title: Amino acid stress response genes promote L-asparaginase resistance in pediatric acute lymphoblastic leukemia [ATAC-seq]

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Understanding the genomic and epigenetic mechanisms of drug resistance in pediatric acute lymphoblastic leukemia (ALL) is critical for further improving treatment. The role of transcriptomic response in conferring resistance to l-asparaginase (LASP) is poorly understood, beyond asparagine synthetase (ASNS). We defined reproducible LASP response genes in LASP resistant and sensitive ALL cells lines as well as primary leukemia samples from newly diagnosed patients. Defining ATF4 target genes in ALL cell lines using ChIP-seq revealed 25% of genes that changed expression after LASP treatment were direct targets of the ATF4 transcription factor.  SLC7A11 was found to be a response gene in cell lines and patient samples as well as a direct target of ATF4. SLC7A11 was also one of only 2.4% of response genes with basal level gene expression that also correlated with LASP ex vivo resistance in primary leukemia cells. Experiments using chemical inhibition of SLC7A11 with sulfasalazine, gene overexpression, and partial gene knockout recapitulated LASP resistance or sensitivity in ALL cell lines. These findings show the importance of assessing changes in gene expression following treatment with antileukemic agent for their association with drug resistance and highlight that many response genes may not differ in their basal expression in drug resistant leukemia cells.

overall_design: ATAC-seq performed in ALL cell lines. Cells grown in standard culture conditions were treated with or without L-asparaginase (1IU/ml) for 4 hrs and subjected to an ATAC-seq protocol. Four independent experiments were conducted for each cell line.


title: Comparison of Methylation Episignatures in KMT2B and KMT2D-related human disorders

status: Public on Apr 17 2022

city: Cambridge

first: Sunwoo

last: Lee

address: Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus

department: Medical Genetics

country: United Kingdom

institute: University of Cambridge

type: Methylation profiling by high throughput sequencing

summary: We compared the DNA methylation patterns in blood from individuals with two rare neurodevelopmental disorders (Childhood-onset dystonia (DYT-KMT2B) and Kabuki syndrome) and healthy control samples

overall_design:
Aim&Methods: To investigate peripheral blood methylation episignatures in KMT2B-related dystonia (DYT-KMT2B), we undertook genome-wide methylation profiling of ~2M CpGs using a next-generation sequencing based assay and compared the findings to those in controls and patients with Kabuki syndrome Type 1 (KS1-KMT2D).
Results: 1,812 significantly differentially methylated CpG positions (DMPs) (FDR < 0.05) were detected in DYT-KMT2B samples compared to controls. Multi-dimensional scaling analysis showed that the 10 DYT-KMT2B samples clustered together and separately from 29 controls and 10 with pathogenic variants in KMT2D. We found that most DMPs were specific to one disorder and that all (DYT-KMT2B) and most (KS1) methylation alterations in CpG islands were gain of methylation events
Processed data include 1) bismark CpG coverage file for all 20 samples and 29 healthy controls and 2) significant differentially methylated DMPs for each cohort group (DYT-KMT2B vs Control, KS1 vs Control, DYT-KMT2B and KS1 (without KMT2D_5) vs Control, and KS1 (without KMT2D_5 vs Control). Final betavalues, CpG site information and NGS-ID (generated by RnBeads package) per sample are provided in each file. In detail, we found 1,812 significantly differentially methylated CpG positions in DYT-KMT2B cohort, 89 DMPs in KS1 cohort, 677 DMPs in DYT-KMT2B+KS1 (without KMT2D_5) cohort, and 136 DMPs in KS1 (without KMT2D_5) cohort.

first: Eguzkine

last: Ochoa

first: Eamonn

middle: R

last: Maher


title: Effects of PAMK on lncRNA, miRNA, and mRNA expression profiles of thymic epithelial cells

status: Public on Apr 15 2022

city: Guangzhou

first: Yugu

last: Li

address: Wushan street

country: China

institute: South China Agricultural University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore the effects of PAMK on MTEC1 cell proliferation, we first determined PAMK concentration that could promote MTEC1 cell proliferation, and then detected the effects of PAMK on the expression profiles of lncRNA, miRNA and mRNA of MTEC1 cells by RNA-seq.

overall_design: The PAMK concentration that promoted the proliferation of MTEC1 cells was determined according to CCK-8 and EdU tests, and then 3 samples of MTEC1 cells treated with PAMK for 12h and 3 samples of MTEC1 cells cultured for 6h were collected under this concentration for RNA-SEQ analysis.

first: Qingru

last: Wu

first: Bingxin

first: Ying

first: Fenfen

last: Liu

first: Lin

last: Yang


title: RNA-Seq identification of LGK974 early and late gene targets in AsPC-1

status: Public on Apr 19 2022

city: Los Angeles

first: David

last: Dawson

state: CA

address: 650 Charles E Young Dr, S

department: Pathology & Laboratory Medicine

country: USA

institute: UCLA

summary: RNA sequencing with differential gene expression analysis was performed on AsPC-1 pancreatic ductal adenocarcinoma (PDAC) cells at multiple time points with a Porcupine inhibitor (LGK974) to identify mechanisms underpinning transcriptional effects.

overall_design: Time course profiling of AsPC-1 PDAC cells treated with LGK974

first: Kristina

middle: Y

last: Aguilera

middle: W


title: T-cell immunogenicity, gene expression profile and safety of four heterologous prime-boost combinations of HIV vaccine candidates in healthy volunteers – results of the randomized multi-arm phase I/II ANRS VRI01 trial

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

summary:
Heterologous prime-boost strategies are of interest for HIV vaccine development. The order of prime-boost components could be important for the induction of T-cell responses.
In this phase I/II multi-arm trial, three vaccine candidates were used as prime or boost: MVA HIV-B (coding for Gag, Pol, Nef); HIV LIPO-5 (5 lipopeptides from Gag, Pol, Nef); DNA GTU-MultiHIV B (coding for Rev, Nef, Tat, Gag, Env gp160 clade B). Healthy volunteers (n=92) were randomized to four groups: 1) MVA at weeks (W) 0/8 + LIPO-5 at W20/28 (M/L); 2) LIPO-5 at W0/8 + MVA at W20/28 (L/M); 3) DNA at W0/4/12 + LIPO-5 at W20/28 (G/L); 4) DNA at W0/4/12 + MVA at W20/28 (G/M).
Frequency of IFNγ-ELISpot responders at W30 was 33%, 43%, 0% and 74%, respectively. Only MVA-receiving groups were further analyzed. Gene expression profiles of 79 subjects at different timepoints were analyzed by Illumina Whole-Genome Gene Expression BeadChips. Significant whole blood gene expression changes were observed two weeks after the first MVA injection, regardless of its use as prime or boost. An MVA gene signature was identified, including 86 genes mainly related to cell cycle pathways. Three prime-boost strategies led to CD4+ and CD8+ T cell responses and to a whole blood gene expression signature primarily due to their MVA HIV-B component.

overall_design: Randomized trial with four parallel arms, evaluating the following prime-boost combinations of HIV vaccine candidates: 1) MVA at weeks (W) 0/8 + LIPO-5 at W20/28 (M/L); 2) LIPO-5 at W0/8 + MVA at W20/28 (L/M); 3) DNA at W0/4/12 + LIPO-5 at W20/28 (G/L); 4) DNA at W0/4/12 + MVA at W20/28 (G/M).

first: L

last: Richert

first: M

last: Durand

first: C

last: Lefebvre

first: B

last: Hejblum

first: H

last: Hocini

first: P

last: Tisserand


title: Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication

status: Public on Apr 18 2022

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors underlying genome topology, such as CTCF and cohesin, leads to modest alterations in gene expression, while genomic rearrangements involving boundaries of topologically associating domains (TADs) disrupt normal gene expression and can lead to pathological phenotypes. Here we inverted an almost entire TAD (245kb out of 300kb) within the X-inactivation centre (Xic), leaving its boundaries intact, which led to a significant rearrangement of topological contacts within the TAD, mostly in accordance to the orientation of underlying CTCF binding sites, and to an increase in contact insulation with the neighbouring TAD. Expression of most genes within the TAD remained unaffected in mutant mouse embryonic stem cells and during differentiation. Interestingly, expression in the neighbouring TAD of the noncoding transcript Xist, which controls X-chromosome inactivation, was ectopically upregulated. The same inversion in mouse embryos led to slight biases in Xist expression but normal patterns of X-chromosome inactivation. Our study suggests that the wiring of regulatory interactions within a TAD can influence the expression of genes in neighbouring TADs, highlighting the existence of mechanisms for inter-TAD communication.

overall_design: Our dataset includes 2 5C-samples.

first: Rafael

last: Galupa

first: Christel

last: Picard

first: Yinxiu

last: Zhan

first: Fatima

last: ElMarjou

first: Colin

last: Johanneau

first: Maud

last: Borensztein

first: Katia

last: Ancelin

first: Luca

last: Giorgetti

first: Edith

last: Heard


title: Transcriptomic response in the heart and kidney to different types of antihypertensive drug administration [heart]

city: Shinjuku-ku

first: Fumihiko

last: Takeuchi

state: Tokyo

address: 1-21-1 Toyama

department: Research Institute

country: Japan

institute: National Center for Global Health and Medicine

summary: To unravel antihypertensive drug-induced gene expression changes that are potentially related to the amelioration of end-organ damages, we performed in vivo phenotypic evaluation and transcriptomic analysis on the heart and the kidney, with administration of antihypertensive drugs to two inbred strains of (i.e., hypertensive and normotensive) rats. We chose to use six antihypertensive classes: enalapril (angiotensin converting enzyme inhibitor), candesartan (angiotensin receptor blocker), hydrochlorothiazide (diuretics), amlodipine (calcium-channel blocker), carvedilol (vasodilating beta-blocker) and hydralazine. In the tested rat strains, four of six drugs, including two renin-angiotensin system (RAS) inhibitors, were effective for BP lowering, whereas the remaining two drugs were not. Besides BP lowering, there appeared to be some inter-drug heterogeneity in phenotypic changes, such as suppressed body weight (Bw) gain and Bw-adjusted heart weight reduction. For the transcriptomic response, a considerable number of genes showed prominent mRNA expression changes either in a BP-dependent or BP-independent manner with substantial diversity between the target organs. Noticeable changes of mRNA expression were induced particularly by RAS blockade, e.g., for genes in the natriuretic peptide system (Nppb and Corin) in the heart and for those in the RAS/ kallikrein-kinin system (Ren and rat Klk1 paralogs) and those related to calcium ion binding (Calb1 and Slc8a1) in the kidney. The heart data comprises of this submission and part of ArrayExpress E-MTAB-9244.

