title: Horizontal Meta-Analysis Identifies Common Deregulated Genes across AML Cytogenetic Subgroups that provide robust prognostic signature

city: Montreal

first: Ali

last: Nehme

state: Quebec

address: 740 avenue Dr. Penfield

department: Human Genetics

institute: McGill University

type:
Expression profiling by array
Third-party reanalysis

summary: Advances in transcriptomics have impacted the way of looking atimproved our understanding of leukemic development and helped  enhancing the stratification of patients. Analyses of individual cohortsTranscriptomics studies often combined AML samples regardless of cytogenetic abnormalities. , which would lead to bias in Hence, deregulated genesdifferential gene expression analysis that may result from the differential representation of in less frequent AML subgroups have low weight, contrarily to those in abundant subgroups. We, thusHence, we performed a horizontal meta-analysis that integrated transcriptomic data of AML from multicentric  multiple studies to enrich the less frequent cytogenetic subgroups and to uncover common genes involved in AML development and response to therapy. A total of 28 Affymetrix microarray datasets harboring 3940 AML samples were downloaded from the GEO database. After stringent quality control, transcriptomics data of 1523 samples from 11 datasets, covering 10 AML cytogenetic subgroups, were retained and merged with the transcriptomic data of 198 healthy bone marrow samples. Differentially expressed genes between each cytogenetic subgroup and normal samples were extracted, allowing the unbiased identification of 330 commonly deregulated genes (CODEGs)., which CODEGs showed enriched expression profiles in myeloid differentiation, leukemic stem cell status and relapse. Most of these genes were downregulated, in accordance with DNA hypermethylation. CODEGS were then used to create a prognostic score based on the weighted sum of expression of 22 core genes (CODEG22). The score was validated in on microarray data of five independent cohorts, and by qRT-PCR in a cohort of 142 samples, by qRT-PCR. CODEG22 stratified patients globally, as well as in subpopulations of cytologically normal and elderly patients. , and hence, couldSo, it may complement the European LeukemiaNet classification for a more accurate prediction of AML outcomes.

overall_design:
After stringent quality control, transcriptomics data of 1523 samples from 11 datasets, covering 10 AML cytogenetic subgroups, were retained and merged with the transcriptomic data of 198 healthy bone marrow samples. The data set was RMA normalized using RMAexpress software then batch-adjusted using ComBat algorithm.

List of reanalyzed Samples and normalized data for reanalyzed Samples, linked below as a supplementary files.
The metadata.txt contains the clinical information associated with the data set.

first: Hassan

last: Dakik

first: Frédéric

last: Picou

first: Meyling

last: Cheok

first: Claude

last: Preudhomme

first: Hervé

last: Dombret

first: Juliette

last: Lambert

first: Emmanuel

last: Gyan

first: Arnaud

last: Pigneux

first: Christian

last: Recher

first: Marie

last: Béné

first: Fabrice

last: Gouilleux

first: Kazem

last: Zibara

first: Olivier

last: Herault

last: Mazurier


title: DNA copy number alterations in radiation-induced rat renal carcinomas

status: Public on Oct 29 2020

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

summary: To investigate DNA copy number changes in rat renal carcinomas induced by ionizing radiation.

overall_design: DNA copy number changes in radiation-induced rat renal carcinomas were analyzed using array-CGH microarray.

last: Daino

first: Toshiaki

last: Kokubo

first: Shizuko

last: Kakinuma


title: A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of Ythdf2 in haematopoiesis [RNA-seq]

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

summary: The mRNA m6A reader YTHDF2 is overexpressed in human acute myeloid leukaemias.  To understand the role of YTHDF2 in normal haematopoiesis and ageing, we performed SMART-seq on haematopoietic stem cells (HSCs) derived from young and aged (1 year old) mice.  In parallel, to identify transcripts likely methylated in HSCs we performed meRIP-seq analysis of c-Kit+ cells.

overall_design:
In young mice, two samples per mouse were taken from 4 WT vs 4 KO mice, but since replicate samples taken from each mouse behaved as biological replicates, they were treated as such. In aged mice, two samples were taken per mouse from 4 WT vs 5 KO mice, and again, because replicate samples from the same mouse acted as biological replicates, these samples were treated as such.
Please note that the 'aged_WT99_HSC_B' sample has low read counts and is excluded from further analysis.

first: Louie

middle: N

last: van de Lagemaat

first: Christopher

last: Mapperley


title: Effect of Ythdf2 in haematopoiesis [meRIP-seq]

overall_design: meRIP-seq was performed on c-KIT positive cells.


title: RNA sequencing of sciatic nerves from ZH3 and WT mice

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: The transcriptome of sciatic nerves was investigated by RNA sequencing. We compared the transcriptome of ZH3 sciatic nerves to WT sciatic nerves in two age groups. Differentially expressed genes were considered as indicators of peripheral nerve damage in ZH3 mice. Then, we compared the sciatic nerve transcriptome of ZH3 mice chronically treated with a dimeric PrP-fusion protein (FT2Fc) to the two control groups treated with either buffer or mouse IgG. This comparison revealed specific changes induced by FT2Fc treatment. Contrary to our hypothesis, FT2Fc treatment did not alter the expression of the genes that were dysregulated in young and old ZH3 mice (as identified in the first part of the study).

overall_design: Sciatic nerve mRNA profiles were obtained by deep sequencing. Number of replicates: young mice (4 months) mice: 3 WT mice, 3 ZH3 mice (both sciatic nerves from one mouse pooled into one sample). Old mice (13-15 months): 4 WT mice, 4 ZH3 mice(both sciatic nerves from one mouse pooled in each sample). Chronically treated ZH3 mice: 4 mice per treatment, each sample comprises one sciatic nerve from one mouse.

first: Anna

last: Henzi

first: Adriano

last: Aguzzi


title: Functional Interrogation of HOXA9 Regulome in Leukemia via Endogenous Reporter-based CRISPR/Cas9 screen

status: Public on Oct 30 2020

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

country: USA

institute: St.Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aberrant HOXA9 expression is a hallmark of most aggressive acute leukemias, including a vast majority of human acute myeloid leukemia (AML) and subtypes of acute lymphoblastic leukemia (ALL). HOXA9 overexpression not only predicts poor patient diagnosis and outcome, but also plays critical roles in leukemia transformation and maintenance. Besides in few clinical cases as a translocation partner, HOXA9 gene generally shows lower frequencies of somatic mutations and is rarely amplified, indicating that transcriptional and epigenetic regulatory mechanisms might be predominantly utilized. However, our current understanding on the upstream regulation of HOXA9 in acute leukemia is still very limited, hindering development of effective methods to treat leukemia driven by aberrant HOXA9 expression. To mitigate these challenges, we have established the first HOXA9 endogenous reporter in an MLL-rearranged leukemia cell line to faithfully dictate HOXA9 expression by mCherry. By utilizing the reporter cell line and CRISPR/Cas9 genome editing tools, we have exploited comprehensive loss-of-function screenings to systematically discover novel transcription factors controlling HOXA9 expression. USF2 was discovered as a novel regulator of HOXA9 that directly binds to HOXA9’s promoter. USF2 depletion significantly down-regulated HOXA9 expression. Notably, in patients with MLL-rearranged B-ALL, transcriptional expression of USF2 and that of HOXA9 were positively correlated. In contrast, chromatin looping factor CTCF was dispensable for controlling HOXA9 expression in MLL-rearranged SEM cells. Collectively, these studies have functionally interrogated the regulome of HOXA9 and advance our understanding of the molecular regulation network in HOXA9-driven leukemia.

overall_design: CUT&RUN ChIP-seq was performed on auxin-inducible degron system  in a human B-cell lymphoblastic leukemia (B-ALL) cell line, SEM, using USF2 (NBP1-92649, Novus) antibodies against USF2 for a pulldown assay

first: Judith

last: Hyle

first: Yang

last: Zhang

first: Shaela

last: Wright


title: A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS (I)

summary: The identification and characterization of rare immune cell populations in humans can be facilitated by their growth advantage in the context of specific genetic diseases. Here, we use autoimmune-lymphoproliferative syndrome to identify a population of FAS-controlled TCRab+ T cells. They include CD4+, CD8+ and double-negative T cells and can be defined by a CD38+CD45RA+T-BET- expression pattern. These unconventional T cells are present in all healthy individuals, generated before birth, enriched in lymphoid tissue and do not expand during acute viral infection. They are characterized by a unique molecular signature that is unambiguously different from other known T-cell differentiation subsets and independent of CD4 or CD8 expression. Functionally, FAS-controlled T cells represent highly proliferative, non-cytotoxic T cells with IL-10 cytokine bias. Mechanistically, regulation of this physiologic population is mediated by FAS and CTLA4 signaling and its survival is enhanced by mTOR and STAT3 signals. Genetic alterations in these pathways result in expansion of FAS-controlled T cells, which can cause significant lymphoproliferative disease.

overall_design: Defined T cell subsets were FACS sorted from 3 ALPS-FAS patients and from 3 control donors for reference, replicates were not included

first: Maria

middle: E

last: Maccari

first: Patrick

last: Kury

first: Sebastian

last: Fuchs

first: Arif

middle: B

last: Ekici

first: Anika

last: Erxleben

first: Rolf

last: Backofen

first: Melanie

last: Boerries

first: Stephan

last: Ehl

first: Anne

last: Rensing-Ehl


title: Effect of needling treatments on GB20 acupoint in EAE model mice

status: Public on Oct 27 2020

city: Beijing

first: Linqing

last: Miao

state: Beijing

address: No.5 Zhongguancun South St, Haidian District

department: Advanced Innovation Center

country: China

institute: Beijing Institute of Technology

summary:
Purpose: We used RNA sequencing to investigate the effect of needling treatments on GB20 acupoint in EAE model mice
Methods: Retinal mRNA profiles of 13-week-old female sham control mice (SHAM), EAE model mice with MOG injection (MOG), EAE model mice with needling treatment at acupoint GB20 (GB20) and its control acupoint GV16 (GV16) were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed with DESeq2 R package to identify differently expressed genes with padj<0.05.
Results: RNA-seq identified total 234 DEGs, with 100 genes upregulated and 134 genes downregulated, comparing MOG group with SHAM group.Further analysis revealed that, among the MOG injection induced 100 up-regulated DEGs, 24 DEGs were reversed and significantly down-regulated by GB20 treatment, while 14 were reversed and significantly down-regulated by GV16 treatment. However, 12 of the 14 reversed DEGs of GV16 treatment were already included in the 24 DEGs of GB20. The left 2 DEGs specific to GV16 treatment were Gfap (glial fibrillary acidic protein) and Fgf2 (fibroblast growth factor 2). As to the MOG injection induced 134 down-regulated DEGs, 12 DEGs were reversed and significantly up-regulated by GB20 treatment, while only 3 DEGs were reversed and significantly up-regulated by GV16 control treatment, and all the 3 DEGs were included in the 12 DEGs of GB20 treatment.
Conclusions: Our research first reported that needling treatment on GB20 had regulation effects on retinal transcriptome of EAE model mice, indicating potential way of therapy for treatment of optic neuritis.

