title: Genome-wide analysis of enhancer landscape in colorectal cancer subgroups (ChIP-seq)

first: Qinglan

last: Li

summary: Colorectal cancer (CRC) is a highly malignant solid tumor and causes millions of cancer related death worldwide. Here, using H3K27ac chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with gene expression data (RNA-seq), we describe the active cis-regulatory landscape across more than seventy diverse CRC patient tissues, including tumor and native tissue. Analysis of the enhancers and super-enhancers with recurrently gained or lost activity revealed novel, clinically relevant insights into CRC biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors which is responsible for tumorigenesis and the maintenance of normal intestinal function. Genomic studies have revealed four distinct consensus molecular subgroups (CMS) with divergent biology and clinical behavior and we reveal that differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity. Our integrated analysis of enhancer elements in a large series of CRC patient paired samples reveals novel insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.

overall_design: Histone modification profiles (H3K27ac and H3K4me3) of tumor and native tissue from 74 CRC patients were generated by ChIP-seq, using Illumina NovaSeq.

first: Qing-lan

first: Xiang

last: Lin

first: Qi-xin

last: Hu

first: Lin

first: Meng

first: Lian-yun

first: Mei

last: Ye

first: Min

last: Wu


title: Chromatin Occupancy of AR, BRD4, and H3K27Ac in MR42D Cells in response to Enzalutamide

status: Public on Jun 22 2021

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

country: USA

institute: Oregon Health & Science University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Epigenetic abnormality due to maternal Zika virus infection

status: Public on Jun 30 2021

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

type: Methylation profiling by high throughput sequencing


title: Distinct chromatin signatures and transcriptional landscape of functional genetic elements in allohexaploid wheat

status: Public on Jun 17 2021

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing


title: STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq]

status: Public on Jun 06 2021

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

summary: Abstract to add later

overall_design: Determination of the sequence of full-length transcripts from mouse embryonic stem cells (ESC) cultured in naïve 2i conditions. PolyA-enriched mRNAs were selected by hybridization to a custom oligo probe set and post-capture, mRNAs were amplified using the Clontech SMARTer PCR cDNA Synthesis Kit with 9 cycles and used in the SMRTbell library prep.  The library was sequenced on the SMRTseq 2000 platform.  PacBio reads were processed through the SMRTLINK v8.0.0 IsoSeq3 pipeline and the PacBio Isoseq transcripts were mapped using minimap2.

first: Dubravka

last: Pezic

first: Wazeer

last: Varsally

first: Samuel

middle: L

last: Weeks


title: PEZIC_STAG1_Pluripotency


title: CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [ChIP-seq]

status: Public on Aug 02 2021

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

summary: CTCF is an 11-zinc-finger DNA-binding protein that acts as a transcriptional repressor and insulator, as well as an architectural protein required for 3D genome folding. CTCF mediates long-range chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), which are sub-megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos, its in vitro removal has only modest effects over gene expression, challenging the generally accepted idea that TADs facilitate enhancer-promoter interactions within gene regulatory landscapes. However, the effects of an altered CTCF-mediated chromatin structure on gene regulation in vivo are poorly understood. Here, we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes, among them many developmental genes. In addition, we show that chromatin accessibility, both at CTCF sites and at developmental cis-regulatory elements (CREs), is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution, we further demonstrate that promoters fail to fully establish long-range contacts with their associated regulatory landscapes, leading to altered gene expression patterns during development. Therefore, our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development, providing the structural basis for the establishment of developmental gene regulatory landscapes.

overall_design:
ChIP-seq assays in wild-type zebrafish embryos at developmental stage 24 hpf
The antibody was kindly provided by Felix Rencillas-Targa (Universidad Nacional Autonoma de Mexico) and previously publised PMID: 29723654. It is a zebrafish-specific antibody generated in rabbit using as epitope a fragment containing aminoacids 723-798 (C-terminal domain) of the zebrafish CTCF protein.

first: Martin

last: Franke

first: Elisa

last: De la Calle-Mustienes

first: Ana

last: Neto

first: María

last: Almuedo-Castillo

first: Ibai

last: Irastorza-Azcárate

first: Rafael

middle: D

last: Acemel

first: Juan

middle: J

last: Tena

middle: M

last: Gómez-Skarmeta


title: Genome-wide analysis of enhancer landscape in colorectal cancer subgroups (RNA-seq)

status: Public on Aug 26 2021

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

overall_design: mRNA profiles of tumor and native tissue from 72 CRC patients were generated by RNA-seq, using Illumina NovaSeq.

first: Qing-lan

first: Xiang

last: Lin

first: Qi-xin

last: Hu

first: Lin

last: Chen

first: Meng

first: Lian-yun

first: Mei

last: Ye

last: Wu


title: Chromatin Occupancy of AR, BRD4, and H3K27Ac in MR42D Cells in response to Enzalutamide [RNA-seq]

first: Zheng

last: Xia

summary: To identify mechanisms that contribute to lineage plasticity and t-NEPC, we focused on enza-resistant cell lines with persistent AR expression that have features of lineage plasticity, including high expression of NEPC markers: the MR42D and MR42F cell lines. We cultured these enzalutamide resistant lines, which are usually maintained in medium with enzalutamide, without enzalutamide for 72 hors to "washout" the effects of enzalutamide, and then either enzalutamide or vehicle was added back to the growing media for 24 hours. Enzalutamide sensitive lines LNCaP and V16D were treated with either enzalutamide or vehicle for 24 hours. Enzalutamide reversibly increased expression neuronal markers in MR42D and MR42F cells, but not enza-sentitive LNCaP and V16D cells, suggesting that the AR may negatively regulate neuronal gene expression in these t-NEPC cells. Moreover, bromodomain inhibitors (BETi) ARV-771 and JQ1 reduced expression of NEPC target genes in MR42D cells.

overall_design: Four cell lines (MR42D, MR42F, LNCaP, and V16D) were treated with the AR-antagonist Enzalutamide (MDV) or Vehicle (DMSO) in biological triplicate. Separately, in culture media with enzalutamide present, the MR42D cell line was also treated with Bromodomain-inhibitors ARV771, JQ1, or Vehicle also in biological triplicates.

first: Dae-Hwan

last: Kim

first: Duanchen

last: Sun

first: Katherine

last: Welker-Leng

first: Joshua

last: Urrutia

first: Joshi

last: Alumkal


title: RNA-Seq analysis identifies to GATA3-AS1 as a lncRNA associated with resistance to neoadjuvant chemotherapy in locally advanced breast cancer patients

status: Public on Jul 12 2021

city: CDMX

first: Luis

middle: Alonso

last: Herrera Montalvo

state: CDMX

address: Av. San Fernando 22

department: Investigación

country: Mexico

institute: Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas

summary:
Purpose: Identified the expression profile of lncRNA associated to neoadjuvant chemotherapy response in 11 tumor of locally advanced breast cancer patients
Methods: We implemented the transcriptomic analysis from 11 breast cancer samples by paired-end RNA-Seq, as a case-control study (responders vs nonresponders group). Differential expression analysis for lncRNA and mRNA were made to identify lncRNA as predictive biomarkers.
Results: We identified the over-expressed lncRNA GATA3-AS1 in nonresponders group. Additionally, we identified the pathways were differentially expressed lncRNA and mRNA are associated in neoadjuvant chemotherapy response.
Conclusion: we propose lncRNA GATA3-AS1 as a potential predictive biomarker for patients with LABC luminal B-like subtype that will not respond to neoadjuvant chemotherapy

overall_design: Transcriptomic analysis of 11 tumor samples from locally advanced breast cancer mexican patients in a case-control study (responders vs nonresponders group), in order to identify lncRNA associated to neoadjuvant chemotherapy response.

first: L

last: Contreras-Espinosa

first: N

last: Alcaraz

first: I

middle: A

last: De La Rosa-Velázquez

first: J

last: Díaz-Chávez

first: P

last: Cabrera-Galeana

first: R

last: Rebollar Vega

last: Reynoso-Noveron

last: González-Barrios

last: Montiel-Manríquez

first: D

last: Bautista-Sánchez

first: C

last: Castro-Hernández

last: Álvarez-Gómez

first: F

last: Jiménez-Trejo

first: M

last: Tapia-Rodríguez

last: García-Gordillo

first: A

last: Pérez-Rosas

first: E

last: Bargallo-Rocha

last: Arriaga-Canon

last: Herrera


title: Expression profile in the progression of the gastric cancer

status: Public on Jul 09 2021

city: wuxi

first: fangmei

last: an

state: jiangsu

address: NO 299,QingYang Road

institute: Wuxi Public Hospital


title: Expression data of the livers of male C57Bl6/N mice after chronic adminitstration of CCl4 for up to one year

city: Heidelberg

first: Christian

middle: H.

last: Holland

address: Im Neuenheimer Feld 267

department: Institute for Computational Biomedicine

country: Germany

institute: Heidelberg University

summary: Chronic administration of CCl4 represents a frequently applied technique to induce liver cirrhosis in mice.

overall_design: A mouse model with 8 to 10 week-old male C57BL/6N mice (Janvier Labs, France) was applied. Carbon tetrachloride (CCl4, 1 g/kg b.w. in olive oil) was injected intraperitoneally (i.p.) twice a week for 2, 6, and 12 months. The used CCl4 was obtained from Sigma-Aldrich (289116-1L, Germany). The vehicle controls received only olive oil in the same way as the CCl4 groups. Vehicle controls were processed after 2 and 12 months. Samples were collected on day 6 after the last CCl4 or oil injection. The mice received a standard diet (Ssniff, Soest Germany) ad libitum before and after CCl4 administration.

