title: Reduced A-to-I editing of endogenous Alu RNAs in severe COVID-19 disease

city: Nashville

last: Aune

state: Tennessee

address: 1161 21st Avenue S.

department: Medicine - Rheumatology

institute: Vanderbilt University Medical Center

summary: Severe COVID-19 disease is associated with elevated inflammatory responses.  One form of Aicardi-Goutières Syndrome caused by inactivating mutations in ADAR results in reduced A-to-I editing of endogenous double-stranded RNAs (dsRNAs), induction of IFNs, interferon-stimulated genes (ISGs), other inflammatory mediators, morbidity and mortality.  Alu elements, ~10% of the human genome, are the most common A-to-I editing sites.  Using leukocyte whole-genome RNA sequencing data, we find reduced A-to-I editing of Alu dsRNAs in patients with severe COVID-19 disease. Unedited Alu dsRNAs, but not edited Alu dsRNAs, are potent inducers of IRF and NF-kB transcriptional responses, IL6, IL8 and ISGs.  Thus, decreased A-to-I editing that may lead to accumulation of unedited Alu dsRNAs and increased inflammatory responses, is associated with severe COVID-19 disease.

relation:
Reanalysis of: GSM4509015
Reanalysis of: GSM4509023
Reanalysis of: GSM4509024
Reanalysis of: GSM4509029
Reanalysis of: GSM4509011
Reanalysis of: GSM4509012
Reanalysis of: GSM4509019
Reanalysis of: GSM4509020
Reanalysis of: GSM4509021
Reanalysis of: GSM4509022
Reanalysis of: GSM4509025
Reanalysis of: GSM4509026
Reanalysis of: GSM4509027
Reanalysis of: GSM4509028
Reanalysis of: GSM4509030
Reanalysis of: GSM4509013
Reanalysis of: GSM4509014
Reanalysis of: GSM4509016
Reanalysis of: GSM4509017
Reanalysis of: GSM4509018
Reanalysis of: GSE149689

overall_design:
We employed whole-genome RNA-sequencing (RNA-seq) files from NCBI Gene Expression Omnibus (GSE149689) for analysis of A-to-I editing. We used the following workflow to identify RNA A-to-I editing sites from paired FASTQ sequencing files.  The main identification tool was a python-based package called the SPRINT toolkit that accepts sequence files and produces text files with the following information for each edit site: (A) genomic location; (B) type of edit (e.g., A-to-G; T-to-C); strand (+ or -); (C) number of edits per site and total number of reads per site. Mathematica programs were developed to synthesize data: numbers of samples in groups with shared editing sites, mean numbers of total reads and edits for each editing site, and editing sites common and unique to group pairs (e.g., HC versus COV-S).  This information was tied to an Alu database to annotate each site: gene locations (intronic, ncRNA, intergenic, 3UTR), and if sites were Alu or non-Alu elements.  To create genome-wide A-to-I editing indices, we identified all A-to-I editing sites present in one sample and summed edit/read ratios for all editing sites across the genome for each HC, COV-M, COV-S or FLU-S sample.
Data Processing:
Input FASTQ RNA-seq files into SPRINT toolkit
recover text files with the following information for each edit site: (A) genomic location; (B) type of edit (e.g., A-to-G; T-to-C); strand (+ or -); (C) number of edits per site and total number of reads per site.
Mathematica programs were developed to synthesize data: numbers of samples in groups with shared editing sites, mean numbers of total reads and edits for each editing site, and editing sites common and unique to group pairs (e.g., HC versus COV-S).
This information was tied to an Alu database to annotate each site: gene locations (intronic, ncRNA, intergenic, 3UTR), and if sites were Alu or non-Alu elements.
To create genome-wide A-to-I editing indices, we identified all A-to-I editing sites present in one sample and summed edit/read ratios for all editing sites across the genome for each HC, COV-M, COV-S or FLU-S sample.
assembly: hg19

first: Philip

last: Crooke III


title: Differential Genome Expression in AhR-KD and Control HCMV-Infected Fibroblasts

status: Public on Mar 05 2021

city: Princeton

first: Thomas

middle: E

last: Shenk

state: NJ

address: Washington Road

department: Molecular Biology

country: USA

institute: Princeton University

type: Expression profiling by high throughput sequencing

summary: Here we report the effect of Aryl hydrocarbon Receptor (AhR) on the transcriptome of HCMV-infected fibroblasts.

overall_design: Total RNA profiles of HFF cells, treated with either Negative Control (NC) or AhR-targeting Locked Nucleic Acids (LNS's), and infected with AD169 HCMV in biological duplicate, at one early time-point.

first: Pooya

last: Naseri-Nosar


title: TT-seq and RNA-seq in TX1072 XXΔXic and XO mESCs during differentiation

status: Public on Mar 04 2021

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use TT-seq and RNA-seq to profile nascent and processed RNA transcription within the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: TT-seq was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at day 2 and day 4 of differentiation (via 2i+LIF-withdrawal).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

first: Michael

last: Robson

first: Robert

last: Schöpflin

first: Liat

last: Ravid

first: Lennart

last: Brandenburg

first: Ilona

last: Dunkel

first: Carolina

last: Vechiatto

first: Evgenia

last: Ntini

first: Verena

last: Mutzel

first: Vera

last: Schmiedel

first: Annalisa

last: Marsico

first: Stefan

last: Mundlos

first: Edda

middle: G

last: Schulz


title: ChIP-exo of HH514-16 treated with NaB or left untreated

city: Gainesville

first: Sumita

middle: A

last: Bhaduri-McIntosh

state: FL

address: ARB  R1-118G, 1600 SW Archer Road

department: Depts. of Pediatrics & of Molecular Genetics and Microbiology

institute: University of Florida

type: Genome binding/occupancy profiling by high throughput sequencing

summary: How Krüppel-associated box-domain zinc finger protein (KRAB-ZFP) transcriptional repressors recruit TRIM28/KAP1 to recognizes target sequences or foreign genomes is unclear.  Here, we used Epstein-Barr virus-infected cells in which a KRAB-ZFP, SZF1, silences lytic/replicative-phase genes of the virus to determine how the ZFP-footprints on cell and viral genomes to target pericentromeric regions. We observed that it uses non-consensus sites to target viral genes. This heterochromatin machinery employed by the host silences and regulate an invader without deregulating itself.

overall_design: We treated HH514-16 Burkitt Lyphoma cells with NaB to induced the lytic phase of the life cyle of EBV or left untreated. After 24hrs, the cells were harvested, stained with reference EBV-seropositive and EBV-seronegative serum, washed, and sorted by Fluorescence Activated Cell Sorting (FACS) into EBV lytic and latent/refractory cell populations. We next performed ChIP-exo and barcoded library for each sample treatment. The sequencing reads were processed by Peconic Genomics for peak-calling. Reads were mapped to GRC hg38 assembly of human genome and EBV reference genome (NC_007605). Peaks were called and identified using default parameters of the GeneTrack and GEM algorithms.

first: Eric

middle: M

last: Burton

first: Ibukun

last: Akinyemi

first: Tiffany

middle: R

last: Frey

first: Huanzhou

last: Xu

first: Xiaofan

last: Li

first: Lai

middle: J

last: Su

first: Jizu

last: Zhi

middle: T

last: McIntosh


title: PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

first: Till

last: Schwämmle

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use polyA-tail enriched RNA-seq within the wildtype TX1072 XX cell line after two days of differentiation.

overall_design: RNA-seq enriched for polyadenylated fragments was performed in differentiating TX1072 XX mESCs using the TruSeq RNA Sample Preparation Kit v2 (Illumina).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

first: Michael

last: Robson

first: Robert

last: Schöpflin

first: Liat

last: Ravid

first: Lennart

last: Brandenburg

last: Dunkel


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

city: Iowa City

middle: S

last: Chimenti

state: IA

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 and ATAC-Seq showed that the differentially expressed genes in YAP-TFE3 cells with knockdown of YEATS2 or ZZZ3 are nested in regions of open chromatin unique to YAP-TFE3.
The altered transcriptional program of the fusion proteins is modulated by the Ada2a-containing histone acetyltransferase complex.

overall_design: mRNA profiles of SW872 liposarcoma cells transduced with fusion gene constructs with shRNAs targeting YEATS2 or  ZZZ3 were generated by deep sequencing, in duplicate.

first: Munir

last: Tanas


title: Capture Hi-C in TX1072 XXΔXic and XO mESCs in the naive pluripotent state and during differentiation

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use capture Hi-C to profile chromatin contacts within the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: Capture Hi-C was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines on a 3 megabase region surrounding the Xist gene (chrX:102238718-10521426). The data was collected in two replicates from cells in 2i+LIF medium (day 0), as well at day 2 of differentiation (via 2i+LIF-withdrawal).

first: Ilona

first: Carolina

last: Vechiatto

first: Evgenia

last: Ntini

first: Verena

last: Mutzel

first: Vera

last: Schmiedel

first: Annalisa

last: Marsico

first: Stefan

last: Mundlos

first: Edda

last: Schulz


title: Non-coding CRISPR interference screen to identify regulatory elements of Xist in TX1072 XX SP107 mESCs at the onset of random X inactivation

last: Schwämmle

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use an inducible CRISPRi system in a non-coding CRISPR screen to profile 138 candidate regulatory elements on their effect on Xist upregulation during early differentiation of mouse Embryonic Stem Cells (mESCs).

