung adenocarcinoma (LUAD) show MDM2 amplification that is associated with poor survival. Mouse double minute 2 (MDM2) is frequently amplified in lung adenocarcinoma (LUAD) and is a negative regulator of p53, which binds to p53 and regulates its activity and stability. Genomic amplification and overexpression of MDM2 together with genetic alterations in p53 leads to genomic and genetic heterogeneity in LUAD that represents a therapeutic target.  In vitro assays in a panel of LUAD cell lines showed that tumor cell response to MDM2 targeted therapy is associated with MDM2 amplification.

overall_design:
Transcriptomic analyses of MDM2 amplified LUAD cell lines with p53 WT(A549) and p53 mutant (H1792) treated with MDM2 inhibitor

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Ayushi

last: Patel


title: Transcriptome analysis using RNA sequencing of the perilesional cortex in traumatic brain injury mice treated with CSF1R inhibitor or vehicle

status: Public on Dec 28 2022

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Goethe University Frankfurt

summary: C57BL6 mice were subjected to a controlled cortical impact (CCI) to induce a unilateral traumatic brain injury (TBI). After surgery, mice were treated for 5 days with the CSF1R antagonist, PLX3397 or vehicle by daily i.p. injections. PLX3397 is an inhibitor of Colony Stimulating Factor receptor 1 (CSF1R) that leads to a depletion of microglial cells which was confirmed by immunohistochemistry in a subgroup of mice at day 5. Termination of PLX3397 allows for a repopulation of microglial cells which was near complete at 30 days, as assessed by immunofluorescence studies. Perilesional cortical tissue was obtained at the late time point of 30 days after TBI to assess lasting effects of microglia depletion for cortical reorganization that manifested at the transcriptional level. The RNAseq study was done in male and female mice (PLX3397 n = 5 male, 5 female; vehicle n = 5 male, 5 female). Behavioral scores for well-being and motor functions were obatined repeatedly during the observation time. Histology of brain lesion size, indices of neuronal damage and neuroinflammation were obtained at 5d and 30d after TBI. Microglia depletion (PLX3397 treatment) did not reduce the lesion volume and hindered phagocytosis and removal of the hematoma at 5 days, but reduced structural brain damage and neuron loss at 30 days after the injury. Neuroinflammatory markers tended to be lower in PLX3397 treated male than female mice which was associated with better neurological outcome. Overall, CSF1R inhibition provided only subtle lasting beneficial effects.

overall_design: RNA was extracted from perilesional cortex 30d after TBI in mice treated with PLX3397 (n = 10) or vehicle (n = 10) from d1-d5. RNA and was analyzed by RNA sequencing in 10 biological replicates per treatment group using an Illumina NovaSeq 6000 system.

first: Michael

middle: E

last: Schäfer

first: Matthias

last: Klein


title: MTA mediated m6A modification promotes chilling tolerance by regulating gene translation efficiency in Arabidopsis

status: Public on Dec 13 2022

city: Nanjing

first: Wang

last: Haiyan

address: Weigang NO.1

department: State Key Laboratory for Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

summary: Plants can respond to low temperatures with diverse mechanisms occurred at transcriptional and translational levels. N6-methyladenosine (m6A) is the most prevalent mRNA modification in eukaryotes that acts as a new emerging layer of epitranscriptomic gene regulation. However, the cellular roles of m6A in plant response to low temperatures remain largely unknown. Here we show that mRNA m6A modification is indispensable for Arabidopsis growth under chilling conditions.

overall_design: Gene expression,translation efficiency and m6A peaks were identified from wild type Columbia-0 and AmiR-mta mutant under chilling and normal conditions in two biological replicates.

first: Shuai

last: Wang

first: Haiyan

first: Zhihui

last: Xu


title: Adipose-derived mesenchymal stem cells inhibit JNK-mediated mitochondrial retrograde pathway to alleviate acetaminophen-induced acute liver injury

status: Public on Dec 17 2022

city: Hang Zhou

first: Yelei

last: Cen

address: Yuhangtang Road No.388,Zhejiang Province,P.R.China

institute: Zhejiang University

summary: Acetaminophen (APAP) is the major cause of drug-induced liver injury, with limited treatment options. APAP overdose invokes excessive oxidative stress that triggers mitochondria-to-nucleus retrograde pathways, contributing to APAP-induced liver injury (AILI). Mesenchymal stem cell therapy is a promising tool for acute liver failure. Therefore, the purpose of this study is to investigate the beneficial effects of adipose-derived mesenchymal stem cell (AMSC) therapy on AILI and reveal the potential therapeutic mechanisms. C57BL/6 mice are used as the animal model and AML12 normal murine hepatocytes as the cellular model of APAP overdose. Immunohistochemical staining, western blotting, immunofluorescence staining, and RNA sequencing assay are used for assessing the efficacy and validating mechanisms of AMSC therapy. We found AMSC therapy effectively ameliorated AILI, while delayed AMSC injection lost its efficacy related to the c-Jun N-terminal kinase (JNK)-mediated mitochondrial retrograde pathways. We further found that AMSC therapy inhibited JNK activation and mitochondrial translocation, reducing APAP-induced mitochondrial damage. The down-regulation of activated Ataxia telangiectasia mutated (ATM) and DNA damage response proteins in AMSC treated mice liver indicated AMSC blocked the JNK-ATM pathway. Overall, AMSC may be an effective treatment for AILI by inhibiting JNK-ATM mitochondrial retrograde pathway, which improves APAP-induced mitochondrial dysfunction and liver injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NC, APAP overdosed-mice and AMSC-treated mice.

first: Yanning

last: Liu

first: Guohua

last: Lou


title: Whole-organism C. elegans L2 GRH-1 ChIP-seq (experiment 2 of 2)

first: Helge

last: Grosshans

summary: We performed ChIP-seq to determine chromatin regions binding Transcription Factor GRH-1, and thereby potential binding motifs and sites, in C. elegans (larval stage 2) whole organisms.

overall_design: One sample was used as "input", ie non-specific pulldown. 1 new GRH-1-specific pulldown sample was generated. Samples were collected at two time points to broadly cover the L2 stage, before pooling. Additionally, two samples (1 input and 1 pulldown, 500mM salt) from experiment 1 were re-extracted, prepared and sequenced.