overall_design: Retinal mRNA profiles of 13-week-old  mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.


title: Transcriptomic analysis of human alveolar type II cell organoids post infection of SARS-CoV-2

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University

summary: We performed unbiased transcriptomic profiling on organoids cultures after SARS-CoV-2 infection to gain insights into AT2s response to SARS-CoV-2 infection.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Bulk RNA-seq was perfomed using human alveolar type II cell organoids at 48 hours after SARS-CoV-2 infection

first: Hiroaki

last: Katsura

first: Vishwaraj

last: Sontake

first: Aleksandra

last: Tata

first: Purushothama


title: Characterization of Lactobacillus plantarum gene expression in the acidic conditions

city: GwangJu

first: JongHee

last: Lee

state: GwangJu

address: kimchiro 86

department: Advanced Process Technology and Fermentation Research Group

country: South Korea

institute: WIKIM

summary: Characterization of Lactobacillus plantarum gene expression in the acididic conditions such as kimchi fermentation

overall_design: To characterize the Lactobacillus plantarum gene expression in the kimchi fermentation, we incubate the Lactobacillus plantarum in the MRS media adjusted with pH 5.0 or 5.5.

first: Jong-Hee

first: Sera

last: Jung


title: Co-cultivation of colorectal cancer cells and human skin fibroblasts in 3D collagen gel and comparison of co-cultivated fibroblasts with CAFs

city: Moscow

first: Olga

last: Rakitina

address: 117997, Russian Federation, Moscow, GSP-7, Ulitsa Miklukho-Maklaya, 16/10

department: Department of Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

summary: Despite the growing recognition of the role of the stroma in cancer growth, invasive behavior and metastasis, the exact mechanisms of its participation remain unclear. We have explored the relationships between the epithelial/mesenchymal (E/M) state of colorectal cancer cells, their ability to activate fibroblasts, and the expression of collagen related genes. To this end, we studied (i) co-cultures of colorectal cancer cells with different hybrid E/M states and normal fibroblasts in a collagen matrix and (ii) patient-derived cancer-associated fibroblasts (CAFs). Using RNA-sequencing, we found that the different cancer cells can activate normal fibroblasts, which could form dense collagen networks. The functional enrichment analysis of differentially expressed genes indicates more mesenchymal phenotype and greater motility of SW480 cells compared to HT29 cells. The genes related to collagen biosynthesis and catabolism tend to be more active in SW480 cells rather than HT29 cells. Moreover, LOXL2 and LOXL3 genes, which are necessary for collagen fibril organization, are SW480 specific, which may indicate greater input of this cell line in collagen remodeling compared to HT29 cells. The expression of several CAF marker genes is activated in NFs upon co-cultivation with HT29 and SW480. Interestingly, a more-epithelial cell line HT29 activates the fibroblasts to a greater extent, than does SW480. The co-cultivation of colon cancer cell lines HT29 or SW480 with NFs leads to the activation of collagen biosynthesis and collagen fibril organization genes in NFs. Our findings suggest that the normal fibroblasts, activated by cancer cells, contribute to the organization of the extracellular matrix. Therefore, targeting the ability of cancer cells to activate normal fibroblasts can be considered as a new therapeutic strategy.

overall_design: Examination of mRNA profiles of monocultures of colorectal cancer cell lines, HT29 and SW480, normal skin fibroblasts (NFs), two cultures of patient-derived colorectal CAFs (CAF1 and CAF2); mRNA profiles of HT29 or SW480 co-cultivated with NFs, and NFs co-cultivated with HT29 or SW480. The preparation of the libraries was performed in technical triplicate for mono- and co-cultivated HT29, SW480, and NFs, while for CAF1 and CAF2, the preparation of the libraries was performed in technical duplicate.

first: Dmitry

last: Didych

first: Alexey

last: Kuzmich


title: A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS (II)

first: Geoffroy

last: Andrieux

first: Maria

last: Maccari

first: Patrick

last: Kury

first: Sebastian

last: Fuchs

first: Arif

first: Anika


title: poly A+ RNA sequencing of cell cycle-synchronized RNA from U2OS cells

city: Urbana

first: Prasanth Kumar

middle: Vijayan

last: Kannanganattu

state: Illinois

address: 601S, Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

summary: We performed paired-end poly A+ RNA sequencing using total RNA isolated from U2OS cells that are synchronised into G1, G1/S, S, G2 and M phase of cell cycle.

overall_design: M-phase cells were collected using Nocadozole treatment. G1 cell are isolated using Nocadozole arrest followed by release. G1/S, S and G2 cells were collected by performing double-thymidine block and release.

first: Qinyu

last: Hao

first: Kannanganattu

middle: V

last: Prasanth

last: Sun


title: ZNF354C is a transcriptional repressor that inhibits angiogenesis in endothelial cells

status: Public on Oct 28 2020

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: RNA-Sequencing of human microvascular endothelial cells (HMEC) that overexpressed ZNF354C demonstrated that this transcription factor is a potent transcriptional repressor

overall_design: mRNA-seq profile after overexpression of pCMV6-ZNF354C or pCMV6-Entry (negative control) for 24h in HMECs.

first: Matthias

middle: S

last: Leisegang

first: James

middle: A

last: Oo

first: Barnabas

last: Irmer

first: Ralf

middle: P

last: Brandes


title: The transcription factor M1BP targets CP190 to chromatin to regulate transcription and chromatin insulator activity (ChIP-Seq)

city: bethesda

first: Elissa

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

summary: Chromatin insulators are DNA-protein complexes that establish distinct higher order transcriptional domains.  In Drosophila, CP190 is the only common factor for all the DNA-binding insulator protein complex. Insulators harbour two properties: they can block communication between an enhancer and a promoter, and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy insulator complex contains three core components; Su(Hw), CP190 and Mod(mdg4)67.2. In our studies, using mass-spec analysis and of immunopurified complexes from Drosophila embryonic nuclear extracts, we identified the transcription factor Motif 1 Binding Protein (M1BP) associated with CP190 and verified this interaction by coimmunoprecipitation. Furthermore, depletion of M1BP results in loss of both enhancer-blocking and barrier activities, also disrupts the nuclear localization of CP190-marked insulator bodies within the developing fly. ChIP-seq analysis of both factors in Kc167 cultured hemocytes revealed extensive overlap of the two factors, particularly at Motif 1 containing promoters. Depletion of M1BP results in extensive loss of CP190 chromatin association, and depletion of CP190 also greatly affects M1BP chromatin association. Moreover, EU-seq analysis after depletion of either CP190 or M1BP suggests they regulate gene expression in similar fashion. Further analysis using reporter assays verifies that CP190-dependent gene expression changes are dependent on the presence of Motif 1. Our results suggest a novel mechanistic relationship between CP190 and M1BP function with respect to transcriptional regulation and higher order chromatin organization.

overall_design: Examination of overlapping of M1BP with insulator proteins Su(Hw), CP190 and Mod(mdg4) genome wide in Kc167 embryonic cell lines and also to investigate whether association of these insulator factors are dependent on M1BP or binding of M1BP dependent on CP190.

first: I

last: Bag

first: S

last: Chen

first: C

last: Liu

first: E


title: Effect of Ythdf2 in haematopoiesis

first: Kamil

last: Kranc


title: The transcription factor M1BP targets CP190 to chromatin to regulate transcription and chromatin insulator activity (RNA-Seq)

overall_design: Examining the transcriptional regulation of M1BP, CP190 and Mod(mdg4)67.2 by performing nascent EU-RNA seq in depletion of each factor in Kc167 cells.


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [mifinder Phenotypes]

city: Bhubaneswar

first: Munmun

last: Chakraborty

state: Odisha

address: MTC campus,Patia

department: Reasearch

country: India

institute: L.V Prasad Eye Institute

summary: Human peripheral mononuclear cells were purified from control and diseased patient volunteers blood using ficol and miRNA was extracted using QIAGEN miRNeasy kit

overall_design: QPCR array profiling. PBMC from control and diseased patients (Cl.PXF and Pig. PXF) were collected as mentioned in summary followed by extraction of miRNA from the same prior to QPCR based miRNA expression array

first: Akash

last: Roy


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [mifinder Stages]

summary: Human peripheral mononuclear cells were purified from control and diseased patient (Psedoexfoliation (PXF),  Ocular Hypertension (OHT), Psedoexfoliation Glaucoma (PXG))  volunteers blood using ficol and miRNA was extracted using QIAGEN miRNeasy kit

overall_design: QPCR array profiling. PBMC from control and diseased patients (OHT and PXG) were collected as mentioned in summary followed by extraction of miRNA from the same prior to QPCR based miRNA expression array


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC)


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [UPR Stages]

summary:
Human peripheral mononuclear cells(PBMC) were purified from control and diseased volunteers' blood (Pseudoexfoliation(PXF), Ocular Hypertension(OHT), Pseudoexfoliation Glaucoma(PXG)) and mRNA was extracted using QIAzol® lysis reagent.
complemenatry DNA(cDNA) was prepared and expression was analysed using PCR based arrays. We used QIAGEN online software to quantitate the differential gene expression .

overall_design: PCR array profiling.  PBMC from Ocular Hypertension(OHT), Pseudoexfoliation( PXF) and pseudoexfoliation glaucoma(PXG) donors blood were used for analysis as indicated in the summary. Equal amount total RNA from each donor was used for gene expression analysis.


