title: Developmental programs in childhood neuroblastoma [scRNA-seq SK-N-AS]

summary: Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. We investigate the developmental origin of neuroblastoma, the role of oncogenic MYCN in blocking normal differentiation and evaluate therapeutic interventions to overcome differentiation blocks. Here, we provide single cell expression profiles (scRNA-seq MARS-seq) of SK-N-AS cells (n=603).

overall_design: Single-cell RNA-seq in cell line SK-N-AS (n=603) under the following culture conditions:  RPMI1640 medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2 and subcultured every 3-4 days.


title: The DNA methylomes of hyper-IgM syndrome type 2 B cells provide insights into the roles of activation-induced deaminase prior to the germinal center reaction

status: Public on Dec 31 2020

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

type: Methylation profiling by high throughput sequencing

summary: Inactivating mutations in activation induced deaminase (AID) lead to hyper-IgM syndrome type 2 (HIGM2), a rare primary antibody deficiency. AID-mediated cytosine deamination has been proposed as mediating active demethylation, although there is evidence both to support and cast doubt on such a role. We here made use of HIGM2 B cells to investigate direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation defects. For genes that undergo demethylation in the transition from naïve to memory B cells but not in HIGM2 individuals, we did not observe AID involvement but a participation of TET enzymes. DNA methylation alterations in HIGM2 naïve B cells are related to premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data supports a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns without involvement of its cytosine deaminase activity.

overall_design: Tagmentation-based whole-genome bisulfite sequencing of naïve (NBC) and non-class-switched memory B cells (ncsMBC) of two HIGM2 patients and two controls

first: Francesc

last: Català-Moll


title: Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1 deficient cases

status: Public on Dec 18 2020

city: Hamburg

first: Dörthe

last: Holdhof

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of ATRTs and extracranial malignant rhabdoid tumors (eMRTs) samples harboring mutations in SMARCA4 and of small cell carcinoma of the ovary hypercalcemic type (SCCOHT) was performed . The Illumina Infinium HumanMethylation450 BeadChip and the Illumina Infinium MethylationEPIC arrays were used to obtain DNA methylation profiles across approximately 450,000 CpGs and 850,000 CpGs, respectively, in FFPE derived tumor samples. In total n=14 ATRT, n=6 eMRTs and n=28 SCCOHT  samples were analyzed.

overall_design: Bisulphite converted DNA from the 14 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip and the Illumina Infinium MethylationEPIC BeadChip Array.

first: U

last: Schüller

first: D


title: Developmental programs in neuroblastoma [RNA-seq SK-N-BE(2)C ATRA]

city: Heidelberg

first: Frank

last: Westermann

address: Im Neuenheimer Feld 280

institute: Hopp Children's Cancer Center (KiTZ) and German Cancer Research Center (DKFZ)

type: Expression profiling by high throughput sequencing

summary: Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. We investigate developmental origins of neuroblastoma, the role of oncogenic MYCN in blocking normal differentiation and evaluate therapeutic interventions to overcome differentiation blocks. Here, we provide expression profiles of SK-N-BE(2)C cells upon treatment with ATRA or solvent control.

overall_design: RNA-seq in cell line SK-N-BE(2)C after treatment with 10 µM ATRA or solvent control (ethanol) for 144 hours


title: Cytoplasmic mRNA decay represses RNAPII transcription during early apoptosis

status: Public on Dec 29 2020

city: Berkeley

first: Christopher

last: Duncan-Lewis

state: California

address: Li Ka Shing Center

department: Molecular and Cell Biology

country: USA

institute: University of California Berkeley

summary: We report that a majority of RNAPII transcripts are transcriptionally downregulated during early apoptosis, prior to the fragmentation of the genome that occurs during the late stages of programmed cell death.

overall_design: Examination of transcript fold changes upon 2 hr TNF-related apoptosis inducing ligand (TRAIL), both in the presence and absence of the pan-caspase inhibitor zVAD.

first: Ella

last: Hartenian

first: Valeria

last: King

first: Britt

last: Glaunsinger


title: Developmental Programming: Adipose Depot-Specific Transcriptional Regulation by Prenatal Testosterone Excess in a Sheep Model of PCOS

status: Public on Dec 30 2020

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary: This study seeks to undertake an assessment of the effects of prenatal exposure of female sheep to excess testosterone, the estrogen precursor, in four different adipose depots. The depots investigated are subcutaneous adipose tissue (SAT) - a fat beneath the skin storing >80% of total body fat in the human body, visceral adipose tissue (VAT) - an intra-abdominal fat primarily associated with digestive system organs, and smaller depots such as epicardial adipose tissue (ECAT) and perirenal adipose tissue (PRAT) that serve specialized functions associated with the organs/tissues in their proximity. The goals are to 1) determine gene expression and gene network profiles in the depots; 2) assess prenatal T-treatment induced disruptions in adipose depot-specific gene expression and gene networks; and 3) identify common and divergent gene and gene pathways underlying depot-specific disruption in prenatal T-treated female sheep.

overall_design: 8 sheep, 4 per treatment group. From each sheep, 4 adipose depot samples. 32 samples total.

first: John

last: Dou

first: Muraly

last: Puttabyatappa

first: Vasantha

last: Padmanabhan

middle: M


title: Pro-inflammatory monocyte phenotype during acute progression of cerebral small vessel disease

status: Public on Dec 09 2020

city: Nijmegen

first: Marlies

last: Noz

state: Nederland

address: Geert grooteplein 8

department: Internal medicine

country: Netherlands

institute: Radboudumc

summary: The aetiology of cerebral small vessel disease (SVD) remains elusive, though currently evidence is accumulating that inflammation contributes to its pathophysiology. In this prospective high-frequency imaging study, we showed that the incidence of acute SVD progression coincides with a functional and transcriptional pro-inflammatory monocyte phenotype. To detect SVD progression, individuals with SVD underwent monthly magnetic resonance imaging (MRI) for 10 consecutive months. RNA sequencing revealed a pro-inflammatory monocyte signature with upregulation of the EGR2 gene. Collectively, we showed that individuals with progressive SVD have pro-inflammatory circulating monocytes characterized by an augmented cytokine production capacity and a pro-inflammatory transcriptional signature.

overall_design: RNA sequencing profiles of isolated monocytes of individuals with progressive SVD and individuals without progression of SVD.

first: Simone

last: Kersten

first: Charlotte

last: Kaffa

first: Alexander

last: Hoischen

first: Niels

last: Riksen


status: Public on Dec 08 2020

city: Jining

first: Chunyu

last: bai

address: NO133，Hehua Road

country: China

institute: Jining Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNAs profiles in extracellular vesicles derived from human  beta cells were analyzed using RNA-seq

overall_design: For analysis the change of miRNAs profile in extracellular vesicles derived from human beta cells, the human beta cells were incubited with solution of low glucose (2 mM) and high glucose (20 mM) respectively for 30 min, then the cell supernatant were selected to isolate the extracellular vesicles using XX method,

last: Bai


title: Sprague Dawley Whole Egg MicroRNA & Total RNA Sequencing

status: Public on Dec 15 2020

city: Ames

first: Joe

last: Webb

state: IA

address: 2302 Osborn drive, 220 Mackay Hall

institute: Iowa State University

summary: In order to understand the effects that egg consumption has on tissue-specific microRNA and  gene expression, we examined the role of whole egg consumption (20% protein, w/w) on differentially  expressed genes (DEGs) between male rat (n =12) transcriptomes in the prefrontal cortex (PFC), liver, kidney  and adipose tissue.

overall_design: 12 rats were randomly assigned to either a Casein based diet or whole egg based diet with N=6 per group

first: Amanda

last: Bries

first: Elizabeth

last: McNeill

first: Matthew

last: Rowling

first: Kevin

last: Schalinske


title: Setd2 Epidermal Deficiency Promotes Cutaneous Wound Healing via Activation of AKT/mTOR Signaling (RNA-Seq)

status: Public on Dec 25 2020

city: shanghai

first: xiaoxue

last: li

address: huashan road

institute: shanghai jiaotong university

summary: Skin wound healing is one of the major prevalent medical problems in the worldwide. Wound healing involves multi-process synergy and re-epithelialization is an essential part of wound healing. Histone H3K36 tri-methylase Setd2 has been extensively studied in different biological processes and diseases. However, the function of Setd2 in the wound healing remains unclear. To elucidate the biological role of Setd2 in the skin wound healing, conditional gene targeting was employed to establish epidermis-specific Setd2-deficient mice. We found that Setd2 deficiency resulted in accelerated re-epithelialization during cutaneous wound healing by promoting keratinocytes proliferation and migration. Furthermore, we demonstrated that loss of Setd2 activated the AKT/mTOR pathway, and pharmacological inhibitions of AKT and mTOR with MK2206 and rapamycin delayed wound closure, respectively. In conclusion, our results reveal the essential role of Setd2 in skin wound healing that is Setd2 loss promotes cutaneous wound healing via activation of AKT/mTOR signaling.

overall_design: mRNA profiles of 12-week-old Setd2fl/fl and Setd2K5-KO skin tissues were generated by deep sequencing

first: Xiaoxue

last: Li


title: RNA sequencing analysis of DLEU2 knockdown in CaSki cells

status: Public on Dec 05 2020

city: Chongqing

first: Min

last: He

address: Yixueyuan Road, Yuzhong District

department: Molecular Medicine and Cancer Research Center

institute: Chongqing Medical University

summary: To further explore the molecular mechanism of DLEU2 in CC cells, RNA sequencing analysis was performed to investigate the differential gene expression profiles between DLEU2 knockdown group and comtrol group in CaSki cells.

overall_design: To investigate the differential gene expression profiles between DLEU2 knockdown group and control group in CaSki cells.