first: Chiara

middle: A


title: Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression [RNA-seq]

status: Public on Nov 26 2022

city: Boston

first: Xinlei

last: Gao

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Excess cholesterol accumulation in lesional macrophages elicits complex responses in atherosclerosis. Epsins, a family of endocytic adaptors, fuel the progression of atherosclerosis; however, the underlying mechanism and therapeutic potential of targeting Epsins remains unknown. In this study, we determined the role of Epsins in macrophage-mediated metabolic regulation. We then developed an innovative method to therapeutically-target macrophage Epsins with specially-designed S2P-conjugated lipid nanoparticles (NPs), which encapsulate small interfering RNAs to suppress Epsins.Our findings suggest that targeting Epsins in lesional macrophages may offer therapeutic benefits for advanced atherosclerosis by reducing CD36-mediated lipid uptake and increasing ABCG1-mediated cholesterol efflux.

overall_design: We performed RNA-seq analysis of WT, ABCG1-KO and Epsin-DKO macrophages.

first: Kui

last: Cui

first: Beibei

first: Kaifu

last: Chen

first: Hong


title: Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression.

overall_design: Refer to individual Series


title: Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression [scRNA-seq]

overall_design: The aortas were isolated from WT and DKO mice on normal or western diet. The aorta cells were used to perform single-cell RNA-seq.


title: Effects of matrine on gene expression of myeloid leukemia cells

status: Public on Nov 09 2022

city: Huizhou City

first: Wangjing

last: Zhong

state: Guangdong Province

address: No. 1, Xuebo Street, Huicheng District

institute: Huizhou Third People's Hospital

summary: To investigate the molecular mechanism of matrine's anti-myeloid leukemia effect, Acute myeloid leukemia cells HL-60 and U937 and chronic myeloid leukemia cells K562 were treated with 0.8mg/mL matrine for 30min and 24h, respectively. Then, RNA-Seq data before and after matrine treatment were used for gene expression profile analysis

overall_design: Comparative gene expression profile analysis of RNA-Seq data of myeloid leukemia cells before and after matrine treatment

first: Wang-jing

first: Fanfan

last: Yang

first: Lingdi

last: Ma


title: Spatial transcriptomics landscape of non-communicable inflammatory skin diseases

status: Public on Nov 14 2022

city: Munich

first: Christina

last: Hillig

address: Ingolstaedter Landstraße 1

department: ICB

institute: Helmholtz Center Munich

summary: We investigated the landscape of non-communicable inflammatory skin diseases by spatial transcriptomics resulting in a large repository of spatially defined human cutaneous transcriptomes of 31 patients.

overall_design: Dataset containing 90 spatial transcriptomic sequencing samples of skin biopsies taken from 31 patients diagnosed with psoriasis, atopic dermatitis or lichen planus, including duplicates of 31 lesional and 14 matched non-lesional samples. Samples  21L008958-21L008973 contain 2-3 specimen on a capture area from different patients and diseases.

first: Alexander

last: Schaebitz

first: Menatullah

last: Mubarak

first: Manja

last: Jargosch

first: Ali

last: Farnoud

first: E.

last: Scala

first: Nils

last: Kurzen

last: Pilz

first: N.

last: Bhalla

first: J.

last: Thomas

first: M.

last: Stahle

first: T.

last: Biedermann

last: Schmidt-Weber

first: Fabian

last: Theis

first: Thomas

last: Walzthoeni

first: Natalie

last: Garzorz-Stark

first: Kilian

last: Eyerich

first: Michael

last: Menden

first: Stefanie


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation (Iso-Seq)

status: Public on Oct 18 2022

city: Bethesda

first: Ashish

last: Lal

address: 37 Convent Drive, Bldg 3, Room 6134

department: Genetics Branch

institute: NCI, NIH

summary:
The goal of our study is to investigate the role of the p53-induced lncRNA PURPL in the context of liver cancer.
To achieve this, we identified transcript variants of PURPL expressed in liver cancer cells and assayed for the transcriptome changes caused by PURPL knockdown after p53 induction.

overall_design: 1. Transcriptome profiling using Illumina and isoform profiling using PacBio of SKHEP1 and HepG2 liver cancer cell lines to check the expression of PURPL and identify transcript variants. 2. mRNAseq profile of established SKHEP1 PURPL CRISPRi cell lines.

first: Corrine

middle: R

last: Hartford

first: Lorinc

last: Pongor

first: Yongmei

last: Zhao

first: Xiongfong

last: Chen

first: Caroline

last: Fromont

first: Ritu

last: Chaudhary

first: Xiao

last: Li

first: Katherine

last: Pasterczyk

first: Ravi

last: Kumar

first: Bruna

last: Muys

first: Dimitrios

last: Tsitsipatis

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Mirit

last: Aladjem

first: Ioannis

last: Grammatikakis


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation (RNA-Seq II)


title: Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease

status: Public on Dec 21 2022

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer’s disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10x Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identify unique marker genes for cortical layers and the white matter, and layer-specific differentially expressed genes (DEGs) in human AD compared to CT. Deconvolution of the Visium spots showcases the significant difference in particular cell types among cortical layers and the white matter. Gene co-expression analyses reveal eight gene modules, four of which have significantly altered co-expression patterns in the presence of AD pathology. The co-expression patterns of hub genes and enriched pathways in the presence of AD pathology indicate an important role of cell-cell-communications among microglia, oligodendrocytes, astrocytes, and neurons, which may contribute to the cellular and regional vulnerability in early AD. Using single-molecule fluorescent in situ hybridization, we validated the cell-type-specific expression of three novel DEGs (e.g., KIF5A, PAQR6, and SLC1A3) and eleven previously reported DEGs associated with AD pathology (i.e., amyloid beta plaques and intraneuronal neurofibrillary tangles or neuropil threads) at the single cell level. Our results may contribute to the understanding of the complex architecture and neuronal and glial response to AD pathology of this vulnerable brain region.