overall_design: 48 samples in total which consist of 4 biological replicates (or rats) per each of the 12 conditions. This dataset is also available in ArrayExpress (E-MTAB-10667).

first: Norihiro

last: Kato


title: Mucosal viral infection induces a regulatory T cell activation phenotype distinct from tissue residency in mouse and human tissues [bulk RNA-seq]

city: Seattle

first: Brianna

last: Traxinger

state: Washington

address: 1100 Eastlake Ave E

department: Vaccine and Infectious Disease Division

institute: Fred Hutch

summary: Vaginal tissue Tregs acquire a inflammatory cytokine-dependent, infection-specific phenotype after local infection with HSV-2

overall_design: CD4+ FoxP3+ Tregs were isolated from the draining lymph nodes and vaginal tissue of FoxP3GFP mice +/- HSV-2 infection. These cells were then processed for 3' bulk transcriptional profiling (Takara, Illumina)

first: Sarah

last: Vick

first: Amanda

last: Woodward-Davis

first: Valentin

last: Voillet

first: Jami

last: Erickson

first: Julie

last: Czartoski

first: Candice

last: Teague

first: Martin

last: Prlic

first: Jennifer

middle: M

last: Lund


title: Combining phenotypic profiling and targeted RNA-Seq reveals linkages between transcriptional perturbations and chemical effects on cell morphology: Retinoic acid as an example

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: The United States Environmental Protection Agency has proposed a tiered testing strategy for chemical hazard evaluation based on new approach methods (NAMs). The first tier includes in vitro profiling assays applicable to many (human) cell types, such as high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). The goals of this study were to: (1) harmonize the seeding density of U-2 OS human osteosarcoma cells for use in both assays; (2) compare HTTr- versus HTPP-derived potency estimates for 11 mechanistically diverse chemicals; (3) identify candidate reference chemicals for monitoring assay performance in future screens; and (4) characterize the transcriptional and phenotypic changes in detail for all-trans retinoic acid (ATRA) as a model compound known for its adverse effects on osteoblast differentiation. The results of this evaluation showed that (1) HTPP conducted at low (400 cells/well) and high (3000 cells/well) seeding densities yielded comparable potency estimates and similar phenotypic profiles for the tested chemicals; (2) HTPP and HTTr resulted in comparable potency estimates for changes in cellular morphology and gene expression, respectively; (3) three test chemicals (etoposide, ATRA, dexamethasone) produced concentration-dependent effects on cellular morphology and gene expression that were consistent with known modes-of-action, demonstrating their suitability for use as reference chemicals for monitoring assay performance; and (4) ATRA produced phenotypic changes that were highly similar to other retinoic acid receptor activators (AM580, arotinoid acid) and some retinoid X receptor activators (bexarotene, methoprene acid). This phenotype was observed concurrently with autoregulation of the RARB gene. Both effects were prevented by pre-treating U-2 OS cells with pharmacological antagonists of their respective receptors. Thus, the observed phenotype could be considered characteristic of retinoic acid pathway activation in U-2 OS cells. These findings lay the groundwork for combinatorial screening of chemicals using HTTr and HTPP to generate complementary information for the first tier of a NAM-based chemical hazard evaluation strategy.

overall_design: We evaluated the Templated Oligo with Sequencing Readout (TempO-Seq) assay for High-throughput transcriptomic screening of a small set of environmental chemicals. This assay yields sequencing reads of exactly 50 base pairs that can be rapidly aligned to generate gene counts, and is compatible with cell lysates prepared in multiwell format. The version of the TempO-Seq assay we evaluated provides nearly whole transcriptome coverage (>20,000 genes). This study encompasses 2 replicates of a 384-well plate design. The majority of wells contain U-2 OS cells exposed to 11 test chemicals at 7 different concentrations (two replicate per test chemical, concentration, and plate), and additional reference samples and controls. Controls include DMSO vehicle treatments (22 per plate). Reference samples include bulk lysate MCF7 samples (2 DMSO treated and 2 TSA treated samples per plate), reference chemical treatments (3 chemicals at single conc each, per plate), and vendor-provided reference RNA mixtures (UHRR and HBRR).

first: Johanna

last: Nyffeler

first: Clinton

last: Willis

first: Felix

last: Harris

first: Laura

last: Taylor

first: Richard

last: Judson

first: Joshua

middle: A

last: Harrill


title: Molecular landscape of immature neurons in the human hippocampus in Alzheimer's disease

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

overall_design: Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity and unique brain functions in rodents and they are dysregulated in many human neurological disorders. Little is known about molecular characteristics of adult human hippocampal imGCs and even their existence is under debate. Here we performed single nucleus RNA-sequencing (snRNA-seq) aided by a validated machine learning-based analytic approach to identify imGCs in both Alzheimer's disease and control and found a decreased number of imGCs with altered gene expression in AD.

first: Yi

last: Zhou

first: Hongjun

last: Song

first: Guo-li

last: Ming


title: Circulating extracellular vesicles exhibit a differential miRNA profile in gestational diabetes mellitus pregnancies

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: We have reported differntial abundance of miRNAs present in the secretory Extracellular vesicles during Gestetional Diabetes Mellitus or Ischemic placental disease

overall_design: miRNAs were extracted from secretory Extracellular Vesicles isolated from maternal blood samples collected at different trimesters of pregnency. miRNA libraries were prepared, sequenced and analysed to identify the differential abundance during various pregnancy complications.

first: Shanthie

last: Thamotharan

last: Allen

first: Carla

last: Janzen

first: Sherin

last: Devaskar


title: Single-cell RNAseq libraries derived from brainstem tissue containing the pre-Bötzinger complex

city: Solna

first: Wiktor

middle: Samuel

last: Phillips

address: Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

summary: We produced single-cell RNAseq libraries using STRT-seq-2i (Hochgerner et al Sci Rep 2017 Nov 27;7(1):1632) with methanol-fixed cells sampled from medullary tissue biopsies that captured the pre-Bötzinger complex inspiratory pattern generating circuit in mice.

overall_design: 2513 single-cell transcriptomic libraries isolated from a pooled sample of dissociated cells (n = 10 mice)

middle: S

first: Jan

middle: P

last: Reising

first: Naify

last: Ramadan

first: Eric

last: Herlenius


title: Amino acid stress response genes promote L-asparaginase resistance in pediatric acute lymphoblastic leukemia

first: Daniel

last: Savic

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Z-DNA is Remodeled by ZBTB43 in Prospermatogonia to Safeguard the Germ Line Genome and Epigenome

status: Public on Apr 14 2022

city: Grand Rapids

first: Piroska

middle: E

last: Szabó

state: MI

address: 333 Bostwick ave NE

department: Epigenetics

institute: Van Andel Institute

overall_design: ZBTB43 in vitro affinity-sequencing was done with purified MBP-ZBTB43 full length protein using fully unmethylated DNA and fully methylated DNA. ZBTB43 in vivo binding was detected by ChIP-seq using FACS-purified fetal mouse male germ cells at 15.5 dpc. DNA methylation was mapped in Zbtb43-/- and wild type spermatozoa from adult male mice using MIRA-seq.


title: Z-DNA is Remodeled by ZBTB43 in Prospermatogonia to Safeguard the Germ Line Genome and Epigenome (ChIP-seq)

summary: Mutagenic purine-pyrimidine repeats can adopt the left-handed Z-DNA conformation. DNA breaks at potential Z-DNA sites can lead to somatic mutations in cancer or to germ line mutations which are transmitted to the next generation. It is not known whether any mechanism exists in the germ line to control Z-DNA structure and DNA breaks at purine-pyrimidine repeats. Here, we provide genetic, epigenomic, and biochemical evidence for the existence of a biological process that erases Z-DNA specifically in germ cells of the mouse male fetus. We show that a previously uncharacterized zinc finger protein, ZBTB43, binds to and removes Z-DNA, preventing the formation of DNA double-strand breaks. By removing Z-DNA, ZBTB43 also promotes de novo DNA methylation at CG-containing purine-pyrimidine repeats in prospermatogonia. Therefore, the genomic and epigenomic integrity of the species is safeguarded by remodeling DNA structure in the mammalian germ line during a critical window of germline epigenome reprogramming.

overall_design: ZBTB43 in vivo binding was detected by ChIP-seq using 500,000 or 100,000 FACS-purified fetal mouse male germ cells at 15.5 dpc. IgG controls and input controls are provided.

first: Yingying

last: Meng

first: Guliang

last: Wang

first: Hongjuan

last: He

first: Kin

middle: H

last: Lau

first: Allison

last: Hurt

first: Brianna

last: Bixler

first: Andrea

last: Parham

first: Seung-Gi

last: Jin

first: Xingzhi

last: Xu

first: Karen

last: Vasquez

first: Gerd

last: Pfeifer

last: Szabo


title: Next Generation Sequencing Facilitates Quantitative Analysis of HCC827 and HCC827/GR cells Transcriptomes

city: Hangzhou

first: linying

last: Wu

address: qingchun road

institute: Zhejiang University

summary: HCC827 cells were obtained from American Type Culture Collection,  and the gefitinib resistant HCC827/GR cells were established by gradient dose treatment for parental cells more than 6 months.Our study established an acquired gefitinib-resistant cell line, which exhibited epithelial-mesenchymal transition (EMT) and stem cell-like properties ann transcriptional sequencing and bioinformatics analysis confirmed that.

overall_design: Examination of gefitinib-sensitive and gefitinib-resistant NSCLC cells.

first: Linying

first: Yuehong

first: Jianying

last: Zhou

first: Yuman

last: Yu

first: Liming

first: Xiaoling


title: coculture SAEC and HMVEC exposed to MWCNT

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

summary:
This study compared global multi-walled carbon nanotube (MWCNT)-induced miRNA expression from human lung epithelial and microvascular endothelial cells in monoculture and coculture with miRNA expression from mouse lungs exposed to MWCNT.
The concordant miRNA in human cell lines, mouse lung  tissues and blood will be potential biomarkers for occupational and medical surveillance.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Global miRNA expression profiles in monoculture and coculture HMVEC and SAEC cell lines are compared with the miRNA profiles in mouse lung tissues and blood samples exposed to MWCNT. The miRNAs with concordant MWCNT-induced reguation are identified.