first: Ahmed

last: Ghallab

middle: H

first: Jan

middle: G

last: Hengstler


title: Acute myeloid leukemia cell line RNA-Seq

status: Public on May 26 2021

city: Berkeley

first: Brian

last: Li

state: California

address: 2521 Hearst Avenue

institute: University of California, Berkeley

summary: We performed RNA-Seq on acute promyelocytic leukemia (APL) cells treated with both all-trans retinoic acid (ATRA) and trichostatin A (TSA) to identify transcriptional changes potentially associated with changes in APL cell mechanical properties. As a control, we performed the same treatments and RNA-Seq analysis on HL-60 cells, which were derived from a patient diagnosed with APL but whose cells lacked the hallmark fusion gene associated with APL. We performed RNA-Seq on these three cell lines (AP-1060, NB4, HL-60) under different conditions (untreated, TSA, ATRA, TSA + ATRA), and identified differentially expressed genes between samples and conditions. This study identified differentially expressed genes and enriched gene sets associated with (1) a resistance to differentiation induced by ATRA or (2) changes in mechanical properties. Overall, we find evidence that ATRA resistance and mechanical properties may be linked by the degree of chromatin condensation in APL cells.

overall_design: A total of 36 samples were analyzed. For each of the 3 cell lines, there were 3 experimental groups (+ATRA, +TSA, +ATRA+TSA) and one untreated control. Each of these experimental groups were analyzed in triplicate.

first: Annie

last: Maslan

first: Aaron

last: Streets

first: Lydia

last: Sohn


title: Transcriptomic Analysis of Laser Capture Microdissected Tumors of Pancreatic Ductal Adenocarcinoma

city: Boston

first: Andrew

middle: S

last: Liss

state: MA

address: 55 Blossom St

department: Surgery

institute: Massachusetts General Hospital

summary: In this study, we performed laser capture microdissection (LCM) of PDAC samples to define their cancer- and stroma-specific molecular subtypes and identify a prognostic gene expression signature for short-term and long-term survival. LCM and RNA-seq analysis of cancer and adjacent stroma of 19 treatment-naïve PDAC tumors were performed. Gene expression signatures were tested for their robustness in a large independent validation set. An RNA in situ hybridization (RNA-ISH) assay with pooled probes for genes associated with disease-free survival (DFS) was developed to probe 111 PDAC tumor samples. Gene expression profiling identified four subtypes of cancer cells (C1-C4) and three subtypes of cancer-adjacent stroma (S1-S3). These stroma-specific subtypes were associated with DFS (p=5.55E-07), with S1 associated with better prognoses when paired with C1 and C2. Thirteen genes were found to be predominantly expressed in cancer cells and corresponded with DFS in a validation using existing RNA-seq datasets. A second validation on an independent cohort of patients using RNA-ISH probes to six of these prognostic genes demonstrated significant association with overall survival (median 17 versus 25 months; p<0.02). Our results identified specific signatures from the epithelial and the stroma components of PDAC, which add clarity to the nature of PDAC molecular subtypes and may help predict survival.

overall_design: Gene expression analysis of cancer cells and adjacent (<280 μm) stromal cells

first: David

last: Birnbaum

first: Sebastian

middle: K

last: Begg

first: Pascal

last: Finetti

first: Charles

last: Vanderburg

first: Anupriya

last: Kulkarni

first: Azfar

last: Neyaz

first: Thomas

last: Hank

first: Eric

last: Tai

first: Vikram

last: Deshpande

first: Francois

last: Bertucci

first: Daniel

first: Keith

last: Lillemoe

last: Warshaw

first: Mari

last: Mino-Kenudson

first: Carlos

last: Fernandez-Del Castillo

middle: T

last: Ting


title: Serum miRNA-based signature to identify radiation exposure and dose in humans

status: Public on May 20 2021

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary: Previously, we used mouse and non-human primate models to show that serum miRNAs may predict the biological impact of lethal and sublethal radiation doses. We hypothesized that these results can be replicated in humans treated with total body irradiation (TBI), and that miRNAs may be used as clinically feasible biodosimeters. To test this hypothesis, serial serum samples were obtained from 25 patients who underwent allogeneic stem-cell transplantation and profiled for miRNA expression using next-generation sequencing. Differential expression results were largely consistent with previous studies and allowed us to select miRNAs, including miR-150-5p, miR-126-5p, miR-375, miR-215-5p, miR-144-5p, miR-122-5p, miR-320d and miR-10b-5p to build classifiers using qPCR-based quantification. We therefore conclude that serum miRNAs reflect radiation exposure and dose for humans undergoing TBI and may be used as functional biodosimeters for precise identification of people exposed to clinically significant radiation doses.

overall_design: Serial serum and serum-isolated exosome miRNA profiles of 25 patients (children and adults) subjected to total body irradiation (total 71 samples)

first: Wojciech

last: Fendler

first: Zuzanna

last: Nowicka


title: Single cell characterization of the immune microenvironment of melanoma brain and leptomeningeal metastases

status: Public on May 14 2021

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: Melanoma brain metastases (MBM) and leptomeningeal metastases (LMM) are two manifestations of melanoma CNS metastasis with vastly different survival outcomes. Using single cell RNA-Seq analysis we uncovered a unique, immune-suppressed T-cell landscape in the LMM microenvironment distinct from that of brain and skin metastases. An LMM patient with an unusually long survival demonstrated an immune repertoire that was distinct from those of poor survivors and more similar to CSF from non-LMM patients. Upon response to PD-1 therapy, this extreme responder showed increased levels of T-cells and dendritic cells in their CSF, whereas poor survivors showed little improvement in their T-cell responses. In MBM patients, systemic therapy was associated with increased immune infiltrate, with similar T-cell transcriptional diversity noted between skin metastases and MBM - suggestive of immune cell trafficking into the brain. A correlation analysis across the entire immune landscape identified the presence of a rare population of dendritic cells (DC3s) that correlated with increased overall survival and positively regulated the immune environment through modulation of activated T-cells and MHC expression. Our study provides the first atlas of two distinct sites of melanoma CNS metastases and identifies rare populations of cells that underlie the biology of this devastating disease.

overall_design: Single cell rnaseq of immune microenvironment of cutatneous melanoma, and brain, leptomeningeal metastases.

first: Inna

first: Zhihua

last: Chen

first: Yian


title: Role of thiosulfate as a source of energy in the bathypelagic North Atlantic Ocean

status: Public on Apr 30 2021

city: Vienna

first: Juan

last: Garcia

address: Althanstraße 14

country: Austria

institute: University of Vienna

summary: The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.

overall_design: Samples collected at 2000 m depth were amended with thiosulfate, thiosulfate plus glucose and acetate, or not amended (control), and incubated for up to 72h, in the dark, at in situ temperature. At the end of the incubation, samples were filtered onto 0.2µm policarbonate filters. The filters were stored at -80ºC until extraction of the RNA. RNA was paired-end sequenced on Illumina HiSeq.

first: Abhishek

last: Srivastava

first: Brandon

last: Swan

first: Ramunas

last: Stepanauskas

first: Gerhard

last: Herndl

first: Eva

last: Sintes


title: Long-range effects of centromeres on the binding of the meiotic chromosome axis factor Red1

status: Public on May 21 2021

city: New York

first: Andreas

last: Hochwagen

state: New York

address: 100 Washington Square East, 1009 Silver Center

department: Biology

institute: New York University

summary: A chromosome size-dependent bias in meiotic recombination is in place to ensure that homologous chromosome pairing occurs for all chromosomes, including the smallest ones. This bias is clearly detectable during the assembly of the meiotic protein axis, the structure that compacts meiotic chromosomes and promotes recombination.To investigate the origin of the size bias, we mapped genome-wide occupancy of the meiotic axis protein Red1 in yeast strains containing chromosome fusions and synthetic chromosomes. Meiosis studies of the fusion and synthetic chromosomes further revealed that core centromeres influence the deposition of the axial element protein Red1 over distances >100kb, while pericentromeric regions co-evolved to reduce Red1 binding near centromeres and spread out Red1 along the chromosomes.

overall_design:
ChIP-seq analysis of Red1 DNA binding 3 hrs after induction of synchronous meiosis in SK1/S288C hybrid budding yeast strains containing fusions of SK1 chromosomes.

Grant: March of Dimes FY16-208
Title: Meiotic segregation of small chromosomes
PI: Andreas Hochwagen, New York University, New York, NY, United States

Grant: NSF MCB-1616111
Title: Complete synthesis of designer eukaryotic genome, Sc2.0
PI: Jef D. Boeke, New York University Medical Center, New York, NY, United States

first: Adhithi

middle: R

last: Raghavan

first: Jonna

last: Heldrich

first: Luis

last: Vale-Silva

first: Jingchuan

last: Luo

first: Jef

last: Boeke


title: Single-cell polyadenylation sequencing (scPolyA-seq) reveals the dynamic of polyA site usage during cell cycles in tumor cell lines [C1]

status: Public on Jun 16 2021

city: Shenzhen

first: Wenfei

last: Jin

state: Guangdong

address: 1088 Xueyuan Rd #faculty research building 1

department: Department of Biology

institute: Southern University of Science and Technology

summary: Alternative polyadenylation (APA) plays an important role in post-transcriptional gene regulation. But how genes' APA usages are influenced by cell cycle remains largely unknown. Here we developed single cell polyadenylation sequencing (scPolyA-seq), a strand-specific approach for sequencing 3’ end of transcripts which can get very deep sequencing level around polyA site for each cell, to investigate the landscape of APA at single cell level, based on Fluidigm C1. We compared APA changes before and after thymidine double blocking (TdR) synchronization of HeLa cells. We then identify 6 gene clusters whose distal polyA site usages fluctuate during cell cycle.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We performed scPolyA-seq, a single-cell RNA sequencing method we devised based on fluidigm C1, on cell line mixtures of Mouse embryonic fibroblasts (MEFs) + synchronized HeLa and MDA-MB-468 + HeLa. We used a Fluidigm C1 HT IFC chip, which could separate 800 single cells, including 20 columns and 40 rows. Cell mixture1 (suspensions of MEFs containing ~10% synchronized HeLa cells, column 1 to 10) and cell mixture 2 (suspensions of MDA-MB-468 containing ~10% HeLa cells, column 11 to 20) were loaded into two independent inlets of a C1 HT integrated fluidics circuit (IFC), thus up of 400 cells could be captured for each cell suspension. Totally 16 columns passed library quality control and were sequenced in PE 150bp. Read 1 was only used as cell barcode, while Read 2 was used in further analysis. Each column of data would be then demultiplexed into 40 cells by a Perl script named “mRNASeqHT_demultiplex.pl” according to the cell barcode in Read 1. Two bulk libraries of MDA-MB-468 cells were also constructed using the same protocol. This series includes mouse and human cell lines, but we mainly focus on analyzing human cell lines in our paper.