overall_design: Human MTG was cryosectioned at 10 µm and mounted on the Visium GE slide for Visium profiling. Spatial resovled transcriptomic (SRT) was performed using the 10x Genomics Visium Spatial Gene Expression Kit (Slide Kit, Part# 1000188. Reagent Kit, Par# 1000189) by following 10x Visium user guide (CG000239 Rev A).

first: Shuo

first: Yuzhou

last: Chang

first: Liangping

first: Diana

last: Acosta

first: Yang

first: Qi

last: Guo

first: Emir

last: Turkes

first: Cody

last: Morrison

first: Dominic

last: Julian

first: Mark

last: Hester

first: Douglas

last: Scharre

first: Chintda

last: Santiskulvong

first: Xue

middle: Y

last: Song

first: Jasmine

middle: T

last: Plummer

first: Geidy

last: Serrano

first: Thomas

last: Beach

first: Karen

last: Duff

first: Qin

last: Ma

first: Hongjun

last: Fu


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation

first: Ashish

last: Lal

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


title: Hepatic PPARα dysfunction in porcine sepsis

status: Public on Nov 28 2022

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Despite decades of research, sepsis remains one of the most urgent unmet medical needs. Clinical trials in sepsis have mainly focused on targeting the inflammatory pathway, however, recent data indicate that sepsis should also be seen as a metabolic disease. Targeting metabolic dysregulations that take place in sepsis might uncover novel therapeutic opportunities to treat human sepsis patients. The role of PPARα in liver dysfunction during sepsis has recently been described, and restoring PPARα signaling proves to be successful in murine sepsis. To find out whether this therapy might also be helpful in human sepsis patients, we analyzed metabolic perturbations in liver of a porcine fecal peritonitis model. Resuscitation with fluids, antimicrobial therapy and abdominal drainage were applied to the pigs in order to mimic human clinical care. By using RNA-seq, we detected problems with PPARα signaling in the livers of septic pigs and reduced PPARα levels correlated well with disease severity. As PPARα regulates the expression of many genes involved in FA oxidation, reduced expression of these target genes concomitant with increased FFAs in plasma and ectopic lipid deposition in the liver was observed. The results obtained in pigs are in agreement with earlier observations in mice and support the potential of targeting defective PPARα signaling in the clinic.

overall_design: Comparative gene expression profiling between livers from sham (3 biological replicates) and sepsis (9 biological replicates) pigs. Samples were taken between 14 and 18 hours after initiating the model for RNA-seq

first: Jolien

last: Vandewalle

first: Bruno

last: Garcia

first: Tineke

last: Vanderhaeghen

first: Lise

last: Van Wyngene

first: Melanie

last: Eggermont

first: Hester

last: Dufoor

first: Céline

last: Van Dender

first: Siska

last: Croubels

first: Antoine

last: Herpain

first: Claude

last: Libert


title: A comprehensive characterisation of fetal and mature retinal cell identity to assess the fidelity of retinal organoids

status: Public on Dec 10 2022

city: Sydney

first: Hani

middle: Jieun

last: Kim

address: The University of Sydney

country: Australia

institute: The University of Sydney

summary: Retinal organoids derived from pluripotent stem cells have been widely used to model development and disease of the human eye. Yet there is a lack of studies that have systematically evaluated the fidelity of the organoids to their in vivo counterpart. This is particularly relevant for evaluating the efficacy of therapeutic applications and culture protocol performance. To this end, we performed an extensive meta-atlas characterisation of cellular identities of the human eye, covering a wide range of developmental stages. The resulting map uncovered previously unknown biomarkers of major retinal cell types and those associated with cell-type specific maturation. Using these retinal identities from fetal and adult tissue as the map, we systematically assessed the fidelity of the retinal organoids to mimic the human eye, enabling us to comprehensively benchmark the current protocols for retinal organoid generation.

overall_design: Single-cell RNA sequencing of 3-month-old retinal organoids

first: Michelle

last: O’Hara-Wright

first: Daniel

first: To

last: Loi

first: Robyn

last: Jamieson

first: Anai

last: Gonzalez-Cordero

first: Pengyi

last: Yang


title: The transcriptomic and proteomic map of human primary cells

city: Rochester

first: Akhilesh

last: Pandey

state: Minnesota

address: 200 First Street SW

department: Laboratory Medicine and Pathology

institute: Mayo Clinic

summary: Molecular profiling of human primary cell types is essential for holistic understanding of human biology. Here we present a map of 28 human primary cell types with comprehensive measurements of expressed transcripts and proteins. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed both at transcriptome and proteome level along with discovery of several cell type specific proteins. Among them, we characterized the novel epithelial specific protein C1orf116 which was further validated with immunohistochemistry across various human tissues. Comprehensive proteome profiling across cell types allowed characterization of ten orphan proteins including TMEM252 and TM4SF18 which lacked protein level evidence. Exhaustive protein database search considering 27 biologically relevant post-translational modifications and 12 chemical modifications was performed, thanks to the increased performance of cloud-based search engine. This, for the first time, provided the catalog of post-translational modifications across cell types, which serve as a resource of PTMs for future studies. We characterized proteins such as protein EEF1A1with various types of PTMs and understudied PTMs including histidine methylation, and O-acetylation of serine. Interestingly, the unexpected higher frequency of dioxidation on tryptophan than that of methionine led us to characterize oxidative mitochondria complex subunit proteins modified through oxidative phosphorylation in mitochondria, which was mostly considered as chemical artifact so far. Overall, these indicated that considering various PTMs during protein database search from non-enriched samples could be routinely used in proteomics experiments. Further, protein database search strategy considering alternative translational start sites, splice junctions, and translational readthrough provided a unique opportunity to refine genome annotation with their proteomic evidence. We believe that our data with the large catalog of transcriptome and proteome of normal human primary cells provide a cornerstone for holistic understanding of cell biology.

overall_design:
Total RNA extracted from 28 human primary cell types are profiled by running on eight lanes of Illumina HiSeq 2500 to study gene expression
Please note that each processed data file was generated from all raw data (lane 1-lane 8) and is linked to the corresponding lane 1 sample records.