middle: L


title: Z-DNA is Remodeled by ZBTB43 in Prospermatogonia to Safeguard the Germ Line Genome and Epigenome (Affinity-seq)

first: Piroska

last: Szabó

overall_design: ZBTB43 in vitro affinity-sequencing was done using purified MBP-ZBTB43 full length protein and fully unmethylated DNA isolated from Dnmt1/Dnmt3a/Dnmt3b triple knockout (TKO) ES cells (Tsumura, A. et al. Genes Cells 11, 805-814 2006) and also fully methylated lung DNA prepared with SssI bacterial CpG DNA methyltransferase, in duplicates. Background affinity was detected using MBP (vector). ZBTB43 affinity -seq was also caried out on DNA from Zbtb43-/- and wild type spermatozoa.

first: Yingying

first: Guliang

first: Hongjuan


title: Z-DNA is Remodeled by ZBTB43 in Prospermatogonia to Safeguard the Germ Line Genome and Epigenome (MIRA-seq)

overall_design: DNA methylation was mapped in Zbtb43-/- and wild type spermatozoa from adult male mice using MIRA-seq.

last: Meng

first: Kin

first: Allison

first: Brianna

first: Andrea


title: scRNAseq analysis of rat and human dorsal root ganglions

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

summary: Peripheral sensory neurons located in dorsal root ganglia relay sensory information from the peripheral tissue to the brain. Satellite glial cells (SGC) are unique glial cells that form an envelope completely surrounding each sensory neuron soma. This organization allows for close bi-directional communication between the neuron and it surrounding glial coat. Morphological and molecular changes in SGC have been observed in pathological conditions such as inflammation, chemotherapy-induced neuropathy, viral infection and nerve injuries. SGC play critical roles in neuronal excitability and nociception, as well as contribute to promote axon regeneration. Whether findings made in rodent model systems are relevant to human physiology has not been investigated. Here we present a detailed characterization of SGC across species. We characterized the transcriptional profile of SGC in mouse, rat and human at the single cell level.  Our findings suggest that key features of SGC in rodent models are conserved in human. These results support the notion that SGC in the sensory system are largely conserved between species. Our study provides the potential to leverage on rodent and human SGC properties and unravel novel mechanisms and potential targets for treating nerve injuries.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: We have applied the high-throughput single-cell mRNA sequencing technique, using the Chromium Single Cell Gene Expression Solution (10x Genomics) to rat L3, L4 DRG, 2 biological replicates for each sample and human DRG (L4,5) from 5 donors.

first: Valeria

last: Cavalli


title: RNA-Seq analysis of P14 CD8+T cells in B16-GP tumors

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

country: Germany

institute: German cancer research center (DKFZ)

summary: CD8+ T cells play an important role in fighting against tumors. However, CD8+ T cells often become functionally impaired or “exhausted” in the tumor microenvironment. T cell exhaustion is a major hurdle that currently limits the efficacy of immunotherapeutic regimens. The exhausted T cell population is heterogeneous and contains T cells subsets at varying states of differentiation and with a range of effector functions and proliferative potential. Identification of exhausted T cell-specific markers will help to understand the heterogeneity of this population. Therefore, we have performed RNA-sequencing analysis of mouse tumor-infiltrating CD8+ T cells and splenic CD8+ T cells.

overall_design: We implanted C57BL/6 mice with B16-GP33-41 melanoma cells. On day 11 after tumor cell implantation, TCR-transgenic P14 CD8+ T cells were adoptively transferred to the tumor-bearing mice. The GP33-41 epitope is recognized by the P14 T cells. The tumor-infiltrating P14 CD8+ T cells were FACS-sorted from tumor and spleen for RNA preparation using the Qiagen RNeasy Mini Kit. The DKFZ High Throughput Sequencing Unit prepared and sequenced the library (Illumina HiSeq 2000 v4 Single-Read 50 bp).

first: Nina

last: Weisshaar


title: Renal gene expression after acute kidney injury in the absence and presence of bone marrow CCR2

city: Bonn

first: Sibylle

last: von Vietinghoff

address: Venusbergcampus 1

institute: University Clinic Bonn

summary: We compared renal gene expression after ischemic reperfusion injury in mice reconstituted with bone marrow with or without myeloid CCR2 prior to injury.

overall_design: 8-week old male LDLr-/- mice were lethally irradiated, reconstituted with either wildtype or Ccr2-/- bone marrow and subjected to unilateral renal ischemia reperfusion (IR)  or control (ctrl.) surgery followed by a high fat diet for three weeks.

first: Anne

last: Hüsing


title: RNA-seq analysis of the effect of loss of Tp53, NF1 or CBS in telomerase-reverse transcriptase (TERT)-immortalized human BJ fibroblasts (BJ-TERT) overexpressing myristoylated AKT1

status: Public on Apr 13 2022

city: Melbourne

first: Jian

last: Kang

state: Victoria

address: 9 Princes street, Fitzroy

department: research division

country: Australia

institute: St Vincent's institute of medical research

summary: Overexpression myristoylated AKT1 in human BJ-TERT fibroblasts induces senescence (AIS). We depleted CBS, Tp53 or NF1 gene by shRNA in AIS cells and performed RNA-seq analysis to investigate the regulatory effect of these genes in AIS maintenance.

overall_design: BJ-TERT cells were transduced with pBabe-puro empty vector (EV) or pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with either pGIPZ-shRNA against CBS, Tp53 and NF1, or the control vector pGIPZ-NTC, pBabe-EV cells transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. There are five samples including pBabe-NTC, AKT1-NTC, AKT-shTP53, AKT-shNF1, AKT-shCBS with three replicates.

first: Haoran

last: Zhu

first: Keefe

middle: T

last: Chan

first: Richard

middle: B

last: Pearson


title: Activation of Xist by An Evolutionarily Conserved Function of the KDM5C Demethylase

city: Ann Arbor

first: Clair

last: Harris

address: 3710 Med Sci II 1241 Catherine St

department: Human Genetics

institute: University of Michigan


title: Transcriptomic response in the heart and kidney to different types of antihypertensive drug administration [kidney]

first: Fumihiko

last: Takeuchi

summary: To unravel antihypertensive drug-induced gene expression changes that are potentially related to the amelioration of end-organ damages, we performed in vivo phenotypic evaluation and transcriptomic analysis on the heart and the kidney, with administration of antihypertensive drugs to two inbred strains of (i.e., hypertensive and normotensive) rats. We chose to use six antihypertensive classes: enalapril (angiotensin converting enzyme inhibitor), candesartan (angiotensin receptor blocker), hydrochlorothiazide (diuretics), amlodipine (calcium-channel blocker), carvedilol (vasodilating beta-blocker) and hydralazine. In the tested rat strains, four of six drugs, including two renin-angiotensin system (RAS) inhibitors, were effective for BP lowering, whereas the remaining two drugs were not. Besides BP lowering, there appeared to be some inter-drug heterogeneity in phenotypic changes, such as suppressed body weight (Bw) gain and Bw-adjusted heart weight reduction. For the transcriptomic response, a considerable number of genes showed prominent mRNA expression changes either in a BP-dependent or BP-independent manner with substantial diversity between the target organs. Noticeable changes of mRNA expression were induced particularly by RAS blockade, e.g., for genes in the natriuretic peptide system (Nppb and Corin) in the heart and for those in the RAS/ kallikrein-kinin system (Ren and rat Klk1 paralogs) and those related to calcium ion binding (Calb1 and Slc8a1) in the kidney. This submission includes the kidney data.

overall_design: 40 samples in total which consist of 2 biological replicates (or rats) per each of the 20 conditions. This dataset is also available in ArrayExpress (E-MTAB-10672).

first: Norihiro

last: Kato


title: Infection with herpesviridae in pregnant dams alters midbrain dopaminergic signatures in adult offspring

first: Juozas

last: Gordevicius

state: Michigan

address: 333 Botswick Ave NE

summary: The adult offspring of MHV68 infected dams had a significantly decreased expression of genes linked to dopamine neurons (Th, lmx1b, and foxa1). Deconvolution analysis revealed that the proportion of dopamine neurons in the midbrain was reduced. Pathway analyses indicated mitochondrial dysfunction, with reductions in genes associated with ATP synthesis, mitochondrial respiratory chain, and mitochondrial translation in the offspring of dams infected with MHV68. TIGAR (a negative regulator of mitophagy) and SDHA (mitochondrial complex II subunit) protein levels were increased, and the levels of 3,4-dihydroxyphenylacetic acid (DOPAC) in the striatum were increased in these offspring. No such changes were observed in the offspring of dams infected with MCMV.

overall_design: Pregnant dams were injected with murine cytomegalovirus (MCMV), murine gamma herpes virus (MHV68) or phosphate buffered saline (PBS) at embryonic day 8.5. The young adult offspring were sacrificed at eight weeks of age, and their midbrains processed for unbiased whole genome RNA sequencing as well as targeted protein expression and high-performance liquid chromatography of dopamine and its metabolites.

last: Gordevičius

first: Amanda

last: Burmeister


summary: We performed Kdm5c (Smcx) ChIP-Seq in del_Tsix XY mouse epiblast cells with two genotypes: Smcx-WT and Smcx-KO

overall_design: We performed ChIP-Seq of Kdm5c (listed as Smcx below) as described in PMID: 26804915 in technical duplicates. Libraries were prepared according to Illumina's TruSeq protocol with minor modifications. To achieve optimal normalization, we spiked in Drosophila chromatin and immunoprecipitated with a H2Av antibody (Active Motif), as described in PMID: 25437568.  ChIP-Seq was performed on day 2 differentiated epiblast-like cells (EpiLCs).

first: Robert

last: Porter

first: Patricia

last: Garay

first: Shigeki

last: Iwase

first: Sundeep

last: Kalantry

first: Milan

last: Samanta

first: Srimonta

last: Gayen

first: Emily

last: Maclary

first: Yumie

last: Murata-Nakamura

first: Rebecca

last: Malcore

first: Christina

middle: N

last: Vallianatos

first: Paul

last: Samollow


title: Mitochondrial HSF1 triggers mitochondrial dysfunction and neurodegeneration in Huntington’s disease

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

summary: Aberrant localization of proteins to mitochondria disturbs mitochondrial function and contributes to the pathogenesis of Huntington’s disease (HD). However, the crucial factors and the molecular mechanisms remain elusive. Here, we found that heat shock transcription factor 1 (HSF1) accumulates in the mitochondria of HD cell cultures, a YAC128 mouse model, and human striatal organoids derived from HD induced pluripotent stem cells (iPSCs). Overexpression of mitochondria-targeting HSF1 (mtHSF1) in the striatum causes neurodegeneration and HD-like behavior. Mechanistically, mtHSF1 facilitates mitochondrial fission by activating dynamin-related protein 1 (Drp1) phosphorylation at S616. Moreover, mtHSF1 suppresses single-stranded DNA binding protein 1 (SSBP1) oligomer formation, which results in mitochondrial DNA (mtDNA) deletion. Suppression of HSF1 mitochondrial localization by DH1, a unique peptide inhibitor, abolishes HSF1-induced mitochondrial abnormalities and ameliorates deficits in an HD animal model and human striatal organoids. Altogether, our findings describe an unsuspected role of HSF1 in contributing to mitochondrial dysfunction, which may provide a promising therapeutic target for HD.