Notice: Read 1 carries cell barcode, while Read 2 may contain polyA sites and sequences nearby. Read 2 is used for identifying the polyA sites and calculating gene expression in our work. As some researchers want to re-use our Read 1 data, we also upload these raw data with '_R1' in their file names, but users must be cautious that sequence quality may be quite low after polyT region, which is common issue for NGS.

first: Junliang

last: Wang

first: Wei

first: Ting

last: Ni


title: STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C]

first: Suzana

last: Hadjur

summary: Abstract to be added later

overall_design: To determine the chromatin conformation contact profiles of specifc sites in the mouse genome we used UMI-4C. This allowed us to also calculate cell-type specific contact distributions.

first: Dubravka

last: Pezic

first: Wazeer

last: Varsally

first: Samuel

last: Weeks


title: Genome-wide GR occupancy and chromatin landscape in skeletal muscles.

status: Public on Apr 10 2021

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary:
Purpose: The aim of this study is to identify the GR genome binding profile as well as that of Pol II, H3K27ac, H3K4me1, H3K4me3 and Ctcf in skeletal muscles.
Methods: Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 4000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Data were further analysed using the peak finding algorithm MACS 2 (Zhang et al., 2008) using input as control. All peaks with FDR greater than 0.1 % were excluded from further analysis. The uniquely mapped reads were used to generate the genome-wide intensity profiles, which were visualized using the IGV genome browser (Thorvaldsdottir et al., 2012).
Results: HOMER (Heinz et al., 2010) was used to annotate peaks, to calculate overlaps between different peak files, and for motif searches. The genomic features (promoter, exon, intron, 3’ UTR, and intergenic regions) were defined and calculated using Refseq and HOMER. Genes annotated by HOMER were further used for a pathway analysis in WebGestalt (Heinz et al., 2010; Wang et al., 2013).

overall_design: Nuclei were extracted from skeletal muscles from 10-week-old mice as described in Joshi 2017.

first: Daniel

last: Metzger

first: Daniela

last: Rovito

first: Shilpy

last: Joshi

first: Anna-Isavella

last: Rerra


title: Transcriptomics analysis of differentially expressed genes in subcutaneous and perirenal adipose tissue of sheep as affected by their pre- and early postnatal malnutrition histories

status: Public on Apr 17 2021

city: Tjele

first: Mette

middle: Olaf

last: Nielsen

address: Blichers Alle 20

department: Animal Science

country: Denmark

institute: Aarhus University

summary: This study aimed to identify the genes (including hub genes) and biological pathways that are responsible for the observed changes on subcutaneous and perirenal adipose tissue morphological triats and tissue specific responses to early life malnutrition in a precocial sheep model.

overall_design: This study compared the mRNA expression levels within each adipose tissue (subcutaneous and perirenal adipose tissue) obtained from 2.5-years old sheep that has been subjected to different late gestational nutrition (6 week prepartum, terms=147 days) such as  NORM (normal; fulfilling 100% energy and protein requirement), LOW (undernutrition; 50% of NORM) and HIGH (overnutrition; fulfilling 150% and 110% energy and protein requirement) followed by early postnatal CONV (moderate low fat) or HCHF (high-carbohydrate-high-fat) diet from day 3 until 6 months of age (adolescent). Thereafter, all animals were fed with similar low fat hay-based diet for 2 years.

middle: O

first: Sharmila

last: Ahmad

first: Markus

last: Drag

first: Suraya

last: Salleh

first: Zexi

last: Cai


title: Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer/promoter dynamics [ChIP-seq]

status: Public on Apr 01 2021

city: Cambridge

first: Ernest

last: Laue

address: 80 Tennis Court Road

department: Department of Biochemistry

institute: University of Cambridge

summary:
Enhancer-promoter dynamics are critical for the spatiotemporal control of gene expression, but it remains unclear how these dynamics are controlled by the nucleosome remodelling and deacetylase (NuRD) complex that is found at nearly all active enhancers and promoters.
We show that MBD3-dependent assembly of the intact NuRD complex increases CTCF/Cohesin binding (using ChIP-seq) and the probability of the interaction of intermediate-range (~1Mb) genomic sequences (using population Hi-C).
Using single-molecule imaging, we then revealed that these changes are related to how the chromatin moves, and that the intact NuRD complex increases how fast the nucleus is explored by NuRD-bound enhancers and promoters.

overall_design: Comparison of CTCF and Smc3 binding to chromatin in wild-type and Mbd3-knockout ES cells

first: Brian

last: Hendrich


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [NelfE_Cut&Tag]

status: Public on Mar 18 2021

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

summary: Negative Elongation Factor (NELF) is a critical transcriptional regulator that works through stabilizing paused RNA Polymerase to permit rapid gene expression changes in response to environmental cues. Whilst NELF is essential for embryonic development, its role in adult stem cells remains unclear. Here, through a muscle stem cell-specific deletion, we show that NELF is required for efficient muscle regeneration and replenishing the stem cell pool. Mechanistic studies using PRO-seq, single cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of muscle regeneration whereby it mediates massive expansion of muscle progenitors. Strikingly, transplantation experiments indicate that these progenitors are also necessary for stem cell pool repopulation implying they are able to return to quiescence. Thus, we identified a critical role for NELF in expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to stem cell pool repopulation.

overall_design: Myoblasts were isolated from Wildtype (WT) and NELF-BscKO (KO) mice in biological triplicate, and expanded in vitro. Ex vivo knockout was induced with 4-hydroxy-tamoxifen over 72 hours, and the resulting populations used for sample preparation

middle: C

last: Robinson

first: Morten

last: Ritso

first: Geoffrey

last: Nelson

first: F


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [S5_RNApolII_Cut&Tag]


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [RNAseq_48hrs]

overall_design: RNA-seq was performed on myogenic progenitor cells which were FACS isolated from regenerating skeletal muscle 48-hours after skeletal muscle damage was induced with Cartiotoxin. Three replicates were performed for Wildtype (WT) populations, and three replicates performed for NELF-BscKO (KO) populations.


title: STAG proteins mediate heterochromatin organization to support translation and cell identity [RNA-Seq]

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

institute: Ucl

summary: Abstract to be added later

overall_design: To determine the effect on the transcriptome upon Stag1 loss.  Mouse embryonic stem cells (ESC) were cultured in serum (FCS) or naïve (2i) conditions. ESCs were treated for 24hrs with siRNA pools to Stag1 (SA1) including, SmartPool (SP), 5' or 3’ end of Stag1 (5p and 3p) and two sets of control siRNAs, scrambled (SCR) and Luciferase (Luc).  There are three replicate sets for SP KD and two for the siRNA pools. Total RNA was first depleted of rRNA (ES FCS) or enriched for PolyA (ES 2i).  RNA-seq libraries were prepared using NEBNext Ultra directional RNAseq kit with 8-10 cycles of PCR. Libraries were sequenced on the Illumina HiSeq3000 platform, 75bp paired-end reads

first: Dubravka

last: Pezic

first: Wazeer

last: Varsally

first: Samuel

middle: L

last: Weeks


title: Chromatin architecture transitions from zebrafish sperm through early embryogenesis [Hi-C]

status: Public on Apr 05 2021

city: Salt Lake City

first: Bradley

last: Cairns

state: UT

address: 2000 Cir of Hope Dr

department: oncological Sciences

institute: Huntsman Cancer institute/HHMI

summary: Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps.  Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control.  We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable.  Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.

overall_design: Zebrafish sperm, and Embryos of 2.25, 4, 5.3 and 24 hours after fertilization were processed for Hi-C. ChIP-seq at 4hpf for RNA polymerase II and ATAC-seq performed at 4hpf.

first: Candice

last: Wike


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [single-cell RNA]

summary: Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation.

overall_design: RNA-seq performed on myogenic precursors which were isolated from regenerating skeletal muscle (mouse) at 5 days post-injury for wild type and NELF-B knockout populations.

first: Daniel


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation {ChIP-seq]

overall_design: RNA Pol II position in wild type cultured primary myoblasts


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [RNA-seq]

summary: Negative Elongation Factor (NELF) is a critical transcriptional regulator that works through stabilizing paused RNA transcripts to permit rapid gene expression changes in response to environmental cues. Whilst NELF is essential for embryonic development, its role in adult stem cells remains unclear. Here, through a muscle stem cell-specific deletion, we show that NELF is required for efficient muscle regeneration and replenishing the stem cell pool. Mechanistic studies using PRO-seq, single cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of muscle regeneration whereby it mediates massive expansion of muscle progenitors. Strikingly, transplantation experiments indicate that these progenitors are also necessary for stem cell pool repopulation implying they are able to return to quiescence. Thus, we identified a critical role for NELF in expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to stem cell pool repopulation.


title: Differentially Expressed Mitochondrial Circulating mRNA in Hypothyroidism Could Be Useful as a Survivor Biomarker in Nonthyroidal Illness Syndrome

status: Public on Jun 05 2021

city: SAO PAULO

first: Robson

middle: José de

last: Almeida

state: SAO PAULO

address: RUA VERGUEIRO 235 249

department: Pós Graduação Stricto Sensu em Medicina

country: Brazil

institute: Universidade Nove de Julho

summary: RNA libraries were constructed from whole blood. We called hypothyroidism differentially expressed genes with the Noiseq. We found a total of 4,197 transcripts regulated by the thyroid hormone present in the peripheral blood. We also found that three hundred and thirty-six (8.01%) were mitochondrial genes type.

overall_design: It was constructed libraries of four subjects with TSH within reference range to compose the control (CTL) group and four hypothyroidism patients (HT).