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [UPR Phenotypes]

summary:
Human peripheral mononuclear cells(PBMC) were purified from control and diseased (Cataract, Classical Pseudoexfoliation(Cl PXF),  Pigmentary Pseudoexfoliation(Pig PXF))  volunteers' blood and mRNA was extracted using QIAzol® lysis reagent.
complemenatry DNA(cDNA) was prepared and expression was analysed using PCR based arrays. We used QIAGEN online software to quantitate the differential gene expression .

overall_design: PCR array profiling.  PBMC from Cataract(Control), Classical Pseudoexfoliation( CL PXF) and Pigmentary pseudoexfoliation (Pig PXF) donors blood were used for analysis as indicated in the summary. Equal amount total RNA from each donor was used for gene expression analysis.


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [miRNA Fibrosis Stages]

summary: Human peripheral mononuclear cells were purified from control and diseased (Psedoexfoliation (PXF), Ocular Hypertension (OHT), Pseudoexfoliation Glaucoma (PXG)) patient volunteers blood using ficol and miRNA was extracted using QIAGEN miRNeasy kit


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [miRNA Fibrosis Phenotypes]

summary: Human peripheral mononuclear cells were purified from control and diseased (Cataract, Classical PXF, Pigmentary PXF) patient volunteers blood using ficol and miRNA was extracted using QIAGEN miRNeasy kit

overall_design: QPCR array profiling. PBMC from control and diseased patients (Cl.PXF and Pig.PXF) were collected as mentioned in summary followed by extraction of miRNA from the same prior to QPCR based miRNA expression array


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [Fibrosis Phenotypes]

summary:
Human peripheral mononuclear cells(PBMC) were purified from control and diseased (Cataract, Classical Pseudoexfoliation(Cl PXF), Pigmentary Pseudoexfoliation(Pig PXF)) volunteers' blood and mRNA was extracted using QIAzol® lysis reagent.
complemenatry DNA(cDNA) was prepared and expression was analysed using PCR based arrays. We used QIAGEN online software to quantitate the differential gene expression .


title: RNA-seq data from three Saccharomyces cerevisiae strains with different protein productivity

status: Public on Oct 26 2020

city: Gothenburg

first: Qi

last: Qi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: The budding yeast Saccharomyces cerevisiae is a popular host to be used to produce recombinant proteins. Here we studied three yeast strains with different productivity using the RNA-seq data to elucidate the mechanisms for improving protein production.

overall_design: Three strains were grown under chemostat cultures at two dilution rates, 0.1/h and 0.2/h. Samples used for RNA-seq analysis were collected at the steady state for each condition.

first: Rosemary

last: Yu

first: Jens

last: Nielsen


title: Real-time quantitative PCR analysis of human peripheral mononuclear cells (PBMC) [Fibrosis Stages]

summary:
Human peripheral mononuclear cells(PBMC) were purified from control and diseased (Pseudoexfoliation (PXF), Ocular Hypertension(OHT), Pseudoexfoliation Glaucoma(PXG)] volunteers' blood and mRNA was extracted using QIAzol® lysis reagent.
complemenatry DNA(cDNA) was prepared and expression was analysed using PCR based arrays. We used QIAGEN online software to quantitate the differential gene expression .

overall_design: PCR array profiling.  PBMC from Ocular Hypertension(OHT), Pseudoexfoliation( PXF) and pseudoexfoliation glaucoma(PXG) donors blood were used for analysis as indicated in the summary. Equal amount total RNA from each donor was reverse transcribed and used for gene expression analysis.


title: Analysis of anti-CD3e-induced transcriptional changes in WNK1-deficient thymocytes

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

summary: RNAseq was used to analyse transcriptional changes occuring in WNK1-expressing or WNK1-deficient DN3 thymocytes following injection of anti-CD3e

overall_design: Wnk1fl/+;CD2Cre;Rag1KO (HET, WNK1-expressing) or Wnk1fl/fl;CD2Cre;Rag1KO (KO, WNK1-deficient) mice were injected intraperitoneally with anti-CD3e and thymi was harvested after 3, 24 and 48 hours. Uninjected mice were used for the 0 hour timepoint. Thy1.2+, CD44- thymocytes were sorted by flow cytometry and RNA was extracted and sequenced. There were three replicates for each genotype/time point except for 4 replicates for WNK1-deficient mice at 0 h time point.

first: Robert

last: Köchl

first: Miriam

last: Llorian Sopena


title: Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory [single-cell RNA-seq]

status: Public on Oct 25 2020

city: Oxford

first: Wojciech

last: Siwek

state: Oxfordshire

address: Department of Biochemistry, South Parks Road

department: Biochemistry

institute: Oxford University

summary: Cytokine activation of cells induces gene networks involved in inflammation and immunity. Transient gene activation can have a lasting impact even in the absence of ongoing transcription, known as long-term transcriptional memory. Here we explore the nature of the establishment and maintenance of IFNγ-induced priming of human cells. We find that while both ongoing transcription and local chromatin signatures are short-lived, the IFNγ-primed state stably propagates through at least 14 cell division cycles. Single cell analysis reveals that memory is manifested by an increased probability of primed cells to engage in target gene expression, correlating with the strength of initial gene activation. Further, we find that strongly memorized genes tend to reside in genomic clusters and that long-term memory of these genes is locally restricted by cohesin. We define the duration, stochastic nature and molecular mechanisms of IFNγ-induced transcriptional memory, relevant to understanding of enhanced innate immune signaling.

overall_design: Single cell transcriptome measurements of polyA mRNA for naïve HeLa cells (N=90), induced with interferon gamma (50ng/mL) for 24h (priming) (N=89) and 24h reinduced with interferon gamma (50ng/mL) after 48h washout (reinduction) (N=91).

first: Lars

last: Jansen


title: Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory [RNA-seq_SCC1-AID]

overall_design: Transcriptome measurements of polyA mRNA for HeLa cells with SCC1 component of cohesin tagged with an AID degron (SCC1-AID). osTIR1 E3 ligase either present (TIR1+) or not (TIR1-). Measurement for naïve HeLa cells; induced with interferon gamma (50ng/mL) for 16h (priming); 48h after interferon gamma washout (primed); 24h reinduced with interferon gamma (50ng/mL) (reinduction) and 24h induction with interferon gamma (50ng/mL) (induction). Cells were additionally treated (IAA+) or not (IAA-) during priming stage with auxin (500µM). Three biological replicates for each condition.


title: Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory [RNA-seq]

overall_design: Transcriptome measurements of polyA mRNA for naïve HeLa cells, induced with interferon gamma (50ng/mL) for 24h (priming), 48h after interferon gamma washout (primed) and 24h reinduced with interferon gamma (50ng/mL) (reinduction). Three biological replicates for each condition.


title: G9a plays distinct roles in maintaining DNA methylation, retrotransposon silencing and chromatin looping

city: Hong Kong

first: Qinghong

last: Jiang

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: G9a is a lysine methyltransferase that regulates epigenetic modifications, transcription and genome organization. However, whether these properties are dependent on one another or represent distinct functions of G9a remains unclear. In this study, we observe widespread DNA methylation loss in G9a depleted and catalytic mutant embryonic stem cells. Furthermore, we define how G9a regulates chromatin accessibility, epigenetic modifications and transcriptional silencing in both catalytic dependent and independent manners. Reactivated retrotransposons provide alternative promoters and splice sites leading to upregulation of neighboring genes and production of chimeric transcripts. Moreover, while topologically associated domains and compartments A/B definitions are largely unaffected, the loss of G9a leads to altered chromatin states, aberrant CTCF and cohesin binding, and differential chromatin looping especially at retrotransposons. Taken together, our findings reveal how G9a regulates the epigenome, transcriptome and higher-order chromatin structures in distinct mechanisms.

overall_design: ChIP-seq, RNA-seq, ATAC-seq, WGBS and Hi-C were conducted for WT, G9a KO, G9a/GLP DKO, G9a-/-Tg(Y1120V; Y1207F), Dnmt3a/3b DKO and Dnmt1/3a/3b TKO mESCs

first: Julie

last: Ang

first: Ah Young

last: Lee

first: Danny

last: Leung


title: Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory

summary:
Cytokine activation of cells induces gene networks involved in inflammation and immunity. Transient gene activation can have a lasting impact even in the absence of ongoing transcription, known as long-term transcriptional memory. Here we explore the nature of the establishment and maintenance of IFNγ-induced priming of human cells. We find that while both ongoing transcription and local chromatin signatures are short-lived, the IFNγ-primed state stably propagates through at least 14 cell division cycles. Single cell analysis reveals that memory is manifested by an increased probability of primed cells to engage in target gene expression, correlating with the strength of initial gene activation. Further, we find that strongly memorized genes tend to reside in genomic clusters and that long-term memory of these genes is locally restricted by cohesin. We define the duration, stochastic nature and molecular mechanisms of IFNγ-induced transcriptional memory, relevant to understanding of enhanced innate immune signaling.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory [ATAC-seq]

overall_design: Chromatin accessibility measurements by ATAC-seq for naïve HeLa cells, induced with interferon gamma (50ng/mL) for 24h (priming), 2 days after interferon gamma washout and 7 days after interferon gamma washout.


title: Expression data from docetaxel-resistant and cabazitaxel-resistant prostate cancer cell lines

city: Barcelona

first: Begoña

last: Mellado

address: Villarroel 170

department: Oncology

country: Spain

institute: Hospital Clínic of Barcelona

summary:
Docetaxel and cabazitaxel are the chemotherapy agents used in castration-resistant prostate cancer. However, most patients eventually develop resistance to these treatments.
The aim of the study was to identify key molecular genes and networks associated with taxanes resistance in 2 models of docetaxel-resistant and cabazitaxel-resistant castration-resistant prostate cancer cell lines.