first: Fangzhou

last: Song


title: Chemical inhibition of ENL/AF9 YEATS domains in acute leukemia [RNA-Seq]

status: Public on Dec 04 2020

city: La Jolla

first: Michael

last: Erb

state: CA

address: 10650 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

summary: Transcriptional co-regulators, which mediate chromatin-dependent transcriptional signaling, represent tractable targets to modulate tumorigenic gene expression programs with small molecules. Genetic loss-of-function studies have recently implicated the transcriptional co-activator, ENL, as a selective requirement for the survival of acute leukemia – particularly those driven by multiple lineage leukemia (MLL)-fusion oncogenes. The YEATS domain of ENL, which binds to chromatin by interacting with acyl-lysine side chains, is critical for its pathogenic function in acute leukemiaand highlighted an essential role for its chromatin reader YEATS domain. Motivated by these recent discoveries, we executed a screen of nearly 300,000 small molecules to identify chromatin-competitiveand identified an amido-imidazopyridine inhibitors of the ENL YEATS domain (IC50 = 7 µM). Leveraging a SuFEx-based high-throughput approach to Optimizing an amido-imidazopyridine scaffold with highly parallelized, SuFEx-based medicinal chemistry optimization, we discovered SR-0813 (IC50 = 25 nM), a potent and selective ENL/AF9 YEATS domain inhibitor that exclusively inhibits the growth of ENL-dependent leukemia cell lines. Armed with this tool and a first-in-class ENL PROTAC, SR-1114, we detailed the response of AML cells to pharmacological ENL disruption for the first time. Most notably, displacement of In AML cells, SR-0813 evicts ENL from chromatin, by SR-0813 preferentially suppresseselicited a strikingly selective suppression of ENL target genes, including HOXA9/10, MYB, MYC and a number of other leukemia proto-oncogenes. Our study reproduces a number of key observations previously made by CRISPR/Cas9 loss of function and dTAG-mediated degradation, and therefore, both reinforces ENL as an emerging leukemia target and validates SR-0813 as a high-quality chemical probe.

overall_design: mRNA-seq samples in MV4;11 acute leukemia cell lines.

first: Erb

last: Michael

first: Bishop

last: Timothy

first: Garnar-Wortzel

last: Leopold


title: Chemical inhibition of ENL/AF9 YEATS domains in acute leukemia [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ENL ChIP-seq samples in MV4;11 acute leukemia cell lines.


title: A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: To elucidate key pathways in the host transcriptome of patients infected with SARS-CoV-2, we used RNA sequencing (RNA Seq) to analyze nasopharyngeal (NP) swab and whole blood (WB) samples from 333 COVID-19 patients and controls, including patients with other viral and bacterial infections. Analyses of differentially expressed genes (DEGs) and pathways was performed relative to other infections (e.g. influenza, other seasonal coronaviruses, bacterial sepsis) in both NP swabs and WB. Comparative COVID-19 host responses between NP swabs and WB were examined. Both hospitalized patients and outpatients exhibited upregulation of interferon-associated pathways, although heightened and more robust inflammatory and immune responses were observed in hospitalized patients with more clinically severe disease. A two-layer machine learning-based classifier, run on an independent test set of NP swab samples, was able to discriminate between COVID-19 and non-COVID-19 infectious or non-infectious acute respiratory illness using complete (>1,000 genes), medium (<100) and small (<20) gene biomarker panels with 85.1%-86.5% accuracy, respectively. These findings demonstrate that SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for differential diagnosis of COVID-19 disease.

overall_design:
Comparison of the gene expression profile of nasopharyngeal swabs from individuals with SARS-CoV-2 infection, other viral acute respiratory infections, non-viral acute respiratory illness, and donor controls as well as of whole blood from individuals with SARS-CoV-2 infection, influenza, bacterial sepsis, and donor controls.
*** Raw sequence data are not provided because patient informed consent could not be obtained in this study. ***

middle: Y

first: Dianna

middle: L

last: Ng

first: Andrea

middle: C

last: Granados

first: Yale

middle: A

last: Santos

first: Venice

last: Servellita


title: Single Cell RNA-Seq data for Cancer Stem Like Reversal Project

status: Public on Dec 07 2020

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Primary breast cancer samples were obtained from malignant pleural effusions or ascites after completely red blood cells depletion. For single cell RNA sequencing, frozen vials were thawed and viable breast cancer cells were obtained after depletion of dead cells and CD45+ cells. The purifed patient cells were cultured in Renaissance medium (3D) and treated with chemotherapy (doxorubicin 0.1 µM, carboplatin 0.1mM, paclitaxel 1µM) for 72 hours, and then replaced with Renaissance medium containing DMSO/belinostat (1µM) for 72 hours incubation. The cells were collected, purified with Dead Cell Removal Kit, and subjected to ICELL8® Single-Cell System.

overall_design:
Chemotherapy and belinostat strongly reprogrammed transcriptome of patient cells for cancer stem-like promotion and reversal. In total, two patients samples (#5 and #6)  with three chemothrapies plus belinostat/DMSO treatment sequentioally were analyzed.

***  Raw data not provided due to patient privacy concerns.  ***

first: Feng

last: Chi

first: Jiayi

last: Liu

first: Samuel

middle: W

last: Brady

first: Patrick

last: Cosgrove

first: Aritro

last: Nath

first: Jasmine

last: McQuerry

first: Sumana

last: Majumdar

first: Philip

middle: J

last: Moos

middle: T

last: Kahn

middle: H

last: Bild


title: Homotypic clustering of L1 and B1 repeats organizes 3D genome

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

summary:
We postulated that the primary DNA sequences, particularly abundant repetitive elements embedded in the genome, may instruct genome folding. Short and long interspersed nuclear elements (SINEs and LINEs, respectively) are two predominant sub-families of retrotransposons in most mammals. LINE-1 (LINE1 or L1) constitutes the most abundant type of repeat subclasses, making up to 18.8% and 17% (0.9~1.0 million copies) of the genome in mouse and human, respectively. B1 in mouse and its closely related, primate-specific Alu elements in human are the most abundant subclass of SINEs, constituting 2.7%~10% (0.6~1.4 million copies) of mouse and human genomes. Here, we demonstrate that B1/Alu and L1 repeats demarcate the genome into the A/B compartments and serve as the blueprint for the three-dimensional (3D) organization of mammalian genomes. Our finding explains the robustness and evolutionary conservation of nuclear chromatin organization in mammals.

H3K9me3 ChIP-seq upon L1 AMO treatment;
We electrotransfected L1 AMO into mESC to block L1 transcripts for 36 h and a standard control from GenTools was used as control -"SCR". We performed H3K9me3 ChIP-seq in mESCs treated with L1 or SCR AMO for 36 h. We found that L1 AMO did not alter the genome-wide binding of H3K9me3, ruling out the possibility that the loss of organization relates to changes in local heterochromatin marks.

overall_design:
All HiC were designed to reveal the role of LINE1 RNA in higher-order chromatin structure
Examination of L1 AMO treatment on H3K9me3 modification distribution genome-wide in mESC.

first: Yuyang

last: Lu

first: L

first: Tong

last: Li

first: Y

last: Sun

first: X

last: Shen


title: Developmental programs in neuroblastoma

first: Frank

last: Westermann

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

overall_design: Refer to individual Series


title: Single cell mRNA profiling of bone marrow disseminated tumor cells from breast cancer patients

status: Public on Dec 01 2020

city: Saint Louis

first: Sanjay

last: Jain

state: MO

address: 660 S. Euclid Ave.

department: Division of Nephrology

institute: Washington University in Saint Louis

summary: A bone marrow aspirate from a patient with advanced stage breast cancer was subject to size-based disseminated tumor cell (DTC) enrichment using the Parsortix (Angle LLC) 8 micron fluidics device. Cells eluted from the device were used for single cell RNA sequencing to demonstrate the capabilities of the device to enrich for DTCs in an unbiased manner

overall_design: A single clinical bone marrow specimen from an advanced stage breast cancer patient was used as a proof of principle

first: Mark

last: Watson

first: Rebecca

last: Aft

first: Madhurima

last: Kaushal


title: The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [rnaseq_sw872]

city: Iowa City

first: Michael

middle: S

last: Chimenti

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary:
The WWTR1(TAZ)-CAMTA1 and YAP1-TFE3 gene fusions are disease defining gene alterations for epithelioid hemangioendothelioma, a vascular cancer. The resultant fusion proteins fuse the C terminus of CAMTA1 and TFE3 in frame to the N terminus of TAZ and YAP, respectively. An unbiased BioID-mass spectrometry/RNAi screen identified YEATS2 and ZZZ3 as components of the Ada2a-containing histone acetyltransferase complex and key interactors of both TAZ-CAMTA1 and YAP-TFE3.
An integrative NGS approach including RNA-Seq, ChIP-Seq, and ATAC-Seq showed TAZ-CAMTA1 and YAP-TFE3 transcriptional programs overlap with TAZ and YAP but also drive expression of a novel transcriptome.
The altered transcriptional program of the fusion proteins owing to altered DNA binding as well as shifts in the chromatin landscape.

overall_design: mRNA profiles of SW872 liposarcoma cells transduced with fusion gene constructs were generated by deep sequencing, in triplicate, using Illumina HiSeq4000.

first: Munir

last: Tanas


title: Bradyrhizobium diazoefficiens USDA110 nodulation of Aeschynomene afraspera is associated with atypical terminal bacteroid differentiation and suboptimal symbiotic efficiency

status: Public on Dec 11 2020

city: Gif sur Yvette

first: Florian

last: Lamouche

address: 1, Avenue de la Terrasse

department: Institute of Integrative Biology of the Cell (I2BC)

country: France

institute: Centre national de la Recherche Scientifique (CNRS)

summary: Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions is varying from non-fixing associations to symbioses that are highly beneficial for the plant. Bradyrhizobium diazoefficiens USDA110 was isolated as a soybean symbiont but it can also establish a functional symbiotic interaction with Aeschynomene afraspera. In contrast to soybean, A. afraspera triggers terminal bacteroid differentiation, a process involving bacterial cell elongation, polyploidy and membrane permeability leading to loss of bacterial viability while plants increase their symbiotic benefit. A combination of plant metabolomics, bacterial proteomics and transcriptomics along with cytological analyses was used to study the physiology of USDA110 bacteroids in these two host plants. We show that USDA110 establish a poorly efficient symbiosis with A. afraspera, despite the full activation of the bacterial symbiotic program. We found molecular signatures of high level of stress in A. afraspera bacteroids whereas those of terminal bacteroid differentiation were only partially activated. Finally, we show that in A. afraspera, USDA110 bacteroids undergo an atypical terminal differentiation hallmarked by the disconnection of the canonical features of this process. This study pinpoints how a rhizobium strain can adapt its physiology to a new host and cope with terminal differentiation when it did not co-evolve with such a host.

overall_design: 3 conditions with 3 replicates each for each condition are analyzed. Two nodule bacteria conditions are considered : one from G.max nodules and from A. afraspera nodules, as well as a culture reference in rich medium

first: Quentin

last: Nicoud

first: Peter

last: Mergaert

first: Benoit

last: Alunni


title: A single cell atlas of the human liver tumor microenvironment

status: Public on Dec 02 2020

city: Rehovot

first: Hassan

last: Massalha

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

summary: We identify the specific contribution of each cell type to the human liver tumor microenvironment and reconstructed hepatocytes zonation of the human liver using a combined approach of single-cell RNA sequencing and laser capture microdissection. Our work constitutes an important resource for identifying potential sources of vulnerabilities in liver tumors and metastases.