first: R

first: A

last: Hirata

first: L

last: Rocha

first: M

last: Motta

first: P

last: Varela

last: Silva

first: J

middle: B

last: Pesquero

first: C

middle: P

last: Camacho


title: Vector-borne Trypanosoma brucei parasites develop and persist in artificial human skin as skin tissue forms

status: Public on May 30 2021

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the infective quiescent metacyclic stage into the mammalian skin at the site of the fly’s bite. In the skin, the metacyclic parasites reactivate and differentiate into proliferative trypanosomes before colonizing the host's blood and tissues. We have generated an advanced human skin equivalent and used tsetse flies to naturally infect the artificial skin with trypanosomes. We have detailed the chronological order of the parasites' development in the skin and found a rapid activation and differentiation of the tsetse-transmitted cell cycle‑arrested metacyclic trypanosomes to proliferative parasites. Single-parasite transcriptomics documented the biological events during differentiation and host invasion at five different time points. After the establishment of a proliferative trypanosome population in the skin, the parasites entered a reversible quiescence program characterized by slow replication and a strongly reduced metabolism. We termed these quiescent trypanosomes skin tissue forms (STF), which may play an important role in maintaining the trypanosome infection in aparasitemic, asymptomatic individuals.

sample_organism:
Trypanosoma brucei
Homo sapiens

platform_organism:
Trypanosoma brucei
Homo sapiens

overall_design: After natural infection, skin equivalents were cultured for another 4 h, 12 h, 24 h, and 7 d, respectively. In addition, freshly collected MCFs obtained from tsetse flies were used. Skin equivalents were dissociated and single viable parasites were sorted based on their tdTomato and Calcein AM signal with a FACSAria III cytometer (BD Biosciences) into 48-well plates containing 2.6 µl of 1x lysis buffer (Takara) supplemented with 0.01 µl of RNase inhibitor (40 U/µl; Takara). Immediately after sorting, cells were placed on ice for 5 min and stored at -80 °C. Library preparation and sequencing was carried out as described previously (Muller et al., 2018). Briefly, 0.2 µl of a 1:20 x 106 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher Scientific) were added to the lysates of single parasites and libraries were prepared using SMART-Seq v.4 Ultra Low Input RNA Kit (Takara) using a quarter of the reagent volumes recommended by the manufacturer. 27 cycles were used for PCR amplification and cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter) using 15 μl of elution buffer (Takara). Library quantification was performed with a Qubit 3 Fluorometer with dsDNA Hs Assay kit (Life Technologies) and the quality of the libraries was assessed using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended volumes, 10 min for tagmentation at 55 °C and 1 min extension time during PCR amplification. Libraries were pooled and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina’s NextSeq 500.

first: Christian

last: Reuter

first: Fabian

last: Imdahl

first: Laura

last: Hauf

first: Ehsan

last: Vafadarnejad

first: Philipp

last: Fey

first: Tamara

last: Finger

first: Heike

last: Walles

first: Florian

last: Groeber-Becker

first: Markus

last: Engstler


title: Genome-wide binding profiles of KDM5 in Drosophila GMCs and immature neurons

status: Public on Mar 17 2021

city: Bronx

first: Hayden

middle: A. M.

last: Hatch

address: 1300 Morris Park Avenue, Ullmann 809

department: Dominick P. Purpura Department of Neuroscience; Department of Genetics

institute: Albert Einstein College of Medicine

summary: Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding the spatiotemporal requirements or neurodevelopmental contributions of KDM5 proteins. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is specifically required within ganglion mother cells and immature neurons for proper neurodevelopment. Within this cellular subpopulation, we identify a core network of KDM5-regulated and -bound genes that are critical modulators of neurodevelopment. Significantly, we find that a majority of these genes are direct targets of Prospero (Pros), a transcription factor with well-established roles in neurodevelopment in other neuronal contexts. We demonstrate that Pros is essential for MB development and show that KDM5 binds to pros and regulates its expression. We therefore provide evidence for a KDM5-Pros axis that orchestrates a transcriptional program critical for proper neurodevelopment.

overall_design: 9 samples with 6 biological replicates for R71C09 > dam:kdm5 with tubulin-Gal80[ts] and 3 biological replicates for R71C09 > dam with tubulin-Gal80[ts].

first: H

middle: M

last: Belalcazar

first: O

middle: J

last: Marshall

last: Secombe


title: Single cell RNA-seq of the spinal cord in a neuropathic pain model.

status: Public on Mar 04 2021

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

institute: University of North Carolina at Chapel Hill

summary: We produced single-cell transcriptomes from the mouse spinal cord using Drop-seq in animals modeling neuropathic pain and superficial injury (SI) controls. We used the spared nerve injury (SNI) model of neuropathic pain. ~10,000 cells from sham surgery controls and ~9,000 cells from SNI animals were sequenced. Unbiased cell clustering yielded 66 spinal cell subtypes sequenced at relatively low depth (~1200 transcripts/cell). Comparisons between SI and SNI cells were performed to investigate cell-specific differences during a neuropathic pain state.

overall_design: SNI and superficial injury (SI) surgeries were conducted on the left hindleg of adult male mice. Two cohorts of mice were used (2x 5SI + 5SNI), which were batch corrected downstream. 14-days post-injury, lumbar spinal cord segments were dissociated and cells were methanol fixed. Drop-seq was performed across 4 days in groups to be batch-corrected downstream. Transcriptomes from 10 SI surgery mice and 10 SNI mice were generated. One SNI sample was removed due to dorsal root ganglion contamination (based on transcripts unique to the DRG).

first: Mark

last: Zylka


title: To determine whether AhR KO has an effect on cell differentiation and/or global gene expression profiles in individual sorted colonic stem cells

status: Public on Feb 27 2021

city: College Station

first: Robert

middle: S.

last: Chapkin

state: TX

address: 373 Olsen Blvd.

department: College of Agriculture and Life Sciences

institute: Texas A&M

summary: To study the role of Ahr in intestinal stem cell fate determination, we generated inducible, stem cell-specific Ahr-/- KO mice and then used scRNAseq to generate data for them. We conducted scTenifoldKnk analysis to knock out Ahr from the scGRN of WT mice and identified 53 top genes and associated pathways. We also conducted GESA analysis and identified 60 non-redundant functional gene sets, including many related to cell cycle and cell proliferation signaling pathways. It showed that enterocytes were the most significant hit, suggesting that Ahr KO induces a change in the expression of enterocyte marker genes, which may be responsible for the alteration of enterocyte differentiation fate. Taken together, our comprehensive analysis revealed the multifactorial functions of Ahr as a key player of enterocyte cell differentiation and proliferation, which is consistent with the known functions of Ahr.

overall_design: Single-cell transcriptome analysis on colonic stem cells from five wild-type (WT) and five Ahr-/- gene knockout (KO) mice

first: Laurie

middle: A

last: Davidson


title: Deep RNA sequencing of HeLa secreted exosomes after 10ng/ml TGF-b1 treatment or no treatment

status: Public on Feb 17 2021

city: jinan

first: Xuewu

last: You

address: wenhua xi road

institute: shandong university

summary: Deep RNA sequceing was performed to explore the expression level of miRNAs in HeLa cell exosomes after treatment with or without 10 ng/ml TGF-β1 for 24 h. The results showed that 48 miRNAs were enriched in exosomes of HeLa cells after treated with TGF-β1 compared with non-treated cells (negative control), proving that TGF-β1 affects HeLa cell exosomes miRNA profile.

overall_design: Explore the differentially expressed miRNAs in HeLa cell exosomes after 10ng/ml TGF-b1 treatment

first: Youzhong

last: Zhang


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation

first: Jeffrey

last: Dilworth

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

overall_design: Refer to individual Series


title: Caveolin1 Deficiency: A Type I Endothelial Interferonopathy Associated with Pulmonary Arterial Hypertension

status: Public on Feb 24 2021

city: Bethesda

first: Gabriela

last: Ferreyra

state: MD

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

summary: CAV1 loss-of-function mutations have been associated with the development of pulmonary arterial hypertension (PAH). CAV1 is an integral component of endothelial caveolae, specialized lipid rafts that attach to the actin cytoskeleton and modulate receptor/signal transduction coupling.  CAV1 loss in pulmonary artery endothelial cells produced a proliferative, hypermigratory cellular phenotype with a disrupted cytoskeletal architecture, mirroring known features of PAH pathobiology. Gene expression on Human Pulmonary Arterial Endothelial Cells (PAECs) transfected with non-targeting siRNA control pool or siRNA (ON-TARGET plus CAV1) in the presence or absence of TNF-alpha was evaluated

overall_design: Human Pulmonary Arterial Endothelial Cells (PAECs) (Lonza Walkersville, MD) were seeded on type I collagen coated plates and cultured in endothelial basal media-2 (EBM-2) supplemented with growth factors (EGM™-2 SingleQuot kit) and 2% FBS (Lonza). PAECs (Passage 1)  were transfected with non-targeting siRNA control pool (ON-TARGET plus Non-targeting pool; Dharmacon) or 10 nM siRNA (ON-TARGET plus CAV1; Dharmacon, Lafayette, CO) with DharmaFECT1 transfecting reagent (Dharmacon) as described in the manufacture’s protocol for 48 h follow by 4 h stimulation with or without TNF-alpha 0.5 ng/ml (Sigma, St. Louis, MO). Five complete independent experiments were analyzed by microarray.

first: Salina

last: Gairhe

first: Jason

last: Elinoff

first: Cumhur

middle: Y

last: Demirkale

last: Danner


title: single cell RNA-sequencing on triple negative G422-glioma(G422TN)

status: Public on Feb 11 2021

city: Wuhan

first: Liu

last: Feng

state: Hubei

address: 13 Hangkong Road, Hankou

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

summary: The aim was to reveal cellular heterogeneity of orthotropic G422TN-glioma

overall_design: Control group:The seventh day after G422TN(5*104) inoculation into the brain, brain tumor tissue was taken for single cell isolation. LTS group: After combined therapy, the mice survived for more than 100 days, and the contralateral side of the brain received the same tumor inoculation again. The tumor-bearing mice survived again for more than 100 days. At this time, on the 7th day after tumor inoculation, the tumor tissue was obtained for single cell sequencing.

