title: Gene expression profile of the human myometrium in preterm spontaneous labor (PSL)

summary: Preterm birth, defined as delivery before the 37th week of gestation, is the most common cause of neonatal mortality and the second leading cause of death in children under five years of age. Preterm birth is associated with immediate and long term morbidity as well as growth and developmental delay. Currently there is no treatment that can prevent or block preterm labor. In order to identify the molecular regulators of preterm spontaneous labor in the human myometrium, we studied the gene expression profiles of samples with Preterm Spontaneous Labour (PSL) and compared them with the gene expression profiles of samples with Preterm No Labor (PNL).

overall_design: We used myometrial tissue samples from women delivering by cesarean section with informed consent. We generated gene expression profiles using the Illumina HTv1.4 microarray and compared the differential gene expression between the preterm spontaneous labor (PSL, n=8) group and the preterm no labor (PNL, n=8)group.

middle: J

first: Martijn

last: Oudijk

first: Marlies

last: Kampman

first: Karst

middle: Y

last: Heida

first: Louise

last: Lagendijk


title: TBX2 a novel upstream regulator of labor

status: Public on Apr 29 2021

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

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

overall_design: Refer to individual Series


title: cIAP1/2 antagonism eliminates MHC class I negative tumors through T cell-dependent reprogramming of mononuclear phagocytes

status: Public on Apr 30 2021

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

country: USA

institute: Dana-Farber Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Induction of non-canonical NF-kB signaling with IAP antagonists mimics costimulatory signaling, augmenting anti-tumor immunity. We show that induction of non-canonical NF-kB signaling induces T-cell dependent immune responses even in B2M-null tumors, demonstrating that direct CD8 T cell recognition of tumor cell expressed MHC class I is not required. Instead, T cell-produced cytokines reprogram macrophages to be tumoricidal. We characterized by single-cell RNA-Seq the transcriptional profile of immune cells infilitrating mouse pancreatic tumors treated with the IAP anatagonist LCL161.

overall_design: CD45+ cells were sorted by FACS from orthotopic 6694c2 pancreatic tumors implanted in C57BL/6 mice treated with vehicle or the IAP antagonist LCL161 for 12 days.

first: Kevin

last: Roehle

first: Li

last: Qiang

first: Katherine

last: Ventre

first: Daniel

last: Heid

first: Lestat

middle: R

last: Ali

first: Patrick

last: Lenehan

first: Max

last: Heckler

last: Crowley

first: Courtney

middle: T

last: Stump

first: Anze

last: Godicelj

first: M

middle: A

last: Bhuiyan

first: Annan

last: Yang

first: Maria

middle: Q

last: del Rey

first: Tamara

last: Biary

first: Adrienne

middle: M

last: Luomo

last: Bruck

first: Jana

middle: F

last: Tegethoff

first: Svenja

middle: L

last: Nopper

first: Jinyang

last: Li

first: Katelyn

last: Byrne

first: Marc

last: Pelletier

first: Kai

middle: W

last: Wucherpfennig

first: Ben

middle: Z

last: Stanger

first: James

last: Akin

first: Joseph

middle: D

last: Mancias

first: Judith

last: Agudo

first: Michael

middle: K


title: HiChIP data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma. Using a CRISPR/Cas9 approach, we generated two STAG2 knock-out isogenic clones (A673_SA2m#1 and TC71_SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. A STAG2 rescue model (A673_SA2r) was generated by correcting the CRISPR mutation in the A673_SA2m#1 model. These STAG1/2 proficient and deficient models were profiled by CTCF HiChIP experiments.  STAG2 isogenic models were also profiled by H3K27ac HiChIP experiments. Analyses of HiChIP data allowed to show that STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions.

overall_design: Using a CRISPR/Cas9 approach, we generated two STAG2 knock-out isogenic clones (A673_SA2m#1 and TC71_SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. A STAG2 rescue model (A673_SA2r) was generated by correcting the CRISPR mutation in the A673_SA2m#1 model. These STAG1/2 proficient and deficient models were profiled by CTCF HiChIP experiments.  STAG2 isogenic models were also profiled by H3K27ac HiChIP experiments. All HiChIP data were generated from at least two independent biological replicates.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête

first: Virginie

last: Raynal

first: Sylvain

last: Baulande

first: Véronique

last: Hill


title: Reactivation of Zeta-Globin by deletion of BCL11A and LRF in HUDEP cells (ChIP-seq)

status: Public on Apr 28 2021

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

summary: The alpha and beta-globin loci harbour genes that are expressed during development and silenced throughout post-natal life. Learning to reactivate these genes may offer new therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address the mechanisms underlying the regulation of the gene encoding zeta-globin, the embryonically expressed alpha-like globin.

overall_design: CRISPR/Cas9 editing was carried out to generate homozygous clones where LRF, BCL11A and BCL11A/LRF were homozygously deleted.  Effects of edited variants were determined by ChIP-seq of chromatin marks in technical replicates.  Experiments were carried out at Day 10 of differentiation on unsorted cells.

first: Andrew

last: King

first: Chris

last: Babbs


title: Reactivation of Zeta-Globin by deletion of BCL11A and LRF in HUDEP cells (ATAC-seq)

overall_design: CRISPR/Cas9 editing was carried out to generate homozygous clones where LRF, BCL11A and BCL11A/LRF were homozygously deleted.  Effects of edited variants were determined by ATAC-seq in technical replicates. Cells were sorted to obtain normoblasts and ensure homogeneity (strong CD235a, weak CD49d, strong Band3). Experiments were carried out at Day 10 of differentiation.


address: 26 rue d'ULM

summary: Expression profiling of Ewing sarcoma samples in the frame of the CIT program from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). STAG2 loss-of-function mutation is the most frequent secondary genetic alteration in Ewing sarcoma, an aggressive bone tumor driven by the chimeric EWSR1-FLI1 transcription factor. STAG2 encodes an integral member of the cohesin complex, a ring-shaped multi-protein structure, which is essential to shape the architecture and expression of the genome with CTCF. Combining this cohort with our previously published series (GSE34620), we show that a signature of commonly downregulated genes upon STAG2 mutation in A673 and TC71 and linked to at least one EWSR1-FLI1 bound GGAA microsatellite enhancer chain element inferred form H3K27ac HiChIP predict poor overall survival in Ewing sarcoma patients.

overall_design: 79 Ewing sarcoma samples were profiled using affymetrix hgu133Plus2 arrays.

first: Franck

last: Tirode

first: Oliver

last: Greiner

first: Gaelle

last: Pierron

first: Stephanie

last: Reynaud


title: STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions


title: Reactivation of Zeta-Globin by deletion of BCL11A and LRF in HUDEP cells


title: RNA-sequencing of control and DMBA-treated WT and Cip2a-/- mouse mammary glands

city: Turku

first: Jukka

last: Westermarck

address: Tykistokatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary: The purpose is to study DMBA-induced transcriptome in WT and in Cip2a-/- mouse mammary gland tissues. We identified differentially expressed genes in DMBA-induced mammary gland in WT vs. Cip2a-/- mouse mammary glands.

overall_design: Examination of transcriptomes in DMBA-induced WT and in Cip2a-/- mouse mammary glands.

first: Srikar

last: Nagelli

first: Anni

last: Laine


title: Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis [hBA-OE]

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

summary: Thermogenic adipocytes possess a therapeutically appealing, energy-expending capacity, which is canonically cold-induced by ligand-dependent activation of b-adrenergic G protein-coupled receptors (GPCRs). Here we uncover an alternate paradigm of GPCR-mediated adipose thermogenesis through the constitutively active receptor, GPR3. We show that the N-terminus of GPR3 confers intrinsic signaling activity, resulting in continuous Gs-coupling and cAMP production without an exogenous ligand. Thus, transcriptional induction of Gpr3 represents the regulatory parallel to ligand-binding of conventional GPCRs. Consequently, increasing Gpr3 expression in thermogenic adipocytes is alone sufficient to drive energy expenditure and counteract metabolic disease in mice. Gpr3 transcription is cold-stimulated by a lipolytic signal and dietary fat potentiates GPR3-dependent thermogenesis to amplify the response to caloric excess. Moreover, we find GPR3 to be an essential, adrenergic-independent regulator of human brown adipocytes. Taken together, our findings reveal a noncanonical mechanism of GPCR control and thermogenic activation through the lipolysis-induced expression of constitutively active GPR3.

overall_design: RNA sequencing of patient-derived non-immortalized brown adipocytes treated with increasing titer of lentivirus carrying GPR3 ORF and EV control.

first: Zachary

last: Gerhart-Hines

first: Olivia

middle: S

last: Johansen

first: Lasse


title: Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis [hWA]

overall_design: RNA sequencing of human fat stromal vascular fraction cells  induced to overexpress GPR3 by lentiviral transduction of core-components of the CRISPRa-SAM system and a GPR3 sgRNA designed to target the GPR3 promotor and EV control cells.


title: Effect of Adolescent Stress on PFC miRNA Gene Expression

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

type: Non-coding RNA profiling by high throughput sequencing

summary: Deaths related to opioid use have skyrocketed in the United States, leading to a public health epidemic. Research has shown that both biological (genes) and environmental (stress) precursors are linked to opioid use. In particular, stress during adolescence – a critical period of frontal lobe development – influences the likelihood of abusing drugs. However, little is known about the biological mechanisms through which adolescent stress leads to long-term risk of opioid use, or whether genetic background moderates this response. Male and female C57BL/6J were exposed to chronic variable social stress (CVSS) or control conditions throughout adolescence and then tested for prefrontal cortex miRNA gene expression. C57BL/6J mice exposed to CVSS had a downregulation of twelve miRNA in the prefrontal cortex compared to control mice.