overall_design: We analyzed six patients who underwent liver resection (colorectal metastasis, primary cholangiocarcinoma, and benign liver cyst). Two samples were extracted from each (malignant and non-malignant). All samples underwent single cells RNA sequencing using MARSseq. In parallel, frozen sections were prepared from each sample. Isolated specific zones of each sections was extracted using laser capture microdissection (LCM) and subjected to bulk sequencing using mcSCRBseq protocol.

first: Keren

middle: B

last: Halpern

first: Samir

last: Abu-Gazala

first: Tamar

last: Jana

first: Efi

middle: E

last: Massasa

first: Andreas

last: Moor

first: Lisa

last: Buchauer

first: Milena

last: Rozenberg

first: Eli

last: Pikarsky

first: Ido

last: Amit

first: Gideon

last: Zamir

first: Shalev

last: Itzkovitz


title: MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis

status: Public on Dec 06 2020

city: Philadelphia

first: PAUL

last: JEWELL

state: PA

address: 3451 Walnut Street Philadelphia

department: Biology

institute: Biociphers

summary: While the effects of confounders on gene expression analysis have been extensively studied there is a lack of equivalent analysis and tools for RNA splicing analysis. Here we assess the effect of confounders in two large public RNA-Seq datasets (TARGET, ENCODE), develop a new method, MOCCASIN, to correct the effect of both known and unknown confounders on RNA splicing quantification, and demonstrate MOCCASIN’s effectiveness on both synthetic and real data.

overall_design:
RNA-Seq samples were simulated based on transcript expression profiles derived from real mouse aorta (N=8) and cerebellum (N=8) samples from GSE54651. 16 simulated samples were based on the ground truth transcipt expression profiles. The remainder of the simulated RNA-Seq samples were based on transcript profiles with batch effects injected at three effect size (0.02, 0.05, and 0.6) and the batch effects were introduced to transcripts from three different proportions of genes (0.02, 0.05, and 0.2).

Data Processing:
1. fastqs from original RNA-Seq samples (GSE54652) were aligned to GENCODE m21 with STAR
2. transcript level TPMs were quantified with Salmon
3. Batch effects were introduced to the mouse aorta and cerebellum sample transcript level TPMs. The aorta samples used were SRR1158521, SRR1158522, SRR1158523, SRR1158524, SRR1158525, SRR1158526, SRR1158527, SRR1158528 and the cerebellum samples used were SRR1158545, SRR1158546, SRR1158547, SRR1158548, SRR1158549, SRR1158550, SRR1158551, SRR1158552. The first four of the aorta samples (SRR1158521...24) and the first four of the cerebellum samples (SRR1158545...48)  were defined as ?batch 1.? The last four of the aorta samples (SRR1158525...28) and the last half of the cerebellum samples (SRR1158549...52) were defined as ?batch 2.?  Batch effect perturbations were only ever introduced to the batch 2 samples and batch effects were restricted to genes with at least two protein coding transcripts and at least one transcript with > 10 reads per kilobase of transcript length in every sample. The procedure to introduce batch effects is as follows: first, the most abundant protein coding transcript per gene was identified as the transcript having the maximum over all transcripts of the minimum reads per kilobase over all samples. This definition ensures the selected transcript is not zero in any sample. Then, for a given gene a batch effect was introduced by (1) selecting a transcript uniformly at random (excluding the most abundant transcript) and (2) reducing TPM of the most abundant transcript by a factor of ?C% Change in Isoform TPM? and correspondingly increasing the TPM of the randomly selected transcript, thus maintaining the overall TPM of the gene and not breaking the definition of TPM (sum of all TPMs in a sample is one million). The ?C% Change in Isoform TPM? factors included 2%, 10%, and 60%. In addition to introducing three different levels of percent changes in isoform TPMs, we also varied the percent of genes batch-effected. We introduced batch effects to G=0%, 2%, 5% or 20% of all genes with protein coding transcripts.
4. simulated fastqs were generated with BEERS algorithm (Grant et. al., 2011)
5. Salmon transcript level TPMs and simulated fastqs are linked below as supplementary files

first: Barry

last: Slaff

first: Caleb

last: Radens

first: Paul

last: Jewell

first: Anupama

last: Jha

first: Nicholas

last: Lahens

first: Gregory

last: Grant

first: Andrei

last: Thomas-Tikhonenko

first: Kristen

last: Lynch

first: Yoseph

last: Barash


title: Adolescent Social Isolation Reprograms the Medial Amygdala: Transcriptome and Sex Differences in Reward

status: Public on Nov 30 2020

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary:
Adolescence is a sensitive window for reward- and stress-associated behavior. Although stress during this period causes long-term changes in behavior in males, how females respond is relatively unknown. Here we show that social isolation stress in adolescence, but not adulthood, induces persistent but opposite effects on anxiety- and cocaine-related behaviors in male vs. female mice, and
that these effects are reflected in transcriptional profiles within the adult medial amygdala (meA). By integrating differential gene expression with co-expression network analyses, we identified crystallin mu (Crym), a thyroid hormone binding protein, as a key driver of these transcriptional profiles. Manipulation of Crym specifically within adult meA neurons recapitulates the behavioral and transcriptional effects of social isolation and re-opens a window of plasticity that is otherwise closed. Our results establish that meA is essential for sex-specific responses to stressful and rewarding stimuli through transcriptional programming that occurs during adolescence.

overall_design: Group housed males, group housed females, socially isolated males and socially isolated females undergo acute cocaine, acute saline, chronic cocaine and chronic saline treatment. Effects are studied.

first: Deena

last: Walker

first: Xianxiao

last: Zhou

first: Hannah

last: Cates

first: Li

last: Shen

first: Bin

last: Zhang

first: Eric

last: Nestler


title: The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [chipseq]

first: Michael

last: Chimenti

overall_design: chromatin binding profile of SW872 liposarcoma cells transduced with fusion gene constructs were generated by chromatin immunoprecipitation and subsequent deep sequencing, in triplicate, using Illumina HiSeq4000.

first: Munir

last: Tanas


title: MicroRNA-802 regulates the innate immune response through Paneth cell expansion and Wnt signaling

city: Zurich

first: Algera

last: Goga

state: Schweiz

address: Otto-Sttern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: Paneth cells are important for maintaining epithelial cell renewal and modulating innate immune function in the intestine through secretion of growth factors and antimicrobial peptides, which help sustain epithelial stem and progenitor cells and contribute to the intestinal barrier and protection against pathogenic bacteria. Here we show that the intestine-enriched miR-802 is a central regulator of intestinal epithelial cell proliferation and Paneth cell function. Genetic ablation of mir-802 in mice leads to amplified ROS generation and Notch/Wnt signaling, increased intestinal epithelial turnover, impaired enterocyte differentiation and nutrient uptake, and increased enterocyte apoptosis. Mice lacking mir-802 in the intestine also exhibit Paneth cell expansion, increased antimicrobial peptide production, and protection against Salmonella infection. This phenotype relies on the miR-802 target gene Tmed9.

overall_design: In total, 6 samples from isolated jejunum enterocyte cells were analyzed. From these, 3 were controls (mir-802fl/fl) and the other 3 were intestine specific KO (Vil-Cre mir-802fl/fl).

first: Markus

last: Stoffel

first: Busra

last: Yagabasan


title: The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [rnaseq_3T3]

summary:
The WWTR1(TAZ)-CAMTA1 and YAP1-TFE3 gene fusions are disease defining gene alterations for epithelioid hemangioendothelioma, a vascular cancer. The resultant fusion proteins fuse the C terminus of CAMTA1 and TFE3 in frame to the N terminus of TAZ and YAP, respectively. An unbiased BioID-mass spectrometry/RNAi screen identified YEATS2 and ZZZ3 as components of the Ada2a-containing histone acetyltransferase complex and key interactors of both TAZ-CAMTA1 and YAP-TFE3.
An integrative NGS approach including RNA-Seq, ChIP-Seq, and ATAC-Seq showed TAZ-CAMTA1 and YAP-TFE3 transcriptional programs overlap with TAZ and YAP but also drive expression of a novel transcriptome.

overall_design: mRNA profiles of NIH 3T3 cells transduced with fusion gene constructs were generated by deep sequencing, in triplicate, using Illumina HiSeq4000.


title: Transcriptomic screen to identify genes regulated by dSET2 in Drosophila third-instar larval nervous system

status: Public on Nov 25 2020

city: Cambridge

first: Rishav

last: Mitra

state: Massachusetts

address: 16 Divinity Avenue

institute: Harvard University

summary: Gene expression changes in neurons are primarily thought to occur via activity driven transcription of immediate-early genes (Chen et al., 2016). Little notice is given to how intracellular Ca2+ changes downstream of myriad signaling pathways affects neuronal gene expression. We recently identified a set of genes whose expression requires IP3R/Ca2+ signals in larval neurons (Jayakumar et al., 2018). This work studies how IP3R/Ca2+ signals regulate changes in gene expression, critical to growth and development, through the histone methyltransferase dSET2. In this study we investigate how  IP3R and dSET2 regulate a common set of developmentally significant genes to enable the larval to pupal transition on a protein deprived diet.

overall_design: mRNA sequencing from three biological replicates of control and  dSET2 knockdown third instar larval brains

first: G

last: Hasan

first: S

last: Richhariya

first: R


title: Impacts of cryopreservation on cell type composition and gene expression in bone marrow biopsy from multiple myeloma patients

status: Public on Nov 19 2020

city: Indianapolis

first: Duojiao

last: Chen

state: INDIANA

address: 410 W. 10th Street

department: Departments of Medical and Molecular Genetics

institute: Indiana University

summary: As the development of the single cell sequencing technology, the workflow of preserving and processing cells needs to be more flexible and manageable to fit the longitudinal or complex single cell study. Consequently, considering the upstream cell cryopreservation protocol instead of using fresh cells become more common in single cell sequencing experiment. There have been several studies reported that cryopreservation protocol could largely preserve the transcriptomic profiles but it brought slight perturbations to the cells. In this case, the effect of cryopreservation on transcriptomic changes needs to be studied to understand whether there will be any bias in the downstream analysis. In this paper, we compared fresh and cryopreserved CD138+ and CD138- cells from multiple myeloma patients’ bone marrow aspirates to evaluate the impact of cryopreservation on cell population frequency and transcriptome. We found the cryopreservation protocol maintained highly consistent gene expression profiles for myeloma cells (R ≥ 0.96) and their microenvironment (R ≥ 0.9), while it slightly impacted the proportion of certain immune cell subtypes in the CD138- samples. In general, our cryopreservation protocol could well preserve bone marrow aspirate samples from multiple patients.