first: Pandey

last: Akhilesh


title: Transcriptome and chromatin accessiblity analysis of Gli1+ and Amhr2+ mesenchymes in the fetal murine reproductive tracts

status: Public on Oct 05 2022

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: Precursors for the male and female reproductive tracts (also known as the Wolffian duct and the Müllerian duct) co-exist in a mammalian embryo before sexual differentiation. The Wolffian duct and Müllerian duct are surrounded by their own mesenchymes in the mesonephros, which can be distinguished by their specific expression of Gli1 and Amhr2, respectively. In the XX embryo, during sexual differentiation, the Wolffian duct degenerates. In this study, by tracking the fate of the Gli1+ Wolffian duct mesenchyme in the tamoxifen inducible genetic lineage tracing model Gli1-CreER; Rosa-Tomato, we demonstrate that the Wolffian duct mesenchyme does not regress along with the Wolffian duct epithelium in the XX embryo. Instead, the Wolffian duct mesenchyme is repurposed and becomes a unique mesenchymal population in the female reproductive tract. Profiling the transcriptomes and chromatin accessibilities of the Gli1+ Wolffian duct mesenchyme in XX and XY during sexual differentiation (E14.5 and E16.5) shows signaling pathways and transcriptional factors that potentially involves the female and male fate differentiation of the Gli1+ Wolffian duct mesenchyme. Comparing the transcriptomes between the Gli1+ Wolffian duct mesenchyme and the Amhr2+ Müllerian duct mesenchyme from the neonatal uterus reveals similarities and differences between the two mesenchymal populations in the female reproductive tract. Ex vivo ablation of the Wolffian duct mesenchyme stunted the growth of the fetal female reproductive tract. In summary, our discovery of the contribution of the Wolffian duct mesenchyme to the female reproductive tract provides new insights into our understanding of sexual differentiation of reproductive tracts.

overall_design: RNA-seq and ATAC-seq on sorted Gli1+ mesenchymal cells from XX and XY mesonpehroi on E14.5 and E16.5; and RNA-seq of sorted Gli1+ and Amhr2+ mesenchymes on neontal uteri

first: Fei

last: Zhao


title: Immunologic adapatations of high grade serous ovarian cancer patients to neoadjuvant carboplatin and paclitaxel therapy

status: Public on Sep 28 2022

city: Providence

first: Jennifer

middle: Renee

last: Ribeiro

state: RI

address: 200 Chestnut St.

department: Obstetrics and Gynecology

institute: Women and Infants Hospital of Rhode Island

summary:
770 genes as well as pathways and deconvoluted immune cell types were determined pre- and post-neoadjuvant chemotherapy in a cohort of 31 stage III-IV high grade serous ovarian cancer (HGSOC) patients, and associations were made with the duration of their platinum-free interval
n/a

overall_design: A total of 31 HGSOC patients were included in this retrospective study. Matched formalin-fixed, paraffin-embedded (FFPE) tumor tissues from treatment naive biopsies and interval debulking surgery following neoadjuvant chemotherapy were obtained from each patient, with associated clinical information, for a total of 62 samples. All patients received frontline carboplatin and paclitaxel although some patients received additional therapies. NanoString nCounter Human PanCancer IO360 panel was used to analyze isolated RNA for 770 genes associated with the tumor immune microenvironment.

first: Nicole

last: James

first: Christoph

last: Schorl

first: Linda

last: Hanley


title: Single-cell sequencing reveals a delicate molecular and cellular interaction during decidualization in humans

status: Public on Nov 24 2022

city: shanghai

first: li

last: mingqing

address: NO.419 fangxie Road, Shanghai

institute: Affiliated obstetrics and Gynecology Hospital of Fudan University

summary: Proper decidualization is a critical determinant of pregnancy success. Deficiencies in decidualization are associated with a variety of pregnancy disorders, including female infertility, recurrent implantation failure, and miscarriage. However, the mechanism for triggering decidualization of human endometrium is largely unknown. Here we characterized the transcriptomes of four major cells in human endometrium and decidua at single-cell resolution. We discovered the dynamic change characteristics of six major stromal cells. More importantly, a dialogue between IGF1+ stromal cells and IGF1R+ stromal cells initiates endometrial decidualization under regulation of progesterone and estrogen, and IL1B+ stromal cells trigger the apoptosis of epithelial cells and functional remodeling during decidualization. We defined a unique AREG+ NK cell for accelerating decidualization by interacting with IGF1+ stromal cells, and observed that extravillous trophoblasts promote decidualization possibly by multiply pathways. Additionally, we developed a systematic repository of cell-cell communication for decidualization via the ligand-receptor complexes interactions. Our study provides deeper insights into the molecular and cellular characterizations during decidualization.

overall_design: Endometrium and decidua mRNA profiles were generated by deep sequencing,using 10X Genomics.

first: Mingqing

last: Li

first: Jiawei

last: Shi


title: Gene expression in manganese-pretreated DNA-stimulated human macrophages

status: Public on Sep 27 2022

city: Frederick

first: Jun

address: P. O. Box B

institute: Leidos Biomedical

summary: A total of 1,302 genes with greater than two-fold increase or decrease and p value less than 0.05 were included in the analysis. 582 genes (cluster 1) were downregulated by Mn2+, and 587 genes (cluster 2) were upregulated by Mn2+. A total of 133 genes (cluster 3) were upregulated by DNA transfection alone. The Venn diagram showed that 351 genes are upregulated in DNA-mediated responses and 247 genes were upregulated by Mn2+ treatment. Of note, the expression of 104 genes were initiated by DNA stimulation alone and then enhanced by Mn2+ treatments. Using a functional enrichment analysis resource (Metascape ), the set of 247 genes (Mn2+-treatment-mediated upregulation) was significantly enriched for the genes involved in multiple biological processes, such as innate immune response and inflammatory cytokines, which include IL-10, IL-4, and IL-13 signaling and the Toll-like receptor signaling pathway. Meanwhile, we noticed that Mn2+ treatment significantly enhanced the responses of the host cells to external stimuli. Similarly, the set of 104 genes was significantly enriched for cytokine signaling in the immune system and for responses to tumor necrosis factor (TNF) or IFN-γ. More interestingly, we found that both functional enrichment analyses for the 247 and 104 genes shared a common category: 38 genes in the 247 genes and 20 genes of the 104 genes were involved in the positive regulation of protein phosphorylation.