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: A non-coding CRISPRi screen for Xist was performed in differentiating mESCs (TX1072 XX SP107) carrying an ABA-inducible dCas9-KRAB system. The library contained 7058 gDNAs targeting 138 candidate regulatory elements within the X inactivation center, as well as 300 non-targeting controls. After 2 days of differentiation via 2i/LIF-withdrawal, the cells were stained for Xist RNA using a FlowFISH protocol and sorted into 4 different fractions (Negative, Low, Medium and High) corresponding to 15% bins of Xist-expression.


title: Identification of intrinsically immunogenic small cell lung carcinoma (SCLC) subpopulations

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

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

institute: Icahn School of Medicine at Mount Sinai

summary: SCLC is molecularly and immunologically heterogenous. Here, using transcriptional and epigenomic profiling of plastic SCLC states in human and mouse cell lines, and patient samples, we define the phenotype of a SCLC population marked by increased MHC Class I antigen presentation.

overall_design: Examination of paired transcriptome and H3K27Me3 ChIP-seq in isogenic SCLC cell lines, and transcriptomes of MHC Class I high vs. low SCLC cell lines and patient samples

first: Navin

last: Mahadevan

first: David

last: Barbie


title: Alternative splicing is a developmental switch for hTERT expression

city: NEW YORK

first: Alex

last: Penev

address: 540 First Ave

institute: NYU Langone Medical Center

summary: Telomere length control is critical for cellular lifespan and tumor suppression. Telomerase is activated in the inner cell mass of the developing blastocyst to reset telomere reserves and its subsequent silencing in differentiated cells leads to gradual telomere shortening. Here, we report that transcriptional control through cis-regulatory elements minimally impact telomerase regulation as a function of pluripotency. Instead, developmental control of telomerase is largely driven by an alternative splicing event, centered around hTERT exon-2. Skipping of exon-2 triggers hTERT mRNA decay in differentiated cells. Conversely, its retention in pluripotent cells promotes telomerase accumulation. Our study also identifies SON as a regulator of exon-2 alternative splicing and we report a patient with insufficient telomerase and short telomeres and harboring a SON mutation. In summary, our study highlights a critical role for hTERT alternative splicing in the developmental regulation of telomerase and implicates defective splicing in telomere biology disorders.

overall_design: Examination of chromatin accessibility and physical chromatin interactions

first: Andrew

last: Bazley

last: Shen

first: Jef

last: Boeke

first: Sharon

last: Savage

first: Agnel

last: Sfeir


title: Transcriptome differences between immortalized brown preadipocytes treated with different paracrine FGFs

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding transcript abundance in primary, immortalized brown preadipocytes from murine, interscapular brown adipose tissue.

overall_design: We prepared primary preadipocytes from the stromal-vascular fraction of murine interscapular brown fat of 129SvEv mice and immortalized these by the SV40 large T antigen method. Cells were treated with 5.56nM Fgf1, Fgf8b or FGF9 for 48h in the presence of 1µg/ml heparin. One group of Ffg8b treated cells was also treated with 2µM Bay-876.  We sequenced total RNA and determined transcript abundance.

first: Thomas

last: Gantert

first: Martin

last: Klingenspor

first: Christine

last: Wurmser


title: STARR-seq in 1.8 XX and XO mESCs during differentiation

first: Till

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use STARR-seq to profile enhancer activity within the X inactivation center at the onset of random X-chromosome inactivation.

overall_design: STARR-seq was performed in the 1.8 XX and 1.8 XO cell lines using the BAC clones of the RPCI-23 Female (C57BL/6J) Mouse BAC Library (RP23-106C4, RP23-11P22, RP23-423B1, RP23-273N4, RP23-71K8) as the input DNA source. The data was collected in 3 replicates from cells in 2i+LIF medium (day 0), as well at day 2 of differentiation (via 2i+LIF-withdrawal).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

first: Michael

last: Robson

first: Robert

last: Schöpflin

first: Liat

last: Ravid

first: Lennart

last: Brandenburg

first: Ilona

last: Dunkel

first: Carolina

last: Vechiatto

first: Evgenia

last: Ntini

first: Verena

last: Mutzel

last: Schmiedel

last: Marsico


title: ATAC-seq in TX1072 XXΔXic and XO mESCs during differentiation

last: Schwämmle

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use ATAC-seq to profile DNA accessibility within the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: ATAC-seq was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at day 2 and day 4 of differentiation (via 2i+LIF-withdrawal).

first: Vera

first: Annalisa

first: Stefan

last: Mundlos

first: Edda

last: Schulz


title: Direct contribution of skeletal muscle mesenchymal progenitors to bone repair

city: Creteil

first: Celine

last: Colnot

state: Val de Marne

address: 8 rue du Général Sarrail

department: INSERM U955, IMRB

country: France

institute: Univ Paris Est Créteil, INSERM

summary: Bone regeneration involves skeletal stem/progenitor cells within periosteum and bone marrow, the formation of a fibrous callus followed by the deposition of cartilage and bone matrix to consolidate the fracture. Interactions between bone and skeletal muscle are known to play a role in bone repair but the underlying mechanisms are poorly understood. To better understand the role of skeletal muscle during bone repair, we characterized stem/progenitor cells within skeletal muscle that participate in bone repair. We show that cells originating from bone marrow, periosteum and skeletal muscle are all derived from the Prx1 embryonic lineage. We developed a mouse polytrauma model combining a non-stabilized tibial fracture and mechanical injury to adjacent skeletal muscles. In this polytrauma model, bone fracture healing is impaired. We characterized the Prx1-derived cell population within skeletal muscle in response to fracture and to polytrauma. To do so, we performed fracture and polytrauma in Prx1Cre;Rosa mTmG mice. We harvested skeletal muscle surrounding the tibia at d0 (uninjured), and surrounding the fracture site at d3 and d5 post-fracture or post-polytrauma. Following enzymatic and mechanical digestion of skeletal muscle tissue, we FACS sorted Prx1-derived GFP+ cells and sequenced them using the 10X Chromium technology.

overall_design: Skeletal muscle Prx1-derived cells GFP+ at d0 (uninjured); Skeletal muscle Prx1-derived cells GFP+ at d3 post-fracture, Skeletal muscle Prx1-derived cells GFP+ at d5 post-fracture, Skeletal muscle Prx1-derived cells GFP+ at d3 post-polytrauma; Skeletal muscle Prx1-derived cells GFP+ at d5 post-polytrauma

first: Colnot

last: Celine

first: Julien

last: Anais


title: Epigenetic regulation of metabolic adaptation predicts response to Inositol hexakisphosphate (IP6) treatment in Group 4 medulloblastoma

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: RNA sequencing analysis for keratinocytes treated with U1 dsRNA and LL34 Alanine Scan Peptides

status: Public on Mar 03 2021

city: San Diego

first: Richard

middle: L

last: Gallo

state: CA

address: 9452 Medical Center Drive

department: Dermatology

institute: UCSD

summary: Summary: We looked at the global changes in gene expression in keratinlcytes treated with selected LL34 Alanine mutants and U1 dsRNA. Methods: Normal human keratinocytes were treated with 2.5 ug/ml U1 dsRNA with or with out co-treatment with LL34 Parent Peptide/ LL34 I24A or LL34 L31A for 18 h. Conclusions: Global gene expression analysis showed pathways related to Type 1 interferon signaling and cytokines where mainly repressed in cells co-treated with either LL34 I24A/ LL34 L31A peptide and U1 dsRNA in comparision to cells co-treated with LL34-Parent peptide and U1 dsRNA.

overall_design: Pooled samples from triplicates were used for RNA seq analysis.

first: Nikhil

middle: N

last: Kulkarni


title: SCFA

city: München

first: Gemma

last: Llovera

address: Feodor-Lynen-Straße 17

institute: Institut für Schlaganfall- und Demenzforschung (ISD)


title: Effect of individual SCFA on microglial polarization

summary: The effect of three individual SCFA were tested in primary microglial cultured cells, we evaluate microglia transcriptome using Nanostring technology

overall_design: Each sample represent an individual microglial cultured well with different SCFA treatment or Saline (control)


title: MicroRNA-221/222 modulate intestinal T helper 17 cell response as a negative feedback rheostat downstream of IL-23

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA-221/222 receive activation signal from IL-23 and suppression signal from TGFb, and target Maf and IL-23R for degradation, therebt acting in an inflammatory arm of Th17 response, and works as a negative feedback rheostat to constrain otherwise feed-forward loop of inflammatory Th17 response in the gut.

overall_design: Next Generation Sequencing Based Quantitative Analysis of Wild Type and miR-221/222-/- CD4+ T cells including ChIP-seq, miRNA-seq, mRNA-seq and scRNA-seq

first: Yohei

last: Mikami

first: Hong-Wei

last: Sun

first: Yuka

last: Kanno

first: John

last: O'Shea


title: Epigenetic regulation of metabolic adaptation predicts response to Inositol hexakisphosphate (IP6) treatment in Group 4 medulloblastoma (HumanMethylation850)

summary: Deregulation of chromatin modifiers plays an essential role in the pathogenesis of medulloblastoma (MB), the most common paediatric malignant brain tumour. Here, we identify a BMI1-dependent sensitivity to deregulation of inositol metabolism in a proportion of medulloblastoma. We demonstrate mTOR pathway activation and metabolic adaptation specifically in medulloblastoma of the molecular subgroup G4 characterised by a BMI1High;CHD7Low signature and show this can be counteracted by IP6 treatment. Finally, we demonstrate that IP6 synergises with cisplatin to enhance its cytotoxicity in vitro and extends survival in a pre-clinical BMI1High;CHD7Low xenograft model.

overall_design: DNA methylation analysis of medulloblastoma cell lines

first: Sara

last: Badodi

first: Nicola

last: Pomella

first: Gabriel

last: Rosser


title: Novel microfluidic platform isolates single cells from tissue faster and more thoroughly for single cell diagnostics and primary culture models.

city: Irvine

first: Jered

last: Haun

address: Nat Sci II 3107

department: Biomedical Engineering

institute: University of California, Irvine

summary: Tissues are composed of highly heterogeneous mixtures of cell subtypes, and this diversity is increasingly being characterized using high-throughput single cell analysis methods. However, these efforts are hindered by the fact that tissues must first be dissociated into single cell suspensions that are viable and still accurately represent phenotypes from the original tissue. Current methods for breaking down tissues are inefficient, labor-intensive, subject to high variability, and potentially biased towards cell subtypes that are easier to release. Here, we present a microfluidic platform consisting of three different tissue processing technologies that can perform the complete tissue to single cell workflow, including digestion, disaggregation, and filtration. First, we developed a new microfluidic digestion device that can be loaded with minced tissue specimens quickly and easily, and then use the combination of proteolytic enzyme activity and fluid shear forces to accelerate tissue breakdown. Next, we integrated dissociation and filter technologies into a single device, which enhanced single cell numbers and fully prepared the sample for single cell analysis. The final multi-device platform was then evaluated using a diverse array of tissue types that exhibited a wide range of properties. For murine kidney and mammary tumor, we found that microfluidic processing produced 2.5-fold more single, viable cells. Single cell RNA sequencing (scRNA-seq) further revealed that device processing enriched for endothelial cells, fibroblasts, and basal epithelium, and did not increase stress responses. For murine liver and heart, which are softer tissues containing fragile cell types, processing time could be reduced to 15 min, and even as short as 1 min. We also demonstrated that periodic recovery at defined time intervals produced substantially more hepatocytes and cardiomyocytes than continuous operation, most likely by preventing damage to fragile cell types. In future work, we will seek to integrate additional operations such as upstream tissue preparation and downstream microfluidic cell sorting and detection to create powerful point-of-care single cell diagnostic platforms.