overall_design:
To investigate the impact of cryopreservation on myeloma cells and their microenvironment, scRNA-seq data was used to compare the cellular composition and gene expression profiles of fresh vs. frozen cells that had been isolated from bone marrow aspirates from the six patients. Magnetic beads covalently coupled to CD138-specific antibodies were used to sort cells expressing CD138. Positive and negative CD138 cell populations were then divided into two aliquots each; one was immediately processed for scRNA-seq (fresh) and the other was cryopreserved for sequencing at a later date (frozen)

**Raw data not provided due to patient privacy concerns**

first: Mohammad

middle: I

last: Abu Zaid

first: Magdalena

last: Czader

first: Lin

last: Wang

first: Patrick

last: McGuire

first: Xiaoling

last: Xuei

first: Hongyu

last: Gao

first: Brian


title: RNA-sequencing analysis reveals transcriptomic profile of Dexamethasone-differentiated CAD cells

city: Payathai

first: Witchuda

last: Saengsawang

state: Bangkok

address: 272 Rama 6 Ave.

department: Physiology

country: Thailand

institute: Mahidol University

summary:
Purpose: We applied the next-generation sequencing to explore the differential gene expression in CAD cells differentiated with dexamethasone (Dex), compared to the undifferentiated cells using Illumna -based RNA-sequencing.
Methods: Total RNAs were extracted from undifferentiated CAD cells and Dex-differentiated cells (5 days). Three independent samples were collected from both experimental groups. Samples then underwent to the sequencing step performed on NextSeq with a 75 base-pair end read length. Quality filtered reads were mapped to the mouse reference genome (GRCm38.p6). Feature Counts software was implemented to obtain raw counts for all mouse genes. The gene counts were used for differential expression analysis with the DESeq2 package to identify differentially expressed genes (DEGs) in the Dex-differentiated CAD cells, as compared to the undifferentiated CAD cells.
Results: The sequence reads (expression level) per sample was obtained in a range of 9.8-11.2 million. The high quality of sequence reads was mapped to the mouse reference transcriptome (GRCm38.p6). The gene counts were used for differential expression analysis. The sample-to-sample distance demonstrated that the clustering of the undifferentiated groups was completely separated from the clustering of Dex-differentiated groups. A PCA plot showed that there was a huge variation (PC 1 =99%) between the Dex-differentiated group and the undifferentiated group but less variation was observed within the same group (PC2 = 0%).  These statistic profiles indicate that the transcriptomic profile between Dex-differentiated CAD cells and undifferentiated CAD cells had the different pattern. A total of 1,183 differentially expressed genes (DEGs) were identified in the Dex-differentiated CAD cells compared to the undifferentiated CAD cells (false discovery rate < 0.01 and |log2 [fold change] | > 2). Of these, 803 and 380 genes were significantly upregulated and downregulated in the Dex-differentiated group, respectively.
Conclusion: Dexamethasone causes extensive changes in gene expression of CAD cells.

overall_design: mRNA profiles of the mouse CAD cells differentiated by Dex compared to the undifferentiated  CAD cells

first: Saengsawang

last: Witchuda

first: Khongkla

last: Ekkaphot


title: Gene expression profiles in epigenetically reprogrammed HepG2 cells: analysis of immune response signatures

status: Public on Nov 24 2020

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary: Chronic hepatitis B virus (HBV) infections remain a health burden affecting ~250 million people worldwide. Thus far, available interferon-alpha (IFNα)-based therapies have shown unsatisfactory cure rates, and alternative therapeutic molecules are still required. However, their development has been hampered because accessible cell models supporting relevant HBV replication and appropriate antiviral activity are lacking. Strategies that reverse epigenetic alterations offer a unique opportunity for cell reprogramming, which is valuable for restoring altered cellular functions in human cell lines. This work aimed to investigate the feasibility of converting HepG2 cells that stably overexpress the HBV entry receptor (sodium/taurocholate cotransporting polypeptide, NTCP) toward IFNα-responsive cells using epigenetic reprogramming. Herein, we showed that an epigenetic regimen with non-cytotoxic doses of the demethylating compound 5-azacytidine restored the anti-HBV action of IFNα in epigenetically reprogrammed HepG2-NTCP-C4 cells, named REP-HepG2-NTCP cells. Thus, a significant inhibition in HBV DNA levels was measured in REP-HepG2-NTCP cells after IFNα treatment. This inhibitory effect was associated with the enhancement of IFNα-mediated induction of critical interferon-stimulated genes (ISGs), which was limited in non-reprogrammed cells. In particular, our data indicated that re-expression of 2’-5’-oligoadenylate synthetase 1 (OAS1) and interferon regulatory factor 9 (IRF9) was the result of an epigenetically driven unmasking of these genes in reprogrammed cells. At last, we evaluated the therapeutic potential of the IFN analog CDM-3008 in REP-HepG2-NTCP cells and demonstrated the efficiency of this chemical compound in triggering ISG induction and HBV inhibition. In summary, this study shows that epigenetic reprogramming promotes the IFNα response in HBV-infected cells and is potentially attractive for cell-based experimental screening of IFN-like compounds.

overall_design: To identified the critical gene sets enriched after epigenetic reprogramming, HepG2 cells were treated with the demethylating agent 5-azacytidine (5-AZA) for 10 days.


title: Ikaros and CK2 regulate expression of Bcl-xL and chemosensitivity in high-risk B-cell acute lymphoblastic leukemia

status: Public on Nov 27 2020

city: Hershey

first: chunhua

last: song

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

summary: High-risk B-cell acute lymphoblastic leukemia (B-ALL) is an aggressive disease, often characterized by resistance to chemotherapy. A frequent feature of high-risk B-ALL is loss of function of the Ikaros tumor suppressor. In leukemia, Ikaros’ function is impaired by oncogenic  Casein Kinase II (CK2), which is overexpressed in B-ALL. Phosphorylation by CK2 reduces Ikaros binding to the promoter of its target gene, particularly Bcl-xL. This results in a loss of Ikaros-mediated repression of Bcl-xL and in increased expression of Bcl-xL. Increased expression of Bcl-xL and/or CK2, as well as reduced Ikaros expression, are associated with resistance to doxorubicin treatment. Molecular and pharmacological inhibition of CK2 with a specific inhibitor CX-4945, enhances Ikaros-mediated repression of Bcl-xL and increases sensitivity to doxorubicin. Combination treatment with CX-4945 and doxorubicin show synergistic therapeutic effects in vitro and in preclinical models of high-risk B-ALL. Results reveal a novel signaling network that regulates chemoresistance in leukemia and lays the groundwork for clinical testing of CK2 inhibitors in combination with  doxorubicin for the treatment of hematopoietic malignancies.

overall_design: Examine the genome-wide binding of Ikaros in JM-1, REH and 697 B-ALL leukemia cells and also the effect of CK2 inhibitor-CX-4945 on the Ikaros binding profiling in JM-1 cells.

first: Chunhua

last: Song

first: Zheng

last: Ge

first: Yali

last: Ding

first: Yuka

last: Kawasawa

first: Sinisa

last: Dovat


title: High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human embryonic stem cell gastruloid cultures

status: Public on Nov 18 2020

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

summary: We used circular micropattern cultures to differentiate human embryonic stem cells (H1 hESCs) into microcolonies termed ‘gastruloids’, comprising germ layer and extraembryonic cells. Differentiated gastruloids were dissociated and reseeded onto micropatterns in single cells solution to study cell sorting behaviors. We applied single-cell RNA sequencing to examine transcriptomes of gastruloids and reseeded cells.

overall_design: Single-cell RNA sequencing was performed on gastruloid cells differentiated from H1 hESCs after 44 hours of BMP4 treatment in micropatterns, and dissociated gastruloid cells reseeded onto micropatterns for 48 hours.


title: Chemical inhibition of ENL/AF9 YEATS domains in acute leukemia

city: La Jolla

first: Michael

last: Erb

address: 10650 N Torrey Pines Rd

institute: The Scripps Research Institute


title: EIN3 positive feedback regulation on EIN2C-mediated histone acetylation and gene expression

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: Purpose: Next-generation sequencing (NGS) has been used to study the gene expression amd EIN2C-EIN3DB binding activity in different samples under air and ethylene treatment. The goal of this study is to uncover how EIN3 dimer affect the EIN2C-mediated histone acethylation and gene expression in response to ethylene.

overall_design: Whole seedling mRNA profiles of 3-day old EIN2C-EIN3DB/ein3-1eil-1, EIN2C-EIN3DBK245N/ein3-1eil-1 and EIN2CS645A/ein3-1eil-1 were generated by sequencing, and whole seedling ChIP-seq of 3-day old EIN2C-EIN3DB/Col-0, EIN2C-EIN3DB/ein3-1eil-1 were generated by Illumina NextSeq.

first: Likai


title: Comparison of transcriptional changes in CD103 positive dendritic cells in mice lacking Il33 expression in DCs relative to control mice

status: Public on Nov 13 2020

first: De'Broski

last: Herbert

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

summary: IL33 is an alarmin protein that is known to be released by epithelial cells as a response to damage. There is also evidence that dendritic cells express IL33, however its function in these cells is not well understood.  To investigate the distinct function of IL33 in dendritic cells, deep sequencing of mRNA transcripts was conducted on FACS sorted DCs in mice lacking Il33 expression in CD11c expressing cells compared to control mice.