overall_design: Male C57BL/6J mice were assigned to chronic variable social stress (CVSS) or control conditions.  To minimize litter effects, littermates were evenly distributed between the CVSS and control groups at weaning. CVSS mice underwent the stress protocol during adolescence (PND 25-59) as previously described (Caruso et al., 2017, 2018c, 2018b, 2018a). Following weaning mice sat undisturbed with littermates (PND 21-25). On PND 25, CVSS mice were individually housed for 3 days followed by social rehousing with 1-2 unfamiliar cage mates for 4 days. This procedure was repeated for 5 consecutive weeks. On PND 59, CVSS mice were rehoused with their original cage mates from weaning until behavioral testing or sacrifice. For control mice, cage mates remained the same from weaning to the end of the study. To equate handling between the control and CVSS conditions, each time CVSS mice were transferred to a new cage for individual or social rehousing, control mice were also moved to new cages. Following CVSS, these mice remained undisturbed (i.e. no behavioral testing) until PND 70 when they were euthanized by cervical dislocation and brains removed. A mouse brain matrix was used to obtain 1 mm slices. The PFC was punched from the slice with a blunt needle that captured both hemispheres and immediately place into RNAlater.

first: Helen

last: Kamens

first: Istvan

last: Albert


title: Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis [C-3BO]

overall_design: RNA sequencing of brown adipose tissue from the constitutive Gpr3 brown and beige adipocyte overexpressor mouse model (C-3BO) and control littermates (chow diet vs. HFD diet) as well as wildtype mice exposed to daily IP injections of CL-316,243 and saline-injected control littermates (chow diet vs. HFD diet).


title: Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis [siRNAGPR3]

overall_design: RNA sequencing of patient-derived non-immortalized brown adipocytes treated with GPR3 siRNA and control siRNA.


title: MiRNAs transcriptional and post-transcriptional landscape in T cell activation

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: NGS-based assesement of miRNA expression and post-transcriptional modification kinetics in human primary CD4+ T cells upon short-term stimulation with antiCD3/antiCD28 or IFN I.

overall_design: miRNA samples were obtained from resting CD4+ T cells, isolated from different healthy donors, after stimulation with antiCD3/antiCD28 or IFN I for 3h, 6h and 24h, or no stimulation (t0h). Libraries were produced and subject to NGS with the Illumina HiSeq 2500 system, and sequencing reads processed to obtain expression estimates of known miRNA molecules described in miRBase (release 22).

first: A

last: Rodríguez-Galán

first: F

last: Sanchez-Madrid


title: RNA sequencing for endoscopic biopsy tissue samples from controls and Crohn's disease patients, and organoids derived from these specimens.

status: Public on Apr 27 2021

city: Seoul

first: Sung Noh

last: Hong

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

summary: RNA sequencing for endoscopic biopsy tissue samples from controls (jejunum [S170], n=1; ileum [SN2], n=1) and patients with Crohn's disease (jejunum [non-inflamed area, A2/L2+L4/B2, infliximab maintenance therapy, S93], n=1; ileum, [non-inflamed area, A2/L2/B2, infliximab maintenance therapy, S95], n=1).   Organoid culture was performed using intestinal crypts derived from these specimens, as described previously (Sato et al. Nature 2009; 459: 262–265]. Organoids were sub-cultured at least 6 passages. RNA sequencing was conducted for organoids on day 3, day 6, and day 9 [S170 and S93], and organoids treated with TNFɑ 30 ng/ml on day 3, day 6, and day 9 [S170 and S93]. RNA sequencing was conducted for organoids on day 6 and day 9 [N2 and S95], and organoids treated with TNFɑ 30 ng/ml on day 6 and day 9.

overall_design:
RNA sequencing for tissue samples: Examination of 4 RNA samples of endoscopic biopsy tissue specimens obtained from control (n=2 [S170, SN2]) and patients with Crohn’s disease (n=2 [S93, S95]).   RNA sequencing for organoid samples: Examination of 10 RNA samples of control organoids (5 pair of RNA samples of 2 control organoids treated with and without TNFɑ 30 ng/ml) - control organoids on day 3 [S170_0_D3], day 6 [S170_0_D6, SN2_0_D6], and day 9 [S170_0_D9, SN2_0_D9]), and control organoids treated with TNFɑ 30 ng/ml on day 3 [S170_30_D3], day 6 [S170_30_D6, SN2_30_D6], and day 9 [S170_30_D9, SN2_30_D9]).   Examination of 10 RNA samples of organoids derived from Crohn’s disease patients (5 pair of RNA samples of 2 organoids derived from Crohn’s disease patients treated with and without TNFɑ 30 ng/ml) - organoids derived Crohn’s disease patients on day 3 [S93_0_D3], day 6 [S93_0_D6, S95_0_D6], and day 9 [S93_0_D9, S95_0_D9]), and organoids derived Crohn’s disease patients treated with TNFɑ 30 ng/ml on day 3 [S93_30_D3], day 6 [S93_30_D6, S95_30_D6], and day 9 [S93_30_D9, S95_30_D9]).
Note from submitter: Our data were derived from material obtained from patients at Samsung Medical Center
Therefore, based on the hospital policy and Korean raw, it is difficult to upload raw data because they contained the patient information.

first: Sung

middle: N

first: Chansu

last: Lee


title: Genomewide copy number profiles for breast cancer from Taiwanese women

status: Public on May 05 2021

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

summary: The incidence of breast cancer has been rapidly increasing in East Asia. This is the first study of genome wide copy number of breast cancer in East Asia.   We conducted this study to compare the genetic alterations between East and West.

overall_design: A total of 120  tumor samples from different patients were subjected to genomic DNA extract. The  DNAs were hybridized to Affymetrix SNP 6.0 arrays per the manufacturer’s instructions (Affymetrix, Santa Clara, CA. USA) to obtain the copy number alterations profilings.

first: Ching-Hung

last: Lin

first: Ruby

last: Huang

first: Yen-Shen

first: Chiun-Sheng

first: Ann-Lii

last: Cheng


title: Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells During the Hen Ovulatory Cycle

city: Chengdu

first: Liang

last: Li

state: Sichuan

address: Wenjiangqu huiminlu211hao sichuan nongyedaxue

country: China

institute: Sichuan agricultural university

summary: In this study, gene expression in Rohman layers was investigated at three distinct stages of the ovulatory cycle: zeitgeber time 0 (ZT0, 9:00 a.m.), zeitgeber time 12 (ZT12, 9:00 p.m.), and zeitgeber time 20 (ZT20, 5:00 a.m.) representing the early, middle, and LH surge stages, respectively, of the ovulatory cycle. Gene expression profiles were explored during follicle development at ZT0, ZT12, and ZT20 using Ribo-Zero RNA sequencing.

overall_design: At 210-days, the birds were sacrificed at 9:00 AM (ZT0, N=3), 21:00 PM (ZT12, N=3) and 05:00 AM (ZT20, N=3). For total RNA sequencing, about 4 μg total RNA was isolated from the granulosa cells (a total of 9 samples).

first: Silu

last: Hu

first: Taotao

last: Gui

first: Xun

last: Deng


title: RNA sequencing of control and CIP2A siRNA silenced basal-like breast cancer cell line HCC38

first: Jukka

last: Westermarck

summary: The purpose is to study the transcriptional changes in basal like breast cancer cell line HCC38 on depletion of CIP2A. We have used 3 unique siRNA sequences of CIP2A and  3 control samples (Mock and 2 unique non-targeting sequences) for the RNA Seq. We identified differentially expressed genes in CIP2A knockdown conditions compared to the control samples and identified pathways regulated by CIP2A in this cell line using GSEA.

overall_design: CIP2A was silenced using 3 unique CIP2A siRNAs. Oligofectamine was used as the transfection reagent and standard manufacturer's protocols were followed. Non transfection control (Mock) and two nontargeting control siRNAs were used as controls.

first: Srikar

last: Nagelli

first: Anni

last: Laine


title: scRNA-seq analysis of SARS-CoV-2 infected human islets

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Recent clinical data has suggestedsed a bi-directional relationship  between Coronavirus disease 19 (COVID-19) and diabetes. Here, we showdemonstrateed the detection of SARS-CoV-2 in pancreatic endocrine cells in autopsy samples derived fromof COVID-19 patients. Single cell RNA-seq and immunostaining confirmed that multiple types of pancreatic islet cells can be infected byare susceptible to SARS-CoV-2, eliciting a cellular stress response and the induction of chemokines. SARS-CoV-2 infection causes the increase of chemokine response, cell stress, and interferon signal. Upon SARS-CoV-2 infection, beta cells show a the decreased expression of insulin and the increased expression of alpha and acinar cell markers, including glucagon and , and acinar cell markers, including PRSS1/trypsin1, respectfully, suggesting which suggests that infected beta cells undergocellular dedifferentiation. This was furtherCorroboration of these findings could be further validated using theinex vivo using single cell sequencing of pancreatic tissue from autopsy of COVID-19 patients autopsies.  Trajectory analysis identifiedindicated that the EIF2 pathway that changess along withmediates beta cell dedifferentiation. Furthermore, a, and a high content screen identified trans-integrated stress response inhibitor (trans-ISRIB) that as decreasinges poly-hormonal cells. Finally, trans-ISRIB treatmentwhich rescueds beta cell dedifferentiation upon SARS-CoV-2 exposure. Together, it, suggestings that SARS-CoV-2 infection causes EIF2 pathway-mediated beta cell dedifferentiation. Altogether, tThis study provides a potential mechanism of new onset diabetes in upon the development of COVID-19.