overall_design: single cell transcriptome profiles of Day 30 and Day 60 human brain organoids

first: Yuan

last: Hong

first: Shanshan

last: Wu

first: Xing

last: Guo


title: RIP-Chip of RIN from 0-3 hour Drosophila melanogaster embryos

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: RIN-associated mRNAs were identified in early Drosophila embryos by RNA co-immunoprecipitation of the endogenous protein using a synthetic antibody (anti-RIN D072), followed by microarray analysis (RIP-Chip).

overall_design: Six RNA co-immunoprecipitations were performed. This includes 3 biological replicates of anti-RIN (antibody D072) RNA co-immunoprecipitations from wild-type 0-3 hour embryos, and corresponding control antibody (antibody C1) RNA co-immunoprecipitations.

first: John

last: Laver

first: J

last: Westwood

first: Sachdev

last: Sidhu

first: Craig

last: Smibert


title: Amino acid stress response genes promote L-asparaginase resistance in pediatric acute lymphoblastic leukemia [RNA-seq]

city: Memphis

first: Daniel

last: Savic

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

summary: Understanding the genomic and epigenetic mechanisms of drug resistance in pediatric acute lymphoblastic leukemia (ALL) is critical for further improving treatment. The role of transcriptomic response in conferring resistance to l-asparaginase (LASP) is poorly understood, beyond asparagine synthetase (ASNS). We defined reproducible LASP response genes in LASP resistant and sensitive ALL cells lines as well as primary leukemia samples from newly diagnosed patients. Defining ATF4 target genes in ALL cell lines using ChIP-seq revealed 25% of genes that changed expression after LASP treatment were direct targets of the ATF4 transcription factor.  SLC7A11 was found to be a response gene in cell lines and patient samples as well as a direct target of ATF4. SLC7A11 was also one of only 2.4% of response genes with basal level gene expression that also correlated with LASP ex vivo resistance in primary leukemia cells. Experiments using chemical inhibition of SLC7A11 with sulfasalazine, gene overexpression, and partial gene knockout recapitulated LASP resistance or sensitivity in ALL cell lines. These findings show the importance of assessing changes in gene expression following treatment with antileukemic agent for their association with drug resistance and highlight that many response genes may not differ in their basal expression in drug resistant leukemia cells.

overall_design: RNA-seq performed in seven ALL cell lines. Cells grown in standard culture conditions were treated with L-asparaginase (1IU/ml) for 4 hrs and RNA was extracted. RNA from untreated control samples was also extracted. Three independent experiments were conducted for each cell line.


title: Transcriptomic response in the heart and kidney to different types of antihypertensive drug administration

city: Shinjuku-ku

first: Fumihiko

last: Takeuchi

address: 1-21-1 Toyama

institute: National Center for Global Health and Medicine

overall_design: Refer to individual Series


title: CD102- MHCII+ (F4/80lo) resident peritoneal macrophages exhibit limited sexual dimporphism in gene expression

city: Edinburgh

first: Stephen

last: Jenkins

address: 47, Little France Crescent

department: Centre For Inflammation Research

institute: University of Edinburgh

summary: CD102- MHCII+ (F4/80lo) peritoneal macrophages  were FACS-sorted from unmanipulated male and female C57BL/6 mice and compared by RNAseq.

overall_design: Population-level transcriptomic data are presented from single CD45+ SiglecF- CD19- CD3- Ly6G- CD11b+ CD102- CSF1R+ MHCII+ peritoneal macrophages from male and female C57BL/6 mice.

first: Calum

last: Bain

first: Nichlolas

last: Steers


title: Amino acid stress response genes promote L-asparaginase resistance in pediatric acute lymphoblastic leukemia [ChIP-seq]

overall_design: ATF4 ChIP-seq performed in Nalm6 cells with or without L-asparaginase treatment. Cells grown in standard culture conditions were treated with L-asparaginase (1IU/ml) for 2 hrs. Twenty million cells were cross-linked for each replicate and 5ug of ATF4 antibody were used for IP. Three independent experiments were conducted for each condition


title: Role of Idax and Rinf in ESC differentiation

city: New York

first: Meelad

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

summary: In this study we assessed transcriptomic changes that occur due to loss of Rinf or Idax or both during differentiation of ESCs to EBs by  subjecting EBs derived from Idax knockout, Rinf knockout or Idax/Rinf double knockout (DKO) ESCs by RNA-seq to identify differentially expressed genes.

overall_design: We studied the role of Idax and Rinf in regulating differentiation gene expression programs by performing RNA-seq of wildtype, Idax knockout, Rinf knockout and Idax/Rinf double knockout embryoid bodies (EBs). EBs were collected at day 6 and total RNA was extracted by (OMEGA E.Z.N.A. Total RNA kit). RNA was quantified by NanoDrop 2000 and 1 µg of RNA was sent to Novogene for mRNA-sequencing analysis (en.novogene.com). Sequencing libraries were prepared by Novogene using NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were subjected to 150-bp paired-end sequencing on Illumina Novoseq 6000 platform. Details for downstream analysis of mRNA-seq data are described in the manuscript methods section.

first: Julioi

last: Flores


title: Aortic gene expression after acute kidney injury

first: Sibylle

last: von Vietinghoff

summary: The risk of cardiovascular events rises after acute kidney injury. Leukocytes promote atherosclerotic plaque growth and instability. We here established a model of enhanced remote atherosclerosis after renal ischemia reperfusion injury and investigated the underlying inflammatory mechanisms.

overall_design: Male LDLr-/- mice were subjected to unilateral ischemia reperfusion (IR)  or control (ctrl.) surgery followed by a high fat diet for three or ten weeks.


title: TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation

city: Houston

first: Jianfang

last: Li

address: 2121 W. Holcombe Boulevard

institute: Texas A&M University

summary: Current knowledge about the role of epigenetic modifiers in pancreas development has been exponentially increased. However, the precise function of TET dioxygenases in pancreas specification remains poorly understood. Using a stepwise human embryonic stem cell (hESC) differentiation system, TET1/TET2/TET3 triple-knockout (TKO) cells displayed severe defects in pancreatic differentiation. Whole-genome analysis revealed TET depletion led to aberrant DNA methylation and chromatin remodeling. In comparison with methylome and hydroxymethylome datasets previously generated from hESCs, we identified unique pancreas-specific hyper-methylated and hypo-hydroxymethylated regions in TKO cells, where binding of pioneer transcription factor FOXA2 was remarkably enriched. Interestingly, transduction of full-length TET1 in TKO cells effectively rescued pancreatic differentiation and the expression of PAX4, a key determinant for -cell specification. Taking these findings together with genome-wide mapping of TET1 in pancreatic progenitors, we uncovered that TET1 co-occupied at a specific subset of FOXA2-bound loci featuring high levels of active chromatin. Locus-specific DNA methylation analysis revealed significant increases of 5-methylcytosine at the PAX4 enhancer in a TET1-dependent manner, consistent with defective generation of functional beta-cells from TET1-knockout hESCs. Thus, our study not only highlights the importance of TET-dependent epigenetic regulation in pancreas development but also unveils an essential role of TET1 in establishing beta-cell identity.

overall_design: We generated TET single-, double-, and triple-knockout hESCs and differentiated them towards the pancreatic endocrine fate. Two replicates were used for sequencing. We performed RNA-seq for WT and TET triple deficient lines (clone 2 and clone 6) of hESC, definitive endoderm (DE) and pancreatic progenitor (PP), as well as TET1 single-deficient line of PP. We performed WGBS (one replicate), CMS-IP, ATAC, H3K4me1, H3K27ac ChIP-seq data for WT and TET triple deficient lines. One replicate of WT TET1 ChIP-seq were also sequenced.

first: Xinwei

first: Jie

last: Ke

first: Minjung

last: Lee

first: Qingping

last: Lan

first: Jia

first: Yun

last: Huang

first: Deqiang

last: Sun

first: Ruiyu

last: Xie


title: Small RNA Sequencing of Different Blood Compartments

status: Public on Apr 12 2022

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: We studied microRNA levels in different blood compartments (erythrocytes, buffy coat, platelets (gel-filtrated or washed), PRP, PPP, and the supernatant of Convulxin-stimulated platelets). The aim of this study was to identify/confirm platelet-enriched miRNAs as biomarkers of platelet activation.

overall_design: Examination of microRNA levels in different blood compartments from four healthy donors.

first: Teresa

last: Krammer

first: Stephan

last: Zeibig

first: Waltraud

middle: C

last: Schrottmaier

first: Anita

last: Pirabe

first: Silvia

last: Goebel

first: Hans-Peter

last: Holthoff

first: Alice

last: Assinger

first: Matthias

last: Hackl


title: AOS10-FMT could rescure the adverse effects induced by high fat diet on the cecum

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of High fat diet on the cecum, and foud that the AOS10-FMT could rescure the side-effect of High fat diet in many factors

overall_design: Exploration of the FMT effects on the damaged cecum induced by High fat diet

first: Yanan

last: Hao


title: PanCancer Immune panel on heart allografts in an antibody mediated Chronic Vasculopathy mouse model

city: cleveland

first: Hidetoshi

last: Tsuda

state: ohio

address: 9500 euclid ave

institute: cleveland clinic

summary: We have developed a novel antibody-mediated CAV model using CCR5 CD8 double knock out mice.Transcroptome analysis using total RNA isolated from the allografts in this recipients  showed differential expression of transcripts in this model.

overall_design: To identify the transcriptome signature of CAV associated with high vs. low titers of de novo DSA, we performed Transcriptomic analysis of the microdisected arteries and the matched apical heart tissue using  a PanCancer immune-profiling gene panel for the NanoString platform.

first: Nina

last: Dvorina

first: Karen

last: Keslar

first: Jessica

last: Nevarez-Mejia

first: Nicole

last: Valenzuela

first: Elaine

middle: F

last: Reed

first: William

last: Baldwin

first: Robert

last: Fairchild


first: Clair

last: Harris

summary: X-inactivation, which equalizes X-linked gene expression between the mammalian sexes, occurs due to the higher expression in females of the X-linked Kdm5c gene.