overall_design: 4 samples total, 2 samples per condition, CD11c-cre-IL33flx/flx versus CD11c-cre

first: Li-Yin

last: Hung

first: Annabel

last: Ferguson

first: Karl

last: Herbine


title: RNA-Seq analysis to assess gene expression levels in MDA-MB-231 cells on treatment with (5-oxo-2-dibenzothienylmethyl)triphenylphosphonium (1-SO) and (2-dibenylthienylmethyl)triphenylphosphonium (1-S) under different UV-A irradiation conditions

status: Public on Nov 17 2020

first: Ryan

last: McCulla

address: 3501 Laclede Ave

department: Chemistry

institute: Saint Louis University

summary:
We report the gene expression levels in MDA-MB-231 cells on treatment with (5-oxo-2-dibenzothienylmethyl)triphenylphosphonium (1-SO) and (2-dibenylthienylmethyl)triphenylphosphonium (1-S) irradiated with UV-A light. These gene expression levels were then compared to control conditions where the cells were treated with the compounds but were not irradiated with UV-A light. The samples were additionally compared to the cells treated with 1% DMSO in DMEM media (with and without UV-A irradiation).
Results: From the first set of experiments, 30 minutes of UV-A irradiation  upregulated 3 and downregulated 5 genes compared to cells with no UV-exposure. The experiments also indicated that 1-SO in UV-A irradiation significantly affected gene expression whereas 1-SO without UV-A did not have a notable effect on expression levels. However, 1-S affected gene expression levels significantly with or without UV-A irradiation.

overall_design: "Two six well plates were plated with MDA-MB-231 cells (600,000 cells/1.8mL/well). Both plates were incubated with compounds (1-SO and 1-S) at final 10μM concentration for 24 hours (VC – 1% DMSO). One plate was irradiated with UV-A light by placing it in a Luzchem photoreactor with 8 LZC-UVA bulbs (fwhm, 325-375 nm) and another plate was kept in the dark by wrapping it in aluminium foil. After UV-exposure, RNA was extracted from these samples using Gen Elute™ Total RNA Purification Kit (Sigma Aldrich, Catalog #RNB100) and the protocol associated with the product kit. The samples were then shipped to Novogene Corporation Inc on dry ice. RNA sequencing and associated bioinformatics analysis (differential gene expression analysis) were performed by Novogene Corporation.  Heatmaps were generated using pheatmap package installed in R." - Isor A. et al., 2020 in prep

first: Ankita

last: Isor

first: Scott

middle: F

last: Grady

first: Christopher

middle: K

last: Arnatt

middle: D


title: Antihypertrophic Memory after Regression of Exercise-induced Physiological Myocardial Hypertrophy

status: Public on Nov 07 2020

city: Guangzhou

first: Hairuo

last: Lin

state: Guangdong

address: 1838 Guangzhou avenue north

department: Department of Cardiology

institute: Nanfang Hospital, Southern Medical University

summary: Background: Exercise can induce physiological myocardial hypertrophy (PMH), and former athletes can live 5-6 years longer than nonathletic controls, suggesting a benefit after regression of PMH. We previously reported that regression of pathological myocardial hypertrophy has antihypertrophic effects. Accordingly, we hypothesized that antihypertrophic memory exists even after PMH has regressed, increasing myocardial resistance to subsequent pathological hypertrophic stress. Methods and Results: C57BL/6 mice were submitted to 21 days of swimming training to develop PMH. After termination of exercise, PMH regressed within 1 week. PMH regression mice (hypertrophic preconditioning group, EHP) and sedentary mice (control group) then underwent transverse aortic constriction (TAC) or a sham operation. At 1 and 4 weeks after TAC, the EHP group showed less increase in myocardial hypertrophy and lower expression of the Nppa and Myh7 genes than the sedentary group. At 4 weeks after TAC, EHP mice had less pulmonary congestion, smaller left ventricular dimensions and end-diastolic pressure, and a larger left ventricular ejection fraction and maximum pressure change rate than sedentary mice. Quantitative polymerase chain reaction (qPCR) revealed that the long noncoding myosin heavy chain associated RNA transcript Mhrt779 was one of the markedly upregulated long noncoding RNAs in the EHP group. Silencing of Mhrt779 attenuated the antihypertrophic effect of EHP in mice with TAC and in cultured cardiomyocytes treated with angiotensin II, and overexpression enhanced the antihypertrophic effect. By chromatin immunoprecipitation assay and qPCR, we found that EHP increased histone 3 trimethylation (H3K4me3 and H3K36me3) at a4 promoter of Mhrt779. Comprehensive identification of RNA-binding proteins by mass spectrometry and Western blot showed that Mhrt779 can bind Brg1 to upregulate Hdac2 and inhibit phosphorylation of Akt and GSK3β. Conclusions: Myocardial hypertrophy preconditioning evoked by exercise increases resistance to pathological stress via an antihypertrophic effect mediated by a signal pathway of Mhrt779 /Hdac2/p-Akt/p-GSK3β.

overall_design: lnc RNA sequencing analysis of exercise prehypertrophic preconditioning(EHP) and sedentary mouse hearts

first: Yinqi

last: Zhu

first: Cankun

last: Zheng

first: Siyuan

last: Ma


title: The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex

last: Chimenti

address: 431 Newton Road

institute: University of Iowa

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [atacseq]

summary:
The WWTR1(TAZ)-CAMTA1 and YAP1-TFE3 gene fusions are disease defining gene alterations for epithelioid hemangioendothelioma, a vascular cancer. The resultant fusion proteins fuse the C terminus of CAMTA1 and TFE3 in frame to the N terminus of TAZ and YAP, respectively. An unbiased BioID-mass spectrometry/RNAi screen identified YEATS2 and ZZZ3 as components of the Ada2a-containing histone acetyltransferase complex and key interactors of both TAZ-CAMTA1 and YAP-TFE3.
An integrative NGS approach including RNA-Seq, ChIP-Seq, and ATAC-Seq showed TAZ-CAMTA1 and YAP-TFE3 transcriptional programs overlap with TAZ and YAP but also drive expression of a novel transcriptome.
The altered transcriptional program of the fusion proteins owing to altered DNA binding as well as shifts in the chromatin landscape.

overall_design: Transcriptionally accessible chromatin of SW872 liposarcoma cells transduced with fusion gene constructs generated by treatment with transposase and subsequent deep sequencing, in triplicate, using Illumina HiSeq4000.

first: Munir

last: Tanas


title: Comparative transcriptome analyses of the Drosophila pupal eye

status: Public on Oct 30 2020

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

institute: Wesleyan University

summary: Investigating Drosophila melanogaster genome-wide gene expression differences in developing pupal eyes comparing 21 hours After puparium formation (APF) to 40 hours APF.

overall_design: Different developmental stage eyes were dissected and genome-wide gene expression levels were compared between these two stages

first: Miles

last: DeAngelis

first: Ruth

last: Johnson


title: A barcoded genome-scale library of inducible alleles reveals principles of synthetic gene control

status: Public on Oct 31 2020

city: South San Francisco

first: Rebecca

last: Wang

address: 1170 Veterans Blvd

institute: Calico Life Science LLC


title: Adaptive responses to HER2-directed therapy in breast cancer cell line models

status: Public on Nov 03 2020

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

institute: Indiana University School of Medicine


title: Control of neurogenic competence in mammalian hypothalamic tanycytes

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N. Broadway Avenue

institute: Johns Hopkins University


title: Control of neurogenic competence in mammalian hypothalamic tanycytes [RNA-seq]

summary: Hypothalamic tanycytes, radial glial cells that share many features with neuronal progenitors, can generate small numbers of neurons in the postnatal hypothalamus, but the identity of these neurons and the molecular mechanisms that control tanycyte-derived neurogenesis are unknown.  We report that tanycyte-specific disruption of the NFI family of transcription factors (Nfia/b/x) stimulates proliferation and tanycyte-derived neurogenesis.  Single-cell RNA- and ATAC-Seq analysis reveals that NFI factors repress Shh and Wnt signaling in tanycytes, and small molecule inhibition of these pathways blocks proliferation and tanycyte-derived neurogenesis in Nfia/b/x-deficient mice.  We show that Nfia/b/x-deficient tanycytes give rise to multiple mediobasal hypothalamic neuronal subtypes that can mature, integrate into hypothalamic circuitry, and selectively respond to changes in internal states.  These findings identify molecular mechanisms controlling tanycyte-derived neurogenesis that can potentially be targeted to selectively remodel hypothalamic neural circuitry controlling homeostatic physiological processes.

overall_design: Single-cell RNAseq for FACS-isolated GFP-positive tanycytes and tanycyte-derived cells from both control and Nfia/b/x-deficient mice.

first: Sooyeon

last: Yoo

first: Juhyun

last: Kim

first: Pin

last: Lyu

first: Thanh

middle: V

last: Hoang

first: Alex

first: Vickie

last: Trinh

first: Weina

last: Dai

first: Lizhi

last: Jiang

first: Patrick

last: Leavy

first: Jae-Kyung

last: Won

first: Sung-Hye

last: Park

first: Jiang

last: Qian

first: Solange

last: Brown


title: Control of neurogenic competence in mammalian hypothalamic tanycytes [ATAC-seq]

overall_design: Single-cell ATACseq for FACS-isolated GFP-positive tanycytes and tanycyte-derived cells from both control and Nfia/b/x-deficient mice.

last: Ma


title: Targeting methylglyoxal in diabetic kidney disease using the novel mitochondria-targeted compound MitoGamide

status: Public on Oct 23 2020

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Diabetic kidney disease (DKD) remains the number one cause of end-stage renal disease in the western world. Currently there is no treatment to cure diabetes or deal effectively with its complications. In experimental diabetes, mitochondrial dysfunction in the kidney has been widely reported with changes in mitochondrial bioenergetics preceding the development of the renal lesion. Glucose-derived molecules generated during diabetes, known as dicarbonyls, such as methylglyoxal, are thought to impair mitochondrial function and may contribute to the pathogenesis of DKD. Here, we sought to target methylglyoxal within the mitochondria using MitoGamide, the novel mitochondria-targeted dicarbonyl scavenger, in an experimental model of diabetes. Male 6-week-old heterozygous Akita mice (C57BL/6-Ins2-Akita/J) or wildtype littermates were randomized to receive MitoGamide (10mg/kg/day) or vehicle by oral gavage for 16 weeks. MitoGamide did not alter blood glucose control or body composition. Akita mice exhibited hallmarks of DKD including albuminuria, hyperfiltration, glomerulosclerosis and renal fibrosis, however, after 16 weeks of treatment, MitoGamide did not substantially improve the renal phenotype. Complex-I-linked mitochondrial respiration was increased in the kidney of Akita mice which was unaffected by MitoGamide. Exploratory studies using transcriptomics identified that MitoGamide induced changes to olfactory signalling, immune system, respiratory electron transport and post-translational protein modification pathways. These findings indicate that targeting methylglyoxal within the mitochondria using MitoGamide is not a valid therapeutic approach for DKD and that other mitochondrial targets or processes upstream should be the focus of therapy.