overall_design: Human islets were infected with SARS-CoV-2 and analyzed using scRNA-seq

first: Xuming

last: Tang

first: Skyler

last: Uhl


title: ChIP-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)

first: Olivier

last: Delattre

summary: STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. Using a CRISPR/Cas9 approach, we generated three STAG2 knock-out isogenic clones (A673_SA2m#1, TC71_SA2m#1 and TC71_SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. Similarly, a STAG1 knock-out isogenic clone (A673_SA1m#1) was generated. Finally, a STAG2 rescue model (A673_SA2r) was generated by correcting the CRISPR mutation in the A673_SA2m#1 model. These STAG1/2 proficient and deficient models were profiled by ChIP-seq for EWS-FLI1, CTCF, cohesin members, and histone marks and allowed to highlight a global conservation of binding for these marks upon STAG2 mutation.

overall_design: ChIP-seq were performed in 2 different Ewing sarcoma cell lines (A673 & TC71) and their respective and derivative STAG1 and STAG2 isogenic deficient and proficient models. In A673, ChIP-seq data were generated from parental A673 (WT), STAG1 KO (A673_SA1m#1), STAG2 KO (A673_SA2m#1) and STAG2 rescue models (A673_SA2r). In TC71, ChIP-seq data were generated from parental TC71 (WT) and in 2 different STAG2 KO (TC71_SA2m#1 and TC71_SA2m#2) clones generated with 2 independent sgRNAs (SA2m#1 and SA2m#2). For all these models, we performed ChIP-seq for CTCF, cohesin members (RAD21, SMC1A, STAG1 and STAG2), EWS-FLI1, H3K4m3 and H3K27ac. Respective inputs were used as normalization controls for all models.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête

first: Virginie

last: Raynal

first: Sylvain

last: Baulande

first: Véronique

last: Hill


title: Small RNA sequencing analysis of Myo-Evs

city: Osaka-Sayama

first: YOSHIMASA

last: TAKAFUJI

state: Osaka

address: 377-2 Ohno-Higashi

department: Facluty of Medicine

country: Japan

institute: Kindai University

summary: As a part of study to characterize the effects of fluid flow shear stress to mouse muscle cells, small RNA sequencing was performed with muscle cell-derived extracellular vesicles (Myo-EVs).

overall_design: small-RNA sequencing was performed with mouse primary osteoblasts, bone marrow cells and C2C12 myoblast-derived extracellular vesicles with/without fluid flow shear stress

first: Yoshimasa

last: Takafuji

first: Masafumni

last: Muratani


title: Circadian phase-dependent myoblast differentiation and muscle regeneration

city: Minneapolis

first: Nobuaki

last: Kikyo

state: Minnesota

department: Stem Cell Institute

institute: University of Minnesota

summary: Circadian rhythms regulate cell differentiation and tissue regeneration; however, their implications in tissue regeneration remain elusive. Here, we present evidence that tissue regeneration efficiency is dependent on the circadian timing of injury affliction in a mouse model of muscle injury. We found that depletion of Per1 or Per2, members of the core circadian regulators in vertebrates, impaired mouse muscle regeneration and myoblast differentiation. Both Per1 and Per2 were necessary to maintain the expression level of Igf2, one of the critical regulators for myoblast differentiation, through epigenetic regulation at the Igf2 promoter and enhancer. Reflecting this, myoblast differentiation was promoted when differentiation was initiated while the level of Pers and Igf2 were high, compared with the time when their expression levels were low. Furthermore, muscle regeneration in the mouse was more efficient when chemical injury was inflicted at night when Pers were highly expressed, compared with morning injury.  This study uncovers circadian timing-based control of myoblast differentiation and muscle regeneration.

overall_design: Per1 and Per2 genes were knocked out in mouse myoblast C2C12 cells with CRISPR-Cas9. The cells were induced to differentiate into myotubes. RNA from undifferentiated (day 0) and differentiating (day 3 and day 5) cells were applied to RNA-seq. n=1. WT is control treated with non-target sgRNA.

first: Nobuko

last: Katoku-Kikyo

first: Ellen

last: Paatela

first: Daniel

last: Houtz

first: Britney

last: Lee

first: Dane

last: Munson

first: Xuerui

last: Wang

first: Mohammed

last: Hussein

first: Jasmeet

last: Bhatia

first: Seunghyun

last: Lim

first: Ce

last: Yuan

first: Yoko

last: Asakura

first: Atsushi


title: The human memory T cell compartment changes across tisses of the female reproductive tract

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

summary: We report transcriptomic analysis of CD4 T cells isolated from vaginal, ectocervical, and endocervical tissues from 4 individuals.

overall_design: Human blood, cervial, and vaginal tissues were collected from healthy women undergoing elective surgeries. Freshly isolated tissues were enzymatically processed into single cell suspensions, and blood was collected into ACD tubes and then the PBMC layer isolated uring a Lymphoprep gradient.  Cells were stained for Live/Dead, CD45, CD3, CD4, CD69, CD103 and Live, CD45+CD3+CD4+ cells were sorted into different CD69/CD103 expressiing populations.

first: Jennifer

last: Lund


title: Differential genetic influences over colorectal cancer risk and gene expression in large bowel mucosa

city: Edinburgh

first: Peter

middle: G

last: Vaughan-Shaw

address: Crewe Road

department: IGMM

institute: University of Edinburgh

summary:
Site-specific variation in colorectal cancer (CRC) incidence, biology and prognosis are poorly understood. We sought to determine whether common genetic variants influencing CRC risk might exhibit topographical differences on CRC risk through regional differences in effects on gene expression in the large bowel mucosa.  We conducted a site-specific genetic association study (10,630 cases, 31,331 controls) to identify whether established risk variants exert differential effects on risk of proximal, compared to distal CRC. We collected normal colorectal mucosa and blood from 481 subjects and assessed mucosal gene expression using Illumina HumanHT-12v4 arrays in relation to germline genotype. Expression quantitative trait loci (eQTLs) were explored by anatomical location of sampling.
Normal colorectal mucosa was analyzed from both CRC patients and healthy controls.

overall_design: Translational gene expression study

first: Maria

last: Timofeeva


title: Maternally expressed imprinted lncRNA and snoRNA are expressed in osteosarcoma and Ewing sarcoma

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

summary: We report on osteosarcoma and Ewing sarcoma tumours resected from human patients that the tumours express long non-coding RNA.

overall_design: Tumour tissue resected from patients.

first: Archana

last: Singh

first: Jasmine

last: Sanghera

first: Vaiyapuri

last: Sumathi

first: Lee

last: Jeys

first: Tamas

last: Dalmay

first: William

last: Fraser


title: Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)

status: Public on Apr 26 2021

city: Stanford

first: Adrian

last: Sanborn

state: CA

address: 299 Campus Drive West

institute: Stanford University

summary: A pooled pull-down experiment for protein fragments, expressed with mRNA display, that bind Med15 or TFIID subcomplex

overall_design: Protein fragments of length 53 amino acids were synthesized as an oligo pool and in vitro translated using mRNA display as a pool of protein fragments covalently tagged with their mRNA sequences. The library was sequenced before and after pull-down with Med15 or Taf4/5/9/6/12 bound to magnetic beads.

first: Benjamin

last: Yeh

first: Jordan

last: Feigerle

first: Cynthia

middle: V

last: Hao

first: Erez

last: Aiden

first: Roger

last: Kornberg


title: Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Activation)

summary: A pooled screen for protein fragments that induce transcriptional activation of a reporter GFP gene.

overall_design: Protein fragments of length 53 amino acids were synthesized as an oligo pool and cloned into a plasmid library. Outgrowth of transformed yeast for five days ensured that each cell contained a unique aTF expression plasmid due to mechanisms maintaining it at single-copy levels. After induction with estrogen, cells with a defined level of aTF expression were selected by mCherry signal and sorted into eight bins based on GFP expression. By next-generation sequencing, the distribution of each protein tile across the bins was determined and the mean value was used to calculate activation—namely, the fold increase in GFP relative to background


title: Gene expression profile of zebrafish pex2 mutant

city: Gifu city

first: Shigeo

last: Takashima

state: Gifu

address: 1-1 Yanagido

department: Life Science Research Center

institute: Gifu University

summary: Transcriptome analysis using microarray was perfomed to reveal mutant-specific gene expression changes that might relate to human Zellweger syndrome.

overall_design: Zellweger syndrome model fish was generated by mutating pex2 gene. Gene expression of pex2  mutant fish was compared with that of wild-type siblings.


title: Single-Cell Transcriptome Analysis of Rb1 Conditional Knockout Prospermatogonia

city: Pullman

first: Nathan

middle: C

last: Law

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

summary: Prospermatogonia, precursors to the mature male germline, undergo a period of sustained quiescence during late fetal and early postnatal development. The purpose of this mitotic arrest is not fully understood. Therefore, utilizing conditional ablation of retinoblastoma protein 1 (Rb1) in mice which blocks entry into quiescence, we analyzed prospermatogonia at the cusp of mitotic arrest at embryonic day 14.5. Prospermatogonia from heterozygous controls or conditional knockout males were isolated via fluorescence-activated cell sorting and profiled via single-cell RNA-sequencing (scRNA-seq). Outcomes of scRNA-seq analysis revealed that a metabolic shift to oxidative phosphorylation and meiotic inhibition are disrupted in prospermatogonia that fail to initiate quiescence. Collectively, these findings and others suggest that biosensing mechanisms eliminate prospermatogonia that fail to mitotically arrest and that key layers of programming are applied during quiescence to ensure proper fate specification.

overall_design: Testicular germ cells were isolated from either control or conditional Rb1 knockout mice at embryonic day 14.5 of development and analyzed by scRNA-seq in triplicate.