overall_design: We performed RNA-Seq from mESC-derived EpiLCs. Libraries were depleted for rRNA and strand-specific according to the protocol described in PMID: 25607527.  Day 2 differentiated EpiLCs were collected from 3 replicates each of 4 genotypes: female wild-type (fWT), female Kdm5c knock-out (fKO), male wild-type (mWT), and male Kdm5c knock-out (mKO)

last: Porter

first: Christina

last: Vallianatos

first: Sundeep

last: Kalantry

first: Shigeki

last: Iwase

first: Milan

last: Samanta

first: Srimonta

last: Gayen

first: Emily

last: Maclary

first: Yumie

last: Murata-Nakamura

first: Rebecca

last: Malcore

first: Paul

last: Samollow


title: AOS10-FMT could rescure the adverse effects of high fat diet on the liver

first: Yong

last: Zhao

summary: We report the side-effects of High fat diet on the liver, and foud that the AOS could rescure the side-effect of High fat diet in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged liver induced by High fat diet

first: Yanan

last: Hao


title: Increased expression of RUNX3 inhibits normal human myeloid development

city: Cardiff

first: Alex

last: Tonks

address: Heath Park Way

department: Department of Haematology

institute: Cardiff University

summary: In this study, RUNX3 expression was analyzed in normal and malignant haematopoiesis and the impact of its dysregulation on myelopoiesis was further determined. We found that RUNX3 was highly expressed in haematopoietic progenitors, with its levels reducing towards granulocytic differentiation. In AML, RUNX3 was overexpressed across all different subtypes except in core binding factor AML where it was downregulated. RUNX3 overexpression in human haematopoietic stem and progenitor cells (HSPC) inhibited myeloid development, particularly granulopoiesis. Further RNA-sequencing studies showed that RUNX3 overexpression downregulates key hematopoietic genes, while upregulating certain lymphoid genes. Overall, this study suggests that increased RUNX3 expression could contribute to the myeloid block characteristic of AML by possibly driving a competing transcriptional program favoring the lymphoid fate.

overall_design: To model the effect of RUNX3 overexpression in AML, human CD34+ HSPC were transduced with either a GFP control or RUNX3 GFP recombinant retrovirus. Following infection, cells were sorted by FACS for GFP positivity and RNA was harvested for RNA sequencing. 5 biological replicates were analyzed in total (Control vs RUNX3).

first: Ana

last: Menezes


title: AOS10-FMT could rescure the adverse effects induced by high fat diet on the small intestinal

summary: We report the side-effects of High fat diet on the small intestinal, and foud that the AOS10-FMT could rescure the side-effect of High fat diet in many factors

overall_design: Exploration of the FMT effects on the damaged small intestinal induced by High fat diet


title: Single cell RNAseq of Th17 and Th22 cells with Gpr65_WT versus KO

city: Cambridge

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

summary: scRNAseq of in vitro polarized Th17 and Th22 cells (Gpr65_WT versus KO), to compare metabolism gene expression in Gpr65_WT versus KO.

overall_design: scRNAseq of in vitro polarized Th17 and Th22 cells (Gpr65_WT versus KO, for Th17, 2WT_vs_2KO, for Th22, 2WT_vs_2KO), to compare differential gene expression in WT versus KO.

first: Xiangjun

last: Chen

first: Daniel

last: Graham

first: Ramnik

last: Xavier


title: Dual-transcritome analysis of germinating Arabidopsis seeds in response to  necrotrophic fungus Alternaria brassicicola

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

summary: We analyzed dual-transcriptome changes in germinating Arabidopsis seeds at three development stages (3, 6 and 10 days after sowing) with or without Alternaria brassicicola. Differentailly expressed genes were identified from both seed and fungus.

overall_design: Three replicates of at least 360 mg of seeds at three developemental stages using the model pathosystem Arabidopsis thaliana/Alternaria brassicicola

first: Philippe

last: Grappin


title: RNA-Seq of U251 glioblastoma cell line with and without (-)-SDS-1-021.

status: Public on Apr 11 2022

city: Bethesda

first: Uma

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary: RNA-Seq analyses polysome-bound mRNAs of glioblastoma cell line NSC11 after 10nM (-)-SDS-1-021 treatement to evaluate drug-induced changes in mRNA translation

overall_design: Vehicle Control (3), 10nM (-)-SDS-1-021 (3)

first: Stacey

last: Lehman

first: Theresa

last: Wechsler

first: Kayla

last: Schwartz

first: Lauren

last: Brown

first: John

last: Porco

first: Willian

middle: G

last: Devine

first: Jerry

last: Pelletier

first: Kevin

last: Camphausen

first: Philip

last: Tofilon


title: Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

city: Chengdu

first: Mengnan

last: He

address: Huimin road 211#

institute: Sichuan Agriculture University

summary: Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

sample_organism:
Danio rerio
Gallus gallus
Macaca mulatta
Homo sapiens
Canis lupus familiaris
Felis catus
Sus scrofa
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

overall_design: To comprehensively explore the evolutionary principles governing 3D genome architecture and to assess the contributions of genome architecture to transcriptional regulation across species, we performed comparative analyses of high-throughput chromosome conformation capture (Hi-C) in fibroblast cells of 12 vertebrates, including two representative mammalian lineages: euarchontoglires including humans, rhesus macaques, mice, rats, and rabbits; boreoeutheria including dogs, cats, pigs, sheep, and cows; as well as two non-mammals including birds (chickens) and fish (zebrafish). We performed the Hi-C experiments in 25 fibroblasts from 11 vertebrates with 1 to 5 biological replicates (distinct cell lines or primary cells derived from different individuals) for each species, produced a total of ~ 5.75-billion uniquely aligned contacts with an average depth of ~230 million (M) contacts per library (range from ~102 M for zebrafish with a relatively small genome size of ~ 1.23 Gb to ~442 M for mouse with a genome size of ~2.73 Gb). We also combined the resulting datasets with those previously generated by us for four pig fibroblasts (pig_DB-2, pig_DB-3, pig_RC-7, and pig_RC-8) (X Tian et al.,2020) and two mouse fibroblasts (mouse_3T6 and mouse_MEF) (M He et al.,2018) using the same experimental protocol. Among these, ~ 63.03% are intra-chromosomal contacts, of which ~74.40% were occurred within 10 Mb. After KR-normalization and quantile-normalization, we generated 31 intra-chromosomal contact maps at 20-kb resolution for each of 31 libraries. With the bin size at 20-kb, there are about 83.12% of bins have at least 1,000 intra-chromosomal contacts. TAD and compartment A/B were also identified by using the 20-kb matrix.

first: Diyan

last: Li

first: Qianzi

last: Tang

first: Shilin

last: Tian


title: Comparative 3D Genome Architecture in Vertebrates (Hi-C)

sample_organism:
Danio rerio
Gallus gallus
Macaca mulatta
Homo sapiens
Canis lupus familiaris
Felis catus
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus


city: Zhengzhou

first: Ding

state: Henan

address: Dongming Road 127

institute: The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital

summary: Since NF-κB plays important roles in DNA repair, we knocked down RELA in KG1α cells and then analyzed whether lncRNAs play a role in DNA repair mediated by NF-κB.

overall_design: KG1α shCtrl and KG1α shRELA cell lines were constructed to evaluate the impact of RELA knockdown on gene expression  in KG1α leukemia cells upon DNA damage

first: Lixian

last: Wu


title: Serum miRNA profile in diabetic patients with ischemic heart disease (IHD) as a promising non-invasive biomarker.

city: Bialystok

first: Agnieszka

last: Bielska

address: Marii Sklodowskiej-Curie 24a

country: Poland

institute: Medical University of Bialytsok

summary:
The aim of this study was to conduct a baseline comparison of serum-circulating miRNA in diabetic patients with and without ischemic heart disease.
We analysed the expression levels of 798 serum miRNAs using the NanoString nCounter Technology Platform. The prediction of the putative miRNAs targets was performed by the Ingenuity Pathway Analysis (IPA) software. Receiver operating characteristic (ROC) analysis was used to assess the diagnostic value of identified miRNAs. Our data showed that 6 miRNAs are significantly upregulated in type 2 diabetes mellitus (T2DM) patients with IHD compared to T2DM patients without IHD. Functional enrichment analysis of target genes by IPA showed networks and canonical pathways involved in the pathology of the cardiovascular system. All tested miRNAs showed high diagnostic value (AUC > 0.75).

overall_design: 44 serum samples of T2DM were collected. 24 of patients developed IHD. The control group (HC) consisted of 16 patients without T2DM and IHD.

first: Adam

last: Krętowski


title: Comparative 3D Genome Architecture in Vertebrates

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

platform_organism:
Danio rerio
Gallus gallus
Macaca mulatta
Homo sapiens
Canis lupus familiaris
Felis catus
Sus scrofa
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Expression profile of BAT and gWAT from adipose tissue-specific Pgam1 deficient mice

city: Niigata

first: Yohko

last: Yoshida

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata University

summary: To analyze the gene expression profile of BAT and gWAT from Pgam1 depletion mice, we performed whole genome microarray expression profiling using brown adipose tissue (BAT) and gonadal white adipose tissue (gWAT) from adipose tissue-specific Pgam1 knockout (KO) mice.

overall_design: Gene expression profile of mice BAT and gWAT were analyzed at 14-16 weeks of age.  Four independent samples were subjected to the microarray analysis.


title: Transcriptomics of Aedes aegypti derived Aag2 cells in response to chikungunya virus infection

city: New Delhi

first: Sujatha

last: Sunil

state: Delhi

address: Aruna Asaf Ali Road

department: Vector Borne Disease Group

country: India

institute: International Centre for genetic engineering and Biotechnology

summary: The study provides a comparative of transcript levels in uninfected and CHIKV-infected Aedes aegypti derived Aag2 cells using RNA Seq

overall_design: 2 samples (each contains 3 triplicates) = 6 samples

first: Divya

last: Mehta

first: Sakshi

last: Chaudhary


title: Single-cell RNA sequencing of the retina in a model of retinitis pigmentosa reveals early responses to degeneration in rods and cones

city: Basel

first: Duygu

last: Karademir Sigurdsson

address: Klybeckstrasse 200

country: Switzerland

institute: Institute of Molecular and Clinical Ophthalmology Basel

summary: In inherited retinal disorders such as retinitis pigmentosa (RP), rod photoreceptor-specific mutations cause primary rod degeneration that is followed by secondary cone death and loss of high-acuity vision. Mechanistic studies of retinal degeneration are challenging because of retinal heterogeneity. Moreover, the detection of early cone responses to rod death is especially difficult due to the paucity of cones in the retina. To resolve heterogeneity in the degenerating retina and investigate events in both types of photoreceptors during primary rod degeneration, we utilized droplet-based single-cell RNA sequencing in an RP mouse model, rd10.