overall_design: DU-145 and PC-3 cells were converted to docetaxel-resistant cells (DU-145DR and PC-3DR, respectively) and to cabazitaxel-resistant cells (DU-145CZR and PC-3CZR, respectively). Whole-genome arrays were used to compare global gene expression between these 6 cell lines. Arrays were performed by triplicate for each cell line.

first: Natalia

last: Jiménez

first: Òscar

last: Reig

first: Mercedes

last: Marín-Aguilera


title: Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in relapsed acute myeloid leukemia [RNAseq]

status: Public on Oct 22 2020

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

summary: Resistance to chemotherapy is the most common cause of treatment failure in acute myeloid leukemia and the drug efflux pump ABCB1 is a critical mediator. Here we demonstrate that in vitro daunorubicin exposure can induce activating ABCB1 promoter translocations in human myeloid cells, similar to those recently described in recurrent high-grade serous ovarian and breast cancer. We then develop a targeted nanopore sequencing approach that enables efficient identification of ABCB1 structural variants in high-grade serous ovarian cancer. Finally, we confirm that ABCB1high cases of relapsed AML are not characterized by ABCB1 promoter translocations but instead show high-level activity of native promoters, consistent with endogenous regulation.

overall_design: THP-1 cells were from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies, Carlsbad, CA) and 10% fetal bovine serum (Sigma Aldrich). Whilst under drug selection cells were counted and replated every third day. Cell lines were confirmed mycoplasma-free and authenticated by short tandem repeat DNA profiling. THP-1 were exposed to escalating doses of daunorubicin over 142 days, generating a resistant line (THP-1_R) which exhibited a 28.3-fold increase in daunorubicin IC50 compared with the sensitive parental cell line (THP-1_S). Total RNA was extracted from 5x10e5 cells using QIAshredder spin columns and an RNeasy® Plus Micro kit (Qiagen, Manchester, UK). RNA sequencing was performed using two replicates for both the sensitive (THP-1_S1 and THP-1_S2) and resistant (THP-1_R1 and THP-1_R2) lines. Prior to sequencing RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). PolyA libraries were prepared using a SureSelect PolyA kit (Agilent Technologies) and samples were then barcoded and pooled. Sequencing was performed using a NextSeq system (Illumina, San Diego, CA). Two replicates were sequenced for each cell line (THP-1_S and THP-1_R). A single run of 150bp paired-end sequencing produced a mean of 55.1M reads per sample.


title: Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in relapsed acute myeloid leukemia [Targeted Resequencing]

type: Genome variation profiling by high throughput sequencing

overall_design: THP-1 cells were from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies, Carlsbad, CA) and 10% fetal bovine serum (Sigma Aldrich). Whilst under drug selection cells were counted and replated every third day. Cell lines were confirmed mycoplasma-free and authenticated by short tandem repeat DNA profiling. THP-1 were exposed to escalating doses of daunorubicin over 142 days, generating a resistant line (THP-1_R) which exhibited a 28.3-fold increase in daunorubicin IC50 compared with the sensitive parental cell line (THP-1_S). Known to contain an ABCB1 promoter fusion, THP-1_R was subjected to genomic target enrichment and sequencing by both long-read nanopore sequencing and conventional illumina sequencing (this data).


title: Rare genetic variation at transcription factor binding site modulates local DNA methylation profiles

status: Public on Oct 24 2020

city: New York

first: Alejandro

last: Martin Trujillo

address: Hess Center for Science and Medicine at Mount Sinai,1470 Madison Avenue, 8th Floor

institute: Icahn school of medicine at mount sinai hospital

summary: Recently, it has been proposed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Combining blood genome-wide DNA methylation profiles (Illumina Infinium MethylationEPIC BeadChiP), whole genome sequencing-derived single nucleotide variants (SNVs) along with predicted transcription factor binding site (TFBS), we were able to observe that rare regulatory variants, i.e, SNVs that disrupt TFBSs, are associated with DNA methylation at both local and, to a lesser extent, broader locations. Interestingly, we also observed that this directed DNA methylation can have consequences on genome regulation by altering expression levels of nearby genes.

overall_design:
About 500ng of genomic DNA was bisulfite-converted and analyzed for genome-wide methylation patterns using the Infinium MethylationEPIC BeadChiP platform at the New York Genome Center (New York, USA), according the manufacturer's recommendation for Illumina Infinium Assay.
All samples are from individuals with congenital heart defects.

Contributor: Pediatric Cardiac Genomics Consortium (PCGC)

first: Andrew

middle: J

last: Sharp

first: Michael

last: Wagner


title: Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory [ChIP-seq]

overall_design: Chromatin occupancy measurements by ChIP-seq (ChIPmentation) for naive HeLa cells, induced with interferon gamma (50ng/mL) for 24h (priming), 2 days after interferon gamma washout and 7 days after interferon gamma washout.


title: RNAseq from nasopharyngeal swab RNA prior to intranasal live attenuated influenza vaccine in children

status: Public on Oct 23 2020

city: Fajara

first: Karim

last: MANE

address: Atlantic Boulevard

department: Statistics and Bioinformatics

country: Gambia

institute: MRCG @ LSHTM

summary: The goal of this study was to identify pre-challenge transcriptomic signatures associated with viral replication of LAIV strains in the nasopharynx.

overall_design:
Open label cohort study.
clinicaltrials.gov entry for the larger study:
https://clinicaltrials.gov/ct2/show/NCT02972957

first: Thushan

last: de Silva

last: Mane


title: Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in relapsed acute myeloid leukemia [Nanopore]

overall_design: THP-1 cells were from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies, Carlsbad, CA) and 10% fetal bovine serum (Sigma Aldrich). Whilst under drug selection cells were counted and replated every third day. Cell lines were confirmed mycoplasma-free and authenticated by short tandem repeat DNA profiling. THP-1 were exposed to escalating doses of daunorubicin over 142 days, generating a resistant line (THP-1_R) which exhibited a 28.3-fold increase in daunorubicin IC50 compared with the sensitive parental cell line (THP-1_S). Primary human AML and HGSC cells were obtained from the Manchester Cancer Research Centre Tissue Biobank (approved by the South Manchester Research Ethics Committee). The Biobank archive was searched for samples from patients with relapsed AML with high blast counts. Primary AML and HGSC samples were selected for targeted nanopore sequencing on the basis of high ABCB1 expression by quantitative PCR. THP-1_R was also sequenced.


title: DMD-targeted RNA-seq data in C25Cl48 muscular cell line treated with siRNA targeting 16 different RBPs

city: Montpellier

first: Sylvie

last: Tuffery-Giraud

address: 641, av du Doyen Gaston Giraud

country: France

institute: Univ Montpellier

summary:
Purpose: The goal of this study was to identify the RBPs that regulate the inclusion of the exons in the muscular isoform of the DMD gene (Dp427m). We compared the splicing pattern of the Dp427m from C25Cl48 treated with a control siRNA or siRNA targeting 16 different RBPs.
Method: The C25Cl48 were treated by RNAi in duplicates (or n=4 for the control condition) and submitted to 3 days of myogenic differentiation. The RBPs tested were CELF1, DAZAP1, DDX5/DDX17, hnRNPA1, hnRNPA2, MBNL1, PTBP1, QKI, RBFOX1, RBFOX2, RBM4, SRSF1, SRSF2, TDP-43 and Tra2b. The silencing efficiency was controlled by RT-qPCR and Western blotting analysis. RNA was reverse transcribed using oligodT and the Dp427m (11.3kb) coding sequence was amplified by Long-Range PCR and sequenced on a 454 GS junior platform. Reads that passed quality filters were mapped to the human X chromosome with STAR. The Percent-Spliced-In (PSI) was calculated for each splicing event using intron-centric metrics (Pervouchine et al., 2013), with the SJPIPE pipeline, from the ipsa package. Junctions were filtered to keep only those covered by a minimum of 5 reads in at least one out of the two biological replicates or 2/4 in the control condition.
Results: Using this DMD-targeted RNA-seq approach, we obtained an average read depth of 1638X, allowing reliable detection of alternative splicing events. Based on a cutoff of |[delta]PSI|≥0.05, we identified 8 exons that were deregulated in at least one of the RBPs tested, and 15 RNAi conditions induced splicing changes.
Conclusion: The 8 deregulated exons identified here are mainly exons that were previously found alternatively spliced in other dystrophin isoforms.

overall_design: si-control and si-RBP treated cells were performed in 4 and 2 biological replicates, respectively.

last: Miro

first: Anne-Laure

last: Bougé

first: Eva

last: Murauer

first: Emmanuelle

last: Beyne


title: Defining the Functional Targets of Cap’n’collar Transcription Factors NRF1, NRF2, and NRF3.

status: Public on Oct 21 2020

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

summary: The NRF transcription factors NRF1, NRF2, and NRF3, are a subset of Cap’n’collar transcriptional regulators which modulate the expression of genes harboring antioxidant-response element (ARE) sequences within their genomic loci. Despite the emerging physiological importance of NRF family members, the repertoire of their genetic targets remains incompletely defined. Here we use RNA-sequencing-based transcriptional profiling and quantitative proteomics to delineate the overlapping and differential genetic programs effected by the three NRF transcription factors. Comparing our data to recent profiling analyses, we create consensus target gene sets regulated by NRF1, NRF2, and NRF3, genetic programs which we determine to be differentially regulated in human tissues. Together, our data provide a quantitative assessment of how NRF family members sculpt proteomes and transcriptomes, essential information for future studies evaluating the role of NRF factors in normal physiology and disease.

overall_design: Comparisons of the transcriptomes of HEK293T cells expressing empty vector, FLAG-NRF1, FLAG-NRF2(T80D), or FLAG-NRF3.