first: Xiao-qian

last: Chen

first: Feng

last: Liu


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of adipose stem cells from diabetic, old and young patients

status: Public on May 17 2021

city: wuhan

first: sen

last: ren

state: hubei

address: donghu road

department: Department of Neurosurgery

institute: Zhongnan Hospital of Wuhan University

summary:
Purpose: Whole-transcriptome sequencing technology and bioinformatics analysis were applied to systematically analyze the differentially expressed mRNAs, lncRNAs, circRNAs and miRNAs in adipose stem cells (ASCs) from diabetic, old and young patients.
Methods: MRNAs, lncRNAs and cirRNAs profiles of adipose stem cells were generated by RNA sequencing, in triplicate, using Illumina HiSeq X Ten . MiRNAs profiles of adipose stem cells were generated by RNA sequencing, in triplicate, using BGISEQ-500. The sequence reads that passed quality filters were analyzed at the transcript isoform level by using sequence analysis programs, including HISAT, Stringtie, CIRI, find_circ and DESeq. qRT–PCR validation was performed using Takara, Vazyme and Clontech kits.
Results: The data showed that 1377 mRNAs, 5353 circRNAs, 932 lncRNAs and 85 miRNAs were significantly differently expressed in adipose stem cells from old patients compared with young patients, with a fold change ≥2 or ≤ -2 and q value <0.001. The data showed that 1878 mRNAs, 22988 circRNAs, 2638 lncRNAs and 122 miRNAs were significantly differently expressed (DE) in adipose stem cells from old patients compared with diabetic patients, with a fold change ≥2 or ≤ -2 and q value <0.001. The results of qRT-PCR confirmed 25 mRNAs, 9 lncRNAs, 8 circRNAs and 13 miRNAs which were consistent with the RNA-seq data. GO and KEGG analyses demonstrated DE mRNAs were significantly enriched in aging and cell senescence terms separately.
Conclusion: Our group simultaneously examined the changing expression of miRNAs, mRNAs, lncRNAs and circRNAs in ASCs associated with diabetes and aging. GO and KEGG pathway analyses were conducted to annotate the possible function of the differentially expressed mRNAs. PPI networks were established in order to find critical protein genes highly involved in our disease models. The ceRNA networks including lncRNA-miRNA-mRNA and cirRNA-miRNA-mRNA interactions were successfully constructed based on the bioinformatic analyses and PCR results. Thus, this study may contribute to our understanding of the underlying mechanisms of ASCs instability and provide novel targets to reverse the dysfunction of ASCs isolated from diabetic and old patients.

overall_design: MRNAs, lncRNAs, circRNAs and miRNAs profiles of adipose stem cells from diabetic, old and young patients were generated by RNA sequencing.

first: Sen

last: Ren

first: Hewei

last: Xiong

first: Jing


title: Chromatin architecture transitions from zebrafish sperm through early embryogenesis

first: Bradley

last: Cairns


title: Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. [single nucleus sequencing]

status: Public on Feb 10 2021

city: San Francisco

first: Stephanie

last: Redmond

state: CA

address: 35 Medical Center Way, 933D Box 0525

department: Neurosurgery

institute: University of California San Francisco

summary:
Purpose: While great progress has been made in understanding the differences in regional stem cell potential using viral and genetic lineage tracing strategies, the core molecular heterogeneity that underlies these regional differences is largely unknown.
Methods: Here we present a single nucleus sequencing dataset of four microdissected regions of adult CD1 wild type mouse ventricular-subventricular zones (V-SVZ). Four samples (anterior-ventral, AV; anterior dorsal, AD; posterior ventral, PV; posterior dorsal, PD) were generated at the same time from the same mice, and each sample was run on its own lane of a 10x Chromium Single Cell Controller chip for single nucleus barcoding.
Results: Here we present single nucleus and single whole cell sequencing datasets of microdissected adult mouse V-SVZ, and evidence for the existence of two broad subtypes of adult neural stem cells. By using spatially resolved microdissections in the single nucleus sequencing dataset as a reference, and mapping marker gene expression in the V-SVZ, we find that these two populations reside in largely non-overlapping domains in either the dorsal or ventral V-SVZ. Furthermore, we identified two subpopulations of newly born neurons that have gene expression consistent with dorsal or ventral origins. Finally, we identify genes expressed by both stem cells and the neurons they generate that specifically mark either the dorsal or ventral adult neurogenic lineage. These datasets, methods and findings will enable future study of region-specific regulation of adult neurogenesis.

overall_design: Single nucleus profiles of regionally micro-dissected ventricular-subventricular zones of 17 postnatal day 35 male (8 mice) and female (9 mice) CD1 wild type mice.

first: Arantxa

last: Cebrian Silla

first: Marcos

last: AssisNascimento

first: Benjamin

last: Mansky

first: David

last: Wu

first: Kirsten

last: Obernier

first: Ricardo

last: Romero Rodriguez

first: Daniel

last: Lim

first: Arturo

last: Alvarez-Buylla


title: Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [H3K4me3_Cut&Tag]

first: Jeffrey

last: Dilworth

overall_design: Myoblasts were isolated from Wildtype (WT) and NELF-BscKO (KO) mice in biological triplicate, and expanded in vitro. Ex vivo knockout was induced with 4-hydroxy-tamoxifen over 72 hours, and the resulting populations used for sample preparation

last: Robinson

first: Morten

last: Ritso

first: Geoffrey

last: Nelson

first: F


title: Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages.


title: Transcriptomics of mouse wildtype and Hoxa2-/- pharyngeal arches 1 and 2

status: Public on Feb 09 2021

city: Kansas City

first: Irina

last: Pushel

state: MO

institute: Stowers Institute for Medical Research


title: Impact of mPGES-1 on the resolution of zymosan-induced peritonitis in mice

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

summary: Despite the progress to understand inflammatory reactions, mechanisms causing their resolution remain poorly understood. Prostanoids, especially prostaglandin E2 (PGE2), are well characterized mediators of inflammation. PGE2 is produced in an inducible manner in macrophages (Mf) by microsomal PGE2-synthase-1 (mPGES-1), with the notion that it also conveys pro-resolving properties. We aimed to characterize the role of mPGES-1 during resolution of acute, zymosan-induced peritonitis. Experimentally, we applied the mPGES-1 inhibitor compound III (CIII) once the inflammatory response was established and confirmed its potent PGE2-blocking efficacy. mPGES-1 inhibition resulted in an incomplete removal of neutrophils and a concomitant increase in monocytes and Mf during the resolution process. mRNA-seq analysis identified enhanced C-X3-C motif receptor 1 (CX3CR1) expression in resident and infiltrating Mf upon mPGES-1 inhibition. Besides elevated Cx3cr1 expression, its ligand CX3CL1 was enriched in the peritoneal lavage of the mice, produced by epithelial cells upon mPGES-1 inhibition. CX3CL1 not only increased adhesion and survival of Mf, but its neutralization also completely reversed elevated inflammatory cell numbers, thereby normalizing the cellular, peritoneal composition during resolution. Our data suggest that mPGES-1-derived PGE2 contributes to resolution of inflammation by preventing CX3CL1-mediated retention of activated myeloid cells at sites of injury.

overall_design: mRNA-seq of peritoneal F4/80lo and F4/80hi macrophages isolated from C57/BL6 mice at day 6 of a zymosan-induced peritonitis model receiving daily i.p. injections of mPGES-1 inhibitor compound III or the respective vehicle control starting at day 1 (n=3)

first: Peter

last: Rappl


title: Transcriptomes of mouse wildtype and Hoxa2-/- pharyngeal arches 1 and 2 at E9.0, E9.5, E10.0, and E10.5.

summary: The Hox genes play a key role in specifying the axial identity of neural crest cells (NCCs) migrating into the pharyngeal arches of the developing mouse embryo. In the absence of Hoxa2, NCC derivatives of the second pharyngeal arch (PA2) duplicate those formed by NCCs of the first arch (PA1). In this study, we use bulk and single-cell RNAseq to establish the molecular mechanisms driving this phenotypic reversion to a ground state. Comparing the transcriptomes of PA1 and PA2 in wildtype and Hoxa2-/- embryos during NCC migration and differentiation, we find that Hoxa2-/- PA2 does not revert to a molecular ‘ground state’ corresponding to the NCC derivatives. This separation of phenotypic and molecular states has significant implications for our understanding of NCC biology. We also identify putative targets through which HOXA2 likely acts to impart PA2 identity. The heterogenous expression of these targets within the PAs and their responses to the absence of HOXA2 suggest that subsets of NCCs may respond to HOXA2 activity in distinct manners related to their ultimate fate. To understand the specification of axial identity in neural crest cells (NCCs), we collected pharyngeal arches (PAs) 1 and 2 from mouse embryos at four time points during NCC migration and the beginning of differentiation (E9.0, E9.5, E10.0, and E10.5). We collected these tissues from both wildtype embryos and embryos homozygous for a mutation abrogating Hoxa2 expression. By performing comparative analysis of these tissues, we set out to understand the molecular underpinnings of NCC axial identity, as well as the mechanistic role of Hoxa2 in establishing PA2 identity.

overall_design: We examine 3-5 biological replicates of PA1 and PA2 collected from a single embryo for each genotype at each timepoint.

first: Paul

last: Trainor

first: Robb

last: Krumlauf


title: Single cell RNA Sequencing of ovarian antral follicle cells

status: Public on Mar 06 2021

city: New York

first: Daylon

last: James

state: NY

address: 515 East 71st Street

institute: Weill Cornell Medicine

summary: We isolated cells from human antral follicles of various stages and sources and subjected them to 10x Chromium single cell sequencing

overall_design: Sequencing libraries prepared from cell populations that were prospectively isolated from antral follicles of patient or xenograft origin


title: Single-cell transcriptomics of mouse wildtype and Hoxa2-/- pharyngeal arches 1 and 2 at E10.5.