overall_design: Heterozygous Ins2-Akita mice (C57BL/6J-Ins2Akita) and their wild type littermates underwent treatment with mitoGamide or mitoQ or their respective vehicle controls at 6 weeks of age via oral gavage. The treatment was continued until mice were 22 weeks of age, at which time the kidneys were harvested and renal cortex tissue underwent RNA extraction and sequencing. Only male mice were used.

first: Gavin

last: Higgins

first: Sih

middle: M

last: Tan

first: Runa

last: Lindblom

first: Cesare

last: Granata

first: Matthew

last: Snelson

first: Vicki

last: Thallas-Bonke

first: Assam

last: El-Osta

first: Carlos

last: Baera-Garza

first: Stuart

last: Caldwell

first: Richard

last: Hartley

first: Thomas

last: Krieg

last: Cooper

first: Michael

last: Murphy

first: Melinda

last: Coughlan


title: Single cell RNA-sequencing data of normal human epidermal melanocytes (N) and in 3 patient-derived xenografts (PDX) (M12, M15, M27)

status: Public on Oct 19 2020

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: We report that AXL, GLI1, ST3GAL1 and SOX2 are elevated in a subset of melanoma cells

overall_design: Single cell RNA-seq was used to evaluate the cocomitant expression of the aforementioned genes in three melamoma tumor models

first: Silvia

last: Pietrobono

first: Barbara

last: Stecca

first: Alexander

last: Meves

first: Martin

last: Fernandez-Zapico


title: Lung expression of human ACE2 sensitizes the mouse to SARS-CoV2 infection

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Development of nonclinical mouse models that show some COVID-19 symptoms such as pneumonia and viral load in targeted tissues such as lung will facilitate the preclinical studies and our understanding of pathogenesis and host responses.

overall_design: 6 paired end samples with 3 controls as indicated; The mice inoculated Ad5-hACE2 or Ad5-empty and infected SARS-CoV2 at each time point.

first: Xuebin

last: Qin


title: A barcoded genome-scale library of inducible alleles reveals principles of synthetic gene control [Seq]

first: Rebecca

middle: Y

last: Wang

state: CA

summary: Characterization of Z3EV-inducible genome-scale library using BarSeq, Whole Genome Sequencing, and RNAseq

overall_design: 341 samples total - 42 for BarSeq, 107 for Whole Genome Sequencing, 207 for RNAseq

first: Gina

last: Turco

first: Manuel

last: Hotz

first: Emily

last: Stoops

first: Griffin

last: Kim

first: Anastasia

last: Baryshnikova


title: Mechanism for the selective sequestration of a histone H3K9 methyltransferase at heterochromatin by the H3K9M mutation

status: Public on Oct 26 2020

city: New York

first: Songtao

last: Jia

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

summary: Oncogenic histone lysine-to-methionine mutations block the methylation of their corresponding lysine residues on wild type histones, but the mechanisms by which these mutations function are highly controversial. We have previously shown that in fission yeast, H3K9M containing nucleosomes sequesters the H3K9 methyltransferase Clr4 to block H3K9 methylation{Shan, 2016 #119}. Using ChIP-sequencing, here we show that even though H3K9M containing nucleosomes are broadly distributed across the genome, Clr4 is mainly sequestered at pericentric repeats. The selective sequestration of Clr4 depends not only on H3K9M, but also on H3K14 ubiquitylation (H3K14ub), a modification deposited by a Clr4 associated E3 ubiquitin ligase complex. In vitro, H3K14ub enhances the interaction between H3K9M and Clr4 and potentiates the inhibitory effects of H3K9M on Clr4 enzymatic activity. Using bio-layer interferometry, we show that the H3K9M mutation reduced association rates (kon) of Clr4 with histone tails, suggesting that Clr4 intrinsically disfavors H3K9M. More importantly, H3K9M reduced the dissociation rate (koff) of Clr4 with histone tails, demonstrating that H3K9M slows down the turnover of Clr4 once it is bound. Finally, we generated mutations on Clr4 that specifically disrupt its interaction with H3K14ub and show that they reduce the inhibitory effects of H3K9MK14ub on Clr4 enzymatic activity in vitro and relieve the sequestration of Clr4 at pericentric repeats in vivo. Therefore, the selective sequestration of Clr4 at pericentric repeats by H3K9M is due to the presence of H3K14ub at these regions, which overcomes Clr4’s aversion of H3K9M and reduces the dissociation of Clr4.

overall_design: ChIP-seq of Flag-Clr4 with/without H3K9M, of H3-Flag and H3K9M-Flag and controls

first: Chun-Min

last: Shan

first: Jin-Kwang

first: Jiyong

first: Kehan

last: Bao

first: Yadong

last: Sun

first: Huijie

last: Chen

first: Jia-Xing

last: Yue

first: Alessandro

last: Stripe

last: Schalch

first: Gianni

last: Liti

first: Peter

middle: L

last: Nagy

first: Liang

last: Tong

first: Feng

last: Qiao


title: Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy

city: Seattle

first: Marcus

last: Woodworth

state: Washington

address: 36 Bagley Hall

department: Department of Chemistry

institute: University of Washington

summary: Proper regulation of genome architecture and activity is essential for the development and function of multicellular organisms. Histone modifications, acting in combination, specify these activity states at individual genomic loci. However, the methods used to study these modifications often require either a large number of cells or are limited to targeting one histone mark at a time. Here, we developed a new method called Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) that uses Expansion Microscopy (ExM) to visualize and quantify multiple histone modifications at non-repetitive genomic regions in single cells at a spatial resolution of ∼75 nm. Using SCEPTRE, we distinguished multiple histone modifications at a single housekeeping gene, quantified histone modification levels at multiple developmentally-regulated genes in individual cells, and evaluated the relationship between histone modifications and RNA polymerase II loading at individual loci. We find extensive variability in epigenetic states between individual gene loci hidden from current population-averaged measurements. These findings establish SCEPTRE as a new technique for multiplexed detection of combinatorial chromatin states at single genomic loci in single cells.

overall_design: Examination of 3 different histone modifications (H3K4me3, H3K27me3 and H3K27ac) across the genome of retinal pigmented epithelial hTERT-immortalized cell line using CUT&RUN sequencing.

middle: A

first: Joshua

middle: C

last: Vaughan

first: Hao

last: Kueh


title: Determination of the regulons of 7 XRE-cupin regulators by DAP-seq

status: Public on Oct 01 2020

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

summary: Determination of the binding sites of 7 transcription factors (PA0535, PA1359, PA1884, PA2312, PA4499 (PsdR), PA4987 and PA5301 (PauR)) in Pseudomonas aeruginosa PAO1.

overall_design: DAP-seq analysis of His-tagged purified proteins binding to sheared genomic DNA of Pseudomonas aeruginosa PAO1.

first: Ina

last: Attrée

first: Sylvie

last: Elsen


title: A deep mutational scan of the MHC class I-specific chaperone tapasin

status: Public on Oct 09 2020

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: Tapasin acts as the principal MHC-I-specific chaperone for facilitating folding and antigenic peptide loading of nascent MHC class I substrates in the cell.  In cells where tapasin has been knocked out, the processing and surface trafficking of the human MHC-I allele HLA-A2 is substantially reduced.  Over-expression of tapasin rescues HLA-A2 surface expression.  Using this assay as the basis for a fluorescence-based selection, tapasin was deep mutationally scanned at 108 positions in the core, at the interface with MHC-I, and on the ‘backside’ distal from where MHC-I binds.  Critical residues of tapasin for rescue of HLA-A2 processing map to sites that contact the underside of the MHC-I alpha-2 domain, to the surface contacting the MHC-1 beta2m and alpha-3 domains, and to the base of a protruding loop that rests above the peptide-binding groove (but not to the tip of the loop itself).

overall_design: A synthetic sequence of tapasin was constructed. A library was generated of tapasin in which 108 positions were diversified with degenerate NNK codons.  The library was transfected into tapasin-knock out Expi293F cells after 1500-fold dilution with a carrier plasmid; this ensures most cells express no more than a single sequence variant and there is a tight connection between genotype and phenotype.  Illumina sequencing data to validate the introduction of indel mutations in exon 2 of the tapasin gene is in GEO Series Acc. No. GSE126206.  Cells expressing the tapasin library were stained for surface HLA-A2 with R-phycoerythrin-conjugated anti-HLA-A2 clone BB7.2, and the 0.5% of cells with the highest fluorescence were collected by FACS.  Following Illumina sequencing, the frequencies of mutations from transcripts in the sorted cells were compared to their respective frequencies in the naive plasmid library.  The calculated enrichment ratios are a proxy for relative activity of the tapasin sequence variants.

first: Christine

last: Devlin


title: Specific ectodermal enhancers control the expression of Hoxc genes in developing mammalian teguments [RNA-seq]

status: Public on Oct 05 2020

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

summary: Vertebrate Hox genes are key players in the establishment of structures during the development of the main body axis. Subsequently, they play important roles either in organizing secondary axial structures such as the appendages, or during homeostasis in postnatal stages and adulthood. Here we set up to analyze their elusive function in the ectodermal compartment, using the mouse limb bud as a model. We report that the HoxC gene cluster was globally co-opted to be transcribed in the distal limb ectoderm, where it is activated following the rule of temporal colinearity. These ectodermal cells subsequently produce various keratinized organs such as nails or claws. Accordingly, deletion of the HoxC cluster led to mice lacking nails (anonychia) and also hairs (alopecia), a condition stronger than the previously reported loss of function of Hoxc13, which is causative of the ectodermal dysplasia 9 (ECTD9) syndrome in human patients. We further identified, in mammals only, two ectodermal-specific enhancers located upstream the gene cluster, which act synergistically to regulate Hoxc genes in these ectodermal organs. Deletion of these enhancers alone or in combination revealed a strong quantitative component in the regulation of these genes in the ectoderm, suggesting that these two enhancers may have evolved along with mammals to provide the level of HOXC proteins necessary for the full development of hairs and nails.