first: Guihua

last: Du

first: Jon

last: Oatley


title: Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

summary:
Activation: A pooled screen for protein fragments that induce transcriptional activation of a reporter GFP gene. A pooled pull-down experiment for protein fragments, expressed with mRNA display, that bind Mediator Med15 or TFIID subcomplex.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Saccharomyces cerevisiae
synthetic construct

overall_design: Refer to individual Series


title: Kdm3b haploinsufficiency impairs the consolidation of cerebellum-dependent optokinetic response memory in mice

first: Joon Yong

last: An

address: 145 Anam-ro, Anam-dong, Seongbuk-gu

institute: Korea University

summary: Bulk RNA samples were recruited from GCE of the cerebellar vermis. We obtained two WT and two Kdm3b+/- mice samples for RNA-sequencing analysis. After trimming low-quality bases, the sequence reads were aligned using the STAR algorithm. Then, we quantified gene expression using the StringTie, resulting 16,447 genes expressed in cerebellum tissues.

overall_design:
RNA-seq analysis of heterozygous mutant of Kdm3b gene, compared to wild-type mice
*** Submitter declaration: "We lost our fastq files for the analysis so we are able to submit only processed data files for submission." ***

first: Joon

middle: Y


title: Bone Marrow Derived SH-SY5Y Neuroblastoma Cells Infected by Kaposi’s Sarcoma Herpes Virus (KSHV) Display Unique Infection Phenotypes and Growth Properties

city: Lincoln

first: Charles

last: Wood

state: Nebraska

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

summary:
Abstract: The Kaposi’s sarcoma-associated herpesvirus (KSHV) is an important oncogenic virus previously shown to be neurotropic, but studies on neuronal cells infection and pathogenesis are still very limited. Here we characterized the effects of KSHV infection on neuronal SH-SY5Y cells by the recombinant virus rKSHV219, which expresses both GFP and RFP to reflect latent and lytic phases of infection. We demonstrated that infected cells have a faster growth rate and the KSHV infection can be sustained. Interestingly, the infected cells can transition spontaneously back and forth between lytic and latent phases of infections, producing progeny viruses but without any adverse effects on cell growth. In addition, transcriptome analysis of viral and cellular genes in latent and lytic cells showed that unlike other infected cell lines, the latently infected cells expressed both latent and most, but not all the lytic genes required for infectious virion production. The uniquely expressed viral genes by the lytic cells were mainly involved in the early steps of virus binding. Some of the cellular genes that were deregulated in both latent and lytically infected cells are involved in cell adhesion, in cell signal pathways and tumorigenesis. The downregulated cellular CCDN1, PAX5, NFASC and upregulated CTGF, BMP4, YAP1, LEF1 and HLA-DRB1 genes were found to be associated with the cell adhesion molecules (CAM), hippo signaling and cancer. These deregulated genes may be involved in creating an environment that are unique in the neuronal cells to sustain cell growth upon KSHV infection not observed in other infected cell types.
IMPORTANCE: Our study has provided evidence that the neuronal SH-SY5Y cells displayed unique cellular responses upon KSHV infection. Unlike other infected cells, this neuronal cell displayed a more rapid growth rate upon infection and can spontaneously transition back and forth between latent and lytic phases of infection. Unlike other latently infected cells, a number of lytic genes were also expressed in the latent phase of infection in addition to the established latent viral genes. They may play a role in deregulating a number of host genes that are involved in cell signaling and tumorigenesis in order to sustain the infection and growth advantages for the cells. Our study has provided novel insights on KSHV infection of neuronal cells and a potential new model for further studies to explore the underlying mechanism in viral and host interaction for neuronal cells, and the association of KSHV with neuronal diseases.

overall_design: Study KSHV latent and lytic infections on bone marrow derrived SH-SY5Y Neuroblastoma cells.


title: 3D genomics across the tree of life reveals condensin II as a determinant of architecture type [DamID-seq]

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

institute: Netherlands Cancer Institute

summary: We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.

overall_design: Examination of lamina associated DNA (LADs) in WT cells and two different ∆CAP-H2 Hap1 clones.

first: Tom

last: van Schaik

first: Claire

last: Hoencamp

first: Ahmed

last: Elbatsh

first: Bas

last: van Steensel

last: Rowland


title: 3D genomics across the tree of life reveals condensin II as a determinant of architecture type [RNA-Seq]

overall_design: mRNA profiles of WT and ∆CAP-H2 Hap1 cells were generated in two different clones in triplicate.

first: Benjamin


title: Chicken (Gallus gallus) Transcriptome of Intestinal, Immune, and Reproductive Cell and Tissue Types

first: David

last: Hawkins

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

summary: We report the transcriptomes of 10 different chicken (Gallus gallus) cell/tissue types. The goal of this project was to determine similarities and differences between different cell/tissue types, with respect to protein coding genes, lncRNA, isoform counts, and differential gene expression. We provide raw data and bigWig files for UCSC visualization. The findings described here will be useful towards a complete annotation of chicken tissue and cellular transcriptomes.

overall_design: 10 cell/tissue types (B cell, bursa, ileum, jejunum, proximal cecum, macrophage (lung), monocytes (blood), ovary, T cells (spleen), and thymus. Two biological replicates per tissue. Average sequencing depth of 43.7 million paired reads per library.

first: R

first: Eliah

last: Overbey

first: Yvonne

last: Drechsler

first: Theros

last: Ng


title: Hakai is required for stabilizing core components of the m6A mRNA methylation machinery

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: N6-methyladenosine RNA (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions, including circadian clock, metabolism and embryonic stem cell differentiation. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila. Its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerisation and interaction with other members of the m6A machinery, while its catalytic activity seems dispensable. Finally, we demonstrate that the loss of Hakai destabilizes the level of several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Thus, our work adds new functional and molecular insights into the mechanism of the m6A mRNA writer complex.

overall_design: S2R+ cells were treated with corresponding double stranded RNA three times during 6 days

first: Tina

last: Lence

first: Nastasja

last: Kreim


title: DNA G-quadruplexes modulate highly transcribed genes in human chromatin [RNA-seq]

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

summary: G4s are nucleic acids secondary structures that form in the presence of four or more runs of gunanine. In vitro results suggested that G4s are involved in the regulation of both transcription and replication processes. In vitro results suggested that G4s are involved in the regulation of both transcription 6–10 and replication 11–13 processes allowed to demonstrate the actual folding of G4s in live cells, but also inserted them in a more biologically relevant context. . In the present work we mapped G4s in the chromatin of a WD-LPS cell line (93T449), we integrated the information of G4 folding with their chromatin context, the transcriptional level of the associated genes and compared the results with data obtained in a cell line of different origin (HaCaT).

overall_design: Transcriptional analysis in untreated and c-exNDI treated 93T449 cells.

first: Sara

last: Lago

first: Gunnar

last: Schotta

first: Filippo

last: Richter


title: DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ChIPseq]

overall_design: G-quadruplexes analysis in 93T449 (ATCC #CRL-3043) cells.


title: 3D genomics across the tree of life reveals condensin II as a determinant of architecture type [Hi-C]

first: Angela

last: Sedeno Cacciatore

overall_design:
Hi-C was performed in CAPH2 depleted HAP1 cells and compared to previously published wild type HAP1 Hi-C data (GEO accession: GSE95014 - combination of GSM2494290, GSM2494294, and GSM2494298).

The hg38_*.hic is generated with a different genomebuild (hg38) and complements the .aca analyses;
The hg38_CAPH2.hic file contains the contact matrix of samples GSM4983062 and GSM4983063.
The hg38_wildtype.hic incorporates data from the previously published GSMs (GSM2494290,GSM2494294, and GSM2494298).

first: Jonne

last: Raaijmakers

first: Ángela

last: Sedeño Cacciatore

first: Hans

last: Teunissen

first: Elzo

last: de Wit


title: DNA G-quadruplexes modulate highly transcribed genes in human chromatin

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


title: 3D genomics across the tree of life reveals condensin II as a determinant of architecture type

status: Public on Apr 23 2021

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

sample_organism:
Arachis hypogaea
Triticum aestivum
Saccharomyces cerevisiae
Agaricus bisporus
Caenorhabditis elegans
Aplysia californica
Aedes aegypti
Culex quinquefasciatus
Drosophila melanogaster
Strongylocentrotus purpuratus
Ciona intestinalis
Branchiostoma lanceolatum
Xenopus laevis
Gallus gallus
Notamacropus eugenii
Homo sapiens
Muntiacus reevesi
Muntiacus muntjak
Pleurobrachia bachei
Pygocentrus nattereri
Acropora millepora
Cristatella mucedo
Clonorchis sinensis
Chiloscyllium punctatum
Python bivittatus
Hypsibius dujardini
Lethenteron camtschaticum

overall_design: 26 species across the tree of life were included in the analysis, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

first: Erez

last: Lieberman Aiden


title: Genome-wide EML1 binding sites in Arabidopsis thaliana seedlings

city: Columbus

first: Jelena

last: Brkljacic

address: 1060 Carmack Rd

institute: The Ohio State University

type: Genome binding/occupancy profiling by genome tiling array

summary: To identify genomic targets involved in the EML-dependent control of seed development, we performed ChIP-chip using whole genome Arabidopsis tiling arrays from p35S::EML1-GFP seedlings using GFP antibodies. The analysis showed that EML1 displayed preferential binding to transposable elements (TEs), while showing no preference for protein coding genes.