overall_design: Macrophages were pretreated with MnCl2 at 25 µM, then transfected with DNA. The gene expression profiles in untreated, Mn2+-treated, DNA-transfected, and a combination of Mn2+- and DNA-treated cells were compared

first: Hongyan

last: Sui

first: Qian

last: Chen

first: Tomozumi

last: Imamichi


title: Single-cell transcriptome profiling of the human endometrium from patients with recurrent implantation failure

status: Public on Sep 16 2022

summary: Despite great advances in assisted reproductive technology (ART), unexplained recurrent implantation failure (RIF) due to disorder of endometrial receptivity still cannot be effectively avoided. More importantly, cell characteristics and cell communication that regulate endometrial receptivity and differentiation, and its disorders in RIF at the window of implantation (WOI) remain rudimentary. Here we characterized the transcriptomes of four major cells in human endometrium from healthy control and RIF patients at single-cell resolution. We discovered the dynamic change characteristics of four major endometrial fibroblast-like cells with different endometrial receptivity, reported a novel pluripotent endometrial glandular epithelial cell with high levels of progesterone receptor and exosomes, and defined a unique ITGA1+CXCR4+ NK cell for connecting endometrial nonimmune cells and immune cell infiltration at the WOI. Additionally, we developed a systematic repository of cell-cell communication for endometrial differentiation and the opening of endometrial receptivity via the ligand-receptor complexes interactions. Our study provides deeper insights into aberrant molecular and cellular characterizations, and the endometrial microenvironmental disorders of RIF patients that are potentially applicable to improve the etiological diagnosis and therapeutics of unexplained RIF.

overall_design: Endometrium mRNA profiles of the Ctrl and RIF patients were generated by deep sequencing,using 10X Genomics.

first: Zhenzhen

last: Lai


title: The hypoxia induced changes in mRNA in RNA-induced silencing complexes  in hypoxia exposed human endothelial cells

status: Public on Sep 15 2022

city: GDANSK

first: Rafal

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

summary: What governs the transition between the two HIFs (the HIF switch) and the role of miRNAs in this regulation is not completely clear. Using genome-wide expression studies on the miRNA content of RNA-induced silencing complex (RISC) in HUVECs exposed to hypoxia compared to the global miRNA-Seq analysis revealed dramatic differences between the two. In our analyses, compared the miRNA and mRNA levels in RISC at 2 hours (mainly HIF-1 driven), 8 hours (HIF-1 and HIF-2 elevated), and 16 hours (mainly HIF-2 driven) in a gene ontology context. This allowed for determining the direct impact of the miRNAs in modulating the cellular signaling pathways involved in the adaptive response. Furthermore, we demonstrate that the hypoxic levels of the vast majority of HIF-1-dependent miRNAs (including miR-210-3p) are also HIF-2 dependent, and that HIF-2 specifically governs the expression of 11 specific miRNAs

overall_design: Examination of mRNA profiles in HUVECs exposed to hypoxia, hypoxia mimetics, with and without HIF1A and EPAS1 silencing


title: Low red to far-red light environments alter nitrogen assimilation in corn (Zea mays)

city: Guelph

first: Clarence

last: Swanton

state: Ontario

address: 50 Stone Road East

department: Plant Agriculture

institute: University of Guelph

summary:
The goal of this work was to investigate the influence of low red to far-red  (R:FR) signals generated by a biological weedy and an artificial source of far-red light on the nitrate assimilation pathway in maize.
In the absence of direct resource competition, far-red light reflected from neighboring weeds compromises light quality (red to far-red ratio; R/FR) and causes a wide range of morphological and physiological responses at early growth stages of crop plants. This study has investigated the effects of low R/FR light signals on nitrate assimilation in maize seedlings. The transcript levels of genes, metabolites, and activities of enzyme in the nitrate assimilation pathway under a biological and a simulated low R:FR light environment were compared with a high R:FR control environment. Low R:FR signals stimulated nitrate accumulation in maize leaves, which  did not appear to result from the upregulation of nitrate transporter genes. A significant reduction in ferredoxin-dependent glutamine:2-oxoglutarate aminotransferase activity appears to play a major role in nitrate accumulation under low R:FR light environments, while activities of other enzymes of the nitrate assimilation pathway remain unchanged.

overall_design: In total, 9 samples were analyzed. Samples consisted of 3 treatments. A weed-free control (WF), a biological (weedy) low R:FR (W), and an artificial low R:FR (FR) with 3 replicates. Each replicate consisted of a pool of second leaves from 3 individual plants (9-day-old).

first: William

last: Kramer

first: Sasan

last: Amirsadeghi


title: The hypoxia induced changes in miRNA in RNA-induced silencing complexes and HIFs induced miRNAs in human endothelial cells

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Examination of miRNA profiles in HUVECs exposed to hypoxia, hypoxia mimetics, with and without HIF1A and EPAS1 silencing


title: Cortical wiring by synapse type-specific control of local protein synthesis

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Neurons use local protein synthesis to support their morphological complexity, which requires independent control across multiple subcellular compartments up to the level of individual synapses. Here we identify a signaling pathway that regulates the local synthesis of proteins required to form excitatory synapses on parvalbumin-expressing (PV+) interneurons in the mouse cerebral cortex. This process involves regulation of the TSC subunit 2 (Tsc2) by the Erb-B2 receptor tyrosine kinase 4 (ErbB4), which enables local control of mRNA translation in a cell type-specific and synapse type-specific manner. Ribosome-associated mRNA profiling reveals a molecular program of synaptic proteins downstream of ErbB4 signaling required to form excitatory inputs on PV+ interneurons. Thus, specific connections use local protein synthesis to control synapse formation in the nervous system.

overall_design: RNAseq of ribosome-associated RNAs from P15 synaptosomes of MGE-derived interneurons in 4 samples from ErbB4 conditional knockout mice and 4 samples from control mice

first: Clémence

last: Bernard

first: Oscar

last: Marín

first: Beatriz

last: Rico


title: RNA-seq of METTL4-mediated Nuclear N6-Deoxyadenosine Methylation Promotes Metastasis through Activating Multiple Metastasis-inducing targets

status: Public on Nov 21 2022

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

summary: Understanding the gene profiling in METTL4/6mA/RP11-390F4.3 axis.