overall_design: Six (6) samples were included. Three (3) from murine kidney tissue and three (3) from mammary tumor tissue samples. For each tissue type, there were two samples that were processed using the device platform and collected at 15 and 60 min intervals, and we also evaluated the 60 min control.

first: Jeremy

last: Lombardo

first: Marzieh

last: Aliaghaei

first: Quy

middle: H

last: Nguyen

first: Kai

last: Kessenbrock

middle: B


title: Indole-3-carbinol-dependent aryl hydrocarbon receptor signaling attenuates the inflammatory response in experimental necrotizing enterocolitis

city: Chapel Hill

first: Misty

last: Good

state: NC

address: 101 Manning Drive 4th Floor CB 7596

department: Pediatrics

institute: University of North Carolina at Chapel Hill

summary: Necrotizing enterocolitis (NEC) causes significant morbidity and mortality in premature infants; therefore, the identification of therapeutic and preventative strategies against NEC remains a high priority. The ligand-dependent transcription factor aryl hydrocarbon receptor (AhR) is well known to contribute to the regulation of intestinal microbial communities and amelioration of intestinal inflammation. However, the role of AhR signaling in NEC is unclear. Experimental NEC was induced in four-day-old wild-type mice or mice lacking AhR expression in the intestinal epithelial cells (AhRΔrIEC) or in CD11c+ cells (AhRΔrCD11c) by subjecting animals to twice daily hypoxic stress and gavage feeding with formula supplemented with lipopolysaccharide and enteric bacteria. During NEC, compared to wild-type mice treated with vehicle, littermates treated with an AhR pro-ligand, indole-3-carbinol (I3C), had reduced expression of Il1b and Marco, a scavenger receptor that mediates dendritic cell activation and the recognition and clearance of bacterial pathogens by macrophages. Furthermore, I3C treatment lead to the downregulation of genes involved in cytokine and chemokine as revealed by pathway enrichment analysis. AhRΔrIEC and their cre-negative mouse littermates were similarly susceptible to experimental NEC, whereas AhRΔrCD11c mice with NEC exhibited heightened inflammatory responses compared to their cre-negative mouse littermates. In seeking to determine the mechanisms involved in this increased inflammatory response, we identified the Tim-4- monocyte-dependent subset of macrophages as increased in AhRΔrCD11c mice compared to their cre-negative littermates. Taken together, these findings demonstrate the potential for AhR ligands as a novel immunotherapeutic approach to the management of this devastating disease.

overall_design: Study the effect of the pro-ligand for Indole-3-carbinol-dependent aryl hydrocarbon receptor on neonatal necrotizing enterocolitis in mice

first: Lila

last: Nolan

first: Belgacem

last: Mihi

first: Pranjal

last: Agrawal

first: Qingqing

last: Gong

first: Jamie

last: Rimer

first: Shay

last: Bidani

first: Sarah

last: Gale

first: Martin

last: Goree

first: Elise

last: Hu

first: Wyatt

last: Lanik

first: Elizabeth

last: Huang

first: Jennifer

middle: K

last: Bando

first: Victoria

last: Liu

first: Angela

last: Lewis

first: Aiza

last: Bustos

first: Zerina

last: Hodzic

first: Marie

last: Laury


title: Discrete limbal epithelial stem cell populations mediate corneal homeostasis and wound healing

status: Public on Mar 02 2021

city: Haifa

first: Anna

last: Altshuler

address: 1, Efron Street

department: Genetics & Developmental Biology

country: Israel

institute: Technion

summary: Stem cells (SCs) are traditionally viewed as rare, slow-cycling cells that follow deterministic rules dictating their self-renewal or differentiation. It was several decades ago, when limbal epithelial SCs (LSCs) that regenerate the corneal epithelium were among the first sporadic, quiescent SCs ever discovered. However, LSC dynamics, heterogeneity and genetic signature are largely unknown. Moreover, recent accumulating evidence strongly suggested that epithelial SCs are actually abundant, frequently dividing cells that display stochastic behavior. In this work, we combined single-cell RNA sequencing and advanced quantitative lineage tracing for in-depth analysis of the murine limbal epithelium. The generated data provides an atlas of cell states of the entire corneal epithelial lineage and reveales the co-existence of two novel LSC populations that reside in separate and well-defined sub-compartments. In the “outer” limbus, we discovered a primitive widespread population of quiescent LSCs (qLSCs) that uniformly express Krt15/Gpha2/Ifitm3/Cd63 proteins that serve as SC reservoire and in boundary formation. In the “inner” peri-corneal limbus, we identified prevalent active LSCs (aLSCs) that express Krt15-GFP/Atf3/Mt1-2/Socs3 and maintain homeostasis. We propose that these SC populations are abundant, follow stochastic rules and neutral drift dynamics. Notably, we provide evidence that T cells serve as niche cells for qLSCs, regulating quiescence and wound response. Taken together, we propose that divergent regenerative strategies are tailored to properly support tissue specific physiological constraints.

overall_design: Epithelial cells were isolated from the limbus of 5 individual adult mice (2.5 months old, n=10 eyes). The limbus together with marginal conjunctiva and corneal periphery were carefully dissected, a protocol for isolating mainly epithelial cells was applied, and suspended cells were subjected to 10x Chromium Single-Cell RNA sequencing (scRNA-seq).

first: Aya

last: Amitai-Lange

first: Noam

last: Tarazi

first: Sunanda

last: Dey

first: Lior

last: Strinkovsky

first: Shira

last: Hadad-Porat

first: Swarnabh

last: Bhattacharya

first: Waseem

last: Nasser

first: Jusuf

last: Imeri

first: Gil

last: Ben-David

first: Ghada

last: Abboud-Jarrous

first: Beatrice

last: Tiosano

first: Eran

last: Berkowitz

first: Nathan

last: Karin

first: Yonatan

last: Savir

first: Ruby

last: Shalom-Feuerstein


title: Precocious metamorphosis of silkworm by BmNPV infection in the latter half of the fifth instar larvae

city: Zhenjiang

first: Pingzhen

last: Xu

state: Jiangsu

address: sibaidu road 16

department: School of Biotechnology,

country: China

institute: Jiangsu University of Science and Technology

summary: The silkworm, Bombyx mori, is a complete metamorphosis insect and an economically important for silk production, the model to study insect physiology and biochemistry. Bombyx mori nucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with silkworm larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. In this study, day-4 fifth instar silkworm larvae were infected by BmNPV, the wandering silkworms appeared in the infected groups were 12 hours earlier than that in the control groups, and the ecdysone titer in infected larvae was significantly higher than that of the control larvae. Then, we used RNA sequencing (RNA-seq) to analyze silkworm PGs 48 h after BmNPV infection. The classifications of the 15 differential expression genes (DEGs) were mainly involved in the metabolic processes and pathways. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected at 24, 48, and 72 h were generally consistent with the transcriptome data. The transcripts of BmTrypsin-1 and BmACSS3 were significantly increased from 24 to 72 h after BmNPV infection that they may be involved in the maturation process in the latter half of silkworm fifth instar larvae. These findings will help to address the interactions between BmNPV infection and host developmental response.

overall_design: To analyze the differentially expressed genes, in particular the interactions between BmNPV infection and host developmental response, after BmNPV infection that they may be involved in the maturation process in the latter half of silkworm fifth instar larvae, the silkworm prothoracic glands (PGs) are used for RNA-Seq.

first: Meirong

last: Zhang

first: Yangchun

last: Wu


title: ApoE expression marks microglial activation upon SCFA supplementation

first: Gemma

last: Llovera

summary: Transcriptomic Nanostring analysis from control and SCFA upplemented GF APPPS1 mice at 3 months of age

overall_design: Each sample represent an individual animal


title: Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with motif analysis and deep learning

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

summary: Genomic sequence variation within enhancers and promoters can have a significant impact on the cellular state and phenotype. However, sifting through the millions of candidate variants in a personal genome or cancer genome, to identify only those variants that impact enhancer function, remains a major challenge. Prioritization of non-coding genome variation benefits from explainable AI to predict and interpret the impact of a mutation on gene regulation. Here we apply a specialized deep learning model to 10 phased melanoma genomes and identify functional enhancer mutations with allelic imbalance of chromatin accessibility and gene expression.

overall_design:
Accessible chromatin profile of A375 and MM047 lines with ATAC-seq. ChIP-seq against cFos, cJun, Fra-1 and JunB in MM099 line.