overall_design: 1 input and 1 ChIP sample

first: Milica

last: Milutinović

first: Benson

middle: E

last: Lindsey III

first: Asela

last: Wijeratne

first: Kengo

last: Morohashi

first: J

last: Hernandez

first: Nikolas

last: Grotewold

first: Virginia

last: Fernández

first: Erich

last: Brkljačić


title: Transcriptomic data from  lymphocytic choriomeningitis virus-infected and mock-infected A549 cells

city: Wuhan

first: Qingxing

last: Wang

state: Wuchang

address: NO 44 in xiaohongshan Central District, Wuhan, China

institute: Wuhan institude of virology, CAS

summary: We reported the transcriptomic analysis on A549 cells infected with lymphocytic choriomeningitis virus (LCMV).

overall_design: A549 cells were infected with lymphocytic choriomeningitis virus strain Amstrong at an MOI of 0.01 or mock-treated. At 36 hours post infection, cells were collected for mRNA extraction and sequencing. Each treatment has three independent repetitions.

first: Qilin

last: Xin

first: Weijuan

last: Shang

first: Weiwei

last: Wan

first: Gengfu

last: Xiao

first: Leike

last: Zhang


title: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions

status: Public on Apr 22 2021

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University


title: DNA G-quadruplexes contribute to CTCF and cohesin recruitment

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites within topologically associating domains (TADs) or at TAD boundaries. We investigated three mechanisms by which G4s may contribute to CTCF recruitment. One involved direct interactions between CTCF and G4s that persisted in the G0/G1 phase of the cell cycle. Synthetic G4s from CpG islands (CGIs) formed complexes with CTCF in vitro, and CTCF occupancy at the respective sites in the genome was modulated by a G4-stabilizing ligand. Another possible mechanism was through G4 interference with DNA methyltransferase activity in CGIs. Bioinformatics analysis confirmed that G4s underlie the association between CTCF and CGIs, but did not support a critical role for methylation in CTCF recruitment to G4-harboring CGIs. The third mechanism was through attracting additional protein factors. We found that G4s are recognized by the nucleosome density modulating high-mobility group (HMG) proteins and the cohesin-interacting protein additional sex combs-like 1. The affinity for these proteins is the basis for indirect G4 contributions to CTCF positioning and TAD demarcation.

overall_design: CTCF ChIP-seq data for PDS-treated and non-treated K562 cells

first: Anna

last: Varizhuk

first: Renat

last: Sultanov


title: Global transcriptomic changes in alveolar epithelial type II (ATII)  cells upon GRK6 depletion based on RNA-seq

status: Public on Apr 24 2021

city: Southampton

first: Yihua

address: University Road

institute: University of Southampton

summary: G protein coupled receptor kinase 6 (GRK6) is a member of the GRKs family, which is expressed in various tissues and involved in the development of several diseases, including lung adenocarcinoma. Our previous study suggested that GRK6 expression was significantly down-regulated in lung adenocarcinoma patients, and its level was an independent prognostic factor for overall survival. Here, by performing RNA-sequencing (RNA-seq) in alveolar epithelial type II (ATII)  cells transfected with either short interfering RNA (siRNA) oligos against GRK6 or control siRNAs, several disease related alterations were identified.

overall_design: To assess the global transcriptomic changes in alveolar epithelial type II (ATII)  cells (kindly provided by Prof Julian Downward, The Francis Crick Institute, UK) upon GRK6 depletion based on RNA-seq. In the GRK6 RNAi group (siGRK6), ATII  cells were transfected with short interfering RNA (siRNA) oligos against GRK6 for 72 hours. In the control group (control), ATII cells were transfected with control siRNA oligos for 72 hours. After that, ATII  cells were subjected to RNA-seq (n=3 for each group).

first: Y

last: Zhou

first: L

last: Yao

first: S


title: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [titration]

summary: Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e. paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are co-expressed in the cell, and thus can compete for target sites across the genome. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data shows that Cbf1 and Pho4 greatly influence each other’s occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs' expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.

overall_design: Eight  protein binding microarray (PBM) experiments were performed for recombinant, full-length, yeast transcription factors Cbf1 and Pho4. Briefly, the PBMs  measured the binding of GST-tagged Pho4 and His-tagged Cbf1 to double-stranded 60k Agilent microarrays at four different concentrations, for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the PBM signal intensity of Cbf1 and Pho4 for each spot.


title: Lsr2 and its novel paralogue mediate the adjustment of Mycobacterium smegmatis to unfavorable environmental conditions

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: In this study, we analyze the role of Lsr2 as a transcription factor in M. smegmatis, a saprophytic bacterium whose natural habitat (soil and water) substantially differs from that of the obligatory mycobacterial pathogens. In summary, the combined RNA-seq and ChIP-seq data revealed that Lsr2 controls gene expression either directly by binding their promoter regions or indirectly through DNA loop formation.

overall_design: Examination of M. smegmatis Lsr2 protein binding sites in optimal growth condition.

first: Marta

last: Kołodziej

first: Tomasz

last: Łebkowski

first: Przemysław

last: Płociński

first: Joanna

last: Hołówka

first: Mariola

last: Paściak

last: Wojtaś

first: Jarosław

last: Dziadek

first: Jolanta

last: Zakrzewska-Czerwińska


first: Angela

last: Sedeno Cacciatore

overall_design: Refer to individual Series


title: High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

summary: Using a high throughput splicing reporter assay, we tested 1,080 single nucleotide variants in POU1F1, a key transcription factor essential for pituitary development.  Our saturation splicing effect map identifies 96 splice disruptive variants, including 14 synonymous variants, of which 8 were found in unrelated patients diagnosed with hypopituitarism.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: Saturation mutagenesis was used to generate libraries comprising all SNVs within POU1F1 exon 2 and flanking introns (-85 bp to +178 bp). These libraries, comprising 1,080 variants, were transferred to the exon trap construct pSPL3. Degenerate 20mer barcodes were added to the downstream 3'UTR, and paired end sequecning was used to associate each barcode with the POU1F1 variant(s) present on the same plasmid copy. COS-7 cells were transfected with the pooled minigene library, and targeted RNA-seq of the spliced minigene transcripts were measure the splicing outcome associated with each barcode/variant.

middle: O


title: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [competition]

first: Raluca

last: Gordan

overall_design: Seven competition protein binding microarray (competition PBM) experiments were performed for recombinant, full-length, yeast transcription factors Cbf1 and Pho4. Briefly, the PBMs involved binding of GST-tagged Pho4 and His-tagged Cbf1 to double-stranded 60k Agilent microarrays under direct competition from each other in order to determine their competitive binding patterns for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the PBM signal intensity of Cbf1 and Pho4 respectively for each spot.


title: Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

institute: Institut Pasteur


title: Expression profiling by high throughput sequencing of THP-1 cells treated with AT or HA

city: Muenster

first: Maria

last: Yusenko

address: Wilhelm-Klemm-Str. 2

department: Institute of Biochemistry

institute: University of Muenster

summary: Deregulation of transcription factor MYB contributes to the development of leukemia and other human cancers, making MYB an attractive target for drug development. We demonstrate that the natural sesquiterpene lactone (STL) 4,15-iso-atriplicolide tiglate (AT) is a novel potent inhibitor of MYB-dependent transcription. Further analysis revealed that C/EBPb, a transcription factor cooperating with MYB in myeloid cells, rather than MYB itself is inhibited by AT and related STLs. We show that these compounds induce apoptosis and differentiation in human acute myeloid leukemia (AML) cell lines and that ectopic expression of C/EBPbor of an activated version of MYB counteract these effects. Furthermore, gene expression profiling shows that AT as well as helenalin acetate, a compound previously shown to inhibit C/EBPb, affect the expression of a significant number of MYB-regulated genes although neither of these compounds targets MYB directly. Taken together these results suggest that C/EBPbp  lays a key role in AML cells by cooperating with MYB and supporting its activity. Finally, we show that AT inhibits primary murine and human AML patient cells in colony formation assays significantly stronger than normal hematopoietic progenitor cells. In summary, our work identifies several related STLs as novel potential drugs targeting AML and highlights a novel role of C/EBPbas a pro-leukemogenic factor in AML cells. We hypothesize that MYB and C/EBPbact together in a transcriptional module to maintain an undifferentiated state of AML cells and that targeting of this module via MYB or C/EBPbmay have therapeutic potential against AML.

overall_design:
Purpose: to reveal gene expression changes induced by AT or HA in THP-1 cells
THP-1 cells were grown in the presence or absence of 1 µm AT or 0.5 µm HA for 24 hs. RNA profiling was obtained in triplicate using Illumina NextSeq

first: Karl-Heinz

last: Klempnauer


title: Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [Ribo-Seq]

summary: In Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remain unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1 to synthesize 22G-RNAs concurrently with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ-granules. Moreover, differences in germline mRNA codon optimality and ribosome occupancy antagonistically affect the abundance of CSR-1 22G-RNAs and the stability of their mRNA targets. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy adopted in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

overall_design: 14 samples were analyzed by Ribo-seq, including replicates (sample name contains 'rep').

first: Meetali

last: Singh

first: Eric

last: Cornes

first: Blaise

last: Li

first: Pierguissepe

last: Quarato

first: Loan

last: Bourdon

first: Florent

last: Dingli

first: Damarys

last: Loew

first: Simone

last: Proccacia


title: Hypoxia-induced SETX links replication stress with the unfolded protein response

city: Oxford

first: Ester

last: Hammond

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

institute: University of Oxford

summary: Study of Transcriptomic changes upon Senataxin depletion in Normoxia and Hypoxia

overall_design: Examination of RKO under normaxia and hypoxia condition with SETX depletion.