middle: H

first: R

middle: L

last: Wiseman

last: Bollong


title: Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in relapsed acute myeloid leukemia [ChIP-seq]

overall_design: THP-1 cells were from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies, Carlsbad, CA) and 10% fetal bovine serum (Sigma Aldrich). Whilst under drug selection cells were counted and replated every third day. Cell lines were confirmed mycoplasma-free and authenticated by short tandem repeat DNA profiling. THP-1 were exposed to escalating doses of daunorubicin over 142 days, generating a resistant line (THP-1_R) which exhibited a 28.3-fold increase in daunorubicin IC50 compared with the sensitive parental cell line (THP-1_S). Primary human AML cells were obtained from the Manchester Cancer Research Centre Tissue Biobank (approved by the South Manchester Research Ethics Committee). The Biobank archive was searched for samples from patients with relapsed AML with high blast counts and sufficient viable cells from ChIP sequencing. H3K27 acetylation ChIP sequencing was performed using two replicates for both the sensitive (THP-1_S1 and THP-1_S2) and resistant (THP-1_R1 and THP-1_R2) lines and a single aliquot from each patient sample.


title: Distinct activities of bacterial condensins for chromosome management in Pseudomonas aeruginosa

city: Gif-sur-Yvette

first: Virginia

last: Lioy

address: 1 Avenue de la Terrasse

department: Genome Biology

institute: Institute for Integrative Biology of the Cell (I2BC)

summary: Three types of structurally related structural maintenance of chromosomes (SMC) complexes, referred to as condensins, have been identified in bacteria. Smc-ScpAB is present in most bacteria, whereas MukBEF is found in enterobacteria and MksBEF is scattered over the phylogenic tree. The contributions of these condensins to chromosome management were characterized in Pseudomonas aeruginosa, which carries both Smc-ScpAB and MksBEF. In this bacterium, SMC-ScpAB controls chromosome disposition by juxtaposing chromosome arms. In contrast, MksBEF is critical for chromosome segregation in the absence of the main segregation system, and it affects the higher-order architecture of the chromosome by promoting DNA contacts in the megabase range. Strikingly, our results reveal a prevalence of Smc-ScpAB over MksBEF involving a coordination of their activities with chromosome replication. They also show that E. coli MukBEF can substitute for MksBEF in P. aeruginosa while prevailing over Smc-ScpAB. Our results reveal a hierarchy between activities of bacterial condensins on the same chromosome.

overall_design: Chromosome conformation capture of Pseudomonas aeruginosa PAO1 wt cells and mutants.

first: Ivan

last: Junier

first: Valentine

last: Lagage

first: Frédéric

last: Boccard

first: Isabelle

last: Vallet


title: Validated transcriptional regulatory roles for five two-component systems in E. coli

first: Bernhard

middle: O.

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Department of Bioengineering

institute: University of California, San Diego

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

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


title: Tumor-educated platelet RNA for the detection and (pseudo)progression monitoring of glioblastoma

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

summary: We report RNA-sequencing data of 805 blood platelet samples, including 240 tumor-educated platelet (TEP) samples collected from patients with glioblastoma and 126 TEP samples collected from patients with brain metastases. In addition, we report RNA-sequencing data of blood platelets isolated from 353 asymptomatic controls and 86 individuals with multiple sclerosis. This dataset highlights the ability of TEP RNA-based 'liquid biopsy' diagnostics for the detection and (pseudo)progression monitoring of glioblastoma.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 or 4000 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTseq.

middle: G

first: Nik

last: Sol

first: Thomas

last: Wurdinger


title: TBK1-METTL3 axis facilitates antiviral immunity

status: Public on Oct 19 2020

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center


title: Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins [human array]

city: Hannover

first: Rishikesh

last: Lotke

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Virologie

institute: Medizinische Hochschule Hannover

summary: The rhadinoviruses Kaposi’s Sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus (MHV-68) persist in infected hosts in a latent state that is characterized by the absence of virus production and by restricted viral gene expression. Their major latency protein, the latency-associated nuclear antigen (kLANA for KSHV and mLANA for MHV-68), is essential for viral genome maintenance and replication and involved in transcriptional regulation. Both kLANA and mLANA interact with cellular chromatin-associated proteins, among them the Bromodomain and Extra Terminal domain (Brd/BET) proteins, which recruit cellular and viral proteins to acetylated histones through their bromodomains and modulate cellular gene expression. They also play a role in the tethering, replication, segregation or integration of a diverse group of viral DNA genomes. In this study we explored if Brd/BET proteins influence the localisation of the LANAs to preferential regions in the host chromatin and thereby contribute to kLANA- or mLANA-mediated transcriptional regulation. Using ChIP-Seq, we observed a genome-wide co-enrichment of kLANA with Brd2/4 near cellular and viral transcriptional start sites (TSS). Treatment with I-BET151, an inhibitor of Brd/BET, displaced kLANA and Brd2/4 from TSS in the viral and host chromatin but did not affect the direct binding of kLANA to kLANA-binding sites (LBS) in the KSHV latent origin of replication. Similarly, mLANA, but not a mLANA mutant deficient for binding to Brd2/4, also associated with cellular TSS. We compared the transcriptome of KSHV-infected with uninfected and kLANA-expressing human B cell lines, as well as a murine B cell line expressing mLANA or a Brd2/4-binding deficient mLANA mutant. We found that only a minority of cellular genes, whose TSS are occupied by kLANA or mLANA, is transcriptionally regulated by these latency proteins. Our findings extend previous reports on a preferential deposition of kLANA on cellular TSS and show that this characteristic chromatin association pattern is at least partially determined by the interaction of these viral latency proteins with members of the Brd/BET family of chromatin modulators.

overall_design: Gene expression profiles of BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 cells in the absence and presence of 0.5 µM I-BET151. Microarray experiment was performed for each condition in three biological replicates.

first: Ulrike

last: Schneeweiß

first: Marcel

last: Pietrek

last: Günther

first: Adam

last: Grundhoff

first: Magdalena

last: Weidner-Glunde

middle: F

last: Schulz


title: Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)

summary: Escherichia coli use two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress, and KdpDE, PhoRB, and ZraSR, which were stimulated by potassium, phosphate, and zinc, respectively. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data was used to validate condition-specific target gene binding sites. Based on this data we (1) identify the target genes for each TCS; (2) show how the target genes are transcribed in response to stimulus; and (3) reveal novel relationships between TCSs, which indicate non-cognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress.  Our understanding of the TRN in E. coli is thus notably expanded.

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

overall_design: Expression profiling data for five two-component system deletion strains and wild type were generated by RNA-seq, in duplicate

first: Kumari

last: Choudhary

first: Julia

last: Kleinmanns

first: Ye

last: Gao

first: Richard

last: Szubin


title: Unravelling the molecular mechanisms of Abscisic acid-mediated drought-stress alleviation in pomegranate (Punica granatum L.)

status: Public on Oct 20 2020

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: Pomegranate (Punica granatum L.) is sensitive to drought stress, which largely affects its transplantation survival rate, fruit yield and quality. Abscisic acid (ABA) treatment can reduce the drought-induced adverse impacts on plants. However, no studies have ever applied ABA as an exogenous supply to alleviate the drought stress on pomegranates. In this study, we performed comparative transcriptome analysis between the ABA-treated and untreated pomegranates to reveal the ABA-induced mechanisms in response to drought-stress. Our results showed that exogenous ABA application substantially enhanced pomegranate drought resistance by strengthening metabolic pathways, such as BRs synthesis, peroxisome biogenesis, photosynthesis and hemicelluloses synthesis. Furthermore, treatments with different ABA concentrations may provoke different transcriptional responses and, once the concentration exceeds the optimal (60 μM), it might induce some potential adverse impacts on plant growth and stress resistance.

overall_design: To investigate the molecular mechanisms underlying ABA-induced drought-stress resistance, we conducted transcriptome-wide bulk RNA-seq of the ABA-treated (30, 60 and 90 μM) and untreated pomegranates (0 μM as control).

first: Jingjing

last: Qian


title: Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in relapsed acute myeloid leukemia [4C-seq]

first: Tim

last: Somervaille

overall_design: THP-1 cells were from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies, Carlsbad, CA) and 10% fetal bovine serum (Sigma Aldrich). Whilst under drug selection cells were counted and replated every third day. Cell lines were confirmed mycoplasma-free and authenticated by short tandem repeat DNA profiling. THP-1 were exposed to escalating doses of daunorubicin over 142 days, generating a resistant line (THP-1_R) which exhibited a 28.3-fold increase in daunorubicin IC50 compared with the sensitive parental cell line (THP-1_S). To investigate fusion partners and other potential regulatory interactions we performed 4C sequencing using a view point centred on the ABCB1 promoter using THP-1_S and THP-1_R.


title: Validated transcriptional regulatory roles for five two-component systems in E. coli (ChIP-exo dataset)

first: Bernhard

last: Palsson

overall_design: ChIP-exo profiling data for five two-component system deletion strains, in duplicate:  BaeR myc tagged cells, CpxR myc tagged cells, KdpE myc tagged cells, PhoB myc tagged cells, ZraR myc tagged cells.


title: Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in relapsed acute myeloid leukemia

overall_design: Refer to individual Series


title: Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Aprepitant, an antiemetic agent, displays potent synergistic interactions with azole drugs against emerging multidrug-resistant Candida auris

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Combination therapies can be a promising tool to augment the antifungal activity of azole drugs against resistant Candida species. Here, we report the interaction between aprepitant, an antiemetic agent, and azole drugs against different Candida species including the emerging multidrug-resistant C. auris. Particularly, aprepitant enhanced the antifungal activity of itraconazole against C. auris by reducing its minimum inhibitory concentration (MIC) by 2-8 folds.  Using Caenorhabditis elegans as an in vivo infection model, the aprepitant/itraconazole combination significantly prolonged the survival of the infected nematodes by ~90% and reduced the fungal burden by ~92% relative to the untreated control. Interestingly, the aprepitant/itraconazole combination exerted a potent fungicidal activity against both planktonic and adherent C. auris biofilms. Further, aprepitant/itraconazole displayed broad-spectrum synergistic interactions against other medically important Candida species including C. albicans, C. krusie, C. tropicalis, and C. parapsilosis (ƩFICI ranged from 0.08 to 031). Comparative transcriptomic profiling indicated aprepitant/itraconazole interferes significantly with metal ions homeostasis and compromises the ROS (reactive oxygen species) detoxification ability of C. auris. This study presents aprepitant as a novel, potent and broad-spectrum azole chemosensitizing agent that warrants further investigation.