overall_design: Most of sample are replicates. For CRISPR-cont, METTL4-DPPW mutant clone1 and clone2 only once.

first: Kai-Wen

last: Hsu

first: Joseph

first: Chuan

last: He


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (RNA-Seq H187)

status: Public on Sep 12 2022

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Molecular classification of small cell lung cancer (SCLC), a lethal and heterogeneous disease, was recently proposed based on expression of four lineage-defining transcription factors SCLC-A (ASCL1), SCLC-N (NEUROD1), SCLC-Y (YAP1), and SCLC-P (POU2F3). In this study, unsupervised clustering of genome-wide histone H3K27 acetylation profiles uncovered previously unappreciated epigenomic heterogeneity of this recalcitrant disease. Specifically, the major SCLC-A subtype, which accounts for approximately 70% of all SCLC cases, was subdivided into two new subtypes SCLC-A1 and SCLC-A2. SCLC-A1 is distinguished by the presence of super-enhancer at the NKX2-1 locus, also observed in a murine SCLC model and human SCLC specimens. We found NKX2-1, a master regulator of lung lineages as well as a critical lineage factor in central nervous system, is uniquely functionally relevant in SCLC-A1, where it maintains neural lineage rather than pulmonary epithelial identity. Through integrative proteomic, transcriptomic and cistromic analyses, we found that maintenance of this neural identity in SCLC-A1 is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1

overall_design:
Transcriptomic profile of NCI-H187 cells genetically engineered to deplete the expression of SOX1 or NKX2-1 with control

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Ranran

last: Kong


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (ChIP-Seq K27ac)

overall_design:
Genome-wide profiles of histone H3K27 acetylation in SCLC cell lines.

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation (RNA-Seq I)

first: Ashish

last: Lal

overall_design: 1. Transcriptome profiling using Illumina and isoform profiling using PacBio of SKHEP1 and HepG2 liver cancer cell lines to check the expression of PURPL and identify transcript variants. 2. mRNAseq profile of established PURPL CRISPRi cell lines.

first: Corrine

last: Hartford

first: Lorinc

last: Pongor

first: Yongmei

last: Zhao

first: Xiongfong

first: Caroline

last: Fromont

first: Ritu

last: Chaudhary

first: Xiao

middle: L

last: Li

first: Katherine

last: Pasterczyk

first: Ravi

last: Kumar

first: Bruna

last: Muys

first: Dimitrios

last: Tsitsipatis

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Mirit

last: Aladjem

first: Ioannis

last: Grammatikakis


title: RNA transcriptome sequencing analysis of primary human keratinocytes transfected with shRNA-NR037661 or control shRNA

status: Public on Aug 30 2022

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

summary: a RNA transcriptome sequencing analysis was performed in primary human keratinocytes that were transfected with  shRNA-NR037661 or control shRNA

overall_design: mRNA profiles of   primary human keratinocytes transfected with shRNA-NR037661 or control shRNA

first: Chunxiao

first: Mingzhe


title: Microarray analysis of long noncoding RNAs in primary human keratinocytes in response to CaCl2 stimulation

status: Public on Sep 02 2022

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

summary: A microarray analysis of long noncoding RNAs was performed in primary human keratinocytes in response to CaCl2 stimulation

overall_design: lncRNA profiles of primary human keratinocytes in response to CaCl2 stimulation over time.


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation

first: Hideo

last: Watanabe

overall_design: Refer to individual Series


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (ChIP-Seq TF)

overall_design:
Genomic occupancy of NKX2-1 in SCLC-A1 and 2 LADC cell lines. Genomic occupancy of SOX1 in SCLC-A1 cell lines. Genome-wide profiles of histone H3K27 acetylation in NCI-H187 cells genetically engineered to deplete the expression of SOX1 with control

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Ranran

last: Kong


title: RNA-seq analysis of bead-purified B cells of 5-week-old TLR9-/- MRL/lpr mice stimulated in vitro with TLR7 agonists (CL097, invivogen) or left unstimulated.

status: Public on Aug 03 2022

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose: The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR7 stimulation of TLR9-/- MRL/lpr B cells.
Methods : Bead purified B cells (5M) from three 5-week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample).
Results: a B-cell specific gene signature of induced genes after short term in vitro TLR7 stimulation was cataloged.

overall_design: mRNA profiles of TLR9 deficient (TLR9-/-) B cells stimulated in vitro with TLR7 agonists (CL097, Invivogen) or unstimulated, were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.

first: Claire

last: Leibler

first: Shuchi

last: Smita

middle: J


title: Dioxin-elicited decrease in cobalamin redirects hepatic propionyl-CoA metabolism to the β–oxidation-like pathway resulting in acrylyl-CoA conjugate accumulation

status: Public on Aug 05 2022

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental contaminant which induces diverse biological and toxic effects, including the reprograming of intermediate metabolism, mediated by the aryl hydrocarbon receptor (AHR). Targeted LC-MS analysis of hepatic extracts from mice gavaged with TCDD every 4 days for 28 days detected an increase in S-(2-carboxyethyl)-L-cysteine, a conjugate produced following the spontaneous reaction between the sulfhydryl group of cysteine and highly reactive acrylyl-CoA, an intermediate in the cobalamin (Cbl)-independent β–oxidation-like metabolism of propionyl-CoA.  In addition to repressing genes in both the canonical Cbl-dependent carboxylase and the alternate Cbl-independent β–oxidation-like pathways at 30 µg/kg TCDD, methylmalonyl-CoA mutase (MUT) activity was inhibited at lower doses. Moreover, TCDD decreased serum Cbl levels and hepatic cobalt levels while eliciting negligible effects on gene expression associated with Cbl absorption, transport, trafficking, or the derivatization to 5’-deoxy-adenosylcobalamin (AdoCbl), the required MUT cofactor. In addition to inducing Acod1 that encodes for aconitate decarboxylase 1, the enzyme responsible for the decarboxylation cis-aconitate to itaconate, TCDD also dose-dependently increased itaconate levels in hepatic extracts. MUT inhibition is consistent with itaconate activation to itaconyl-CoA, a MUT suicide inactivator that adducts AdoCbl, that in turn, inhibits MUT activity and reduces Cbl levels. Collectively, these results suggest the decrease in MUT activity is due to Cbl depletion following TCDD treatment that redirected propionyl-CoA metabolism to the alternate Cbl-independent β–oxidation-like pathway. The resulting hepatic accumulation of acrylyl-CoA likely contributes to TCDD-elicited hepatotoxicity and the multi-hit progression of steatosis to steatohepatitis with fibrosis.