overall_design: Droplet sequencing was used to profile and compare single-cell transcriptomes in retinas of postnatal day 21 rd10 mice, a mouse model of retinitis pigmentosa, and wild type controls.

first: Karademir

last: Duygu

first: Grimm

last: Christian


title: Rat model of breast cancer to dissect mechanisms of immune escape and immunotherapy sensitivity

status: Public on Apr 10 2022

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: NMU-induced sprague dawley rat model of breast cancer treated with immunotherapy to prevent tumor progression

overall_design: Bulk RNA-Seq: Gene expression of FACS sorted EpCAM+, SMA+ and double negative (DN) subpopulations from tumors from NMU-induced mammary tumors in rats that were treated with vehicle, anti-PD-L1 antibody, TGFBR1 inhibitor and combination treatment.

first: Gil

last: Del Alcazar

first: Carlos

last: Rodrigo

first: Trinh

last: Anne

first: Masa

last: Aleckovic

first: Nicholas

last: Harper

first: Shanshan

last: Xie

first: Ethan

last: Krop

first: Bethlehem

last: Lulseged

first: Katherine

last: Murphy

first: Gordon

last: Freeman

first: Deborah

last: Dillion

first: Senthil

last: Muthuswamy

first: Polyak

last: Kornelia

first: Ernesto

last: Rojas

first: Michael

last: Oliphant


title: Systematic identification of cell fate regulatory programs using a single-cell atlas of mouse development

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: We performed single-cell RNA sequencing (scRNA-seq) analysis to 10 mouse tissues belonging to seven age groups, ranging from early organ occurrence to mature adult stage (E10.5, E12.5, E14.5, neonatal, day 10, day 21 and adult), all together profiling in more than 500,000 cells. The profiled organs span diverse systems, including brain, heart, intestine, kidney, liver, lung, pancreas, stomach, testis and uterus.These data represent, to our knowledge, the first single-cell atlas of detailed mouse differentiation throughout development.

overall_design: Microwell datasets for ten mouse tissues (brain, heart, intestine, kidney, liver, lung, pancreas, stomach, testis and uterus) covering 5 stages  including E14.5, neonatal, 10d, 3w, 6-8w. Embryo datasets cover E10.5 and E12.5. Some mouse tissues are used from GSE108097.

first: Xiaoping

last: Han

first: Renying

last: Wang

first: Lijiang

last: Fei


title: Transcriptional profiling of human hepatic NK cell subpopulations

status: Public on Apr 09 2022

city: Maynooth

first: Mark

last: Robinson

state: Co. Kildare

address: Department of Biology, Maynooth University

department: Department of Biology

country: Ireland

institute: Maynooth University

summary: To identify potential functional roles of liver-resident NK cells we performed RNA sequencing on FACS sorted NK cell subpopulations from liver perfusates (n=5) and healthy blood controls (n=5). Full-length transcripts were sequenced from low-input samples using a modified version of the SMART-Seq2 protocol. Hepatic CD56brightCD16- and CD56brightCD16+ samples upregulate genes associated with tissue residency.

overall_design: mRNA profiles of FACS sorted NK cell subpopulations from liver perfusates (n=5) and healthy blood controls (n=5).


title: A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 660 S. Euclid Avenue Campus Box 8103

institute: Washington University in St. Louis

summary: The recent derivation of bona fide human trophoblast stem cells (hTSCs) significantly improved our ability to study human placental biology and pathologies, but few studies have investigated the molecular regulators of hTSC identity. Therefore, we utilized a genome-wide CRISPR-Cas9 knockout screen to comprehensively define genes essential for or restricting the fitness of hTSCs. The resulting essential and growth-restricting genes include both well-established and potentially novel trophoblast regulators. We referenced our data to those of similar genetic screens performed in cancer cell lines and primed human pluripotent stem cells (hPSCs), as well as gene expression data of the early human embryos, to identify potential hTSC-specific and -enriched regulators. Among those are TEAD1, a gene previously reported to be dispensable for mouse placentation6. However, in the human trophoblast context, TEAD1 targets many hTSC regulators and plays a major role in its specification and maintenance. Overall, our study presents the first CRISPR/Cas9 knockout screen in a human extraembryonic lineage and provides a valuable resource for future trophoblast research.

overall_design:
CRISPR screening in hTSCs
TEAD1 CUT&Tag in hTSCs
ATAC-seq in naïve hPSCs

first: Chen

last: Dong

first: Bo

last: Zhang

first: Thorold

last: Theunissen


title: Morphine addiction-NAc_RNA sequencing

city: shijiazhuang

first: xiaojie

last: li

address: 361 Zhongshan East Road, Chang'an District, Shijiazhuang, Hebei Province

institute: Hebei Medical University

summary: The current study aimed at addressing two questions: 1) How the expression of key lncRNAs is altered in the NAc during the morphine-induced addiction? 2) Which is/are the target gene(s) and what is/are the regulatory mechanism(s) of gene(s) in response to the candidate lncRNAs? To answer these two questions, the morphine addiction model was first established by using the conditioned place preference (CPP) paradigm. Then, the aberrant expression of lncRNAs was identified in the NAc tissue by RNA-sequencing.

overall_design: The NAc tissues from C57BL/6N mice from the two groups that were subjected to morphine or saline training CPP model were harvested; three samples (6 mice) from each group were used for total RNA isolation. RNA-seq was performed by BioMarker (Beijing, China). In short, following RNA quantification and qualification, RNA integrity was examined with the RNA Nano 6000 Assay Kit and the Agilent Bioanalyzer 2100 library preparation for RNA sequencing system (Agilent Technologies, CA, USA). Any library preparations in this study were sequenced on an an Illumina platform. The known lncRNAs were differentiated from the assembled transcripts if the sequencing species has known lncRNA annotations. The remaining transcripts(unknown transcripts) were used to screen for putative lncRNAs.Three computational approaches include CPC/CNCI/Pfam/CPAT were combined to sort non-protein codingRNA candidates from putative protein-coding RNAs in the unknown transcripts. Putative protein-coding RNAs were filtered out using aminimum length and exon number threshold. Transcripts with lengths more than 200 nt and have more than two exons were selected as lncRNA candidates and further screened using CPC/CNCI/Pfam/CPAT that have the power to distinguish the protein-coding genes from the non-coding genes. As well as the different types of lncRNAs include lincRNA, intronic lncRNA, anti-sense lncRNA ,sense lncRNA were selected using gffcompare.

first: Bing

last: Xie

first: Di

last: Wen

first: Chunling

last: Ma

first: Xiaojie

last: Li


title: Cell Fate Determining Molecular Switches and Signaling Pathway in Pax7-expressing Somitic Mesoderm

city: Hong Kong

first: Angela

last: Wu

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: During development, different cell types are originated from a common progenitor at a specific time frame. Previous lineage tracing of Pax7+ progenitors in somitic mesoderm has built the foundation of its development trajectory towards dermis, brown adipocytes, and skeletal muscle at dorsal trunk. Yet the molecular switches and mechanisms of such differentiation remain unknown. By combining inducible lineage tracing and single-cell RNA sequencing, here we show the transcriptomic profile of the Pax7 lineage, precise differentiation time point, and transcription factors that could drive lineage-specific differentiation. Utilizing surface markers identified in each cell types, we successfully enriched brown adipocytes, dermal fibroblasts, and cell-type specific progenitors for in vitro culture. Further characterization has shown the importance of Wnt5a and Rgcc for lineage development during embryogenesis. We also propose eFAP (embryonic fibro/adipogenic progenitor) that resembles adult FAPs lineage potentials. The work provides further understanding of the Pax7 lineage during embryonic development.

overall_design: Investigate the developmental trajectory of the Pax7 lineage during mouse embryogenesis at single-cell level. Bulk samples for specific population were investigated as well.

first: Cheuk

middle: W

last: Fung

first: Han

last: Zhu

first: Shaopu

last: Zhou

first: Xiuqing

last: Wei

first: Zhenguo


title: Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2 [ATAC-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Majority of RUNX1 mutations in AML are missense or deletion-truncation and behave as loss-of-function mutations. Following standard therapy, AML patients expressing mtRUNX1 exhibit inferior clinical outcome than those without mutant RUNX1. Studies presented here demonstrate that as compared to AML cells lacking mtRUNX1, their isogenic counterparts harboring mtRUNX1 display impaired ribosomal biogenesis and differentiation, as well as exhibit reduced levels of wild-type RUNX1, PU.1 and c-Myc. Compared to AML cells with only wild-type RUNX1, AML cells expressing mtRUNX1 were also more sensitive to the protein translation inhibitor homoharringtonine (omacetaxine) and BCL2 inhibitor venetoclax. HHT treatment repressed enhancers and their BRD4 occupancy, as well as reduced levels of c-Myc, c-Myb, MCL1 and Bcl-xL. Consistent with this, co-treatment with omacetaxine and venetoclax or BET inhibitor induced synergistic in vitro lethality in AML expressing mtRUNX1. Compared to each agent alone, co-treatment with omacetaxine and venetoclax or BET inhibitor also displayed improved in vivo anti-AML efficacy, associated with improved survival of immune depleted mice engrafted with AML cells harboring mtRUNX1. These findings highlight superior efficacy of omacetaxine-based combination therapies for AML harboring mtRUNX1.

overall_design: 12 samples; replicates are included and controls are provided for each data set

first: Christopher

last: Mill

first: Kapil

last: Bhalla


title: Characterisation of Grem1 wild-type and mutant murine pancreatic tumours

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

summary: We performed RNA-seq analysis on Grem1 wild-type and Grem1-deleted pancreatic tumour tissues from Pdx1-Flp;KrasFSF-G12D;Trp53frt/frt (KPF) mice. We compared the transcriptome between these two groups of tumours with the aim to understand their molecular signatures and the relevance to human pancreatic ductal adenocarcinoma subtypes.

overall_design: Transcriptome profiles of Grem1 wild-type and Grem1-deleted tumours were generated by deep RNA sequencing, in five biological replicates (primary KPF murine pancreatic tumours).