first: Shaliny

last: Ramachandran

first: Tiffany

last: Ma

first: Natalie

last: Ng

first: Iosifina

middle: P

last: Foskolou

first: Ming-Shih

last: Hwang

first: Pedro

last: Victori

first: Wei-Chen

last: Cheng

first: Francesca

last: Buffa

first: Katarzyna

middle: B

last: Leszczynska

first: Natalia

last: Gromak


title: Non-Terminally Exhausted Tumor-Resident Memory HBV-specific T Cell Responses Correlate with Relapse-Free Survival in Hepatocellular Carcinoma

status: Public on Apr 21 2021

city: Singapore

first: Hong Kai

last: Lee

address: 8 Biomedical Grove

department: Singapore Immunology Network

country: Singapore

institute: Agency for Science, Technology and Research

summary: Hepatocellular carcinoma (HCC) often develops following chronic hepatitis B virus (HBV) infection and responds poorly to immune checkpoint blockade.   Here we examined the antigen specificities of HCC-infiltrating T cells and their relevance to tumor control. Using highly multiplexed peptide-MHC tetramer staining of unexpanded cells from blood, liver and tumor tissues from 46 HCC patients, we detected 91 different antigen-specific CD8+ T cell populations targeting HBV, neoantigen, tumor-associated and disease-unrelated antigens. Parallel high-dimensional analysis delineated five distinct antigen-specific tissue-resident memory T (Trm) cell populations. Intratumoral and intrahepatic HBV-specific T cells were enriched for two Trm cell subsets that were PD-1-low and TOX-low, despite being clonally expanded. High frequencies of intratumoral terminally exhausted T cells was uncommon. Patients with tumor-infiltrating HBV-specific CD8+ Trm cells exhibited longer-term relapse-free survival. Thus, non-terminally exhausted HBV-specific CD8+ Trm cells show hallmarks of active involvement and effective antitumor response, implying that these cells could be harnessed for therapeutic purposes.

overall_design:
Broad analysis of CD8 T cell antigen specificity in HBV-HCC patient blood/liver/tumor.

*** Raw data is to be made available through EGA due to privacy concerns ***

first: Yang

first: Evan

last: Newell


title: DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ATAC-seq]

first: Filippo M.

last: Cernilogar

overall_design: Chromatin accessibility analysis in 93T449 (ATCC #CRL-3043) human liposarcoma cells.

first: Sara

last: Lago

first: Gunnar

last: Schotta

first: Filippo

middle: M

last: Richter


title: Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [RIP-Seq]

first: Germano

last: Cecere

overall_design: 8 IP- 8 input paired samples were analyzed by sRNA-seq including replicates

first: Meetali

last: Singh

first: Eric

last: Cornes

first: Blaise

last: Li

first: Pierguissepe

last: Quarato

first: Loan

last: Bourdon

first: Florent

last: Dingli

first: Damarys

last: Loew

first: Simone

last: Proccacia


title: Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [ncRNA-seq]

overall_design: 37 samples were analyzed by sRNA-seq, including replicates (sample name contains 'rep').


title: Liver Transcriptomics from Mice on a Control vs Low Isoleucine Diet

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

summary: Mice were put on either a control or low isoleucine diet and their liver transcriptomic expression was measured in both the fasting and fed state. This was to discover the impact of reducing a single branched chain amino acid on the metabolism of the liver.

overall_design: To compare the metabolic effect of a Low Ile diet, 10-week-old male mice were placed on either a Control AA  or a Low Ile diet for 3 weeks. All mice were maintained at a temperature of approximately 22°C. Mice were euthanized by cervical dislocation and livers were harvested and snap frozen in liquid nitrogen following overnight (16-hr) fasting or refeeding.

first: Nicole

last: Richardson

first: Deyang

last: Yu

first: Dudley

last: Lamming


title: Transcriptome analysis of Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)-infected and Influenza A/H1N1-infected nasal turbinate and lung tissues

city: Jerusalem

first: Dana

last: Wolf

address: Ein Kerem

department: Dept. of clinical Microbiology & Infectious Diseases

country: Israel

institute: Hadassah University Hospital

summary: We report the application of RNA sequencing for transcriptome analysis of SARS-CoV-2-infected and Influenza A-infected Human nasal turbinate and lung tissues, enabling the study of tissue responses to viral infections

overall_design: Nasal turbinate tissues from three individuals and Lung tissues from five individuals, were either SARS-CoV-2-, Influenza A- or mock-infected and subjected to transcriptome analysis.

first: Or

last: Alfi


title: SF3B1 deficiency impairs human erythropoiesis via activation of p53 pathway: implications for understanding of ineffective erythropoiesis in MDS

city: New York

first: Xiuli

last: An

address: 310 E 67th St

institute: New York Blood Center

summary: SF3B1 knockdown in human CD34+ cells leads to increased apoptosis and cell cycle arrest of early-stage erythroid cells and generation of abnormally nucleated late-stage erythroblasts. RNA-seq analysis of SF3B1-knockdown erythroid progenitor CFU-E cells revealed altered splicing of an E3 ligase Makorin Ring Finger Protein 1 (MKRN1) and subsequent activation of p53 pathway.Decreased expression of genes involved in mitosis/cytokinesis pathway including polo-like kinase 1 (PLK1) was noted in SF3B1-knockdown polychromatic and orthochromatic erythroblasts comparing to control cells.

overall_design: RNA-seq analyses between normal erythropoiesis and  SF3B1 knockdown erythropoiesis


title: Transcriptome analysis of the extremotolerant Ramazzottius varieornatus exposed to 60Co gamma ray

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

summary: Transcriptome sequencing of Ramazzottius varieornatus exposed to 500Gy gamma ray.

overall_design: 27 samples, of which 3 are non-irradiated samples. All conditions are have 3 technical replicates.

first: Kazuharu

last: Arakawa


title: Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [GRO-Seq]

first: Germano

last: Cecere

overall_design: 6 samples were analyzed by GRO-seq, including replicates (sample name contains 'rep').

first: Meetali

last: Singh


title: Divergent resistance mechanisms to HER2-targeted therapies in breast cancer (scRNA-Seq)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

overall_design: scRNA-Seq of two HER2+ PDX models treated with chemotherapy or HER2-targeting agents

first: Michalina

last: Janiszewska

first: Shayna

last: Stein

first: Franziska

last: Michor


title: Divergent resistance mechanisms to HER2-targeted therapies in breast cancer (bulkRNA-Seq and Exome-Seq)

type: Genome variation profiling by high throughput sequencing

overall_design: Bulk RNA-Seq and exome seq on DNA and RNA of two HER+ PDX models treated with anti-HER2 drugs


title: Divergent resistance mechanisms to HER2-targeted therapies in breast cancer

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

overall_design: Refer to individual Series


title: Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

summary: The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies).  Three biological replicates were assigned for each group and in total 13 groups were prepared for ATAC-seq libraries. We mapped about 30 million reads per sample to D. discoideum with bowtie2 workflow.  Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed D. discoideum have dispartate chromatin accessibility regions throughout the genome.

overall_design: Fresh nuclei from vegetative, streaming, mound and fruiting body stages were extacted and transposed, and cDNA libraries were generated for deep sequencing, in triplicate, using Hiseq 4000

first: Simon

last: Yuan Wang

last: Liberman Greer


title: Next generation sequencing analysis of knockdown-Control and LINC00842-knockdown pancreatic cancer cell lines transcriptomes

city: Guangzhou

first: Xudong

last: Huang

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Gene expression profiling of pancreatic cancer cell PANC-1 and SW1990 when LINC00842 knockdown by CRISPR/Cas9 system. We identified LINC00842 is a novel prognosis related lincRNA in pancreatic cancer and its regulation networks is poorly understood. We used the total RNA from knockdown control and LINC00842-knockdown PANC-1 and SW1990 cells to analyze the differentially expressed genes which were regulated by LINC00842, and further explored the biological processes that LINC00842 may involved.

overall_design: Two-condition experiment, LINC00842-KD vs. KD-Ctrl PANC-1 and SW1990 cells, respectively. For construction of LINC00842 knockdown cells, we knocked in a 3 × poly (A) transcription stop cassette into the 5’ region of LINC00842 to transcriptional inhibited its expression by using CRISPR/Cas9 system. Biological replicates: 1 LINC00842-KD cell, 1 KD-Ctrl cell.

first: Jian

last: Zheng

first: Dongxin

last: Lin


title: The ZMYND8-regulated Mevalonate Pathway Endows YAP-High Intestinal Cancer with Metabolic Vulnerability

city: Shanghai

first: Qiang

last: Pan

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

summary: To elucidate the molecular basis by which ZMYND8 influences intestinal stemness and tumorigenesis, we performed RNA-seq to analyze gene expression in the crypts of 2-month-old Apcmin/+ and Apcmin/+; Zmynd8IEC–/– mice. Next, we performed chromatin immunoprecipitation (ChIP) sequencing (ChIP-Seq) to characterize the genomic distribution of ZMYND8 and SREBP2 in HCT116 WT and SREBP2-KO cells under sterol-depleted conditions.

overall_design: Total RNA was extracted from small intestinal crypts of 2-month-old Apcmin/+ and ZMYND8IEC-/-; Apcmin/+ mice. Each RNA sample contained 3 mice replicates and was pooled by equal mass to diminish variation. For ChIP sequencing, HCT116 WT and SREBP2-KO cells were cultured in LPDS for 24 hours and crosslinked. The pellets were harvested and performed by ChIP seq using ZMYND8 antibody (Bethyl A302-090A) and SREBP2 antibody (Cayman, 10007663).

first: Jun

last: Qin

first: Shanshan

last: Zhong

first: Hanling

last: Wang


title: Assessment of changes in gene expression and splicing in ecd1 homozygous mutant third-instar larvae kept at restrictive temperature (29°C)