summary: The Hox genes play a key role in specifying the axial identity of neural crest cells (NCCs) migrating into the pharyngeal arches of the developing mouse embryo. In the absence of Hoxa2, NCC derivatives of the second pharyngeal arch (PA2) duplicate those formed by NCCs of the first arch (PA1). In this study, we use bulk and single-cell RNAseq to establish the molecular mechanisms driving this phenotypic reversion to a ground state. Comparing the transcriptomes of PA1 and PA2 in wildtype and Hoxa2-/- embryos during NCC migration and differentiation, we find that Hoxa2-/- PA2 does not revert to a molecular ‘ground state’ corresponding to the NCC derivatives. This separation of phenotypic and molecular states has significant implications for our understanding of NCC biology. We also identify putative targets through which HOXA2 likely acts to impart PA2 identity. The heterogenous expression of these targets within the PAs and their responses to the absence of HOXA2 suggest that subsets of NCCs may respond to HOXA2 activity in distinct manners related to their ultimate fate. To understand the heterogeneity of neural crest cells (NCCs) and other tissues of pharyngeal arches (PAs) 1 and 2 in the mouse embryo at E10.5, during NCC differentiation, we collected PA1 and PA2 from wildtype embryos and Hoxa2-/- embryos. We used the 10x Chromium single-cell sequencing system to compare the transcriptional profiles between PA1 and PA2 as well as wildtype and Hoxa2-/- PAs.

overall_design: We manually dissected PA1 and PA2 from six wildtype embryos and five Hoxa2-/- embryos, pooling according to PA and genotype, then produced a single-cell suspension for each and sequenced using 10x Chromium machine.


title: An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses

status: Public on Feb 04 2021

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Wheat (Triticum aestivum) has a large allohexaploid genome. Subgenome-divergent regulation contributed to genome plasticity and the domestication of polyploid wheat. However, the specificity encoded in the wheat genome determining subgenome-divergent spatio-temporal regulation has been largely unexplored. The considerable size and complexity of the genome are major obstacles to dissecting the regulatory specificity. Here, we compared the epigenomes and transcriptomes from a large set of samples under diverse developmental and environmental conditions. Thousands of distal epigenetic regulatory elements (distal-epiREs) were specifically linked to their target promoters with coordinated epigenomic changes. We revealed that subgenome-divergent activity of homologous regulatory elements are affected by specific epigenetic signatures. Subgenome-divergent epiRE regulation of tissue specificity is associated with dynamic modulation of H3K27me3 mediated by Polycomb complex and demethylases. Furthermore, quantitative epigenomic approaches detected key stress responsive cis- and trans-acting factors validated by DNA Affinity Purification and sequencing (DAP-seq), and demonstrated the coordinated interplay between epiRE sequence contexts, epigenetic factors, and transcription factors in regulating subgenome divergent transcriptional responses to external changes. Thus, this study provides a wealth of resources for elucidating the epiRE regulomics and subgenome-divergent regulation in hexaploid wheat, and gives new clues for interpreting genetic and epigenetic interplay in regulating the benefits of polyploid wheat.

overall_design: To systematically characterize RE repertoire of bread wheat, their dynamic regulatory landscape as well as the interplay between REs, we obtained the chromatin activity for a total of 7 typical tissues and 8 external stimuli in bread wheat by performing chromatin immunoprecipitation coupled to massively parallel DNA sequencing (ChIP-seq) for three well-studied histone modifications known to reliably capture enhancer and promoter activities, including acetylated histone 3 at lysine 9 (H3K9ac) and tri-methylated histone 3 at lysine 4 (H3K4me3) associated with active regulatory regions, and tri-methylated histone 3 at lysine 27 (H3K27me3) associated with Polycomb repressed regions, together with gene expression profiles across 15 samples.

first: Yijing

last: Zhang


title: Transcriptome analysis of HEK-293, A549 and HRT18 cells infected with shaan virus

status: Public on Feb 02 2021

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

country: South Korea

institute: Chungbuk National University

summary:
propose: The goals of this study are viral transcript of host cells infected with shaan virus  and host cell responses in HEK293, A549 and HRT18 infected with shaan virus.
Methods: We infected the virus at an MOI of 0.5 to human tissues-derived cell lines including HEK-293, A549 and HRT18. The infected cells were harvested at 24 hours post infection, and a total RNA was extracted from the harvested cells with Trizol LS reagent. The trimmed reads were mapped to shaan virus genome or GRCh37 human genomic DNA reference. The differentially expressed genes (DEGs) between the virus-infected and mock-infected cells were calculated based on the fold changes of FPKM per each gene.
Result: Viral transcripts were expressed differentially depending on the viral genes, it is obvious that the nucleocapsid (N) transcript was most expressed in all infected cells. Gene ontology enrichment analysis based on the DEGs revealed that HEK-293, A549 and HRT18 cells highly expressed the genes related to the antiviral defence system and innate immune response in response to the shaan virus infection.
Conclusion: In this study, we describe transcriptome data from the shaan virus-infected cells. The inferred DEGs and their related biological functions can be further investigated to understand the shaanvirus-host interaction.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: transcriptome profile of HEK293, A549, HRT18 and MARC 145 infected with shaan virus


title: RNA sequencing  in human  iPSCs derived from  bipolar  patients  to identify important therapeutic molecular targets of Valproate(VPA)

status: Public on Dec 31 2020

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

summary: Valproate(VPA) has been used in the treatment of bipolar disorder since the 1990s.  However, the therapeutic targetsof VPA have remained elusive. Here we  used RNA sequencing  in human  iPSCs derived from  bipolar  patients  to further identify important molecular targets. Human iPSCs were homogenized and total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen, Carlsbad, CA) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent, Santa Clara, CA), respectively. Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500. The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality. TopHat2 (v2.0.9) aligned the reads to the mouse reference genome (Mus musculus UCSC mm10) and to the Ensembl human reference genome (GRCh38.p13) using default parameters. Alignments were then converted to expression count data using HTseq (v0.6.1) with default union mode.

overall_design: Human fibroblasts or lymphoblasts from multiple patients were reprogrammed to hiPSCs via non-integrating episomal-mediated, lentivirus-mediated, or retrovirus mediated gene transfer, characterized, and differentiated to NPCs, as previously described (Supplementary Table 2). We used iPSCs from two patients diagnosed with bipolar disorder and classified as Lithium Non-Responsive (Pt-LiNR-1 and Pt-LiNR-2). Patient selection criteria, clinical evaluation and classification were conducted as thoroughly described previously. We use two separate clones from each patient in these experiments. Differentiation into neurons was similar to techniques described previously (PMID: 28500272). Neurons were cultured for 4 weeks prior to pharmacological experiments. Neurons were cultured in four 12-well plates of cells with two plates as technical replicates for each patient. Each of the wells of the 12-well plate were treated with either vehicle (water), VPA (1mM), or ACY957 (3μM), repeated in quadruplicates (2 patients x 2 clones x 3 treatments x 4 replicates = 48 samples). Cells were treated for 72 hrs with daily media and compound changes, then collected, washed (1X PBS), and pelleted then flash frozen for RNA extraction.

first: Colleen

last: McClung

first: Ryan

last: Logan

first: George

last: Tseng

first: Wei

last: Zong


title: BKM120 Treated WHIMs_17 Model Cohort

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

summary: Aberrant activation of PI3K pathway is frequently observed in triple negative breast cancer (TNBC).  However single agent PI3K inhibitors have shown modest anti-tumor activity.  To investigate biomarkers of response, we tested 17 TNBC PDX models with diverse genetic and proteomic background, with varying PI3K pathway signaling activities for their tumor growth response to the pan-PI3K inhibitor BKM120 as well as baseline and treatment induced proteomic changes as assessed by reverse phase protein array (RPPA).  We demonstrated that PI3K inhibition induces varying degrees of tumor growth inhibition (TGI), with 5 models demonstrating over 80% TGI. BKM120 consistently reduced PI3K pathway activity as demonstrated by reduced pAKT following therapy.  Several biomarkers showed significant association with resistance, including baseline levels of growth factor receptors (EGFR, pHER3 Y1197), PI3Kp85 regulatory subunit, anti-apoptotic protein BclXL, EMT (Vimentin, MMP9, IntegrinaV), NFKB pathway (IkappaB, RANKL), and intracellular signaling molecules including Caveolin, CBP, and KLF4, as well as treatment induced increase in the levels of phosphorylated forms of Aurora kinases.  Sensitivity was associated with higher baseline levels of proapoptotic markers (Bak and Caspase 3) and higher number of markers being changed following BKM120 therapy. Interestingly, markers indicating PI3K pathway signaling activation at baseline were not significantly correlated to %TGI.  These results provide important insights in biomarker development for PI3K inhibitors in TNBC.

overall_design: Molecular profiling was completed on 54 microarrays representing different passages and human counterparts for 17 triple negative breast cancer models using 2 channel (tumor:reference) whole human genome Agilent arrays.

first: Jeremy

middle: W

last: Hoog


title: 17 Models: Buparlisib-treated Patient Derived Xenograft (PDX) Reversed Phase Protein Array (RPPA) Data

status: Public on Jan 27 2021

summary: Aberrant activation of PI3K pathway is frequently observed in triple negative breast cancer (TNBC).  However single agent PI3K inhibitors have shown limited anti-tumor activity.  To investigate biomarkers of response and resistance mechanisms, we tested 17 TNBC patient-derived xenograft (PDX) models representing diverse genomic backgrounds and varying degrees of PI3K pathway signaling activities for their tumor growth response to the pan-PI3K inhibitor BKM120.  Baseline and post-treatment PDX tumors harvested following 3 days of BKM120 or vehicle administration were subjected to reverse phase protein array (RPPA) to identify protein markers associated with tumor growth response.  While BKM120 consistently reduced PI3K pathway activity, as demonstrated by reduced levels of phosphorylated AKT, percentage tumor growth inhibition (%TGI) ranged from 35% in the least sensitive to 84% in the most sensitive PDX model at the completion of approximately 3-4 weeks of treatment.  Several biomarkers showed significant association with resistance, including elevated baseline levels of growth factor receptors (EGFR, pHER3 Y1197), PI3Kp85 regulatory subunit, anti-apoptotic protein BclXL, EMT (Vimentin, MMP9, IntegrinaV), NFKB pathway (IkappaB, RANKL), and intracellular signaling molecules including Caveolin, CBP, and KLF4, as well as treatment-induced increase in the levels of phosphorylated forms of Aurora kinases.  Sensitivity to BKM120 was associated with higher baseline levels of proapoptotic markers (Bak and Caspase 3) and a greater number of markers differentially changed following BKM120 therapy. Interestingly, markers indicating PI3K pathway signaling activation or PTEN loss at baseline were not significantly correlated to %TGI.  These results provide important insights into biomarker development for PI3K inhibitors in TNBC.