first: Linxiang

last: Lan

first: Axel

last: Behrens

first: Aasia

last: Hussain

first: Hari

last: ps


title: Parsing the role of NSP1 in SARS-CoV-2 infection

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

country: Israel

institute: Weizmann Institute

summary: NSP1 is a major shutoff factor of the SARS-CoV-2 coronavirus, which is responsible for the COVID-19 pandemic. The functions of NSP1 and its contribution to SARS-CoV-2 propagation is not well understood. We tackled these questions utilizing methods such as RNA sequencing, ribosome profiling, and SLAMseq.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: To decipher SARS-CoV-2 NSP1's functions, we performed RNA sequencing following overexpression and fractionation of the wt protein and of two mutants. We also performed SLAMseq analysis on cell overexpressed with NSP1wt and with a mutated NSP1, and on cells infected with SARS-CoV-2 or with a SARS-CoV-2Δnsp1 mutated virus. Additionally, we performed ribosome profiling on cells infected with SARS-CoV-2 or with the SARS-CoV-2Δnsp1 mutant.

first: Tal

last: Fisher

first: Avi

last: Gluck

first: Makoto

last: Kuroda

first: Aharon

last: Nachshon

first: Jason

last: Hsu

first: Peter

middle: J

last: Halfmann

first: Yfat

last: Yahalom-Ronen

first: Yaara

last: Finkel

first: Michal

last: Schwartz

first: Shay

last: Weiss

first: Chien-Te

middle: K

last: Tseng

first: Tomer

last: Israely

first: Nir

last: Paran

first: Yoshihito

last: Kawaoka

first: Shinji

last: Makino


title: Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3

status: Public on Apr 08 2022

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

summary: CD8+ T cell exhaustion is a distinct differentation state resulting from chronic antigen exposure and leading to hierarchical loss of effector functions. Using a murine model of diabetes, we show that CD8+ T cells derived from the islets of diabetic mice have CD8+ T cells that are canonically exhausted and yet retain sufficient effector function to contribute to pathogenicity in autoimmune diabetes. Genetic deletion of the inhibitory receptor LAG3 restricted to only CD8+ T cells lead to accelerated disease, with LAG3 deficient CD8+ T cells having enhanced effector function and trafficking. These findings reveal a  distinct role of LAG3 in restraining autoreactive CD8+ T cells and implicate LAG3 as a potential therapeutic target in autoimmunity.

overall_design: NOD mice harboring a CD8+ T cell restricted genetic deletion of LAG3 were used to assess the role of LAG3 in autoimmune diabetes and were compared to control mice. CD8+ T cells were isolated from islets and lymph nodes by FACS. Bulk RNAseq, single-cell RNAseq with paired TCRseq, and single-cell ATACseq were performed on these isolated CD8+ T cells from control and LAG3 deleted mice.  CD8+ T cells from three eight-week old female mice per group were pooled across two independent experiments for bulk RNAseq. CD8+ T cells from four eight-week old mice per group were used for scRNAseq experiments. CD8+ T cells from four eight-week old mice were used for scATACseq experiments.

middle: R

first: Stephanie

last: Grebinowski

first: Dario

middle: A

last: Vignali


title: WAT3R: Recovery of T-Cell Receptor Variable Regions From 3’ Single-Cell RNA-Sequencing

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

institute: NIBRT

summary: Diversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3’-biased single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3’ scRNA-seq is not available.  Here we present an analysis pipeline to process TCR variable regions enriched from 3’ scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells (PBMCs) from a healthy donor and detect TCR sequences in a high proportion of single T-cells. Detection of TCR sequences is negligible in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T-cells than other T-cell types, indicating an association between T-cell clonotypes and differentiation states.

overall_design: Paired Single-cell 3' RNA sequencing and T-cell receptor sequencing on 1 peripheral blood sample

first: Duncan

middle: M

last: Morgan

first: Erica

last: DePasquale

first: J

last: Love

first: Felipe

last: Prósper

last: van Galen


title: RNA-seq analysis of various strains of Mycobacterium tuberculosis under normal and redox stress.

city: CHANDIGARH

first: Dibyendu

last: Sarkar

address: SECTOR 39A

institute: CSIR-IMTECH

summary: We have performred RNA-seq analysis of WT, ∆phoP and ∆sigH Mtb H37Rv under normal and redox (Diamide) stress, to investigate the role of PhoP and SigH in maintaning the redox homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India. The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Although recent evidence suggests that at low pH M. tuberculosis encounters reductive stress, the mechanism of integrated regulation of stress response remains unknown. Unexpectedly, we find that PhoP contributes to mycothiol level and a PhoP-depleted bacilli shows enhanced susceptibility to redox stress. Because SigH is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. Our results suggest that while PhoP controls pH homeostasis via its interaction with SigE, SigH-dependent PhoP expression, but not PhoP -SigH interaction, and direct recruitment of SigH, but not PhoP controls expression of mycobacterial thioredoxin genes. Together, these results uncover novel stress-specific interaction events of sigma factors and PhoP or lack thereof, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol homeostasis. The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Although recent evidence suggests that at low pH M. tuberculosis encounters reductive stress, the mechanism of integrated regulation of stress response remains unknown. Unexpectedly, we find that PhoP contributes to mycothiol level and a PhoP-depleted bacilli shows enhanced susceptibility to redox stress. Because SigH is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. Our results suggest that while PhoP controls pH homeostasis via its interaction with SigE, SigH-dependent PhoP expression, but not PhoP -SigH interaction, and direct recruitment of SigH, but not PhoP controls expression of mycobacterial thioredoxin genes. Together, these results uncover novel stress-specific interaction events of sigma factors and PhoP or lack thereof, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol homeostasis.

overall_design: Dissecting the regulation pattern of thioredoxin genes in Mycobacterium tuberculosis.

first: Harsh

last: Goar


title: HIV Tat and cocaine interactively alter genome-wide DNA methylation and gene expression and exacerbate learning and memory impairments [Bisulfite-seq]

status: Public on Apr 07 2022

city: North Chicago

first: Johnny

last: He

state: IL

address: 3333 Green Bay Road, Basic Science Building 2.300

department: Microbiology and Immunology

institute: Rosalind Franklin University

summary: To investigate whole genomic DNA methylation changes after cocaine/saline treatment in iTat mice, we isolated genomic DNA from 24 hippocampus hemispheres of mice and performed whole genomic bisulfite sequencing (WGBS).

overall_design: There were total 24 samples, 12 from iTat mice and 12 from Wt mice. Each iTat/Wt mouse group includes six males and six females, and each sex has three cocaine treated mice and saline treated mice.


title: What goes around comes around: artificial circular RNAs bypass cellular antiviral responses

city: Giessen

first: Oliver

last: Rossbach

address: Heinrich-Buff-Ring 17

department: Biology and Chemistry (FB08)

institute: Institute of Biochemistry - University of Giessen

summary: Natural circular RNAs have been found to sequester microRNAs and suppress their function. We have used this principle as a molecular tool, and produced artificial circular RNA sponges in a cell-free system by in vitro transcription and ligation. Formerly, we were able to inhibit hepatitis C virus propagation by applying a circular RNA decoy strategy against microRNA-122, which is essential for the viral life cycle. In another proof-of-principle study, we used circular RNAs to sequester microRNA-21, an oncogenic and pro-proliferative microRNA. This strategy slowed tumor growth in a 3D cell culture model system, as well as in xenograft mice upon systemic delivery. In the wake of the global use of an in vitro transcribed RNA in Covid-19 vaccines, the question arose if therapeutic circular RNAs trigger cellular antiviral defense mechanisms when delivered systemically. In this study, we present data on the cellular innate immune response as a consequence of liposome-based transfection of the circular RNA sponges we previously used to inhibit microRNA function. We find that circular RNAs produced by the presented methodology do not trigger the antiviral response and do not activate innate immune signaling pathways.

overall_design: A549 cells were transfected with 250 ng of artificial linear and circular RNA sponges ciRS-21-bu and ciRS-21-rnd (PMID: 34316687). 3 hours post transfection A549 cells were harvested, total RNA was isolated and RNA-sequencing was performed.

first: Janina

last: Breuer

first: Patrick

last: Barth


title: Gene expression profile of gWAT SVF from adipose tissue-specific Pgam1 deficient mice

city: Niigata

first: Yohko

last: Yoshida

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata University

summary: Epidydimal WAT from adipose tissue Pgam1 deficient mice shows the phenotype of beiging. We used single cell RNA sequencing (scRNA-seq) to characterize the beiging cells in gWAT.

overall_design: Gene expression profile of stromal vascular fraction (SVF) of mice gonadal whote adipose tissue (gWAT) was analyzed at 13 weeks of age.

first: Goro

last: Katsuumi

first: Masahide

last: Seki

first: Yutaka

last: Suzuki


title: Characterisation of epithelial and mesenchymal cells in murine pancreatic tumours

city: London

first: Linxiang

last: Lan

address: 237 Fulham Rd

institute: The Institute of Cancer Research

summary: We performed RNA-seq analysis on YFP+EpCAM+ and YFP+EpCAM- cell populations freshly isolated from three Pdx1-Cre;KrasLSL-G12D;Trp53fl/fl;Rosa26LSL-YFP (KPCY) murine pancreatic tumours. We compared the transcriptome between these two populations with the aim to understand their molecular interactions that could underlie epithelial-mesenchymal plasticity and tumour heterogeneity.

overall_design: Transcriptome profiles of YFP+EpCAM+ and YFP+EpCAM- cells were generated by deep RNA sequencing, in three biological replicates (primary KPCY murine pancreatic tumours).

first: Theodore

last: Evan

first: Axel

last: Behrens

first: Pablo

last: Soro-Barrio


title: HIV Tat and cocaine interactively alter genome-wide DNA methylation and gene expression and exacerbate learning and memory impairments [RNA-seq]

summary:
To investigate RNA expression changes after cocaine/saline treatment in iTat mice, we isolated RNA from the other 24 corresponding  hippocampus hemispheres of the same mice (used for WGBS) and performed bulky RNA sequencing.
We then did the gene expression analysis and correlated the genen expression data with WGBS data.

overall_design: There were total 24 samples, 12 from iTat mice and 12 from Wt mice. Each iTat/Wt mouse group includes six males and  six females, and each sex has three cocaine treated mice and saline treated mice.