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

institute: CECAD Research Center  Cologne

summary: Pre-mRNA splicing catalyzed by the spliceosome represents a critical step in the regulation of gene expression contributing to transcriptome and proteome diversity. The spliceosome consists of five small nuclear ribonucleoprotein particles (snRNPs) biogenesis of which remains only partially understood. Here we define the evolutionarily conserved protein Ecdysoneless (Ecd) as a critical regulator of U5 snRNP assembly and Prp8 stability. Combining Drosophila genetics with proteomic approaches we demonstrate Ecd requirement for the maintenance of adult healthspan and lifespan and identify the Sm ring protein SmD3 as a novel interaction partner of Ecd. We show that the predominant task of Ecd is to deliver Prp8 to the Sm protein ring within emerging U5 snRNPs. Ecd deficiency leads to reduced Prp8 protein levels and compromised U5 snRNP biogenesis, causing loss of splicing fidelity and transcriptome integrity. Based on our findings, we propose that Ecd acts as a chaperone that delivers Prp8 to the forming U5 snRNP allowing completion of the cytoplasmic part of the U5 snRNP biogenesis necessary to meet the demand of cells for functional spliceosomes.

overall_design: Total RNA of w1118 and ecd1 third instar larvae upshifted to 29°C was isolated, DNase treated and submitted for RNA sequencing

first: Steffen

last: Erkelenz

first: Dimitrije

last: Stanković

first: Tina

last: Bresser

first: Ann-Katrin

last: Claudius

first: Niels

last: Gehring

first: Volker

last: Boehm


title: Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score

city: Irvine

first: Li

last: Liang

address: MedSurge II

institute: University of California Irvine

summary: Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the intensive care unit (ICU), requirement for ventilators, or death. Importantly, anti-Ep9 antibodies can be detected within 6 days post-symptom onset and sometimes within 1 day. Furthermore, anti-Ep9 antibodies correlate with various comorbidities and hallmarks of immune hyperactivity. We introduce a simple-to-calculate, disease risk factor score to quantitate each patient’s comorbidities and age. For patients with anti-Ep9 antibodies, scores above 3.0 predict more severe disease outcomes with a 13.42 likelihood ratio (96.7% specificity). The results lay the groundwork for a new type of COVID-19 prognostic to allow early identification and triage of high-risk patients. Such information could guide more effective therapeutic intervention.

platform_organism: Severe acute respiratory syndrome-related coronavirus

platform_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Antibody profiling against 60 antigens across respiratory virus subtypes including 11 antigens from SARS-CoV-2 was performed on patient sera collected during COVID testing (n= 45).

first: Sanjana

last: Sen

first: Emily

last: Sanders

first: Kristin

last: Gabriel

first: Brian

last: Miller

first: Hariny

last: Isoda

first: Gabriela

last: Salcedo

first: Jason

last: Garrido

first: Rebekah

last: Dyer

first: Rie

last: Nakajima

first: Aarti

last: Jain

first: Ana

last: Caldaruse

first: Alicia

last: Santos

first: Keertna

last: Bhuvan

first: Delia

middle: F

last: Tifrea

first: Joni

middle: L

last: Ricks-Oddie

first: Philip

last: Felgner

first: Robert

middle: A

last: Edwards

first: Sudipta

last: Majumdar

first: Gregory

last: Weiss


title: Microarray expression profile from human dendritic cells (DCs) with or without DENV infection

city: Zhunan

first: Ling-Jun

last: Ho

address: 35, Keyan Road, Zhunan Town

department: Institute of Cellular and System Medicine

institute: National Health Research Institute

summary: To identify which genes could be modulated by DENV infection in human dendritic cells (DCs)

overall_design: Human dendritic cells (DCs) were infected with DENV (MOI=5) or mock infected for 24 h, and microarray analysis was conducted


title: The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription in Saccharomyces cerevisiae

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

summary: RSC (Remodels the Structure of Chromatin) is a conserved ATP-dependent chromatin remodeling complex that regulates many biological processes, including transcription by RNA polymerase II (Pol II). We report that not only RSC binds to nucleosomes in coding sequences (CDSs) but also remodels them to promote transcription. RSC MNase ChIP-seq data revealed that RSC-protected fragments were very heterogenous (~80 bp to 180 bp) compared to the sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC activity promotes accessibility of nucleosomal DNA. Importantly, RSC binding to +1 nucleosomes and CDSs, but not with -1 nucleosomes, strongly correlated with Pol II occupancies suggesting that the RSC enrichment in CDSs is important for efficient transcription. This is further supported by a similar heterogenous distribution of Pol II-protected fragments. As such, the genes harboring high-levels of RSC in their CDSs were the most strongly affected by ablating RSC function. Altogether, this study provides a mechanism by which RSC-mediated remodeling aids in RNA Pol II traversal though coding sequence nucleosomes in vivo.

overall_design: Formaldehyde crosslinked yeast cells were subjected either to MNase digestion or sonication to obtain chromatin. The input MNase, and ChIPed sonicated and MNase chroamtin was subjected to paired-end Illumina 4K sequencing.

first: Emily

last: Biernat


title: Transcriptome analysis in XACT deleted female human pluripotent stem cells

city: Isehara-shi

first: Atsushi

last: Fukuda

institute: Tokai University

summary: In this study, we generated female human pluripotent stem cells with the deletion of large non-coding RNA XACT specifically expressed in human pluripotent stem cells. We obtained heterogenous knock out and compound null clones. In order to examine, the effect of XACT on X-linked genes expression states, we carried out allele specific expression analysis.

overall_design: Using CRISPR-Cas9 system, about 400Kb XACT gene regions are depleted in female human iPS cell (HPS002).


title: Transcriptome analysis in D. discoideium (AX2) in different developmental stages

first: Eric

last: Greer

summary: The goal of RNA-seq is to identify the differential expressed genes in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies).  Two biological replicates were assigned for each group and in total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped about 20 - 30 million reads per sample to D. discoideum with bowtie2 workflow. The analysis pipeline started with pseudo-alignment of the reads using kallisto, followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth. Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05. Our results showed stage-specific gene expression profiles in different developmental stages.

overall_design: Messenger RNA from vegetative, streaming, mound and fruiting body stages were extacted and cDNA libraries were generated for deep sequencing, in duplicate, using Nextseq500

first: Simon

last: Yuan Wang

last: Liberman Greer


title: Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [RNA-Seq]

first: Germano

last: Cecere

institute: Institut Pasteur

summary: In Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remain unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1 to synthesize 22G-RNAs concurrently with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ-granules. Moreover, differences in germline mRNA codon optimality and ribosome occupancy antagonistically affect the abundance of CSR-1 22G-RNAs and the stability of their mRNA targets. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy adopted in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

overall_design: 13 samples were analyzed by RNA-seq, including replicates (sample name contains 'rep').

first: Meetali

last: Singh

last: Cornes

first: Blaise

last: Li

first: Pierguissepe

last: Quarato

first: Loan

last: Bourdon

first: Florent

last: Dingli

first: Damarys

last: Loew

first: Simone

last: Proccacia


title: Transcriptome analysis of gene expression changes in fer-8 and the parental line

city: Vancouver

first: Andrew

last: Wilson

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary: To reveal transcriptional changes in the fer-8 mutant that could explain the increase in Pseudomonas colonization, we performed transcriptional profiling in both shoots and roots from fer-8 and the parental line. We identified 675 up-regulated genes in the shoots of fer-8 relative to wildtype plants. Surprisingly, we found only 82 up-regulated genes in fer-8 roots relative to the parental line, and there were no significantly enriched GO terms. In contrast, we found that the genes upregulated in shoots were enriched in GO terms related to defense, response to fungi, and JA signaling, consistent with previous reports of JA activation in the shoots of another fer mutant fer-4.

overall_design: Using RNAseq approach to disect trangscriptome changes in roots and shoots in a novel mutant deficient in feronia receptor like kinase (fer-8).

first: Cara

last: Haney

first: Yi

last: Song


title: Chromatin accessibility in D. discoideium (AX2) in different developmental stages

country: USA

summary: The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies).  Two biological replicates were assigned for each group and in total 8 groups were prepared for ATAC-seq libraries. We mapped about 10 million reads per sample to D. discoideum with bowtie2 workflow.  Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed D. discoideum have dispartate chromatin accessibility regions throughout the genome.

overall_design: Nuclei from vegetative, streaming, mound and fruiting body stages were extacted and transposed, and cDNA libraries were generated for deep sequencing, in duplicate, using Nextseq500


title: Commensal yeast derived b-1,6-glucan induces regulatory T cells

city: Pohang

first: Gi-Cheon

middle: careful

last: Kim

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

institute: IBS

summary: To characterize the effect of MGCP in colonic dendritic cell phenotypic changes, we performed gene expression RNAseq analysis for colonic CD11c+ dendritic cells from mock or MGCP administered germ-free mice

overall_design: Total RNA was extracted from colonic dendritic cells from mock and CSGG treated germ-free mice.

first: C

last: Lee

first: R

last: Verma

first: E

last: Jeun

first: G

first: S

last: Im


title: Study of heavy metal stress in the basidiomycete Schizophyllum commune

status: Public on Apr 20 2021

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

institute: Friedrich-Schiller-University

summary: Transcriptome changes associated with metal stress were investigated in order to identify tolerance mechanisms and the impact on inositol signaling. The wild type S. commune 12-43 was compared with 12-43 grown with addition of contaminated seepage water (HSW) and another wild type strain W22 grown with 0.01 mM Cd.

overall_design: With microarray analysis, the mRNA expression pattern of heavy metal response was analyzed. The comparisons between the strain 12-43 and 12-43 grown on contaminated seepage water (HSW) and 12-43 with W22 grown with 0.01 mM Cd were observed. For each comparison two replicates were analyzed.