overall_design: RNA-seq datasets of E9.5 to E12.5 distal part of forelimb embryos separated into mesoderm and ectoderm

first: M

last: Fernandez-Guerrero

first: L

first: D

last: Duboule

last: Ros


title: Chronic Malaria drives functional heterogenity in B cell subpopilations and expansion of unswitched atypical memory B cells [Malaria scRNA-seq]

status: Public on Sep 30 2020

city: Atlanta

first: Arun

last: Boddapati

state: GA

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

summary: Human chronic infectious diseases have been shown to alter the composition and phenotype of the B cell compartment, which, in part, can attribute to failure to acquire protective immunity. However, the extent of such alterations is poorly understood. Here, using a combination of bulk and single cell RNA-sequencing (scRNA-seq) of B cells in individuals living in malaria-endemic Africa, we characterized changes in naïve B cell, classical memory B cell (MBC) and atypical MBC subsets. Of particular interest were unswitched atypical MBCs that expanded in children upon the onset of febrile malaria. This subpopulation expressed IgD but only low levels of IgM (IgD+IgMlo), high levels of the atypical MBC markers, Tbet and CD11c, as well as the intrinsically autoreactive VH4-34. IgD+IgMlo atypical MBCs were distinguished functionally by their acquisition of high antigen-affinity thresholds for activation, suggesting the IgD+IgMlo atypical MBC expansion during febrile malaria may reduce responses to low affinity self-antigens during acute malaria

overall_design:
scRNA seq of peripheral blood B cells isolated by negative selection from three adults living in malaria-endemic Mali and three adults from US
The raw data is to be made available through dbGaP (controlled access;  phsnnnnnn)

first: Holla

last: Prasida

first: Abhijit

last: Ambegaonkar

first: Noga

last: Rogel

first: Haewon

last: Sohn

first: Dan

last: Sturdevant

first: Asaf

last: Madi

first: Susan

last: Pierce


title: Shared transcriptional profiles at the single cell level of atypical memory B cells suggest common drivers of expansion and function in malaria, HIV and autoimmune diseases [Malaria VDJ+GEX scRNA-seq]

overall_design:
scRNA seq (VDJ+GEX) of peripheral blood B cells isolated by negative selection from two adults living in malaria-endemic Mali
The raw data is to be made available through dbGaP (controlled access)

first: Prasida

last: Holla

first: Brian

last: Dizon

first: Ella

last: Goldschmidt

first: James

middle: W

last: Austin

first: Lela

last: Kardava

first: Li

last: Yuesheng

first: Poching

last: Liu

last: Moir


title: Shared transcriptional profiles at the single cell level of atypical memory B cells suggest common drivers of expansion and function in malaria, HIV and autoimmune diseases [HIV scRNA-seq]

summary: Human chronic infectious diseases, including malaria and HIV and autoimmune diseases, notably SLE, are accompanied by a striking expansion of a subpopulation of B cells termed atypical memory B cells (MBCs). We compared the single cell transcriptional profiles of B cells in malaria and HIV, characterizing and uncovering heterogeneity within each B cell subset. Remarkably, atypical MBC clusters in these two diseases showed significant similarities to each other as well as to atypical MBCs in autoimmune diseases, suggesting a common driver of their expansion and shared functions. Focusing on atypical MBCs in malaria we identified an IgD+IgMlo subpopulation that expanded in children upon the onset of febrile malaria, showed a distinct V gene usage characteristic of antigen-driven B cell populations and unexpectedly, had acquired high antigen-affinity thresholds for activation. We speculate that in malaria IgD+IgMlo atypical MBCs expand to limit responses to low-affinity self-antigens, a function that may be shared by  atypical MBCs in other chronic infections and autoimmune diseases.

overall_design:
scRNA seq of peripheral blood B cells isolated by negative selection from three HIV-infected adults and three healthy adults, all from the US
The raw data is to be made available through dbGaP (controlled access; phsnnnnnn)


title: A cis-regulatory atlas of maize single cells

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. We describe 92 distinct patterns of chromatin accessibility across more than 165,913 putative CREs, greater than 56,575 cells, and 52 known cell-types using a novel regularized quasibinomial logistic model for estimating single cell accessibility. Cell-type specification could be largely explained by combinatorial accessibility of transcription factors (TFs) and their associated binding. Analysis of cell type-specific co-accessible chromatin recapitulated higher-order chromatin interactions, providing novel insight into cell type-specific regulatory dynamics. Integration of genetic diversity data revealed cell-type specific CREs contributed to specific morphological and molecular phenotypic traits indicative of their cellular functions, expanding our understanding of the molecular influence of complex traits in a eukaryotic species.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design: All samples were integrated into a single all vs. all analysis. Several organs (leaf, axillary buds, embyonic roots, crown roots) were profiled with biological replicates.

first: Alexandre

last: Marand


title: Chronic Malaria drives functional heterogenity in B cell subpopilations and expansion of unswitched atypical memory B cells

first: Arun

last: Boddapati

overall_design: Refer to individual Series


title: Chronic Malaria drives functional heterogenity in B cell subpopulations and expansion of unswitched atypical memory B cells [Malaria bulkRNA-seq]

overall_design:
Differential gene expression between four B cell subsets - Naïve B cells (CD21+CD27-), classical memory B cell (CMBC- CD21+CD27+), activated memroy B cell (AcMBC- CD21-CD27+) and atypical MBC (CD21-CD27-) obtained by sorting peripheral blood B cells (CD19+CD20+CD10-) of three adults living in Malaria-endemic Mali
The raw data is to be made available through dbGaP (controlled access;  phsnnnnnn)

first: Holla

last: Prasida

last: Ambegaonkar


title: ROF1 induction experiments [Agilent]

first: Rebecca

last: Wang

summary: Measure global transcriptional responses to ROF1 induction in S288c budding yeast

overall_design: Experiments with phosphate-limited chemostats were performed as described in Hackett et al (MSB, 2020). Extraction, labeling, and hybridization of RNA were performed as described in Hackett et al (MSB, 2020). Microarrays were imaged using an Agilent SureScan G4900DA Microarray Scanner. Images were processed using Agilent Feature Extraction software and a custom R script. Fluorescence intensities were floored at a value of 50. The resulting data were hierarchically clustered (Pearson distance metric with average linkage) using Cluster 3.0 and visualized in R using the pheatmap package.

first: R

last: McIsaac

first: Bernd

last: Wranik


title: Phenotypically supervised single cell sequencing parses within-cell-type heterogeneity

city: San Diego

first: Stephanie

last: Fraley

address: 9500 Gilman Drive MC 0412

institute: UCSD

summary: We used a phenotypic cell sorting technique to ask whether phenotypically supervised scRNAseq analysis (pheno-scRNAseq) can provide more insight into heterogeneous cell behaviors than unsupervised scRNAseq. Using a simple 3D in vitro breast cancer (BRCA) model, we conducted pheno-scRNAseq on invasive and non-invasive cells and compared the results to phenotype-agnostic scRNAseq analysis. Pheno-scRNAseq identified unique and more selective differentially expressed genes (DEGs) than unsupervised scRNAseq analysis. Functional studies validated the utility of pheno-scRNAseq in understanding within-cell-type functional heterogeneity and revealed that migration phenotypes were coordinated with specific metabolic, proliferation, stress, and immune phenotypes.

overall_design: Transcriptomic examination of human and mouse breast cancer cells for phenotypic heterogeneity. Phenotypic supervision: Cells were phototagged using photoconversion of Dendra2 that was transduced into MDA-MB-231 cells. Cells were then sorted using fluorescence activated cell sorting.  2 samples were phenotypically supervised, 2 samples were phenotype-agnostic.

first: Kevin

last: Chen

first: Kivilcim

last: Ozturk

first: Hannah

last: Carter


title: RNA-seq of mouse testis samples from different treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: The aim of this project was to explore the role of muscarinic receptors (M1, M3, and M5) in spermatogenesis. The lentivirus with the knockdown of M1, M3, M5 were injected into mouse testes. Then the testes were collected. The RNA was used for the RNA-seq analysis to search the role of these receptors in the spermatogenesis.

overall_design: RNA-seq of mouse testis samples from different groups in muscarinic receptor knockdown, control treatment

first: Bohui

last: Xiong

first: Cong

last: Zhang

first: Wei

last: Shen


title: Long-chain saturated fatty acids in breast milk are associated with the pathogenesis of atopic dermatitis via inducing inflammatory ILC3s

city: Hiroshima

first: masamoto

last: kanno

address: 1-2-3, kasumi, Minami-ku

department: Department of Immunology

institute: Hiroshima University

summary: Breastfeeding is thought to influence the immune system development of infants and may even affect various immunological responses later in life. Breast milk provides a rich source of early nutrition for the growth and developmental of infants. However, the presence of certain compounds in breast milk related to an unhealthy lifestyle or the diet of lactating mothers may negatively impact infants6. Based on a cohort study, we found that the composition of mother’s milk containing high amount of long-chain saturated fatty acids (LCSFAs) was related to a higher incidence of atopic dermatitis (AD) in children. Similarly, a mouse model in which breastfed offspring were fed milk high in LCSFAs also resulted in AD onset later in life. We showed that LCSFAs are damage-associated molecular patterns, which initiate a series of inflammatory events in the gut involving type 3 innate lymphoid cells (ILC3s). A remarkable increase in inflammatory ILC3s was observed in the gut, and the migration of these ILC3s to the skin contributed to the pathogenesis of AD. Gene expression analysis of ILC3s isolated from the gut revealed up-regulation of genes that increase ILC3s and chemokines, which may play a role in ILC migration to the skin. Even in the absence of adaptive immunity, Rag1 knockout mice fed a high-LCSFA milk diet developed eczema, accompanied by increased gut ILC3s. Here, we propose that early exposure to LCSFAs in infants may affect the balance of intestinal innate immunity, inducing a highly inflammatory environment with the proliferation of ILC3s and production of interleukin-17 and interleukin-22, which are attributed to the pathogenesis of AD.

overall_design: Examination of ILC3s from intraepithelial and lamina propria layer of two different mice groups, comparison between normal or fed with maternal milk with high saturated fatty acids

first: Weng-Sheng

last: Kong

first: Masamoto

last: Kanno


title: Single-cell RNA transcriptome helps define the limbal/corneal epithelial stem/early transit amplifying cells and how autophagy affects this population in cornea

status: Public on Sep 24 2020

city: Chicago

first: Han

last: Peng

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary:
Purpose: Single-cell RNA-sequencing (scRNA-seq) was used to interrogate the relatively rare stem (SC) and early transit amplifying (TA) cell populations in limbal/corneal epithelia from wild-type and autophagy-compromised mice.
Results: Unbiased clustering detected 10 distinct populations: three clusters of mesenchymal and seven clusters of epithelial cells, based on their unique molecular signatures. A discrete group of mesenchymal cells expressed genes associated with corneal stromal SCs. We identified three limbal/corneal epithelial cell subpopulations designated as stem/early TA, mature TA, and differentiated corneal epithelial cells. Thioredoxin-interacting protein and PDZ-binding kinase (PBK) were identified as novel regulators of stem/early TA cell quiescence. PBK arrested corneal epithelial cells in G2/M phase of the cell cycle. Beclin1+/− mice displayed a decrease in proliferation-associated (Ki67, Lrig1) and stress-response (H2ax) genes. The most increased gene in beclin1+/− mice was transcription factor ATF3, which negatively regulates limbal epithelial cell proliferation.  Conclusions: Establishment of a comprehensive atlas of genes expressed by stromal and epithelial cells from limbus and cornea forms the foundation for unraveling regulatory networks among these distinct tissues. Similarly, scRNA-seq profiling of the anterior segmental epithelia from wild-type and autophagy-deficient mice provides new insights into how autophagy influences proliferation in these tissues.