overall_design: Method: polyA selection of mRNA from treated and untreated Candida auris, sequenced on a NovaSeq 6000

first: Hassan

last: Eldesouky

last: Lanman

first: Tony

last: Hazbun

first: Mohamed

last: Seleem


title: Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins [mouse array]

first: Rishikesh

last: Lotke

overall_design: Gene expression profiles of A20-GFP, A20-mLANA WT and A20-mLANA 3A cells in the absence and presence of 1 µg/ml doxycycline for 24 and 48 hours. Microarray experiment was performed for each condition in three biological replicates. Twenty microarray hybridizations were conducted in dual-colour mode using amplified cRNA populations, fluorescently labeled with either Cy3 or Cy5. Respective pairs of differently labeled samples were co-hybridized on one microarray each. In order to enable inspection of normalized intensity values rather than just ratios or fold changes, dual-colour results were integrated into a single-color GEO matrix.

last: Schneeweiß

last: Pietrek

first: Thomas

last: Günther


title: RNA sequencing of livers from Per2-/- and WT mice following MC38 cancer cells injection reveals transcriptional differences as early as 7 days post injection

status: Public on Oct 15 2020

city: Rehovot

first: Ruth

last: Scherz-Shouval

address: 234, Herzl

country: Israel

institute: The Weizmann Institute of Science

summary: The circadian clock regulates diverse physiological processes by maintaining a 24-hour gene expression pattern. Genetic and environmental cues that disrupt normal clock rhythms can lead to cancer, yet the extent to which this effect is controlled by the cancer cells versus non-malignant cells in the tumor microenvironment (TME) is not clear. Here we set out to address this question, by selective manipulation of circadian clock genes in the TME. In two different mouse models of cancer we find that expression of the core clock gene Per2 in the TME is crucial for tumor initiation and metastatic colonization, whereas another core gene, Per1, is dispensable. We further show that loss of Per2 in the TME leads to significant transcriptional changes in response to cancer cell introduction. These changes may contribute to a tumor-suppressive microenvironment. Thus, our work unravels an unexpected protumorigenic role for the core clock gene Per2 in the TME, with potential implications for therapeutic dosing strategies and treatment regimens.

overall_design: Per2-/- or WT C57Bl/6 male mice were injected with 20,000 MC38 cells (n=4 mice per genotype) or PBS (n=2 control mice per genotype) into the hepatic portal vein. 7 days post-injection, mice were sacrificed and livers  were then dissociated and sequenced.

first: Lee

last: Shaashua

first: Shimrit

last: Mayer

first: Chen

last: Lior

first: Hagar

last: Lavon

first: Alexander

last: Novoselsky


title: RNAseq for WT and oschz1 mutant

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

summary: At genome-wide level, loss of OsChz1 causes mis-regulation of thousands of genes and broad alterations of nucleosome occupancy as well as reduction of H2A.Z-enrichment within chromatin along the gene body and at TSS. While OsChz1 associates with chromatin regions enriched of repressive histone marks (H3K27me3 and H4K4me2), its loss does not affect the genome landscape of DNA methylation.

overall_design: 2 geneotype with 3 replicates

first: Kangxi

last: Du

first: Aiwu

last: Dong

first: Wen-Hui

last: Shen


title: Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin  [EPIC methylation data on cell lines and PDXs]

status: Public on Oct 18 2020

city: Heidelberg

first: Elisa

last: Espinet

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

type:
Methylation profiling by array
Third-party reanalysis

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. Methylationlow tumors are characterized by higher expression of endogenous retroviral (ERV) transcripts and dsRNA sensors which leads to a cell intrinsic activation of an interferon signature (IFNsign). This results in a pro-tumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells preserve lineage traits, respective of normal ductal or acinar pancreatic cells. Moreover, ductal-derived KrasG12D/Trp53-/- mouse PDACs show higher expression of IFNsign compared to acinar-derived counterparts. Collectively, our data point to two different origins and etiologies of human PDACs, with the aggressive Methylationlow/IFNsignhigh subtype potentially targetable by agents blocking intrinsic IFN-signaling.

overall_design:
hPDAC primary cell lines (PACOs) were normalized together. PDAC-PDX tumor samples were normalized together with normal samples. These included HPDE cell line, normal bulk tissue, mixed exocrine DNA, acinar, de-differentiated acinar and ductal cells isolated by FACS from healthy donors, and 4 previously published acinar and ductal replicates (GSE122126, samples GSM3455826, GSM3455827, GSM3455828, GSM3455829). RnBeads was used to process the data. SNP-enriched and sex chromosome associated probes were removed from the analyses. BMIQ normalization was applied.

**Submitter declares that the raw data for 34 Samples were deposited in the European Genome-phenome Archive (EGA) under accession number EGAS00001004660 due to patient privacy concerns.**

first: Andreas

last: Trumpp

first: Efsun

last: Arda

first: Ilse

last: Rooman


title: Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins [ChIP-seq]

last: Lotke

overall_design: Study of host and viral genome-wide binding profiles of KSHV LANA, human BRD2, human BRD4 and MHV-68 LANA. Two biological replicates of KSHV LANA ChIP-seq were performed in BCBL-1, BJAB-kLANA and BJAB-rKSHV.219 cells in the absence or presence of a BRD/BET inhibitor I-BET151. ChIP-Seq for BRD2 and BRD4 was performed in BCBL-1 cells in the absence or presence of I-BEI151. IgG or Input samples were considered as control. mLANA ChIP-Seq was performed in three biological replicates in A20-GFP control and A20-mLANA WT cells. Two biological replicates of ChIP-Seq were performed for mLANA-3A mutant in A20-mLANA 3A cells. A20-mLANA 3A data have been labelled from rep2 onwards to indicate the mLANA WT-matched experiment numbering.

first: Ulrike

last: Schneeweiß

first: Marcel

first: Adam

last: Grundhoff

first: Magdalena

last: Weidner-Glunde

last: Schulz


title: OsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice


title: ChIP-Seq of OsChz1-MYC

overall_design: examination of 1 antibodies with 2 replicates. Samples without antibody were used as input control.


title: Gene expression profiling reveals insights into infant immunological and febrile responses to capsular group B meningococcal vaccine

city: Oxford

first: Daniel

last: O'Connor

address: Churchill Hospital

department: Paediatrics

institute: University of Oxford

summary: We report gene expression profiles, using RNA-sequencing, in whole blood samples taken before and after  infant immunisations.

overall_design: To assess gene expression profiles following routine infant immunisations, and relate these to vaccine immunogenicity and reactogenicity.

last: O’Connor


title: Transcriptome analysis of CHAF1B depletion in Akata EBV+ Burkitt Lymphoma cells

city: Tampa

first: Mingxiang

last: Teng

state: FL

address: 12902 Magnolia Dr

department: Department of Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center and Research Institute

summary: RNAseq was used to identify host and EBV viral transcriptome changes in CHAF1B knock-out Akata EBV+ cells. CHAF1B KO Akata EBV+ cells were subjected to RNAseq analysis. The Akata EBV+ cells expressing control sgRNA was used as the control.

overall_design: CHAF1B KO Akata EBV+ cells and control Akata EBV+ cells were subjected to RNAseq analysis.

first: Yuchen

last: Zhang

first: Chang

last: Jiang

first: Benjamin

last: Gewurz


title: Cell signaling coordinates global Polycomb Repressive Complex 2 recruitment and developmental gene expression in murine embryonic stem cells

status: Public on Oct 13 2020

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy


title: Quantitative Analysis of different NK cell types Transcriptomes

status: Public on Oct 12 2020

city: La Jolla

first: Huang

last: Zhu

address: 2880 Torrey Pines Scenic Dr.

department: Medicine

institute: University of California-San Diego

summary: We compared transcriptome of different types of NK cells including obtained from peripheral Blood (PB-NK), derived from human ES cell, H9-NK, derived from human iPSC (iPSC-NK), derived from CD34+ cells from umbilical cord blood (UCB-NK), NKcell line (NK92) and 3 cancer cell lines (K562, Raji and Jurkat). When comparing the similarity of the NK cells populations by the number of differentially expressed genes to iPSC NK cells, there were the fewest differentially expressed genes in the comparison with the UCB NK cells, followed by the PB-NK cells, followed by the H9 embryonic stem cell derived-NK cells and lastly by the NK92 cell line.

overall_design: mRNA profiles of 5 different NK cell type and 3 cancer cell lines were generated by deep sequencing, in dulpicate, using Illumina Hi-seq 2000.

first: Dan

last: Kaufman


title: Loss of hepatocyte cell division leads to liver inflammation and fibrosis

status: Public on Oct 14 2020

city: Singapore

first: Jin Rong

last: Ow

state: Singapore

address: 61 Biopolis Drive

department: Institute of Molecular and Cell Biology

country: Singapore

institute: A*STAR

summary: Purpose was to identify transcriptomic changes in whole liver and isolated hepatocytes from 2 week old wild type and Cdk1 liver-specific knock-out (Cdk1 Liv-/-) mice.

overall_design: RNA-seq of mRNA extracted from whole liver and isolated hepatocytes of 2 week old wild type or Cdk1 Liv-/- mice.

first: Matthew

middle: R

last: Dewhurst

first: Heike

last: Wollmann

first: Hyungwon

last: Choi


title: MLLT6 maintains PD‐L1 expression and mediates tumor immune resistance

status: Public on Oct 16 2020

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: We present a CRISPR-Cas9 screen in human cancer cells to identify genes that confers tumors with the ability to evade the cytotoxic effects of the immune system. We discovered that the transcriptional regulator MLLT6 (AF17) is required for PD-L1 cell surface presentation and protein expression in multiple cancer types and MLLT6 depletion alleviates suppression of CD8+ cytotoxic T cell-mediated cytolysis. Furthermore, cancer cells lacking MLLT6 exhibit impaired STAT1 signaling and are insensitive to interferon gamma induced stimulation of IDO1, GBP5, CD74 and MHC class II genes, while maintaining MHC class I gene expression. Collectively, our findings establish MLLT6 as a regulator of oncogenic and interferon gamma associated immune resistance

overall_design: Pooled CRISPR-Cas9 based screen to identify genes regulating PD-L1. Cells that expressed low levels of PD-L1 were subjected to deep sequencing to determine frequencies of sgRNAs and their target genes that were enriched, IFNG treated and untreated samples from 3 different time points were used for studying the sgRNA expression profiles by deepsequencing, RNA-seq transcriptome profiling of U2OS wildtype and MLLT6 knockout cells treated with and without IFNG. Samples of each condition was submitted in triplicates for deep sequencing.