Please note that processed data file generated from both ATAC-seq replicates is linked to the corresponding *ATAC-seq A sample records.

first: Z

last: Kalender-Atak

first: I

last: Ihsan-Taskiran

first: J

last: Wouters

first: G

first: S

last: Aerts


title: RNA-seq analysis in papillary thyroid carcinoma cells knocking down LDHA

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

summary: To assess the function of LDHA in PTCs, we performed transcriptome analysis through high-throughput RNA-Seq of control and LDHA knockdown cells

overall_design: We knocked down LDHA in B-CPAP cells and performed the RNA-seq analysis in order to exam the transcriptome after LDHA knockdown

first: Xianle

last: Shi

first: Wei


title: Single cell sequencing reveals phloem loading occurs via the abaxial bundle sheath cells in maize leaves

city: Duesseldorf

first: Margaret

last: Bezrutczyk

state: NRW

address: Universitatstrasse 1

department: Molecular Physiology

institute: Heinrich Heine Universitat


title: Single cell sequencing reveals phloem loading occurs  via the abaxial bundle sheath cells in maize leaves [scRNA-seq]

summary: Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. The observations provide first insights into the unique properties of abBS cells, cells previously considered to fulfill the same functions as other bundle sheath cells (BSCs), and a basis for understanding the C4 syndrome.

overall_design: Distal 6 cm section of leaf 2 from six V2 maize seedlings were selected for protoplast release, and single cell sequencing performed using the 10x Chromium partitioning system.

first: Nora

last: Zoellner

first: Colin

middle: P

last: Kruse

first: Thomas

last: Hartwig

first: Tobias

last: Lautwein

first: Karl

last: Koehrer

first: Wolf

last: Frommer


title: Degradation of intracellular glutathione in Aspergillus nidulans

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Glutathione (GSH) is an abundant and widely distributed antioxidant in fungi. Hence, understanding cellular GSH metabolism is of vital importance to deciphering redox regulation in these microorganisms. In this study, we generated dugB (AN1879), dugC (AN1092), and dugB dugC double deletion mutants which display disruption of the GSH degradation pathway in Aspergillus nidulans. Deletion of dugB, dugC or both resulted in a moderate increase in GSH content under growing conditions and substantially slowed down the depletion of GSH pools under carbon starvation.  Inactivation of dug genes caused reduced accumulation of reactive oxygen species, decreased autolytic cell wall degradation and extracellular enzyme production, increased sterigmatocystin formation but decreased viability in starving cultures. Changes in the transcriptomes suggested that enzyme secretions were controlled at post transcriptional level. In contrast, secondary metabolite production was also regulated at the level of mRNA abundance. Based on these findings, we suggest that GSH connects starvation and redox regulation to each other: A. nidulans cells utilize GSH as stored carbon source during starvation. The reduction of GSH contents of cells alters the redox state activating regulatory pathways responsible for carbon starvation stress responses.   Under glucose rich conditions, inactivation of dug genes reduced conidia production of surface cultures, disturbed sexual development and down-regulated the transcription of genes encoding MAP kinase pathway proteins (e.g. steC, sskB, pbsA, hogA, mkkA) or proteins involved in the regulation of conidiogenesis or sexual differentiation (e.g. flbA,C,E, nosA, rosA, nsdC,D). These finding indicates that the authority of redox regulation goes far beyond the protection against redox stress; it affects development, stress responses (other than redox stress) and secondary metabolism as well.

overall_design: two strains (a DUG pathway mutant and a reference strain) were examined under two conditions (carbon starving conditions and on glucose) with three biological replicates (altogether 12 samples)

first: Tamás

first: Barnabas

middle: C

last: Gila

first: Karoly

last: Antal

first: Heungyun

last: Moon

first: Jae-Hyuk

last: Yu

first: Istvan

last: Pocsi


title: The common germline TP53-R337H mutation is hypomorphic and confers incomplete tumor penetrance and late tumor onset in a mouse model

status: Public on Mar 01 2021

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
The TP53-R337H founder mutation exists at high frequency throughout southern Brazil and represents the most common germline TP53 mutation reported to date. It was originally identified in pediatric adrenocortical tumors in families with no reported history of cancer. The R337H mutation has since been found in association with early-onset breast cancers and Li-Fraumeni syndrome. To study this variability in tumor susceptibility we generated a knockin mutant p53 mouse model (R334H). Endogenous murine R334H is naturally expressed at abnormally high levels in multiple tissues and is functionally compromised in a cell type and stress-specific manner. The mutant p53 mice develop tumors with long latency and incomplete penetrance, consistent with many human carriers being at a low, but elevated risk for cancer
We used microarrays to compare the global programme of gene expression in thymocytes obtained from WT or TP53R337H/R337H mutant mice that had either received 5 Gy whole body irradiation or no irradiation.

overall_design: The missense mutation TP53 R337H was introduced into murine 129 embryonic stem (ES) cells by site-directed mutagenesis. ES clones harboring the mutation were then injected into C57BL6/J blastocysts to achieve germline transmission of the TP53R337H mutant allele. Mice were back-crossed against C57BL6/J mice and heterozygous pups were mated to obtain TP53R337H/R337H offspring. WT or TP53R337H/R337H mutant mice were irradiated using 5 Gy whole body radiation, euthanized 6 hours post-irradiation and thymocytes harvested for RNA extraction.  We used four mice per treatment group, except for the WT irradiated group where duplicate mice were used.

first: John

last: Jeffers

first: Emilia

last: Pinto

first: Jerold

last: Rehg

first: Jinlang

last: Wang

first: Bonald

last: Figueiredo

first: Carlos

last: Rodriguez-Galindo

first: Raul

last: Ribeiro

first: Gerard

last: Zambetti


title: MicroRNA-138 Suppresses Glioblastoma Proliferation through Downregulation of CD44 (NanoString)

city: Houston

first: Zhongming

last: Zhao

state: Texas

address: 7000 fannine St

institute: University of Texas Health Science Center at Houston

summary: 100 ng of total RNA was processed with the Human v3 miRNA Expression Assay using NanoString nCounter system (NanoString, USA). Expression of individual miRNA was measured by quantitative real-time PCR with TaqMan miRNA Expression kit (Applied Biosystems, Thermo Fisher Scientific, USA).

overall_design: This study aimed to identify tumor suppressive miRNAs with a promising therapeutic potential for the treatment of GBM. Our data obtained from miRNA expression profiling on GBM patient samples and patient-derived primary GBM cells have identified miR-138 as one of the most significantly downregulated miRNAs in GBM.

first: T

last: Lee


title: Progenitor cell diversity in the developing mouse neocortex

city: Chicago

first: Xiaochang

last: Zhang

state: IL

address: 920 E 58th St, CLSC 507A

department: Human Genetics

institute: The University of Chicago

summary: In the mammalian neocortex, diverse projection neuron types are generated by the same pool of neural progenitors in sequential waves. How neuronal cell type specification is related to developmental timing remains unclear. To determine whether neural progenitor cell heterogenity correlates with neuronal type spcification, we performed single cell RNA sequencing analysis of the developing mouse neocortex (E10.5 through E18.5) by Drop-Seq. We uncovered cellular and molecular diversity among neuroepithelial cells, radial glial cells, intermediate progenitors and neuron types.

overall_design: Dorsal forebrain tissues were collected from embryonic day 10.5, 12.5, 14.5, 15.5, 16.5 and 18.5 CD-1 mice (Charles River), dissociated into single cells, captured by the Drop-Seq protocol and analyzed for cell clusters and differential gene expression.

first: Bowei

last: Kang


title: PKR2 overexpression in heart

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

summary: Effect of overexpression of PKR2 in mice hearts on the cardiac transcriptome.

overall_design: RNA was isolated from hearts of mice overexpressing PKR2 (n=4) and of WT mice (n=4) and hybridized to microarrays.


title: Single cell sequencing reveals phloem loading occurs  via the abaxial bundle sheath cells in maize leaves [bulk RNA-seq]

first: Margaret

last: Bezrutczyk

overall_design: To determine which genes are affected by protoplasting in order to remove them from the analysis, we performed RNAseq on maize leaf tissue and protoplasts generated from the equilvant tissue

first: Nora

last: Zoellner

first: Colin

last: Kruse

first: Thomas

last: Hartwig

first: Tobias

last: Lautwein

first: Karl

last: Koehrer

first: Wolf

last: Frommer


title: Proteogenomic anlalysis of glioblastoma (GBM)

city: Tel Aviv

first: Tamar

last: Geiger

address: Levanon st

institute: Tel Aviv University

summary: To examine patterns associated with survival, we assembled a cohort of GBM patients whose survival ranges from less than 3 months and up to 10 years, most of which are not bearing isocitrate-dehyderogenase (IDH)-1 mutation and did not undergo prior treatment. We integrated high-resolution mass-spectrometry proteomics and RNA sequencing to examine the yet unresolved proteomic contribution to poor patient outcome, and compared it to the more established transcriptomic contribution and to published single-cell data. Discovering both layer-specific and shared processes, we found that long and short survival are distinguished by immune, metabolic and developmental processes. Additionally, we observed a significant discrepancy in tumor classification between expression layers. Overall, our integrative findings establish proteomic heterogeneity in GBM as a gateway to explaining poor survival.

overall_design: mRNA profiles of clinical tumor samples from 68 GBM patients were generated by deep sequencing, using Illumina HiSeq2500.

first: Gali

last: Yanovich-Arad


title: Single cell gene expresison profiling in human embryonic stem cell derived cardiomyocytes

city: Seattle

first: Charles

last: Murry

state: WA

address: 850 Republican Street

department: Pathology

institute: University of Washington

summary: We applied microfluidics-based single cell transcriptiomics to analize gene expression heterogenity in human embryonic stem cell derived cardiomcytes (hESC-CMs)

overall_design: ~10,000 hESC-CMs at day 30 of differentiation were analyzed using the Chromium NextGEM Single Cell 3’ kit (10X Genomics).

first: Alessandro

last: Bertero

first: Xiulan

last: Yang


title: Caspase-1 from Human Myeloid Derived Suppressor Cells Can Promote T-cell independent Tumor Proliferation

city: Nashville

first: Young

last: Kim

address: 1215 21st Avenue South, Suite 7209

department: Otolaryngology

institute: Vanderbilt University Medical Center

summary: Immunosuppressive myeloid-derived suppressive cells (MDSCs) are characterized by their phenotypic and functional heterogeneity. To better define their T cell-independent functions within the tumor, sorted monocytic CD14+CD11b+HLA-DRlow/- MDSCs (mMDSCs) from squamous cell carcinoma patients showed upregulated caspase-1 activity, that was associated with increased IL1b and IL18 expression. In vitro studies demonstrated that mMDSCs promoted caspase-1-dependent proliferation of multiple squamous carcinoma cell lines in both human and murine systems. In vivo, growth rates of B16, MOC1, and Panc02 were significantly blunted in chimeric mice adoptively transferred with caspase-1 null bone marrow cells under T cell-depleted conditions. Adoptive transfer of wildtype Gr-1+CD11b+ MDSCs from tumor-bearing mice reversed this antitumor response, whereas caspase-1 inhibiting thalidomide-treated MDSCs phenocopied the antitumor response found in caspase-1 null mice. We further hypothesized that MDSC caspase-1 activity could promote tumor intrinsic MyD88-dependent carcinogenesis. In mice with wildtype caspase-1, MyD88-silenced tumors displayed reduced growth rate, but in chimeric mice with caspase-1 null bone marrow cells, MyD88-silenced tumors did not display differential tumor growth rate. When we queried the TCGA database, we found that caspase-1 expression is correlated with overall survival in squamous cell carcinoma patients. Taken together, our findings demonstrated that caspase-1 in MDSCs is a direct T cell-independent mediator of tumor proliferation.