overall_design: 17 PDX models were analyzed under 2 treatment conditions: 50hr buparlisib treatment vs. 3 day vehicle.  3 bioreplicates and 3 technical replicates were analyzed when possible.


title: Ventral tegmental area brain region from wild-type and Clock delta 19 mutant mice in response to valproate or ACY957 compound

summary: We report the gene expression changes in the ventral tegmental area brain region from wild-type and Clock delta 19 mutant mice in response to valproate or ACY957 compound. RNA was extracted from these regions then processed for RNAseq.

overall_design: Brains were extracted and flash frozen from adult male ClockΔ19 or Wildtype mice treated with valproate (VPA), ACY957, or their respective vehicles for 14 days (See above). Tissue was collected at ZT6, approximately 24 hrs after the last treatment. Multiple bilateral 1mm punches were taken centered over the ventral tegmental area (VTA). Individual mice were used as biological replicates (8 mice x 2 genotypes x 4 treatments = 64 samples). Mouse brain tissue punches were homogenized and total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen, Carlsbad, CA) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent, Santa Clara, CA), respectively. Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500. The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality. TopHat2 (v2.0.9) aligned the reads to the mouse reference genome (Mus musculus UCSC mm10) and to the Ensembl human reference genome (GRCh38.p13) using default parameters. Alignments were then converted to expression count data using HTseq (v0.6.1) with default union mode. The RNAseq count data were transformed to log2 count data using voom function of the Bioconductor limma package..


title: Coupled myovascular expansion directs cardiac growth and regeneration

status: Public on Feb 05 2021

city: Durham

first: Ravi

last: Karra

address: 247A CARL Building

department: Department of Medicine

institute: Duke University

summary:
Purpose: The goal of this experiment is to better understand the molecular mediators of myovascular coupling during growth and injury.
Methods: We performed single cell RNA-sequencing (scRNA-Seq) of border zones of cryoinjured murine hearts collected at P7 using the Drop-seq protocol.
Results: Together with in situ hybridization data, results from the scRNA-seq data analysis support a dynamic role for myocardial VEGFA to endothelial VEGFR2 signaling as a regulator of the myovascular expansion during growth and regeneration.

overall_design: Single-cell RNA-seq through Drop-seq technique of border zones from mice hearts collected at P7 pooled into one sample


title: Next Generation Sequencing Facilitates Quantitative Analysis of bHLH6 OV, spx4, and wild-type Transcriptomes

city: Hangzhou

first: He

middle: Qiu

last: ju

address: Yuhangtang road

institute: Zhejiang University

summary:
Purpose: To investigate the expression profiles of genes regulated by bHLH6, we performed RNA-seq analysis using bHLH6 OV, spx4, and wild type treated with high and low P
Methods: Roots and shoots mRNA profiles of 7-day-old bHLH6 OV, spx4, and wild-type (WT) rice seedlings treated with 200 μM or 10 μM Pi for 2 weeks three biological replicates were generated by deep sequencing using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA). The mapped reads of each sample were assembled by Hisat2 (v2.0.5). qRT–PCR validation was performed using SYBR Green assays
Results: RNA-seq data confirmed that in shoots, 4,694 genes were upregulated and 4,126 were downregulated in bHLH6 OV lines compared with wild type under high-P conditions.Among the differentially expressed genes, 1,805 (38.5%) were upregulated in wild type under low-P conditions, whereas 1,598 (38.7%) of the downregulated genes were downregulated in wild type under low-P conditions, suggesting that bHLH6 overexpression upregulates a subset of PSI genes. In total, 971 genes were upregulated and 853 genes were downregulated in spx4 compared to wild type in high-P conditions. Among these upregulated genes, 371 (38.2%) were also upregulated in shoots of bHLH6 OV plants compared to in wild type; 456 (53.4%) of the downregulated genes were also downregulated in shoots of bHLH6 OV compared with wild type. In roots, 311 (10.5%) out of the 2,969 upregulated genes in bHLH6 OV lines under high-P conditions were also upregulated in wild type under low-P conditions; 501 (19.1%) out of the 2,628 downregulated genes in bHLH6 OV were also downregulated in wild type under low-P conditions. However, 313 (60.2%) out of the 520 genes upregulated in spx4 in roots were also upregulated in bHLH6 OV lines compared to in wild type, whereas 497 (54.6%) out of 910 the downregulated genes were also downregulated in bHLH6 OV compared to in wild type. To validate the RNA-seq results, we selected the upregulated PT and PAP (PURPLE ACID PHOSPHATASE) genes for expression analysis using RT-qPCR. The expression levels of PT2, PT10, PAP10a, and PAP21b were considerably higher in roots of bHLH6 OV plants than in those of wild type and bhlh6 mutants, whereas the expression of SPX2 was much lower in bHLH6 OV plants than in wild type
Conclusion: our study is the first to analyze in detail the bHLH6 transcriptome produced by rna-seq technology and perform biological replication. Our results suggest that bHLH6 mediates the regulation of Pi homeostasis by SPX4. Our results advance the current understanding of the Pi-signaling regulatory network and will potentially contribute to the genetic improvement of crop P efficiency.

overall_design: Roots and shoots mRNA profiles of 7-day-old bHLH6 OV, spx4, and wild-type (WT) rice seedlings treated with 200 μM or 10 μM Pi for 2 weeks with three biological replicates.

first: Chuanzao

last: Mao

first: Qiuju

last: He


title: Characterizing microRNAs and their targets in differnt organs of  Camellia sinensis

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

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

overall_design: Refer to individual Series


title: Characterizing microRNAs and their targets in differnt organs of  Camellia sinensis [miRNA-seq]

summary: MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses.  Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance.  Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis.  We sequenced 9 small RNA libraries and 9 RNA-Seq libraries from roots, leaves and flowers tissues.  Through comprehensive computational analyses of 9 small RNA profiles, we identified 200 conserved miRNAs of which 138 have not been reported, and 56 novel miRNAs with 33 have not been reported.  Nearly, two thousands genes have significantly different expression levels in tissues.  In order to identify targets of miRNAs, we sequenced two degradome profiles from leaves and roots, respectively.  Totally, more than 3,000 putative targets of conserved miRNAs were identified in both degradome profiles by using the SeqTar algorithm.  These results clearly enhanced our understanding about small RNA guided gene regulations in Camellia sinensis.

overall_design: Retinal small RNA profiles of leafs, roots and flowers in Camellia sinensis  were generated by deep sequencing.


title: Characterizing microRNAs and their targets in differnt organs of  Camellia sinensis [degradome]

overall_design: Retinal degradome profiles of leaf and root in Camellia sinensis  were generated by deep sequencing.


title: Transcriptional Profiling of Pediatric Cholestatic Livers Identifies Three Distinct Macrophage Populations

status: Public on Dec 22 2020

city: Chicago

first: Deborah

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: We characterize three subpopulations of cholestatic macrophages in pediatric patients with biliary atresia (BA) and Alagille syndrome (ALGS).

overall_design:
single-cell RNA-seq of liver biopsies
Note: This GEO submission contains only processed data. The submitter will upload the raw data files to dbGap due to patient privacy issue.

first: Sarah

last: Taylor


title: Genome-wide maps of chromatin state in renal tubular epithelial cells

city: Shanghai

first: Hanyu

last: Rao

address: No.1954, hua shan Rd. Shanghai

institute: Shanghai Jiao Tong University

summary: To further understand the underlying mechanisms and identify genes directly regulated by SETD2 and H3K36me3 on a genome-wide scale, we performed chromatin immunoprecipitation using a H3K36me3 specific antibody followed by next-generation sequencing (ChIP-seq) assays using the renal tubules isolated from SETD2FL/FL KSPCRE/+ and its control SETD2fl/fl mice.

overall_design: Examination of 2 different histione modifaication in 2 primary renal tubular epithelial cells

first: Wei-Qiang

last: Gao


title: Characterizing microRNAs and their targets in differnt organs of  Camellia sinensis [RNA-seq]

overall_design: Retinal RNA profiles of leafs, roots and flowers in Camellia sinensis  were generated by deep sequencing.


title: Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. [single whole-cell]

first: Stephanie

last: Redmond

summary:
Purpose: While great progress has been made in understanding the differences in regional stem cell potential using viral and genetic lineage tracing strategies, the core molecular heterogeneity that underlies these regional differences is largely unknown.
Methods: Here we present a single whole-cell sequencing dataset of microdissected adult hGFAP:GFP mouse V-SVZ. Four samples were (two samples from male mice, two samples from female mice) multiplexed & combined using MULTI-Seq barcodes (McGinnes et al. 2019), labeled with TotalSeq antibodies against VCAM1 and CD24 proteins (Biolegend), and were split into two technical replicate lanes on a 10x Chromium Single Cell Controller chip for single cell barcoding. Genomic libraries were prepared using standard Illumina protocols, and barcode libraries (MULTI-Seq, TotalSeq) were prepared using MULTI-Seq protocols.
Results: Here we present single whole-cell and single nucleus sequencing datasets of microdissected adult mouse V-SVZ, and evidence for the existence of two broad subtypes of adult neural stem cells. By using spatially resolved microdissections in the single nucleus sequencing dataset as a reference, and mapping marker gene expression in the V-SVZ, we find that these two populations reside in largely non-overlapping domains in either the dorsal or ventral V-SVZ. Furthermore, we identified two subpopulations of newly born neurons that have gene expression consistent with dorsal or ventral origins. Finally, we identify genes expressed by both stem cells and the neurons they generate that specifically mark either the dorsal or ventral adult neurogenic lineage. These datasets, methods and findings will enable future study of region-specific regulation of adult neurogenesis.

overall_design: Single cell profiles of micro-dissected ventricular-subventricular zones of male (postnatal day 35) and female (postnatal day 29) hGFP:GFP mice.