first: Mirko

last: Theis

first: Sandeep

last: Sreevalsan


title: CD200 expression marks leukemia stem cell (LSC) in human AML

status: Public on Oct 10 2020

city: Toronto

first: Jean

last: Wang

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network


title: Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics

status: Public on Oct 11 2020

city: Rockville

first: David

last: Morse

state: Maryland

address: 9800 Medical Center Drive

department: National Center for Advancing Translational Sciences

institute: National Institutes of Health

summary: Single-cell RNA-sequencing (scRNA-seq) is a powerful technique for describing cell states. Unfortunately, identifying the spatial arrangement of these states in tissues remains challenging. Here, we describe SEgmentation by Exogenous Perfusion (SEEP), a rapid and integrated method to link positional location to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of 3D disease models. Classification of sample layers based on dye accessibility permits dissociated and sorted cells to be retrospectively characterized by transcriptomic and regional identity. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs regarding the relationship between cell state and position while also revealing new concepts on how the spatially unique microenvironment of individual cells within tumors influences cell identity.

overall_design: Spatially segmented single-cell RNA sequencing was performed using the SEEP method and the inDrop protocol as detailed in the manuscript related to this work


title: Withdrawal from chronic alcohol exposure leads to tissue-specific recovery of the zebrafish transcriptome

status: Public on Oct 09 2020

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

institute: CSIR Centre for Cellular and Molecular biology

summary: Alcohol consumption can lead to a wide-range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue-specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre-exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even after withdrawal. We also examined gender-specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall, our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue-specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal.

overall_design: Methods: Brain and liver tissue from six groups of zebrafish (Danio rerio, shortfin,’AB’ strain) of both sexes i.e, Male control, Female control, Male alcohol-exposed, Female alcohol exposed, Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control, three replicates of female control, two replicates of Male alcohol-exposed, two replicates of Female alcohol exposed, three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC, mapped to reference genome (danRer10) using STAR, abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.

first: Arif

last: Mohammed

first: Gopal

last: Kushawah

first: Sofia

last: Banu

first: Surabhi

last: Srivastava

first: Divya

middle: T

first: Rakesh

middle: K

last: Mishra


title: A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer

city: Fontenay aux Roses

first: Germain

last: Rousselet

address: 18 route du Panorama

department: Cellular and Molecular Radiobiology (IRCM)

institute: CEA

summary: Interferon beta is a central cytokine in the antiviral response and the immunogenicity of cancer therapies. In monocytes, its expression is modulated by a 60 kb downstream eQTL. We found that this eQTL disrupts binding of the C/EBP-β transcription factor to an enhancer interacting with the IFNB1 promoter. This enhancer, that we have called FIRE for Far IFNB1 Regulatory Enhancer, is conserved in murine myeloid cells, where its looping to Ifnb1 is increased in a genetic model of Ifnb1 deregulation. Precisely, we show that in murine myeloid cells, the TRIM33 chromatin reader partially co-localizes with CTCF and cohesin on the chromatin, and knocking out Trim33 reinforces a loop between Ifnb1 and FIRE.

overall_design: In order to identify CTCF and cohesin peaks in murine myeloid cells, we performed ChIP-seq targeting CTCF and RAD21 in the RAW264,7 cell line. Input were used as controls.


title: BS-Seq for oschz1 mutant

first: Liufan

last: Yin

overall_design: 2 geneotype with 2 replicates

first: Kangxi

last: Du

first: Aiwu

last: Dong

first: Wen-Hui

last: Shen


title: ChIP-Seq of H2A.Z and H3

overall_design: examination of 2 different histone modifications in 2 samples with 2 replicates. Samples without antibody were used as input control.


title: Landscape of N6-methyladenosine modification patterns in human ameloblastoma

status: Public on Oct 08 2020

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

type: Non-coding RNA profiling by high throughput sequencing

summary: N6-methyladenosine (m6A)  is one of the most popular RNA modifications, which is widely found in messenger RNAs (mRNAs) and non-coding RNA like  long no-coding RNA (lncRNAs) and circular RNA (circRNAs).In our study,we provide m6A landscape of human ameloblastoma, which expands the understanding of m6A modifications and uncovers regulation of lncRNAs and circRNAs through m6A modification in ameloblastoma.

overall_design: We employed MeRIP-seq analyses in three pairs of ameloblastoma tumor tissue specimens and corresponding normal oral specimens to explore m6A modification patterns and uncovered m6A modified lncRNAs and circRNAs in ameloblastoma

first: Ming

last: Zhong

first: Xing

last: Niu

first: Lijie

last: Chen

first: Jingping

last: Xu

first: Jinwen

last: Liu

first: Xue

last: Qiao


title: Gene expression profiling from glutamine-depleted and -replete H460 cells.

city: Daegu

first: Keun-Gyu

last: Park

address: Chilgokjungang-daero 136-gil

institute: Kyungpook national university

summary: We performed RNA-seq to compare immune modulators in glutamine-deprived versus glutamine-replete cancer cells.

overall_design: RNA-seq was performed on glutamine-depleted and -replete H460 cells in triplicate, using LEXOGEN QuantSeq 3' mRNA-Seq Library Prep Kit (Cat#015.96).


title: Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin. [Expression profile of human PDAC primary cells]

first: Elisa

last: Espinet

country: Germany

overall_design: Seven different human primary PDAC cells lines were lysed, RNA  was extracted and gene xpression analyses were performed

first: Andreas

last: Trumpp


title: MNase-Seq for nucleosome occupancy

overall_design: 2 genotypes with 2 replicates


title: CD200 expression marks leukemia stem cell (LSC) in human AML part 1

first: Jean

last: Wang

summary: The leukemia stem cell (LSC) populations of acute myeloid leukemia (AML) exhibit phenotypic, genetic and functional heterogeneity that contribute to therapy failure and relapse. Progress towards understanding the mechanistic basis for therapy resistance in LSCs has been hampered by difficulties in isolating cell fractions that enrich for the entire heterogeneous population of LSCs within individual AML samples. We previously reported that CD200 gene expression is upregulated in LSC-containing AML fractions. We demonstrate that CD200 is present on a greater proportion of CD45dim blasts compared to more differentiated CD45high cells in AML patient samples. In 75% of AML cases examined, CD200 was expressed on 10% of CD45dim blasts; of these, CD200 identified LSCs within the blast population in 90% of samples tested in xenotransplantation assays. Notably, CD200 expression captured both CD34- and CD34- LSCs within individual AML samples. Highly purified CD45dimCD200+ LSC-containing blasts were enriched in primitive HSC/progenitor-like signatures, while CD45dimCD200- nonengrafting blasts were enriched in myeloid-like signature. Moreover, analysis of CD45dimCD200+ blasts from NPM1-mutated AMLs also demonstrated an enrichment of primitive gene expression signatures compared to unfractionated (bulk) cells.

overall_design: CD45dim blasts were sorted into CD200+ and CD200- fractions from AML samples functionally validated to contain CD200+ LSCs (Metadata1) before RNA extraction and sequencing. RNA from unfractionated (bulk) cells was extracted and subjected to gene expression analysis using Illumina HumanHT-12 v4 microarrays (Ng et al. Nature. 2016;540:433-437) (Metadata2) or sequencing (Metadata3).

first: Jenny

last: Ho

first: Jessica

last: Macleod


title: Biomarker Discovery in Attention Deficit Hyperactivity Disorder: RNA sequencing of Whole Blood in Discordant Twin and Case-Controlled Cohorts

status: Public on Oct 07 2020

city: Protland

first: Joel

middle: T.

last: Nigg

state: Oregon

address: 3181 S.W. Sam Jackson Park Road

department: Department of Psychiatry

institute: Oregon Health & Science University

type: Expression profiling by genome tiling array

summary: We found RNA markers common to both the discordant twin study and case-controlled subjects further narrowed the putative targets, some of which had been previously associated with ADHD at the DNA level. The potential role of several differentially expressed genes, including ABCB5, RGS2, GAK, GIT1 and 3 members of the galactose metabolism pathway (GALE, GALT, GALK1) are substantiated by prior associations to ADHD and by established mechanistic connections to molecular pathways relevant to ADHD and behavioral control.

overall_design:
Single molecule RNA sequencing via HeliScope sequencer to identify expressed changes in whole blood RNA in ADHD.
*** RNA-Seq raw data to be made available through dbGaP (controlled access) due to patient privacy concerns.

first: Tim

last: McCaffrey

first: Georges

first: Daniel

last: Jones

first: Dmitry

last: Shtokalo

first: Denis

last: Antonets

first: Yuri

last: Vyatkin

first: Eleanor

last: Battison


title: CD200 expression marks leukemia stem cells (LSC) in human AML part 2

first: Amanda

last: Mitchell


title: Cell signaling coordinates global Polycomb Repressive Complex 2 recruitment and developmental gene expression in murine embryonic stem cells (ChIP-Seq)

first: Jin

last: He

summary: In this study, we provide evidence to show that the expression of PRC2-recruting factor Jarid2 is largely reduced in both naïve mESC and Erk1/Erk2 double knockout (Erk1/2-dKO) mESCs, which can be rescued by reactivation of FGF/MARK signaling in naïve mESCs or ectopic Erk1 expression in Erk1/2-dKO mESCs, suggesting the FGF/ERK signaling positively regulates the Jarid2 expression in mESCs. Consistent with the Jarid2 function in the PRC2 recruitment, the global Ezh2 occupancy and histone H3K27me3 are largely reduced at CpG islands (CGIs) and bivalent promoters in both naïve mESCs and Erk1/Erk2-dKO mESCs, which can be fully restored by ectopic expression of Jarid2 expression, suggesting the reduced Jarid2-mediated PRC2 recruitment is a main molecular mechanism leading to the global reduction of PRC2 occupancy at CpG islands and bivalent promoters in naïve mESCs.  At the transcriptional level, although both PRC2 occupancy and histone H3K27me3 modification are reduced at bivalent promoters, there exist two groups of genes with distinct expression status. the FGF/ERK signaling target genes are silenced while the Wnt signaling target genes are largely de-repressed, which is caused by the chemical activation of  Wnt/beta-catenin signaling in naïve mESCs. Further ChIP-seq analyses demonstrate an increased occupancy of β-catenin at its activated gene promoters in naïve mESCs.  These results suggest the transcriptional activation of bivalent genes in naïve mESCs is predominantly determined by the presence of transcriptional factors but not the status of PRC2 occupancy at gene promoters.