overall_design: The project compares mRNA expression of Granulocyte (CD15+, CD14-) to Monocyte (CD15-, CD14+) populations of MDSCs (myeloid derived suppressor cells). There is no specific experimental group. 4 pairs of MDSCs were derived from fresh peripheral blood of patients with squamous cell carcinoma of the head and neck subsequently their mRNA was preserved using Trizole.  Each pair in the above case means that both monocyte and granulocyte populations came from the blood of the same patient with squamous cell carcinoma of the head and neck.

first: Mikhail

last: Gorbounov

first: Richard

last: Blosser

first: C\

last: Talbot Jr


title: Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence

city: Shanghai

first: Wenyue

last: Dong

address: Fenglin road 300

institute: CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Here, we identified a long-chain acyl-CoA-responsive transcriptional repressor, FdmR, as the key regulator of mycobacterial fatty acid catabolism. We employed ChIP-Seq to identify the genomic binding regions for FdmR. FdmR was found to bind upstream of fadA2, fabG4, fadE24, fixA, MMAR_1683, fadE5, icl, desA3, desA3_1, and MMAR_2730.We then demonstrated that FdmR acts as a valve to direct the fatty acid flux from β-oxidation towards lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. This regulatory mechanism enables a high rate of cell growth with modest consumption of fatty acid substrates.

overall_design: The 10% sonicated DNA was stored and named “Input”, 80% was used in immunoprecipitation reactions with Monoclonal ANTI-FLAG® M2 antibody (Sigma) and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”, respectively. No biological replicates.


title: Silencing of unintegrated HIV-1 by SLF2 and the SMC5/6 complex

city: Cambridge

first: Liane

last: Dupont

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Cambridge Institute of Therapeutic Immunology & Infectious Disease

institute: University of Cambridge

summary: Silencing of nuclear DNA is an essential feature of the innate immune response to invading pathogens. Early in lentiviral infection, unintegrated viral cDNA accumulates in the nucleus, yet remains poorly expressed. In HIV-1-like lentiviruses, the Vpr accessory protein enhances unintegrated viral DNA expression, suggesting Vpr antagonises cellular restriction. We previously showed how Vpr remodels the host proteome, identifying multiple cellular targets. We now screen these using a targeted CRISPR-Cas9 library, identifying SMC5-SMC6 complex localization factor 2 (SLF2) as the Vpr target responsible for silencing unintegrated HIV-1. SLF2 recruits the SMC5/6 complex to unintegrated lentiviruses, and depletion of SLF2, or the SMC5/6 complex, increases viral expression. Using ATAC-seq, we show that Vpr-mediated SLF2 depletion increases chromatin accessibility of unintegrated virus, suggesting the SMC5/6 complex compacts viral chromatin to silence gene expression. This work implicates the SMC5/6 complex in nuclear immunosurveillance of extrachromosomal DNA and defines an evolutionarily conserved antagonism by Vpr.

overall_design: A sub-genomic CRISPR-Cas9 knockout screen performed in CEM-T4 T cells using a custom sgRNA library of putative Vpr targets. ATAC-seq of Jurkat T cells infected with a lentiviral reporter.

first: Sergio

last: Martinez Cuesta

first: Paul

last: Lehner


title: Whole Transcriptome RNA-seq from A549 cells exposed to P. californicus serum

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: Whole transcriptome RNA sequencing in A549 human NSCLC cells was generated. A549 cells were cultured in sera isolated from  male P. californicus  that differed in bonding experiences

overall_design: A549 cells RNA profiles treated with serum from P. californicus

first: Naderi

last: Asieh

first: Ji

last: Hao

first: Michael

last: Shtutman

first: Kiaris

last: Hippokratis


title: The PERK signaling controls myoblasts differentiation by regulating microRNA networks

city: Guangzhou

first: Zhang

last: Yin

address: Xin Gang West 135

institute: Sun Yat-sen University

summary: By using small RNA-seq, we report microRNA profilings from Perk knockdown C2C12 cells, differentiated C2C12 cells, Atf4 overexpressed C2C12 cells, Perk knockdown P19 cells and negative control.

overall_design: Small RNA-seq of mouse cell lines upon different treatments.

first: Ye-ya

last: Tan

first: Yin

last: Zhang

first: Liang-hu

last: Qu


title: S100A14 Suppresses Metastasis of Nasopharyngeal Carcinoma by Inhibition of NF-kB Signaling through Degradation of IRAK1

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Nasopharyngeal carcinoma (NPC) is a unique head and neck cancer with highly aggressive and metastatic potential, and distant metastasis is the main reason for treatment failure. The underlying molecular mechanisms of NPC metastasis remains poorly understood. Here, we have identified S100 calcium binding protein A14 (S100A14) as a functional regulator suppressed NPC metastasis via inhibiting NF-kB signaling and reversing epithelial-mesenchymal transition (EMT). S100A14 was downregulated in highly metastatic NPC cells and NPC tissues. Analyzing 202 NPC samples by immunohistochemical staining revealed that lower S100A14 expression significantly correlated with shorter patient overall survival (OS) and distant metastasis-free survival (DMFS), serving as an independent unfavorable prognostic factor. Gain- and loss-of-function studies confirmed that S100A14 suppressed NPC cellular motility in vitro and in vivo. Mechanically, S100A14 promoted ubiquitin-proteasome-mediated degradation of interleukin-1 receptor-associated kinase 1 (IRAK1) to suppress NPC cellular migration. Moreover, S100A14 and IRAK1 established a feedback loop, which can be disrupted by the IRAK1 inhibitor T2457. Overall, our study uncovers the S100A14-IRAK1 feedback loop is a theranostic target for NPC metastasis.

overall_design: To elucidate the molecular mechanisms of S100A14 in suppressing NPC cellular motility, we performed high-throughput sequencing of S18 and 5-8F cells with S100A14 overexpression or vector control.

first: Dong

middle: F

last: Meng

first: Chao

last: Qian


title: RNA seq analysis of kupffer cells isolated from mouse fed a high fat diet, deficient for Lpcat3 or not in macrophages

city: dijon

first: david

last: masson

address: 7 boulevard jeanne d'arc

institute: INSERM

summary: To identify potential role of macrophage LPCAT3 in progression of hepatic steatosis in mice, we isolated Kupffer cells from mice deficient for LPCAT3 in macrophages and fed a high fat diet for 16 weeks

overall_design: After 16 weeks of high fat diet, livers were digested by a two-steps perfusion using collagenase and homogenate were centrifugated to eliminate cell pelets containing primary hepatocytes. F4/80 positive cells contained in supernatant were isolated by MACS strategy using anti-F4/80 microbeads. Total RNA was extracted using RNeasy Mini Kit (Qiagen) and immediatly frozen at -80°C.

first: D

last: MASSON

first: T

last: BOURGEOIS


title: Translatome analysis of dorsal striatum D1-medium spiny neurons (D1-MSNs) lacking the TrkB receptor in mice.

city: Baltimore

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Mice lacking the TrkB receptor and expressing a ribosomal HA tag in dopamine D1 receptor-expressing neurons (D1-Cre-flTrkB-RT mice) were used. A subset of these mice (14.4%) display repetitive, stereotypic rotational behavior. Polyribosome immunoprecipitation from dorsal striatum D1-medium spiny neurons was used to isolate cell-type specific RNA. Translatomes of 4-week old mice with and without repetitive behavior, as well as control (D1-Cre-RT mice) were compared using RNA-sequencing.

overall_design: Cell-type specific RNA-sequencing of D1-MSNs in mice with and without spontaneous repetitive behavior (D1-Cre-flTrkB-RT mice)

first: Michel

last: Engeln

first: Yang

last: Song

first: Ronna

last: Hertzano

first: Mary

last: Lobo


title: Gene expression of T cells stimulated by peritoenal cDC subsets

city: Seoul

first: Moah

last: Sohn

address: 50 YONSEI-RO, SEODAEMUN-GU

country: South Korea

institute: Yonsei University

summary: After injecting OVA (grade V, sigma aldrich) for an hour, OVA-laden peritoneal cDC subsets had been sorted and co-cultured with OT-1 or OT-2 cells for 3 days. Then, mixture of cells, mainly expanded T cells and only a few cDCs, went through mRNA-sequencing.

overall_design: Global mRNA sequencing of OT-1 and OT-2 cells stimulated by peritoneal cDC subsets.

first: Chae

last: Park


title: Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

summary: We develop CoTECH, a combinatorial barcoding method allowing for high-throughput parallel single-cell detection of chromatin occupancy and transcriptome.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Protein A-Tn5 was enriched through specific antibodies to genomic regions and Tn5 generated indexed chromatin. Following tagmentation, mRNA inside cells were captured by oligo dT barcode primers and reversed-transcribed. Combinatorial indexing strategy was implemented on both ChIPed DNA parts and RNA parts.

first: Yingjie

last: Luo

first: Qianhao

last: Wang

first: Aibin

last: He


title: Characterization of Human Bone Marrow Niches with Metabolome and Transcriptome Profiling

city: ANKARA

first: Selda

last: Ayhan

address: SIHHIYE

country: Turkey

institute: HACETTEPE UNIVERSITY

summary: The hematopoietic niches in bone marrow (BM) are specialized compartments working in harmony to regulate all the steps of the hematopoiesis cascade. Little is known about how BM niches in healthy humans. Therefore, we investigated the presence of different niches in healthy human BM using comparative omic technologies (Metabolomic and transcriptomic). We sequenced and comparative analyzed mRNA samples of human bone marrow mesenchymal stem cells (MSCs) to generate the gene expression profiles of these cells which obtained from two anatomically different BM regions (R1 and R2).