overall_design: Beginning on post-natal day (PND) 30, male C57BL/6 mice were repeatedly gavaged at 23° C every 4 days for 28 days with some dose of 2,3,7,8-tetrachlorodibenzo-p-dioxin (0.03 - 30 µg/kg TCDD) or sesame oil vehicle (n = 5 per dose) and sacrificed on PND 58 with CO2. Gavaging and tissue collection always occurred between ZT0 and ZT3. Tissues were flash frozen in liquid nitrogen and stored at -80°C. For total RNA extraction using trizol, 100 mg was used per liver sample. Only samples which passed Nanodrop and RIN quality control were used. 150 bp paired-end RNA reads were sequenced using a NovoSeq 6000.

first: Warren

last: Sink

first: Rance

last: Nault


title: Developmental exposure to low-level saxitoxin affects neuronal gene expression in zebrafish (Danio rerio)

status: Public on Jul 31 2022

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Increasing frequency and geographical distribution of harmful algal blooms (HABs) presents a growing threat to the public health. Saxitoxin (STX) is a potent neurotoxin naturally produced by dinoflagellates and cyanobacteria during HAB events. Consumption of seafood contaminated with STX is responsible for paralytic shellfish poisoning (PSP). STX inhibits voltage-gated sodium channels, affecting the propagation of action potentials. Humans are among the species most sensitive to PSP, and neurological symptoms of exposure range from tingling of the extremities to severe paralysis. To protect humans against PSP, there is a ban on harvesting of seafood when the STX levels reach 80 μg/100 g of shellfish tissue. However, shellfish with toxin levels below this regulatory limit often are harvested for consumption. Our objective is to understand the potential health effects of exposure to low levels of STX during sensitive windows of development. Zebrafish embryos were exposed to STX (24 or 48 pg) or vehicle (0.3 mM HCl) at 6 hours post fertilization (hpf) via microinjection. There was no overt toxicity, but starting at 36 hpf there was a temporary lack of pigmentation in STX-injected embryos, which resolved by 72 hpf. Using HPLC, we found that STX was retained in embryos up to 72 hpf in a dose dependent manner. We examined transcriptional profiles in embryos at 24, 36 and 48 hpf. There were no differentially expressed genes (DEGs) in STX-injected embryos at 24 hpf, but at 36 and 48 hpf there were_x000B_3547 and 3356 DEGs, respectively, in response to STX. KEGG pathway analysis revealed significant enrichment of genes related to focal adhesion, adherens junction and regulation of actin cytoskeleton, suggesting that cell-cell and cell-extracellular matrix interactions were affected by STX. The genes affected are critical for axonal growth and the development of functional neural networks. We also observed differential expression of axon guidance factors (netrins, semaphorins, and ephrins), which can control axon outgrowth. We are currently using immunohistochemistry to confirm these findings. Overall, these results suggest that STX exposure might affect axon outgrowth by modulating cell adhesion molecules. [NIH P01ES021923 and NSF OCE-1314642].

overall_design: Saxitoxin and vehicle (control) injected embryos were sequenced for profiling gene expression patterns. Three biological replicates per treatment and time point were sequenced.

last: Hahn

first: John

last: Stegeman


title: mRNA expression analysis of several cell subset from peripheral blood of SLE patient and Healthy Control

status: Public on Sep 26 2022

city: Kyoto

first: Kenji

last: Okuma

state: Kyoto

address: 53, Shogoin Kawara-cho, Sakyo-ku, Medical Innovation Center

country: Japan

institute: Astellas Pharma Inc.

summary: Isolated T, B, monocyte, mDC, pDC, naiveB, memoryB and PBMC at spontaneous state from peripheral blood

overall_design: SLE, HC

first: Takuma

last: Oku

first: Yoshitaka

last: Hirayama

first: Koji

last: Kitagori

first: Hajime

last: Yoshifuji


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (Fixed-tissue ChiP-Seq Human)

state: NY

overall_design:
Fixed-tissue ChIP-seq (FiTAc-seq) for H3K27ac profiling and super-enhancer analysis of FFPE human SCLC tumors

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************


title: Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [ISO-seq]

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

summary: We explored the regulation of intronic polyadenylation isoforms by cisplatin, and its impact on the translatome. This was done in part by 3'-seq (see GSE119978) and Iso-Seq (this data set).

overall_design: To characterize intronic polyadenylation isoforms regulated by cisplatin, we performed Iso-seq analyses on cisplatin- and vehicle-treated non-small cell lung cancer cells.

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Alexandre

last: DEVAUX

first: Mandy

last: CADIX

first: Sophie

last: MICHALLET

first: Ludovic

last: TESSIER

first: Hussein

last: MORTADA

first: Alina

last: CHAKRABORTY

first: Marc

last: DELOGER

first: Jean-Baptiste

last: CLAUDE

first: Pierre

last: GESTRAUD

middle: M

last: LABBE

first: Sonia

last: LAMEIRAS

first: Virginie

last: RAYNAL

first: Sylvain

last: BAULANDE

first: Didier

last: AUBOEUF

first: Nicolas

last: SERVANT

first: Stéphan

last: VAGNER

first: Béatrice

last: EYMIN


title: Functional analysis across model systems implicates ribosomal proteins in growth and proliferation defects associated with hypoplastic left heart syndrome