overall_design: Examine the Polycomb occupancy and gene expression in wild-type mESCs in different culture conditions and Erk1/Erk2 double knockout mESCs.


title: Cell signaling coordinates global Polycomb Repressive Complex 2 recruitment and developmental gene expression in murine embryonic stem cells (RNA-Seq)


title: Total RNA sequencing in the hippocampus of wild type and APP/PS1 mice

status: Public on Oct 05 2020

city: shanghai

first: song

last: chenghuan

address: south chongqing road

institute: shanghai jiaotong university

summary: Our study aimed to dissect differentially expressed circRNAs in the hippocampus of wild type and APP/PS1 mice and demonstrated the important role of circRNA in Alzheimer's disease.

overall_design: We used deep RNA sequencing (RNA-seq) to examine the circRNA and mRNA in the hippocampus of APP/PS1 mice (which express APP695swe and PS1-dE9 mutations) and wild-type control mice at the 6-month-old stage.

first: Song

last: Chenghuan

first: Huang

last: Wanying


title: Widespread traces of lytic KSHV in primary effusion lymphoma at single-cell resolution

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

summary: Cancer cells of primary effusion lymphoma (PEL) often contain both Kaposi sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). We measured the interplay of human, KSHV, and EBV transcription in a cell culture model of PEL using single-cell RNA sequencing. The data detect widespread trace expression of lytic KSHV genes.

sample_organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8

overall_design: Single-cell RNA-seq transcriptomes of BC-1 primary effusion lymphoma cells

first: Nicole

last: Rondeau

first: Michael

middle: O

last: Finlayson

first: J


title: Smoking induced gene expression changes in adult peripheral blood

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Smoking associated gene expression changes from immune cell type fractions

overall_design: Magnetic bead antibody-purified human immune cell fractions isolated from peripheral blood from smoking and nonsmoking adults were extracted and hybridized on Affymetrix microarrays.

first: Suzanne

middle: N

last: Martos

first: Michelle

last: Campbell


title: Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [scATAC-Seq]

status: Public on Oct 02 2020

city: Durham

first: Anna Mae

last: Diehl

address: Research Drive

institute: Duke University

summary: Adult liver has enormous regenerative capacity as it can regenerate after losing two-thirds of its mass while sustaining essential metabolic functions. How the liver balances dual demands for increased proliferative activity with maintenance of organ function is unknown, but essential to prevent liver failure. Using partial hepatectomy (PHx) in mice to model liver regeneration, we integrated single-cell RNA and ATAC sequencing to map state transitions in ~ 13,000 hepatocytes at single-cell resolution as livers regenerated, and validated key findings with immunohistochemistry, to uncover how the organ regenerates hepatocytes while simultaneously fulfilling its vital tissue-specific functions. After PHx, hepatocytes rapidly and transiently diversified into multiple distinct populations with distinct functional bifurcation: some retained the chromatin landscapes and transcriptomes of hepatocytes in undamaged adult livers while others transitioned to acquire chromatin landscapes and transcriptomes of fetal hepatocytes.  Injury-related signaling pathways known to be critical for regeneration were activated in transitioning hepatocytes and the most fetal-like hepatocytes exhibited chromatin landscapes that were enriched with transcription factors regulated by those pathways.

overall_design: Profiling of chromatin accessibility of liver hepatocytes by high throughput sequencing

first: Anna

middle: M

first: Tianyi

last: Chen


title: Runx1 marks a luminal castration resistant lineage established at the onset of prostate development

city: Macclesfield

first: Renaud

last: Mevel

address: Cancer Research UK, Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge

country: United Kingdom

summary: We performed scRNA-seq to characterize the heterogeneity of RUNX1+ and RUNX1- fractions of the adult mouse prostate. We dissected individual lobes of intact/hormone naive and regressed/castrated mouse prostates, isolated from P2-Runx1:RFP reporter mice, expressing RFP as a surrogate of Runx1 expression. In order to compensate for the relative sparsity of RFP+ and RFP- cells respectively pre- and post-castration, we artificially enriched for under-represented populations by FACS (EPCAM+) prior cell encapsulation. To study the specification of embryonic prostate lineages, we performed scRNA-seq on the EPCAM+ fraction of UGS explant cultures collected at successive time points: E15.5 (D0), day 1 (D1), day 3 (D3), and day 6 (D6).

overall_design: For adult mouse prostate samples, intact and castrated lobes were dissected from P2-Runx1:RFP mouse models. Individually sorted populations (ECPAM+ RFP+ / RFP-) from each lobe were multiplexed using MULTI-seq lipid-tagged indices. 3 independent experiments (run 1, run 2, run 3) were performed. For UGS explant cultures, samples were collected at successive time points of cultures: E15.5 (D0), day 1 (D1), day 3 (D3), and day 6 (D6). Sorted populations (EPCAM+) were multiplexed using MULTI-seq lipid-tagged indices.

first: Georges

last: Lacaud


title: Whole genome RNA-sequencing from roots of Arabidopsis thaliana wild-type and stop1 exposed to low pH, low phosphate (Pi), Aluminum and Iron excess conditions.

city: Irapuato

first: Luis

middle: Rafael

last: Herrera-Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Langebio

country: Mexico

institute: Cinvestav - Langebio

summary: Total mRNA was extracted from the root tips (10 mm from the root apex) of wild-type plants (Col-0 accession) and stop1 mutants grown 5 days after germination under optimum conditions and then transferred for 16 hours to low phosphate(Pi), low pH, Al and Fe excess mediums.

overall_design: Analysis of 6 different treatments (+Pi_pH6, -Pi_pH6, +Pi_pH5, -Pi_pH5, +Al, Fe excess), 2 different genotypes (wild-type, stop1),  2 biological replicates per treatment

last: l Herrera-Estrella

first: Jonathan

last: Ojeda-Rivera


title: Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

summary:
Purpose: Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), has long been associated with the development of lung adenocarcinoma (LUAD) and sarcoidosis. These chronic lung diseases share histopathological similarities that challenge differential diagnosis.
Methods: Human lung tissues were used for total RNA extraction with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed using a Nanodrop ND-2000 (Thermo Scientific), and each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies), and each sample had the RNA Integrity Number (RIN) above 7.0. The ribosomal RNAs (rRNAs) were removed using Ribo-Zero rRNA Removal Kits (Illumina). RNA libraries were then constructed by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and evaluated using the Agilent 2200 TapeStation and Qubit® 2.0 (Life Technologies). Sequencing was performed by RiboBio Co., Ltd. on an Illumina HiSeq 3000 machine with paired-end 150-bp reads.   The adaptors and low quality bases assessed using FASTQC 0.11.3 were trimmed by Trimmomatic 0.39 using the following options: TRAILING:20, MINLEN:235 and CROP:235. Trimmed reads were then aligned to the ensembl 79 (GRCh38.p2) reference genome using STAR 2.4.2a. FeatureCounts 1.6.2 was subsequently employed to convert aligned short reads into read counts for each sample. Genes with less than ten counts in two or more samples were removed. The data were then analyzed using R 3.4.4 and DEseq2 1.18.1. Differentially expressed genes of each disease group were identified using Wald statistics test, with fold-change > 2 and Benjamini–Hochberg (BH)-adjusted P < 0.1 as compared to NC group.
Results: These findings provide novel pathogenic links and molecular markers for better understanding and differential diagnosis of pulmonary TB, LUAD and sarcoidosis.

overall_design: Lung Tissue mRNA profiles of NM, TB, LUAD and sarcoidosis diseases were generated by RNAseq, in five replicates, using Illumina Hiseq 3000.

first: Qiyao

last: Chai

first: Zhe

last: Lu

first: Zhidong

last: Liu

first: Yanzhao

last: Zhong

first: Fuzhen

last: Zhang

first: Changgen

last: Qiu

first: Bingxi

last: Li

first: Jing

last: Wang

first: Lingqiang

first: Yu

last: Pang

first: Cui Hua


title: Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [scRNA-Seq]

first: Anna Mae

last: Diehl

country: USA

overall_design: Profiling of transcriptomes of liver hepatocytes by high throughput sequencing

first: Anna

first: Tianyi


title: Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [RNA-Seq]

last: Chen


title: Anti-cancer activity of Cotyledon orbiculata extract

status: Public on Oct 06 2020

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

summary: We investigated the effects of the crude extract of a South African medicinal plant, Cotyledon orbiculata, on cell survival of colon (HCT116) cancer cell lines. Using RNASeq, we discovered that the extract interfered with mRNA regulatory pathways. Here, we found that the extract of Cotyledon orbiculata, a South African medicinal plant, had an anti-proliferative effect in cancer cells, mediated by apoptosis induced by alternative splicing of hnRNPA2B1 and BCL2L1.

overall_design: RNA sequencing was used to determine the effect of crude extract from the Cotyledone orbiculata on differential gene expression and splicing in human colon cancer cells, relative untreated control cells.

first: David

last: Bates

first: Tshepiso

last: Makhafola

first: Zodwa

last: Dlamini

first: Mzwandile

last: Mbele

first: Kiren

last: Yacqub-Usman

first: Amy

last: Hendren

first: Daisy

last: Haigh

first: Zoe

last: Blackley

first: Mervin

last: Meyer