overall_design: In total, 22 human bone marrow-derived mesenchymal stem cells (hBMSC) samples which were obtained from two anatomically different bone marrow region (R1 and R2) of 11 healthy bone marrow transplantation donors analyzed.


title: Dissecting the effects of preconditioning with inflammatory cytokines and hypoxia on the angiogenic potential of Mesenchymal Stromal Cell (MSC)-derived soluble proteins and Extracellular Vesicles (EVs)

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

summary: Mesenchymal stromal cells (MSCs) are characterized by a regulatory phenotype and respond promptly to the environmental signals modulating their secretory activity. An appropriate preconditioning may induce MSCs to release secretomes with an enhanced regenerative potential. However, it fails to take into account that secretomes are composed by both soluble factors and extracellular vesicles (EVs), whose functions could be altered differently by the preconditioning approach. Here we demonstrate that the MSC secretome is strongly modulated by the simultaneous stimulation with hypoxia and pro-inflammatory cytokines, used to mimic the harsh environment present at the site of injury. The cargo content (in terms of miRNAs) of the corresponding EV fractions was less sensitive to the influence of the external stimuli.

overall_design: miRNAseq of EVs obtained from human MSC treated in 4 different conditions. MSC are derived from 3 donors.

first: Davide

last: Ceresa

first: Cansu

last: Gorgun

first: Federico

last: Villa

first: Roberta

last: Tasso


title: Role of Transforming Growth Factor-β1 in Recessive Dystrophic Epidermolysis Bullosa Squamous Cell Carcinoma

city: Minneapolis

first: Jakub

last: Tolar

state: Minnesota

address: 2001 6th St SE

institute: University of Minnesota - Twin Cities

summary: The goal of this RNA-seq experiment was to determine how gene expression in RDEBSCC cell lines was altered relative to normal culture conditions when the culture media was supplemented with TGFb1 or TGFb1 and a TGFb1 inhibitor (SB431542).

overall_design: Three cell lines derived from squamous cell carcinoma tumors in patients with recessive dystrophic epidermolysis bullosa were used (2, 4, and 70). RNA-seq was performed for three experimental conditions for each cell line. The three conditions were (1) media only, (2) media+TGFb1, and (3) media+TGFb1+SB431542 (TGFb1 inhibitor). Each experimental condition was replicated three times for each cell line, except condition 2 and 3 for cell line 2, where the samples were lost, resulting in a total of 25 paired-end samples.

first: Kirk

last: Twaroski

first: Weili

last: Chen

first: Michael

last: Pickett-Leonard


title: Gene expression in human macrophages stimulated with IFN-alpha and IL10

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

summary: Human monocyte-derived macrophages were stimulated with IFN-alpha or IL-10, and then gene expression was evaluated.

overall_design: Monocytes were differentiated to mature macrophages by coculture with 2% human serum, M-CSF and GM-CSF as described in Cancer Sci. 2016 Nov;107(11):1696-1704. Human monocyte-derived macrophages were stimulated with IFN-alpha or IL-10 (10ng/mL) for 1 day, and then gene expression was evaluated.


title: Transcriptomic biomarker pathways associated with death in HIV-infected patients with cryptococcal meningitis

city: Minnespolis

first: Irina

last: Vlasova-St. Louis

state: MN

department: Medicine

institute: University of Minnesota

summary: to identify transcriptomic biomarker pathways in peripheral blood that are associated with or  predict the development of death or fatal C-IRIS among patients with CM who were enrolled in the Cryptococcal Optimal ART Timing (COAT) Trial.

overall_design: We assessed peripheral blood gene expression using next-generation RNA sequencing in 4 groups of patients with CM: 1) no C-IRIS or Death; 2) C-IRIS survivors; 3) fatal C-IRIS; 4) Death without C-IRIS. Gene expression was assessed at the time of ART initiation, at 1, 4, and 8 weeks on ART, and at the time of C-IRIS events.


title: RNA-seq of primary dissociated cortical Nipbl+/- neurons

status: Public on Feb 28 2021

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: RNA-seq of total RNA from Nipbl+/+ and Nipbl+/- dissociated cortical neurons at Day In Vitro (DIV10)

overall_design: RNA-Seq was performed on total RNA from primary mouse neurons cultured for ten days. Three replicates of each genotype, Nipbl+/+ and Nipbl+/-, were used.

first: Matthias

last: Merkenschlager

first: Lesly

last: Calderon

first: Thomas

last: Carroll

first: Felix

last: Weiss

first: Yi-Fang


title: Single cell RNA-seq defines novel heterogeneity within the pancreatic ductal tree

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

summary: Lineage tracing using genetically engineered mouse models has become an essential tool for investigating cell-fate decisions of progenitor cells and biology of mature cell types, with respect to physiology and disease progression. To study disease development, an inventory of an organ’s cell types and understanding of physiologic function is paramount. Here, we performed single-cell RNA sequencing to examine heterogeneity of murine pancreatic duct cells, pancreatobiliary cells, and intrapancreatic bile duct cells. We isolated duct cells within the murine pancreas using the DBA lectin sorting strategy that labels all pancreatic duct cell types. Our data contest the paradigm suggested by previous single cell studies that murine pancreatic duct cells are homogenous. We describe an epithelial mesenchymal transitory axis among our two subpopulations of pancreatic duct cells and identify SPP1 as a regulator of this phenotype and human duct cell de-differentiation. Our results further define functional heterogeneity of pancreatic duct subpopulations by elucidating a role for Geminin in accumulation of DNA damage in the setting of chronic pancreatitis. Our findings implicate diverse functional roles for subpopulations of pancreatic duct cells in disease progression and establish a comprehensive road map of murine pancreatic duct cell, pancreatobiliary cell, and intrapancreatic bile duct cell homeostasis.

overall_design: We performed single cell analysis of murine pancreatic duct cells and follow up functional studies of pancreatic ductal cells, which include RNA-seq of HPDE E6/E7 SPP1 gRNA cell lines and HPDE E6/E7 scr gRNA controls.

first: Audrey

last: Hendley

first: Arjun

last: Rao

first: Laura

last: Leonhardt

first: Sudipta

last: Ashe

first: Jennifer

last: Bridge

first: Xianlu

last: Peng

first: Honglin

last: Jiang

first: David

middle: I

last: Berrios

first: Mathias

last: Pawlak

first: Lucia

middle: Y

last: Li

first: Jonghyun

last: Lee

first: Eric

last: Collisson

first: Mark

last: Anderson

first: Gabriela

last: Fragiadakis

first: Jen

last: Yeh

first: Jimmie

last: Chun

first: Grace

last: Kim

first: Valerie

last: Weaver

last: Hebrok


title: Gene expression in CD163-deficient resident macrophages

first: Yoshihiro

last: Komohara

summary: To investigate CD163-related signals and cytokine production, mRNA expression of resident peritoneal marophages derived from wild type mice and CD163-deficient mice was analyzed.

overall_design: Following resident peritoneal macrophages were isolated, cells were cultured with 10%FBS/RPMI for 2 days. Cells were then  stimulated with LPS (100 ng/mL) for 1 day. Cells with or without LPS-stimulation were treated and mRNA were isolated.

first: Yukio

last: Fujiwara


title: Loss of ARID1A induces a stemness gene ALDH1A1 expression with histone acetylation in the malignant subtype of cholangiocarcinoma

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

summary: Genomic analyses have recently discovered the malignant subtype of human intrahepatic cholangiocarcinoma (ICC) characterized by frequent mutations of chromatin remodeling gene ARID1A, however, the biological and molecular functions still remain obscure. We here examined the clinical and biological significances of ARID1A deficiency in human ICC. Immunohistochemical analysis demonstrated that loss of ARID1A was an independent prognostic factor for overall survival of ICC patients (P = 0.023). We established ARID1A-knockout (KO) cells by using the CRISPR/Cas9 system from two human cholangiocarcinoma cell lines. ARID1A-KO cells significantly enhanced migration, invasion, and sphere formation activity. Microarray analysis revealed that ALDH1A1, a stemness gene, was the most significantly elevated genes in ARID1A-KO cells. In addition, ALDH enzymatic activity as a hallmark of cancer stem cells was markedly high in the KO cells. ARID1A and histone deacetylase 1 directly recruited to the ALDH1A1 promoter region in cholangiocarcinoma cells with undetectable ALDH1A expression by chromatin immunoprecipitation assay. The histone H3K27 acetylation level at the ALDH1A1 promoter region was increased in cells when ARID1A was disrupted (P < 0.01). Clinically, inverse correlation between ARID1A and ALDH1A expression was also detected in primary ICC (P = 0.018), and ARID1A-negative and ALDH1A1-positve ICCs showed worse prognosis than only ARID1A-negative cases (P = 0.002). In conclusion, ARID1A may function as a tumor suppressor in ICC through transcriptional down-regulation of ALDH1A1 expression with decreasing histone H3K27 acetylation. Our studies provide the basis for the development of new epigenetic approaches to ARID1A-negative ICC.

overall_design: ARID1A-knockout cholangiocarcinoma cells were established by using a lentiviral CRISPR/Cas9 system.

first: Jun

last: Yoshino

first: Yoshimitsu

last: Akiyama

first: Toshiro

last: Ogura

first: Kosuke

last: Ogawa

first: Hiroaki

last: Ono

first: Yusuke

last: Mitsunori

first: Daisuke

last: Ban

first: Atsushi

last: Kudo

first: Shoji

last: Yamaoka

first: Minoru

last: Tanabe

first: Shinji

last: Tanaka


title: RNA-sequencing data of THP-1 cells after the knockdown of KANSL2, KANSL3 or KAT8