first: Lea

last: Traxler

first: Ines

last: Schlunk

first: Susann

last: Erdmann

first: Daniela

last: Freihorst

first: Katrin

last: Krause


title: OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis

city: Xiamen

first: Zhicheng

last: Gong

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

department: School of Life Sciences

institute: Xiamen University


title: Comparison of the specificities of the RGG/RG-domains of FMR1, FXR1 and FXR2 for small RNA

city: Ulm

first: Axel

last: Freischmidt

address: Albert-Einstein-Allee 11

department: Neurology

institute: Ulm University

summary: In previous studies, we identified a sequence motif (GDCGG) in almost all microRNAs downregulated in the serum of patients with amyotrophic lateral sclerosis. We found that FMR1, FXR1 and FXR2 directly and specifically interact with microRNAs containing the GDCGG motif via their RGG/RG-domains. Here, we compare the specificities for microRNAs of the RGG/RG-domains of FMR1, FXR1 and FXR2 on a transcriptome-wide scale using the Affymetrix GeneChip™ miRNA 3.0 Arrays.

overall_design: The recombinant RGG/RG-domains of FMR1, FXR1 and FXR2 (2.9 nmole), respectively, were incubated with 50 µg low molecular weight RNA isolated from HEK293 cells in 14 ml of buffer (25 mM Tris, 150 mM potassium chloride, 2.5 mM magnesium chloride, 0.5% NP-40, pH 7.5). After incubation, the recombinant proteins were isolated using Ni-NTA-Agarose (Qiagen #30210), extensively washed  and the co-purifying RNA compared to the input-RNA to identify binding microRNAs that get enriched by the different RGG/RG-domains. Three biological replicates were used for each RGG/RG-domain.

first: Karlheinz

last: Holzmann

first: Jochen

middle: H

last: Weishaupt


title: Single-cell transcriptome analysis in D. discoideum (AX4) in different developmental stages

first: Eric

last: Greer

summary: The goal of scRNA-seq is to identify the differential expressed genes in the wild-type D. discoideum at different developmental stages (vegetative, streaming, slug and fruiting bodies). Three biological replicates were assigned for each group and in total 12 groups were prepared for scRNA-seq libraries with 10000 cells as starting materials using Chromium Single Cell Gene Expression kit V3 (10x Genomics). Each sample was sequenced to an average of 393 million reads per sample with Illumina Hiseq 4000 and Novaseq 6000 platforms. The raw fastq files were processed by Cell Ranger (v 3.1.0, all with default setting except --normalize=none for aggr function) to generate the cell-barcode matrix. All downstreaming analysis was performed on R (3.6.3). Seurat package (3.1.5) was mainly used for basic analysis. Slingshot package was use for pseudotime analysis.

overall_design: Cells from vegetative, streaming, mound and fruiting body stages were isolated and scRNAseq libraries were generated for deep sequencing, in duplicate, using Hiseq4000 and Novaseq6000.

first: I

last: Wang

first: Simon

first: Paul


title: kidney organoids derived from human induced pluripotent stem cells (iPSC)

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

summary:
iPSCs were maintained on Geltrex coated flat culture dish in E8 media according to manufacturer’s guidelines. Colonies  were  manually harvested at 60-80% confluence. Cells were then collected and dissociated into single cells using EDTA. Cells were put on to ultra low attachment 24 well or 96 well plate  to allow them to form aggregated in suspension with ROCK inhibitor.
Cell aggregates 191were cultured in E8 medium with daily medium change for 6-7 days. Control iPSC-A (iPSC-aggregates) were plated on a Geltrex in 96 well plate or 8 well culture chamber. And then aggregates were treated E8 medium with daily medium change for 12-14 days.

overall_design: Starting from human IPSC in vitro kidney differentiation was performed in order to study transcriptome regulated program during this stage of development: initial human IPSC cell (PB33) was processed in duplicate et resulting kidney organoid was processed in duplicate

first: Jin

middle: W

last: Hwang

first: Christophe

last: Desterke

first: Frank

last: Griscelli

first: Annelise

last: Bennaceur-Griscelli

first: Ali

last: Turhan


title: Commensal yeast cell surface polysaccharide activities unleashed upon removal of b-1,3-glucans restrain inflammatory disorders

first: Changhon

last: Lee

address: 77 Cheongam-Ro, Nam-Gu

institute: POSTECH

summary: To characterize the effect of MGCP in dendritic cell phenotypic changes, we performed gene expression RNAseq analysis from CD8a-CD11b+ dendritic cells that stimulated with mock or MGCP in vitro.

overall_design: Total RNA was extracted from FACs sorted splenic CD8a-CD11b+ dendritic cells stimulated with mock or MGCP.

first: C

first: E

last: Jeun

first: G

last: Kim

first: S

last: Im


title: The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mice

city: Ann Arbor

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Ablation of the gustatory G-protein, GNAT3, in damage and KRAS G12D induced pancreatic transformation enhanced CXCL1 and CXCL2 expression, altered the immunoregulatory gene expression of CXCR2 expressing myeloid-derived suppressor cells, and increased gMDSC presence to promote the progression of metastatic pancreatic ductal adenocarcinoma.

overall_design: Pancreata from Kras LSL-G12D/+; Ptf1a CreERT/+; R26 LSL-EYFP and GNAT3-ablated Kras LSL-G12D/+; Ptf1a CreERT/+; R26 LSL-EYFP mice were subject to single-cell RNA-seq using a droplet partitioning method (10X Genomics Chromium platform).  Tissue from two mice per genotype were used in this study.

first: Megan

middle: T

last: Hoffman

first: Howard

last: Crawford


title: OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis [RNA-seq]

first: Zhicheng

last: Gong

summary: Genomic amplification of OTUD7B is frequently found across human cancers. But its role in tumorigenesis is poorly understood. Lysine‐specific demethylase 1 (LSD1) is known to execute epigenetic regulation by forming corepressor complex with CoREST/histone deacetylases (HDACs). However, the molecular mechanisms by which cells maintain LSD1/CoREST complex integrity are unknown. Here, it is reported that LSD1 protein undergoes K63‐linked polyubiquitination. OTUD7B is responsible for LSD1 deubiquitination at K226/277 residues, resulting in dynamic control of LSD1 binding partner specificity and cellular homeostasis. OTUD7B deficiency increases K63‐linked ubiquitination of LSD1, which disrupts LSD1/CoREST complex formation and targets LSD1 for p62‐mediated proteolysis. Consequently, OTUD7B deficiency impairs genome‐wide LSD1 occupancy and enhances the methylation of H3K4/H3K9, therefore profoundly impacting global gene expression and abrogating breast cancer metastasis. Moreover, physiological fluctuation of OTUD7B modulates cell cycle‐dependent LSD1 oscillation, ensuring the G1/S transition. Both OTUD7B and LSD1 proteins are overpresented in high‐grade or metastatic human breast cancer, while dysregulation of either protein is associated with poor survival and metastasis. Thus, OTUD7B plays a unique partner‐switching role in maintaining the integrity of LSD1/CoREST corepressor complex, LSD1 turnover, and breast cancer metastasis.

overall_design: RNA-seq was perform to illustrate How OTUD7B regulated genes expression

first: Han

last: You

first: Aicun

last: Li

first: Jiancheng

last: Ding


title: OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis [ChIP-seq]

overall_design: ChIP-seq performed in this study was designed to uncover the role of OTUD7B-mediated deubiquitination in LSD1 genome-wide distribution


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [miRNA-Seq]

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

summary: Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.

overall_design: We generated small RNA  sequencing data of  pig tissues with 1-3 replicates.

first: Long

last: Jin

first: Silu

last: Hu

first: Mingzhou

first: Qianzi

last: Tang


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq human]

overall_design: We generated RNA  sequencing (RNA-seq) data of adipose tissue of human with 3 replicates for inter-species comparison.


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [human Hi-C]

overall_design: We generated chromatin conformation capture  sequencing (Hi-C) data of adipose tissue of human with 3 replicates for inter-species comparison.


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [Spatial transcriptomic]

first: Bo

last: Zeng

state: Sichuan

address: 211 Huimin road, Wenjiang district

overall_design: This study takes pig psoas major muscle tissue in two replicates as the object. Through spatial transcriptome research, we clarified the gene expression distribution of different types of muscle fibers in the tissue, and their corresponding marker genes were inentified.


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq for pig and rat]

sample_organism:
Sus scrofa
Rattus norvegicus

platform_organism:
Sus scrofa
Rattus norvegicus

overall_design: We generated RNA sequencing (RNA-seq) data of adipose tissue of rat, rabbit, pig, sheep, cat and dog with 1-6 replicates.


title: Determine the genome-wide localization of histone and histone marks in different stages of D. discoideum

first: Eric

last: Greer

address: 320 Longwood Avenue

institute: Boston Children's Hospital/Harvard Medical School

summary: We report the chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) on H3, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, and H3K36me3.  ChIP-seq were sequenced to a depth of at least 8 million total reads/sample. We found that H3K4me3, H3K27ac and H3K4me1 show separation between unicellular and multicellular stages in principal component analysis (PCA); other marks were unable to show a clear separation in PCA.

overall_design: Examine the localizaiton of histone marks and nucleosome postioning in D. discoideum (AX2) thorughout the genome

first: Simon

last: Yuan Wang

last: Liberman Greer


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq across species]

sample_organism:
Gallus gallus
Macaca mulatta
Canis lupus familiaris
Felis catus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus
Cavia porcellus

overall_design: We generated RNA sequencing (RNA-seq) data of varies tissues across 9 species with 1-3 replicates for inter-species comparison.