title: Fate mapping and scRNA sequencing reveal origin and diversity of lymph node stromal precursors

city: Milan

first: Andrea

last: Brendolan

address: via Olgettina 60

department: Experimental Oncology

country: Italy

institute: San Raffaele Scientific Institute

summary: Lymph node (LN) stromal cells play a crucial role in LN development and in supporting adaptive immune responses. However, their origin, differentiation pathways, and transcriptional programs are still elusive. Here, we used lineage-tracing approaches and single-cell transcriptome analyses to determine origin, transcriptional profile, and composition of LN stromal and endothelial progenitors. Our results showed that all major stromal cell subsets and a large proportion of blood endothelial cells originate from embryonic Hoxb6+ progenitors of the lateral plate mesoderm (LPM), whereas lymphatic endothelial cells arise from Pax3+ progenitors of the paraxial mesoderm (PXM). Single-cell RNA sequencing revealed the existence of different Cd34+ and Cxcl13+ stromal cell subsets and showed that embryonic LNs contain proliferating progenitors possibly representing the amplifying populations for terminally differentiated cells. Taken together, our work identifies the earliest embryonic sources of LN stromal and endothelial cells and demonstrates that stromal diversity begins already during LN development.

overall_design: Droplet-based scRNAseq on non-hematopoietic cells isolated from brachial, inguinal and mesenteric LNs from Islet-YFP mice at embryonic P2 and from C57BL6/N wild-type for embryos at E17.5 and for adults at P60


city: Hangzhou

first: Lijiang

last: Fei

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: We construct single-cell landscapes to study multi-lineage fate decisions and identify Xbp1 as a conserved transcriptional regulator of cell type stabilization.

overall_design: Expression profiling by high-throughput single cell RNA sequencing of E12.5 Xbp1-/- and WT mouse embryos.

first: Xiaoping

last: Han


title: Investigating patterns of chromatin accessibility, histone modifications, and insulation involved in rattlesnake venom gene regulation

city: Arlington

first: Blair

last: Perry

address: 501 S. Nedderman Dr, Life Sciences Building RM 337

department: Biology

institute: The University of Texas at Arlington

summary: We generated ATAC-seq data for pre- and post-extraction venom gland samples and H3K4me3, H3K27ac, and CTCF ChIP-seq from post-extraction venom gland samples from the Prairie Rattlesnake to investigate patterns of chromatin accessibility, transcription factor binding, and insulation during venom production, and to identify open promoters and active enhancer regions.

overall_design: ATAC-seq and ChIP-seq (H3K27ac, H3K4me3, and CTCF) in a rattlesnake venom gland

first: Todd

last: Castoe


title: Genome-wide maps of ER and γH2AX binding and transcriptomes in BRCA1-deficient cells with E2 treatment

city: Guanghzou

first: Zeng

last: Pengguihang

address: No.74, Zhongshan 2nd Road, Guangzhou, Guangdong

institute: Sun Yat-Sen University

summary: The goal of this study is to find out the relationship between ER-mediated transcription and DNA damage induced by estrogen(E2) and BRCA1 deficiency in MCF7. The DNA damage is marked by chromatin binding of γH2AX using ChIP-seq.

overall_design: We used ChIP-seq to obtain chromatin binding of γH2AX and ER in BRCA1 knockdown and control MCF7 with or without 10nM E2 treatment for 12h. DRB is used to inhibit transcription.  mRNA profiles were generated by  RNA-seq in same condition.

first: Junjun

last: Ding

first: Jiahao

last: Chen

first: Jingxin

last: Liu

first: Pengguihang

last: Zeng


title: snoRNA sequencing of sEV isolated from plasma of astronauts

status: Public on Apr 06 2022

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

country: Armenia

institute: Institute of Molecular Biology NAS RA

summary: This study aimed to determine whether the spaceflight-induced snoRNA changes in plasma extracellular vesicles (EV) and astronauts' peripheral blood mononuclear cells (PBMCs) can be utilized as potential biomarkers. Using unbiased small RNA sequencing, we evaluated the EV snoRNA changes in peripheral blood (PB) plasma of astronauts (n=5/group) who underwent median 12-day long Shuttle missions between 1998-2001. Using stringent cutoff (> log 2-fold change, FDR < 0.05), we detected 21 down-regulated snoRNAs and 9 upregulated in PB-EVs at three days after return (R+3) compared to ten days before launch (L-10). Our findings unveiled that spaceflight induced changes in EV and PBMCs snoRNA expression, thus suggesting snoRNAs may serve as novel biomarkers for monitoring astronauts' health.

overall_design: Comparison of snoRNA expression from blood sEVs at 2 time points.

first: David

last: Goukassian

first: Venkata

last: Garikipati

first: Lahouaria

last: Hadri

first: Shizuka

last: Uchida

first: Paul

last: Mills

first: Mattew

last: Coleman

first: Angela

last: Evans

first: Aimy

last: Sebastian

first: Agnieszka

last: Brojakowska

first: Malik

last: Bisserier

first: K

middle: S

last: Rajan

first: Amit

last: Rai


title: Condition- and isoform-dependent UPF1 activity

city: Bethesda

first: J. Robert

last: Hogg

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: HEK-293 cells transfected with non-targeting control siRNA or UPF1LL-specific siRNA were treated with vehicle control, puromycin, or thapsigargin as indicated and used for total RNA-seq.

overall_design: Paired-end high-throughput RNA sequencing of total RNA from triplicate biological replicate treatments of HEK-293 cells. Cells were reverse-transfected with the indicated siRNAs and re-plated 48-hours post-transfection. The next day, cells at 70-75% confluency were treated with vehicle control, 25, 50, or 100 µg/mL puromycin (Sigma) for 4 hours, or 1 µM thapsigargin for 6 hours.

first: Sarah

middle: E

last: Fritz

first: J


title: Loss of Prm1 leads to defective chromatin protamination, impaired PRM2 processing, reduced sperm motility and subfertility in male mice [PRM1]

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

summary: One of the key events during spermiogenesis is the hypercondensation of chromatin by substitution of the majority of histones by protamines. In humans and mice, protamine 1 (PRM1/Prm1) and protamine 2 (PRM2/Prm2), are expressed in a species-specific ratio. Using CRISPR-Cas9-mediated gene editing we generated Prm1-deficient mice and demonstrate, that Prm1+/- mice are subfertile while Prm1-/- are infertile. Prm1-/- and Prm2-/- sperm show high levels of reactive oxygen species (ROS)-mediated DNA damages and increased histone retention. In contrast, Prm1+/- sperm display only moderate DNA damages. The majority of Prm1+/- sperm were CMA3 positive indicating protamine-free DNA. This is not due to increased histone retention in Prm1+/- sperm. Additionally, we found that sperm from Prm1+/- and Prm1-/- mice contain high levels of incompletely processed PRM2. Further, the PRM1:PRM2 ratio is skewed from 1:2 in WT to 1:5 in Prm1+/- animals. Our results reveal that PRM1 is required for proper PRM2 processing to produce the mature PRM2 which, together with PRM1 is able to hypercondense DNA. Hence, the species specific PRM1:PRM2 ratio has to be precisely controlled in order to retain full fertility.

overall_design: Comparative testis gene expression profiling of PRM1 deficient mice compared to WT

first: Gina

last: Merges

first: Julia

last: Meier

first: Simon

last: Schneider

first: Alexander

last: Kruse

first: Andreas

last: Fröbius

first: Gregor

last: Kirfel

first: Klaus

last: Steger

first: Hubert

last: Schorle


title: RNA-Seq of iWAT of Foxp4 KO mouse after 7 days' cold exposure

city: Shanghai

first: Fuhua

last: Wang

address: 800 Dongchuan RD. Minhang District

country: China

institute: SJTU

summary: In order to investage the role of Foxp4 in  adaptive thermogenesis, we knocked out Foxp4 in the adipose tissue of mice by AdipoQ-Cre. After cold exposure for 7 days, we isolated the ingunal white adipose tissue for mRNA expression analysis by RNA-Seq.

overall_design: Inguinal white adipose tissue mRNA profile of 2 months old Foxp4fl/fl mice(ct1,ct2,ct3) and Foxp4AdipoQΔ/Δ mice(ko1,ko2,ko3)

first: Xizhi

last: Guo


title: RNA-sequencing analysis of the OsbZIP83 overexpression rice lines.

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

institute: Ishikawa Prefectural University

summary: We report the comparison of transcript expression in OsbZIP83 overexpression lines b83OX-13, 15 and 19 against non-transformants (NT) in Fe-sufficient roots and leaves by RNA-Seq.

overall_design: Total RNA was extracted from Fe-sufficient roots and leaves of b83OX-13, 15, 19 and NT, and used for RNA-Seq library preparation, sequencing, mapping and quantification of each gene expression as read per million (RPM).

first: Atsushi

last: Nagano


title: HIV Tat and cocaine interactively alter genome-wide DNA methylation and gene expression and exacerbate learning and memory impairments

first: Johnny

last: He

country: USA

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

overall_design: Refer to individual Series


title: Genome-wide binding sites of Foxp4 in beige adipocyte

summary: We found deletion of Foxp4 in mature adipocytes  would augment juvenile and mature beige adipocyte thermogenesis.In order to investage the binding site of Foxp4 in the genome of  beige adipocytes, we did Foxp4 ChIP-Seq with differentiated SVF cells derived from ingunal adipose tissues.

overall_design: The binding sites of Foxp4 and H3K27AC on the genome of beige adipocytes


title: Characterization of microglia polarization states under targeted AAV transduction using bulk and single cell RNA sequencing

city: Beijing

first: Minmin

last: Luo

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: The study of microglia biology and the development of microglia-based gene therapies are in urgent need of efficient and safe vehicles for microglia transgene delivery. To address this, we developed adeno-associated virus (AAV) variants that mediate efficient in vitro and in vivo microglia transduction via directed evolution of the AAV capsid protein. To assess the effect of AAV transduction on microglia, we carried out bulk RNAseq in primary microglia  and found that microglia transduced by AAV remain close to homeostatic state. Furthermore, single-cell RNA sequencing showed that the AAV-MG variants mediate safe in vivo transgene delivery without inducing microglia immune activation. These AAV variants should facilitate the applications of various genetically-encoded sensors and effectors in studying microglia-related biology and therapeutic interventions.

overall_design: RNAseq: mRNA profiles of cultured microglia treated with blank, LPS, IL4 or/and AAV variants. scRNAseq: mRNA profiles of cold-dissociated microglia from mice treated with Saline, LPS, or Poly(i:c), using 10X Chromium (reference dataset); mRNA profiles of cold-dissociated microglia from mice treated with LPS or stereotaxically injected with AAV, using Smart-seq2 (query dataset).

first: Rui

last: Lin

first: Youtong

last: Zhou

first: Ting

last: Yan

first: Ruiyu

first: Xinshuang

last: Zhang

first: Xiangyu

first: Lihui

last: Lu

first: Li