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

institute: The Institute of Cancer Research

summary: Histone acetylation is associated with open chromatin and transcriptionally active genes. Specifically, acetylation of lysine 16 on histone H4 (H4K16ac) has been shown to prevent the assembly of nucleosomal arrays in vitro. This modification is catalyzed by the MYST-family histone acetyltransferase KAT8 (also known as MOF and MYST1), which is part of two distinct chromatin-associated complexes: NSL and MSL. While extensively studied in Drosophila, the functions of H4K16ac and the two KAT8-containing complexes in mammalian cells are not well understood. Here, we demonstrate a surprising complex-dependent activity of KAT8. We found that KAT8 catalyzes H4K5 and H4K8 acetylation as part of the NSL complex, whereas it catalyzes the bulk of H4K16 acetylation as part of the MSL complex. Furthermore, we show that the core proteins of the MSL complex and H4K16ac are not required for cell proliferation and global chromatin accessibility, whereas the NSL complex is essential for cell survival, as it is enriched at the promoters of housekeeping genes and is required for their transcription initiation. In summary, we show that KAT8 switches catalytic activity and function depending on its associated proteins, and that, as part of the NSL complex, it catalyzes H4K5 and H4K8 acetylation required for the expression of genes essential for cell survival.

overall_design: Cells transduced with either a non-targeting sgRNA (sgNegCtrl, 3 biological replicates) or sgRNAs inducing knockowns of KANSL2, KANSL3 or KAT8 (sgKANSL2, sgKANSL3, sgKAT8; 2, 3 and 3 biological replicates, respectively)

first: Kristian

last: Helin


title: 4C contact profiles of the Pcdh-b enhancers HS18-20

first: LMS

last: Bioinformatics Core

summary: We performed 4C-seq to measure the chromatin contact changes between Pcdh-b and their enhancers, HS18-20.

overall_design: Chromatin contact profiles in control or RAD21-TEV cleaved cells were generated by 4C. Contents of processed data files: column 1 - the starting coordinate of the 1kb bin, 2 - the mean of values within a 2kb window, 3 - the 80th quantile of values, and 4 - the 20th quantile of values

first: Ya

last: Guo

first: Yi-Fang

last: Wang

first: Felix

last: Weiss

first: Matthias

last: Merkenschlager


title: Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcriptional regulation and cellular homeostasis (ChIP-sequecing data)

overall_design: 39 ChIP-sequencing samples. Where indicated, input or bait KD was used as a control. Where indicated, spike-in normalization factors are provided


title: RAD21-TEV NLS-TEV RNAseq - extended cohesin depletion

summary: RNA-seq of vehicle and doxycycline treated Rad21-TEV primary neuron transduced with NLS-TEV, inducing extended cohesin depletion

overall_design: Total of 6 samples analysed; 3 replicates of Rad21-tev primary neurons 7 days following doxycyline treatment (24 hours, 100ug/ml), 3 replicates of Rad21-tev primary neurons 7 days following vehicle treatment


title: ATAC-sequencing data of THP-1 cells after the knockout of MSL1

summary: Histone acetylation is associated with open chromatin and transcriptionally active genes. Specifically, acetylation of lysine 16 on histone H4 (H4K16ac) has been shown to prevent the assembly of nucleosomal arrays in vitro. This modification is catalyzed by the MYST-family histone acetyltransferase KAT8 (also known as MOF and MYST1), which is part of two distinct chromatin-associated complexes, NSL and MSL. While extensively studied in Drosophila, the functions of H4K16ac and the two KAT8-containing complexes in mammalian cells are not well understood. Here, we demonstrate a surprising complex-dependent activity of KAT8. We found that KAT8 catalyzes H4K5 and H4K8 acetylation as part of the NSL complex, whereas it catalyzes the bulk of H4K16 acetylation as part of the MSL complex. Furthermore, we show that the core proteins of the MSL complex and H4K16ac are not required for cell proliferation and global chromatin accessibility, whereas the NSL complex is essential for cell survival, as it is enriched at the promoters of housekeeping genes and is required for their transcription initiation. In summary, we show that KAT8 switches its catalytic activity and function depending on its associated proteins, and that it, as part of the NSL complex, catalyzes H4K5 and H4K8 acetylation required for the expression of genes essential for cell survival.

overall_design:
We compared ATAC-seq profiles of the human acute myeloid leukemia cell line THP-1 with and without the knockout of MSL1 protein.
Cells transduced with either a non-targeting sgRNA (sgNegCtrl, 2 biological replicates) or sgRNAs inducing knockout of MSL1 (sgMSL1, 2 biological replicates).

first: Radzisheuskaya

last: Aliaksandra

first: Helin

last: Kristian


title: Gene expression in ATN1-1 cells with or without coculture with macrophages

first: Yoshihiro

last: Komohara

summary: To investigate the cell-cell interaction with macrophages, mRNA expression of control ATN-1 cells and ATN-1 cells cuoculture with macrophages.

overall_design: ATN-1 cells were coultured with human monocyte-derived macrophages for 3 weeks, and macrophages were deleted by anti-CD14 magnet beads and mRNA were isolated from purified ATN1 cells.


title: Human cortical nuclei RNAseq

summary: RNA-seq of NeuN-negative and NeuN-positive nuclei from healthy controls

overall_design: Total of 3 NeuN-negative samples and 3 NeuN-positive samples analysed, all samples age matched


title: RAD21-TEV NLS-TEV rescue RNAseq

summary: RNA-seq of and doxycycline treated Rad21-TEV primary neuron transduced with NLS-TEV

overall_design: Total of 12 samples analysed; 3 replicates of Rad21-tev primary neurons 24h following doxycyline treatment (6 hours, 100ng/ml), 3 replicates of Rad21-tev primary neurons 24h following vehicle treatment. 3 replicates of Rad21-tev primary neurons 7 days following doxycycline treatment (6 hours, 100ng/ml), 3 replicates of Rad21-tev primary neurons 7 days following vehicle treatment.


title: CdLS NeuN-positive RNAseq

summary: RNA-seq of NeuN-positive nuclei from CdLS patients and healthy age-matched controls

overall_design: Total of 10 NeuN-positive samples analysed; 4 of CdLS patient pre-frontal cortex samples, and 6 healthy age-matched controls


title: CdLS NeuN-positive ATACseq

summary: ATAC-seq of NeuN-positive nuclei from CdLS patients and healthy age-matched controls

overall_design: Total of 9 NeuN-positive samples analysed; 4 of CdLS patient pre-frontal cortex samples, and 5 healthy age-matched controls


title: CdLS NeuN-negative RNAseq

summary: RNA-seq of NeuN-negative nuclei from CdLS patients and healthy age-matched controls

overall_design: Total of 9 NeuN-negative samples analysed; 3 of CdLS patient pre-frontal cortex samples, and 6 healthy age-matched controls


title: RAD21-TEV ERt2-TEV RNAseq

summary: RNA-seq of and Ethonal and Tamoxifen-treated Rad21-TEV primary neuron transduced with ERT2-TEV

overall_design: Total of 12 samples analysed; 3 replicates of 24h tamoxifen-treated Rad21-TEV primary neuron transduced with ERT2-TEV, 3 replicates of 24h ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV, 3 replicates of 72h tamoxifen-treated Rad21-TEV primary neuron transduced with ERT2-TEV and 3 replicates of 72h ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV


title: Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize

status: Public on Feb 27 2021

city: Ames

first: Stephen

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 alternative splicing 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 alternative splicing 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 alternative splicing 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: Diane

last: Bassham


title: Conformation/Identification of dPPRrcbL RNA targets using RIPSeq

city: Strasbourg

first: Kamel

last: Hammani

address: 12 Rue du général Zimmer

institute: IBMP-CNRS

summary: Stroma extracts were isolated from 2-week-old transgenic dPPRrbcL or WT plants and incubated with HA-specific antibodies. IgGs were captured with Protein A Dynabeads (Thermo Fisher scientific) and recovered RNA was used for generation of libraries with the NEBNext® Ultra™ II RNA Library Prep Kit. Primary reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench. Reads of the two replicates aligned in CLC Genomics Workbench were extracted as coverage (reads per nucleotide). Graphs were created with excel using the extracted coverage values

overall_design: RNA Immunoprecipitation with HA-specific antibody using WT and dPPRrbcL stroma extracts. As dPPRrbcL is expected to be a soluble chloroplast-localized protein, stroma extracts were used for RNA-Immunoprecipitation to confirm association with the rbcL mRNA and to identify potential off-targets.

first: Nikolay

last: Manavski

first: Andreas

last: Brachmann


title: Partial rescue of neuronal genes deregulated in CdLS by cohesin

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

overall_design: Refer to individual Series


title: Quantitative Analysis of Wild Type and Prmt1 adipocyte-specific KO Epididymal primary adipocyte Transcriptomes

status: Public on Feb 25 2021

first: Seung-Hoi

last: Koo

address: 145 Anam-Ro, Seongbuk-Gu

department: Life Sciences

institute: Korea University

summary: We attempted to analyze the effect of adipocyte-specific knockout of Prmt1 in energy homeostasis in mice. By analyzing the transcriptomics of epididymal primary adipocytes from male mice with wild type and adipocyte-specific Prmt1 knockout mice, we provide the insight into the collective roles of Prmt1 in epididymal white adipose tissues.

overall_design: mRNA profiles of epididymal primary adipocytes from 12 week-HFD fed wild type (WT) and adipocyte-specific Prmt1 KO mice

first: Seri

last: Choi


title: SOX9 modulates cancer biomarker and cilia genes in pancreatic cancer

city: Irvine

first: Michael

last: Parsons

address: 4101 Natural Sciences II

institute: University of California, Irvine

summary: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive form of cancer with high mortality. The cellular origins of PDAC are largely unknown, however, ductal cells, especially centroacinar cells (CACs), have several characteristics in common with PDAC, such as expression of SOX9 and components of the Notch-signaling pathway. Mutations in KRAS and alterations to Notch signaling are common in PDAC; and, both these pathways regulate the transcription factor SOX9. To identify genes regulated by SOX9, we performed siRNA knockdown of SOX9 followed by RNA-seq in PANC-1 cells, a human PDAC cell line. We report 93 differentially expressed (DE) genes, with convergence on alterations to Notch-signaling pathways and ciliogenesis. These results point to SOX9 and Notch activity being in a positive feedback loop; and, SOX9 regulating cilia production in PDAC. We additionally performed ChIP-seq in PANC-1 cells to identify direct targets of SOX9 binding and integrated these results with our DE gene list. Nine of the top ten downregulated genes have evidence of direct SOX9 binding at their promoter regions. One of these targets was the cancer stem cell marker EpCAM. Using whole-mount in situ hybridization to detect epcam transcript in zebrafish larvae, we demonstrated that epcam is a CAC marker and that Sox9 regulation of epcam expression is conserved in zebrafish. Additionally, we generated an epcam null mutant and observed pronounced defects in ciliogenesis during development. Our results provide a link between SOX9, EpCAM, and ciliary repression that can be exploited in improving our understanding of the cellular origins and mechanisms of PDAC.