overall_design: Methods: We conducted scRNA-seq on ocular anterior segmental tissue from wild-type and beclin 1–deficient (beclin1+/−) mice, using a 10X Gemomics pipeline. Cell populations were distinguished by t-distributed stochastic neighbor embedding. Seurat analysis was conducted to compare gene expression profiles between these two groups of mice. Differential protein expression patterns were validated by immunofluorescence staining and immunoblotting.

first: Nihal

last: Kaplan

first: Junyi

first: Brian

last: Wray

first: Priyam

last: Patel

first: Matthew

last: Schipma

first: Wending

last: Yang

first: Robert

last: Lavker


title: cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing

status: Public on Sep 29 2020

city: Edinburgh

first: Yanick

last: Crow

address: Western General Hospital Campus, Crewe Road

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: A disturbance of histone protein composition renders nuclear DNA immunogenic, inducing a type I interferon response to self.

overall_design: We investigated histone pre-mRNA misprocessing in patient and control fibroblasts using RNA-seq. Total RNA was extracted from the cells and transcripts remaining after an initial selection for polyadenylated RNA were ribo-depleted, and both poly(A)+ and poly(A)- fractions then sequenced.


title: Investigating the role of IL-2 in shaping the epigenome in T cells [RNA-seq]

status: Public on Sep 14 2020

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: During T cell activation hundreds of genes are primed for efficient activation. Here we show that IL-2 signaling is required to maintain open chromatin at gene regulatory elements which are associated with alternate pathways of T cell differetiation.IL-2 actiavtes binding of AP-1 and STAT5 at sites that can subsequently bind other STAT and lineage dietermining proteins, depending on what other factors exist in their enviroment.

overall_design: RNA-seq samples were generated in triplicate for T-blast cells cultured in IL-2 with and without activation with PMA and calcium ionophore and in T-blast cells cultured for 16 hours in the absence of IL-2 (IL-2nil) with (+) and without activation with PMA and calcium ionophore

first: Sarah

last: Bevington

first: Peter

last: Keane


title: Investigating the role of IL-2 in shaping the epigenome in T cells [ATAC-seq]

overall_design: ATAC-seq samples from in vivo generated antigen specific Th1 cells, Th17 cells, Il7ra deficient Th1 memory T cells and control littermates


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium [Tube_TiO2_NP]

status: Public on Sep 12 2020

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

summary: In this study, using advanced microscopy, in vivo/in vitro omics experiments and in silico molecular modelling, the long-lasting response to a single exposure of different lung cell types to nanomaterial was determined. The information was further used to build a predictive algorithm that would allow identification of nanomaterials that have the potential to induce inflammation.

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of Tube TiO2NPs. Four different doses were selected:0, 18, 54, or 162 µg/animal. Samples were collected at day 1, and day 28 post-exposure.

first: Luna

last: Rahman

first: Andrew

last: Williams


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium [100_nm_TiO2_NP]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of 100nm TiO2NPs. Four different doses were selected: 0,18, 54, or 162 µg/animal. Samples were collected at day 1, and day 28 post-exposure.


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium [Cube_TiO2_NP]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of Cube TiO2NPs. Four different doses were selected: 0, 18, 54, or 162 µg/animal. Samples were collected at day 1, and day 28 post-exposure.


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium [15_nm_TiO2_NP]

overall_design: This experiment examined the lung transcriptomic responses to single intratracheal instillation of 15nm TiO2NPs. Four different doses were selected: 0,18, 54, or 162 µg/animal. Samples were collected at day 1, and day 28 post-exposure.


title: Predicting Impact of Myeloid Cells on T Cells Effector Function from Spatial Organization of TiME in CRC

city: Penzberg

first: Henrik

last: Failmezger

address: Nonnenwald 2

institute: Roche Diagnostics GmbH

summary: Recent developments in digital computational pathology support not only classical cell density based tumor characterization, but also a more comprehensive analysis of the spatial cell organization in the tumor immune microenvironment (TiME). Leveraging that methodology in the current study, we tried to address the question of how the distribution of myeloid cells in TiME of primary colorectal cancer (CRC) affects the function and location of cytotoxic T cells. We applied multicolored immunohistochemistry to identify monocytic (CD11b/CD14) and neutrophilic (CD11b/CD15) myeloid cell populations together with proliferating and non-proliferating cytotoxic T cells (Ki67/CD8). Through automated object detection and image registration using HALO software (IndicaLab), we applied dedicated spatial statistics to measure the extent of overlap between the areas occupied by myeloid and T cells. With this approach, we observed distinct spatial organizational patterns of immune cells in tumors obtained from 74 treatment-naive CRC patients. Detailed analysis of inter-cell distances and myeloid-T cell spatial overlap combined with integrated gene expression data allowed to stratify patients irrespective of their mismatch repair (MMR) status or consensus molecular subgroups (CMS) classification. In addition, generation of cell distance-derived gene signatures and their mapping to the TCGA data set revealed associations between spatial immune cell distribution in TiME and certain subsets of CD8 and CD4 T cells. Presented study sheds a new light on myeloid and T cell interactions in TiME in CRC patients. Our results show that CRC tumors present distinct distribution patterns of not only T effector cells but also tumor resident myeloid cells, stressing out the necessity of more comprehensive characterization of TiME in order to better predict cancer prognosis. This research emphasizes the importance of multimodal approach combining computational pathology with its detailed spatial statistics and gene expression profiling. Finally, our study presents a novel approach to cancer patients characterization that can potentially be used to develop new immunotherapy strategies, not based on classical biomarkers related to CRC biology.

overall_design: Gene expression in colorectal cancer.

first: Natalie

middle: N

last: Zwing

first: Konstanty

last: Korski


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium

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


title: Profiling of histone modifications in bovine embryonic stem cells

status: Public on Aug 29 2020

city: Fort Collins

first: Michelle

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

summary: Profiling of H3K27me3 and H3K4me3 in bovine embryonic stem cells using Cut&Run.

overall_design: Cut&Run libraries were prepared from bovine embryonic stem cells. Two histone modifications were profiled (H3K27me3 and H3K4me3) and for each mark, two replicate libraries were prepared.

first: Chuan

last: Zhou

first: Micaela

last: Navarro

first: Pablo

last: Ross


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium [DQ_TiO2_NP]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of DQ TiO2NPs. Four different doses were selected: 0,18, 54, or 162 µg/animal. Samples were collected at day 1, and day 28 post-exposure.


title: Investigating the role of IL-2 in shaping the epigenome in T cells

overall_design: Refer to individual Series


title: The transcription factor bZIP60 links the Unfolded Protein Response (UPR) to the Heat Stress Response (HSR) in maize

status: Public on Aug 31 2020

city: Ames

first: Stephen

middle: H

last: Howell

state: Iowa

address: 1111 WOI Road

department: Plant Sciences Institute Department of Genetics, Development and Cell Biology

institute: Iowa State University

summary: This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of heat stress on maize we used a controlled environment facility called the Enviratron to simulate field conditions. For our experiments, maize plants were subjected to conditions simulating normal diurnal rhythms of light and temperature, with increasing maximal daily temperature (MDT). Maize plants were grown continuously under four different temperature regimes with simulated morning temperatures ramped up over 6 hr to the MDT of 31°C, 33°C, 35°C or 37°C and simulated evening/night time temperatures ramped down over 8 hr to 10°C below the MDT. We tracked the gene expression events of maize W22 seedlings grow under different temperatures (MDT of 31°C, 33°C, 35°C or 37°C) to evaluate how different MDTs affect the program of gene expression in maize. At the same time, we analyzed the effects of temperature on gene expression in bzip60-2 and W22 V4 plants (20 DAG) and V5 plants (27 DAG) in the Enviratron as the temperature reached its MDT to investigate whether and how bZIP60 confers heat stress tolerance in maize. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of V4 and V5 W22 plants (at 20 and 27 DAG, respectively). Plants were sampled in triplicates.

overall_design: Each sample was collected in 3 biological replicates, and each replicate from mutiple plants under the same condition.

first: Zhaoxia

last: Li

first: Jie

last: Tang

first: Renu

last: Srivastava

first: Diane

last: Bassham


title: Effects of Tesamorelin on Hepatic Transcriptomic Signatures in HIV-Associated NAFLD

status: Public on Sep 08 2020

city: Boston

first: James

middle: M.

last: Billingsley

state: MA

address: Landmark Center, 3rd Floor East, 401 Park Drive

institute: harvard T.H. Chan school of public health

summary: Nonalcoholic fatty liver disease (NAFLD) is a common comorbidity among people living with HIV with a more aggressive course than in the general population. In a recent randomized placebo-controlled trial, we demonstrated that the growth hormone-releasing hormone analogue tesamorelin reduced liver fat and prevented fibrosis progression in HIV-associated NAFLD over one year. In the current study, we leveraged paired liver biopsy specimens from this trial to identify hepatic gene pathways that are differentially modulated by tesamorelin versus placebo to gain key insights into the biological underpinnings of its clinical effects.

overall_design: We performed whole transcriptome analysis, and subsequent Gene Set Enrichment Analysis (GSEA) on paired liver biopsies, at baseline and 12 months after treatment  with tesamorelin (n = 18) or placebo (n = 21) on all participants who had available data of sufficient quality.

first: Lindsay

middle: T

last: Fourman

first: George

last: Agyapong

first: Shannan

last: Sui

first: Meghan

last: Feldpausch

first: Julia

last: Purdy

first: Isabel

last: Zheng

first: Chelsea

middle: S

last: Pan

last: Aepfelbacher

first: Kathleen

last: Corey

first: Martin

last: Torriani

first: David

last: Kleiner

first: Colleen

last: Hadigan

first: Takara

last: Stanley

first: Raymond

last: Chung

first: Steven

last: Grinspoon