status: Public on Jul 14 2022

city: La Jolla

first: Georg

last: Vogler

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Hypoplastic left heart syndrome (HLHS) is the most lethal congenital heart disease (CHD). The pathogenesis of HLHS is poorly understood and due to the likely oligogenic complexity of the disease, definitive HLHS-causing genes have not yet been identified. Postulating that impaired cardiomyocyte proliferation as a likely important contributing mechanism to HLHS pathogenesis, and we conducted a genome-wide siRNA screen to identify genes affecting proliferation of human iPSC-derived cardiomyocytes (hPSC-CMs). This yielded ribosomal protein (RP) genes as the most prominent class of effectors of CM proliferation. In parallel, whole genome sequencing and rare variant filtering of a cohort of 25 HLHS proband-parent trios with poor clinical outcome revealed enrichment of rare variants of RP genes. In addition, in another familial CHD case of HLHS proband we identified a rare, predicted-damaging promoter variant affecting RPS15A that was shared between the proband and a distant relative with CHD. Functional testing with an integrated multi-model system approach reinforced the idea that RP genes are major regulators of cardiac growth and proliferation, thus potentially contributing to hypoplastic phenotype observed in HLHS patients. Cardiac knockdown (KD) of RP genes with promoter or coding variants (RPS15A, RPS17, RPL26L1, RPL39, RPS15) reduced proliferation in generic hPSC-CMs and caused malformed hearts, heart-loss or even lethality in Drosophila. In zebrafish, diminished rps15a function caused reduced CM numbers, heart looping defects, or weakened contractility, while reduced rps17 or rpl39 function caused reduced ventricular size or systolic atrial dysfunction, respectively. Importantly, genetic interactions between RPS15A and core cardiac transcription factors TBX5 in CMs, Drosocross, pannier and tinman in flies, and tbx5 and nkx2-7 (nkx2-5 paralog) in fish, support a specific role for RP genes in heart development. Furthermore, RPS15A KD-induced heart/CM proliferation defects were significantly attenuated by p53 KD in both hPSC-CMs and zebrafish, and by Hippo activation (YAP/yorkie overexpression) in developing fly hearts. Based on these findings, we conclude that RP genes play critical roles in cardiogenesis and constitute an emerging novel class of gene candidates likely involved in HLHS and other CHDs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from human induced pluripotent stem cells (hPSCs) and hPSC-derived cardiomyocytes (hPSC-CMs) and its KD derivatives (siRPL39, siRPS15A).

last: Colas


title: Expression profiles of transfer RNA-derived small RNAs in esophageal cancer

status: Public on Jul 10 2022

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

summary: We collected 4 paired esophageal cancer (EC) tissues and adjacent normal tissues. Total RNA was extracted from the tissues. Then total RNA was processed and transfer RNA-derived small RNAs (tsRNAs) were profiled using tsRNA sequencing technique. Raw read counts were filtered to remove the tsRNAs that were expressed in low levels. We only kept the tsRNAs with a nonzero raw read count in all 4 EC tissues or all 4 adjacent normal tissues, and normalized the remaining tsRNAs with DESeq2 in the statistical program R (version 4.0.1). Differentially expressed tsRNAs were screened using following criterions: fold change was larger than 2 and adjusted P value was less than 0.05.

overall_design: The tsRNA expression levels in esophageal cancer tissues were compared to those in adjacent normal tissues.

first: Xinnian

last: Yu


title: Effects of  20-week exercise on whole-blood genome-wide DNA methylation profile in children with overweight/obesity

status: Public on Jul 07 2022

city: Granada

first: AUGUSTO

middle: MIGUEL

last: ANGUITA-RUIZ

state: Granada

address: Cruz, 6.

country: Spain

institute: ISGLOBAL

summary: In this project, the effects of a 20-week exercise intervention on whole blood genome-wide DNA methylation signatures (CpG sites level) in boys and girls with overweight/obesity (OW/OB) were investigated. Twenty-three children (10.05 ± 1.39 years, 56% girls) with OW/OB, were randomized to either a 20-week exercise intervention (exercise group [EG]; n=10; 4 boys/ 6 girls), or to  usual lifestyle (control group [CG] (n=13; 6 boys/ 7 girls). Whole blood genome-wide DNA methylation and transcriptome profile (RNA-seq) analyses were performed before and after the intervention period. Changes in the DNA methylation sites of 485 and 386 CpGs were induced by the exercise intervention (compared to the control group) in boys and girls respectively  (p < 0.001). These CpG sites mapped to loci enriched in distinct gene pathways related to metabolic diseases, fatty acid metabolism, and immune function in boys or girls (p < 0.05). In boys, changes on the DNA methylation status of 87 CpG sites (from the subset of 485 significant CpGs) associated with changes in the gene expression levels of 51 gene transcripts which were regulated by exercise (p < 0.05). Among girls, changes on DNA methylation at 46 CpG sites (from the initial 386 significant CpGs) were associated with changes in the gene expression levels of 30 gene transcripts affected by exercise. Gene transcripts affected by exercise-induced DNA methylation were related to obesity, metabolic syndrome, and inflammation. Nevertheless, none of the presented analyses survived multiple testing correction (FDR > 0.05). This multi-omics approach reveals that exercise may regulate gene pathways involved in metabolism and immune functions in blood cells of boys and girls with OW/OB. These preliminary results provide an important first step to characterize the molecular response to exercise interventions in pediatric populations.

overall_design: Bisulphite converted DNA from the 23 individual in two time points (baseline and t1; 46 samples) were hybridised to the Infinium Methylation EPIC array (Illumina, San Diego, CA, USA).

first: Abel

last: Plaza-Florido

first: Augusto

last: Anguita-Ruiz

first: Signe

last: Altmäe

first: Concepción

last: Aguilera-García

first: S

last: Reitzner

first: Carl

last: Sundberg

first: F

middle: B

last: Ortega


title: Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [total RNA-seq]

first: Céline

last: Labbé

summary: We explored the regulation of intronic polyadenylation isoforms by cisplatin, and its impact on the translatome. This was done in part by 3'-seq (see GSE119978) and Total-RNA-Seq (this data set).

overall_design: To characterize intronic polyadenylation isoforms regulated by cisplatin, we performed Total-RNA-seq analyses on cisplatin- and vehicle-treated non-small cell lung cancer cells.

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Alexandre

last: DEVAUX

first: Mandy

last: CADIX

first: Sophie

last: MICHALLET

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