overall_design: 2 ChIP-seq samples against SOX9 and their inputs in PANC-1 cells and 4 RNA-seq samples from SOX9- and control-siRNA treated PANC-1 cells

first: Hannah

middle: E

last: Edelman

first: Sarah

last: McClymont

first: Tori

last: Tucker

first: Santiago

last: Pineda

first: Rebecca

last: Beer

first: Andrew

last: McCallion


title: RNA sequencing of wildtype and homozygous titin A178D mouse left ventricle samples

status: Public on Feb 26 2021

city: Oxford

first: Katja

last: Gehmlich

address: Level 6, West Wing, John Radcliffe Hospital

department: Radcliffe Department of Medicine

institute: Univeristy of Oxford

summary: Truncating variants in titin can cause dilated cardiomyopathy, however, the role of missense titin variants is less clear. In humans the heterozygous titin A178D variant is associated with dilated cardiomyopathy with left ventricular non-compaction. Using CRISPR-Cas9 mediated homology-directed repair the A178D titin variant was introduced  into a mouse model. Homozygous A178D mice showed features of dilated cardiomyopathy. Total RNA was extracted from the left ventricles of WT and homozygous A178D littermate control mice and RNA-sequencing performed. Different patterns of gene expression were identified in wildtype and homozygous A178D left ventricles.

overall_design: RNAseq profiles of 3 wildtype and 4 homozygous titin A178D mouse left ventricle samples

first: Violetta

last: Steeples


title: Using lncRNA sequencing to reveal a putative lncRNA-mRNA correlation network and potential role of PCBP1-AS1 in pathogenesis of cervical cancer

status: Public on Feb 24 2021

city: Nanjing

first: linhan

last: li

address: 168 Gushan Road, Dongshan Street, Jiangning District

institute: Affiliated Jiangning Hospital of Nanjing Medical University

summary: The aim of this study was to construct a lncRNA-mRNA co-expression function network and analyze lncRNAs that might contribute to the pathogenesis of cervical cancer. Transcriptome analysis of 3 cervical cancer samples and 3 adjacent tissue samples was completed in this project.LncRNA-mRNA correlation analysis, enrichment of functions, qPCR, K-M survival, clinicopathology analysis, GSEA and immune infiltration analysis were implemented. Total of 67.600 GB of Clean Data (sequencing Data after quality control) was obtained. The average amount of Clean Data of each sample was 11.267 GB, the percentage of Q30 base was above 91.18%, and the GC content was between 45.46% and 47.18%.Reference species: human;Reference genomic version: GRCH38;Reference genome source: http://asia.ensembl.org/Homo_sapiens/Info/Index;The sequencing data of each sample after quality control was compared with the specified reference genome, and the matching rates ranged from 95.957% to 97.270%, and the unique matching rates ranged from 91.363% to 94.258%. Transcriptomic and lncRNA-mRNA correlation analysis revealed PCBP1-AS1 plays a key role as an independent prognostic factor in patients with cervical cancer.

overall_design: LncRNA profiles of 3 cervical cancer samples and 3 adjacent tissue samples

first: Linhan

last: Li

first: Qisong

last: Peng

first: Min

last: Gong

first: Ling

last: Ling

first: Yingxue

last: Xu

first: Qiaoling

last: Liu


title: Medulloblastoma in adults: Cytogenetic phenotypes identify prognostic subgroups

city: Bonn

first: Tobias

last: Goschzik

address: Venusberg-Campus 1

department: Neuropathology

institute: University of Bonn Medical Center

summary: Medulloblastoma (MB) is a rare disease in adults. In this study we elucidated the genetic landscape and prognostic impact of genetic aberrations in a cohort of 117 adult medulloblastomas. Histological features and pathway activation were evaluated on the protein level; 14.5% showed WNT activation, 63.3% SHH activation and 22.2% were annotated to non-WNT/non-SHH-MB. Genome-wide copy number analysis was performed by molecular inversion probe array technology. MB-related genes were sequenced in WNT- and SHH-activated MBs. 79.7% of SHH-MBs showed desmoplastic/nodular, all other MBs classic histology. WNT-MBs carried oncogenic CTNNB1 mutations in 88.2% and had monosomy 6 in 52.9%. In SHH-MBs, TERT promoter mutations occurred in 97%, mutations in PTCH1 in 38.2%, SMO in 15.5%, SUFU in 7.4%, and TP53-mutations in 4.1%. 84.6% of non-WNT/non-SHH-MBs had an isochromosome 17q. A whole chromosomal aberration (WCA) signature was present in 45.1% of SHH-TP53wt-MBs and 65.4% of non-WNT/non-SHH-MBs. In 98 cases with survival data, WNT-MBs had a 5-year overall survival (OS) of 68.6%. SHH-MBs TP53-wild-type and non-WNT/non-SHH-MBs showed 5-year OS of 80.4% and 70.8%, respectively. TP53-mutant SHH-MBs represented a prognostically unfavorable entity; all patients died within 5 years. Patients with a WCA signature showed significantly increased OS (p-=-0.011 for SHH-TP53wt-MBs, p-=-0.048 for non-WNT/non-SHH-MBs).

overall_design: Bisulphite converted FFPE-DNA from 27 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip (850K)

first: Goschzik

last: Tobias

first: Zur

last: Anja

first: Doerner

last: Evelyn

first: Waha

last: Andreas

first: Friedrich

last: Carsten

first: Hau

last: Peter

first: Pietsch

last: Torsten


title: lncRNA profiles enable prognosis prediction and subtyping for esophageal squamous cell carcinoma

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary: AC007128.1, a long non-coding RNA, was upregulated in both ESCC tissues and cells, and associated with poor prognosis in ESCC. AC007128.1 can promote migration and invasion in ESCC cell lines. By RNA-sequencing analysis, we observed the significant changes of genes important in AC007128.1-depleted cells. We generated two KYSE150 cell lines stably transduced with either a sh-NC lentiviral construct or a shRNA lentiviral construct designed to target AC007128.1 RNA to investigate the consequences on the gene expression profile of AC007128.1 knockdown in KYSE150 cells.

overall_design: The gene expression of 3 samples from shAC007128.1 KYSE150 cell line was compared to 3 samples from shCtrl by RNA sequencing.

first: Shujun

last: Zhang


title: Repeated stimulation of self-presentation pathway by targeting erythrocytes in vivo drives anergy and profound T cell dysfunction

city: Chicago

first: Jeffrey

last: Hubbell

state: Illinois

address: 5640 S. Ellis Ave

institute: University of Chicago

summary: The purpose of this study was to conduct an in-depth analysis of the molecular characteristics of both CD4 and CD8 T cells upon encounter of self-associated antigen bound to erythrocytes, induce therapeutic tolerance in an endogenous repertoire of T cells, and understand the mechanisms involved in uptake and presentation of erythrocyte-associated antigen.

overall_design: Ovalbumin-specific CD4 and CD8 T cell mRNA profiles of WT mice 5 days post adoptive transfer of OTI and OTII cells. At 1 day post transfer mice received either 1ug A8B1-OVA, the molar equivalent of OVA, a higher dose of OVA, or saline. Each replicate was generated from fluorescent activated cell sorted OTI and OTII cells pooled from 3 mice.

first: Elyse

middle: A

last: Watkins

first: Jennifer

last: Antane

first: Andrew

last: Tremain

first: Jaeda

last: Roberts

first: Kristen

last: Lorentz

first: Sarah

last: Zuerndorfer

first: Anya

last: Dunaif

first: Luke

last: Bailey

first: Mindy

last: Nguyen

first: Robert

last: DeLoera

first: Stephan

last: Kontos


title: Sustained splenic contraction after daily cocaine administration in rats

status: Public on Feb 23 2021

city: Tokyo

first: Toshihiko

last: Aki

department: Forensic medicine

summary:
To obtain insight into the  changes in spleen caused by repeated cocaine administration, we performed transcriptome analysis.
Total RNAs from the control and cocaine groups (day 7) were subjected to DNA microarray analysis.

overall_design: We analyzed spleen from 1 control rat and 1 cocaine-administered (50mg/kg, daily for 7days) using the ClariomS platform.

first: Kana

last: Unuma

first: Koichi

last: Uemura

first: Moeka

last: Nomura


title: Transcriptional regulation of plant biomass degradation and carbohydrate utilization genes in Caldicellulosiruptor bescii [RNA-Seq (TSS)]

city: Athens

first: Michael

middle: W

last: Adams

state: Georgia

address: 220 South Jackson Street

department: Department of Biochemistry and Molecular Biology

institute: University of Georgia

summary: Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade various polysaccharide components of plant cell walls. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species C. saccharolyticus and C.bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to fourteen Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose.

overall_design: 5' TSS was analyzed for five different growth substrates (glucose, cellobiose, crystalline cellulose (Avicel), xylose, birchwood xylan (Sigma), 5 g/L each). Growth experiments were performed in triplicate at 78°C as closed cultures without pH control (400 mL volume, shaken at 150 rpm).   Cells were harvested in mid-to-late exponential growth stage (0.5−1.5 × 108 cells mL−1). Cells were pelleted by centrifugation at 6,000 × g for 5 minutes, supernatant was decanted, and cell pellets were frozen in liquid nitrogen.

first: Steven

middle: D

last: Brown

first: Charlotte

last: Wilson

first: Mirko

last: Basen

first: Dawn

middle: M

last: Klingeman