first: Arantxa

last: Cebrian Silla

first: Marcos

last: AssisNascimento

first: Benjamin

last: Mansky

first: David

last: Wu

first: Kirsten

last: Obernier

first: Ricardo

last: Romero Rodriguez

first: Daniel

last: Lim

first: Arturo

last: Alvarez-Buylla


title: Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [RNA-Seq]

status: Public on Dec 02 2020

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: How heterochromatin genes evolve as ‘gene islands’ to fit into the repressive chromatin environment in plants are poorly understood. To address this question, we performed a comprehensive epigenetic profiling in the genus Oryza with high quality BAC-assembled regional sequences and near gap-free genomes. Comparative analyses of a heterochromatin knob demonstrated the dynamics of chromatin states (heterochromatin versus euchromatin) among the Oryza species in a phylogenetic context. LTR (long-terminal repeat) retrotransposons are the main contributor (~99%) to heterochromatin diversity. Heterochromatin genes are distributed as ‘gene islands’ in heterochromatin, but heterochromatin hardly projects expression disturbance to them. Heterochromatin genes are almost free of H3K9me2 histone modifications in exons, and have similar gene structure and transposon invasion rate in introns to its orthologous euchromatin counterparts. Analyses of the rice HiC data verified the topological existence of ‘gene islands’ and demonstrated that ‘gene islands’ are less spatially co-localized with heterochromatin. By examining evolutionarily recent inserted genes in the Oryza species, we found that the active promoters of six inserted genes can elevate CHH (H=A, C, T) methylation at the insertion sites. Our results reveals that heterochromatin genes evolve as heterochromatin-insulated ‘gene islands’ to escape the repressive influence of heterochromatin, contrasting to the ‘integration’ model in Drosophila. We suggest that active gene promoters may contribute to this insulation by acting as an important heterochromatin-euchromatin boundary in plants.

sample_organism:
Oryza brachyantha
Oryza punctata
Oryza glaberrima
Sorghum bicolor
Oryza sativa Japonica Group
Leersia perrieri

overall_design: we conducted a comprehensive heterochromatin study among close-related species with high quality sequences and near-gap free genomes. To achieve this, we generated twenty-six new epigenetic datasets in this study including the heterochromatin hallmark H3K9me2 in six species and DNA methylation of Oryza brachyantha, two siRNA libraries of O. sativa and O.brachyantha.

first: Meijiao

last: Wang

first: Mingheng

last: Chen


title: Mouse sympatho-adrenal system at E13.5

status: Public on Feb 06 2021

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

institute: Medical University of Vienna

summary: We addressed heterogeneity of neural crest-derived lineages developing into sympathoadrenal system during mouse development.

overall_design: Mouse embryos were injected in utero at E8 and collected at embryonic day E13.5. The labelled neural-crest derived cells were sorted with FACS.

first: Alek

last: Erickson

first: Polina

last: Kameneva

first: Michael

last: Ratz

first: Emma

last: Andersson

first: Bettina

last: Semsch

first: Jonas

last: Frisen

first: Erik

last: Sundstrom

first: Igor

last: Adameyko


title: Single-cell transcriptomes and T cell receptor sequences of memory T lymphocytes from the peripheral blood and the synovial fluid of patients with juvenile idiopathic arthritis.

status: Public on Nov 27 2020

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Antigen-experienced (or memory) T lymphocytes were isolated from the synovial fluid of inflamed joints and the peripheral blood of patients with juvenile idiopathic arthritis (JIA). After flow-sort of CD4+CD45RO+CD25- (Tcon), CD4+CD45RO+CD127loCD25+ (Treg) and CD8+CD45RO+ T cells, single-cell RNA-sequencing was conducted to perform paired analyses of gene transcription and T cell receptor (TCR) repertoires in the same cells. The study aimed to identify T memory cells that were stimulated by antigens in inflamed joints of JIA patients and which perpetuate chronic inflammation by expression pro-inflammatory genes. In addition, the study aimed at understanding the clonal relationships of T cells differentiating at chronically inflamed sites, as well as to identify blood-circulating T cell clones that shared gene expression and antigen-specificity with T cells in inflamed joints in order to improve patient stratification and diagnostics of patients with chronic inflammatory diseases in the future.

overall_design: Single-cell RNA-sequencing and TCR immunoprofiling of flow-sorted CD4+CD45RO+CD25-, CD4+CD45RO+CD127loCD25+ and CD8+CD45RO+ T cells from paired blood and synovial fluid samples of patients with JIA were performed.

first: Patrick

last: Maschmeyer

first: Gitta

last: Heinz

first: Christopher

last: Skopnik

first: Frederik

last: Heinrich

first: Katrin

last: Lehmann

first: Imme

last: Sakwa

first: Mir-Farzin

last: Mashreghi

first: Andreas

last: Radbruch


title: Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia

status: Public on Dec 04 2020

city: Boston

first: Barry

last: Zee

state: MA

address: 61 Binney Street

department: Newborn Medicine

institute: Boston Children's Hospital


title: Transcriptional dynamics of ricin-induced ARDS

status: Public on Nov 17 2020

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

summary: We report the presence of pathologic states of epithelial, mesenchymal and vascular endothelial cells and molecular programs involved in immunopathological progression. We also report the transcriptionally functional diversity of neutrophils and identify a previously undetected neutrophil subset undergoing transdifferentiated process. Cell–cell interaction analysis reveal vascular mural cells as potential crosstalk hubs in pulmonary communication network.

overall_design: Examination of dynamic transcriptional signatures of lung structural and immune populations during the early stages of ARDS

first: Huiying

last: Yang

first: Dongsheng

last: Zhou


title: Chromatin modification is not a prerequisite for p63 binding but p63 binding can elicit chromatin remodeling

status: Public on Dec 01 2020

city: Buffalo

first: Michael

last: Buck

address: 701 Ellicott St

institute: SUNY at Buffalo

summary: Transcription factor (TF) p63 is a master regulator playing critical roles in epidermal development and other cellular processes. Our lab’s previous research deciphered a distinct chromatin architecture at p63 bound site in keratinocytes. In order to figure out whether those chromatin modifications already exist before p63 binding, or p63 occupancy contributes to such chromatin marks, we built p63-expressing cell lines. We then obtained p63 bound regions in these overexpressing cell line, and looked at different histone marks at those sites before p63 occupancy. As shown in the results, before p63 binding, the targeting sites have barely detectable histone marks, indicating p63’s capability to approach unmodified chromatins. Moreover, there is no significant difference in chromatin marks between p63 bound sites and unbound sites when no p63 binding happens. Our in vivo findings were confirmed by examining p63 binding to unmodified nucleosomes in vitro, showing that histone modification is not indispensable for p63 binding but binding site positioning on nucleosome does play a role. Overall, our results suggest that histone modifications do not affect p63 binding, and p63 protein can bind to inaccessible, weakly modified chromatin regions in vivo.

overall_design: ChIP-seq of K562 and HepG2 cells

first: Xinyang

last: Yu


title: Cortical single-cell RNA sequencing of the microglia specific TREM2 inducible mouse models in the middle stage of amyloid deposition

status: Public on Nov 11 2020

city: jacksonville

last: Zhao

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: We induced TREM2 expression at 2 months of age in our 5xFAD/TREM2 mouse models and harvested the animals at 5 months of age. The single cells from the cortex were isolated and subjected to the single-cell RNA seq to investigate the effects of TREM2 on microglia transcriptomic profiles in the middle stage of amyloid development. Our data showed that TREM2-WT induced the mTOR/EIF2 signaling pathways and restricted the disease associated microglia (DAM) signature. In contrast TREM2-R47H variant significantly upregulated the MHC class II molecules, enriched the antigen presentation pathway, and exacerbated a signature of antigen presentation contributing to enhanced amyloid pathology.

overall_design: Six mice (3 males and 3 females) were analyzed for each of the four groups, including 5xFAD/TREM2-WT-Ctrl, 5xFAD/TREM2-WT-Induced, 5xFAD/TREM2-R47H-Ctrl, 5xFAD/TREM2-R47H-Induced .

first: Wenhui

last: Qiao

first: Yuka

last: Martens

first: Yingxue

last: Ren


title: The ERβ cistrome in colon cancer

status: Public on Oct 07 2020

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

country: Sweden

institute: Scilifelab

summary: In order to elucidate the mechanism of ERβ in the colon, we validated ERβ antibodies, opti-mized chromatin-immunoprecipitation (ChIP), and performed ChIP-Seq of CRC engineered cell lines re-expressing ERβ.We present for the first time, the cistrome of nuclear receptor ERβ in different CRC cell lines.

overall_design: Each ChIP was performed three times. For further analysis, we focused on sites present in at least two out of three replicates

first: Cecilia

last: Williams


title: Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary

first: Lei

last: Li

sample_organism:
Oryza sativa
Oryza brachyantha
Oryza punctata
Oryza glaberrima
Sorghum bicolor
Oryza sativa Japonica Group
Leersia perrieri


title: Expression data from PTC cell lines transfected with SHCBP1-shRNA

status: Public on Oct 04 2020

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

summary:
The mRNA and protein levels of SHCBP1 were significantly upregulated in PTC cancer tissues compared with paired normal tissue. Knockdown of SHCBP11 in TPC-1 and K1 significantly supressed cell growth, colony formation ability, tumor invasion, and  phase transition of the cell cycle.
We used microarrays to investigate the gene expression alterations of PTC cells after SHCBP1 knockdown by shRNA.

overall_design: SHCBP1-shRNA-expressing and control-shRNA-expressing lentivirus were constructed and infected into PTC cancer cells TPC-1. Then total RNA was prepared for RNA extraction and hybridization on Affymetrix microarrays. Three independent samples were collected for each group.

first: Houfa

last: Geng


title: RNA-seq muscle

status: Public on Oct 01 2020

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

institute: IGBMC

summary: Identify the genes modulated by Glucocorticoid Receptor.

overall_design: We selectively knocked-out GR in myofibers by crossing GR floxed mice to HSA-Cre-ERT2 mice. RNA from gastrocnemius muscle of 16 week-old control (GR floxed mice) and knock-out mice was extracted with trizol according to the manufacturer protocol. RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). We annotated these reads to the mm10 build of the mouse genome using TopHat version 2. The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR and DESeq.

first: Anna-Isavella

last: Rerra

first: Daniel

last: Metzger