title: Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scATAC-seq]

overall_design: scATAC-seq of day 30 of trophoblast conversion together with naïve and primed hPSCs. Nuclei were mixed using the following ratio (H9 primed: Sigma primed: H9 naive: Sigma naive: day 30 ASECRiAV conversion = 1:1:1:1:2)

first: Grigorios

last: Georgolopoulos

first: Alexandre

last: Bruneau

first: Ryan

last: Allsop


title: Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells

status: Public on Aug 01 2022

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_timecourse_naiveTSC]

summary: time course scRNAseq of naïve to trophoblast stem cells and extraembryonic mesoderm conversion and D70 sorted extraembryonic mesoderm. Samples were collected at day 0, 1, 2, 4, 8, 13 and 18.

first: Thi

middle: X

last: Pham

first: Amitesh

last: Panda

first: Harunobu

last: Kagawa

middle: N

first: SanKit

last: To

first: Adrian

last: Janiszewski

first: Michael

last: Oberhuemer

first: Raissa

middle: S

last: Tchinda

first: Frederic

last: Lluis

first: Laurent

last: David

first: Nicolas

last: Rivron

first: Bradley

middle: P

last: Balaton


title: Modulation of type-I interferon responses reduces SARS-CoV-2 replication and inflammation in rhesus macaques

status: Public on Nov 16 2022

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: Inflammation following SARS-CoV-2 infection is a hallmark of COVID-19 and predictive of morbidity and death. However, the inflammatory pathways contributing to host-defense vs immune-mediated pathology have not been fully elucidated. This duality is clearly seen with type-I interferons (IFN-I) which are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to site of infection, a key feature of severe COVID-19. Here, we modulated IFN-I signaling in rhesus macaques (Macaca mulatta) prior to and during acute SARS-CoV-2 infection (day -1 through day 2 post infection) using a mutated IFNα2 (IFN-modulator; IFNmod) which blocks binding to IFNAR2 and signaling of endogenous IFN-I. IFNmod treatment resulted in a highly significant and consistent reduction in SARS-CoV-2 viral load in BAL, lung, and hilar LN (>3-log difference) and upper airways (nasal swabs). IFNmod also potently reduced inflammatory cytokines and chemokines in BAL, expansion of inflammatory monocytes (CD14+CD16+), and lung pathogenesis. Furthermore, Siglec-1 expression, which has been shown to enhance SARS-CoV-2 infection, was rapidly downregulated in the lung and on monocytes of IFNmod-treated SARS-CoV-2 infected RMs. Notably, while RNAseq analysis showed that IFNmod induced a modest upregulation of antiviral IFN-stimulated genes (ISGs) in uninfected RMs, it resulted in a robust reduction in pathways associated with both antiviral and inflammatory ISGs in SARS-CoV-2-infected RMs. In conclusion, IFNmod treatment provides sufficient levels of type I IFN signaling that inhibit viral replication while also limiting hyperinflammation. IFN-I plays a vital role in regulating SARS-CoV-2 replication, but uncontrolled IFN signaling has a detrimental impact on inflammation and pathogenesis. A better understanding of the role of IFN-I pathways is essential for designing therapies targeting these pathways and aimed at limiting COVID-19 pathogenesis.

overall_design: Uninfected Rhesus Macaque Study (n=4): Four uninfected rhesus macaques (RMs) were treated with a four-day course of IFNmod (1mg/day, intramuscularly) to assess the effects of IFNmod in the absence of experimental infection. Brochoalveolar lavage (BAL) fluid was collected prior to treatment initiation (pre-treatment baseline (BL)), 1 day post treatment initiation, and 3 days post treatment initiation. Blood was collected at BL and at days 1, 2, and 3 post treatment initiation.; SARS-CoV-2-infected Rhesus Macaque Study (n=18). 18 RMs were infected with SARS-CoV-2 (USA-WA/2020 strain) intratracheally and intranasally. To investigate the role of type I IFN in SARS-CoV-2 pathogenesis, 9 of these RMs received a four-day course of IFNmod  (1mg/day, intramuscularly) beginning 1 day prior to infection (day-1) and ending on day 2 post infection while the remaining 9 control animals were untreated. Animals were necropsied at 2 days post infection (dpi), 4dpi, or 7dpi. Brochoalveolar lavage (BAL) fluid was collected before treatment was initiated and animals were infected (baseline (BL)), 2 days post infection (dpi), and, depending on necropsy date, at 4dpi and 7dpi. Blood was collected at BL and at days 1, 2, 4, 5 and 7dpi also depending on necropsy date.

first: Mirko

last: Paiardini

first: Timothy

last: Hoang

first: Elise

middle: G

last: Viox

first: Amit

middle: A

last: Upadhyay

first: Maria

last: Pino

first: Arun

last: Boddapati

first: Rayhane

last: Nchioua

first: Maximilian

last: Hirschenberger

first: Matthew

last: Gagne

first: Zachary

last: Strongin

first: Justin

middle: L

last: Harper

first: Kevin

last: Nguyen

first: Kathryn

last: Pellegrini

first: Kirti

last: Karunakaran

first: Steven

middle: E

last: Bosinger


title: A distinct astrocyte subtype in the aging mouse brain characterized by impaired protein homeostasis

status: Public on Jul 19 2022

city: Daejeon

first: Eunbeol

last: Lee

address: Daehak-ro 291

country: South Korea

institute: KAIST

summary: A new population of dysfunctional astrocytes in the aging mouse hippocampus called autophagy-dysregulated astrocytes (APDAs) show impaired protein homeostasis and defective regulation of synapse formation and elimination and appear early in a mouse model of Alzheimer’s disease.

overall_design: Single cell RNA-seq of 2-year-old WT mouse brains, Six hippocampi were analyzed

first: Seongjoon

last: Lim


title: Comprehensive transcriptomic profiles of non-small cell lung cancer by single-cell RNA-seq

status: Public on Jul 30 2022

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

summary: Lung cancer has been the leading cause of cancer death seriously threatening human health. The lung cancers display high heterogeneity in terms of pathology and molecular biomarkers. However, previous studies are mainly based on population of cancer cells due to technical limitations, which would conceal important information from rare single cells. Hence, using a modified STRT-seq technique, we profiled transcriptomes of over 9,000 single cells from 20 primary non-small cell lung cancer (NSCLC) patients diagnosed with stage I-IV. We identified major epithelial cell types, stroma cells and immune cells existed in lung, analyzed the differences between normal and tumor tissues and described the heterogeneity of intra- and inter-tumor tissues at single cell level. Furthermore, we analyzed the potential relationship of malignant epithelial cells, stroma cells and immune cells. In summary, our comprehensive analysis provided maps of transcriptomes characteristics of lung cancers and will be helpful for the prognosis and therapy of lung cancers.

overall_design: We collected tumor tissues and adjacent normal tissues from twenty patients diagnosed with stage I-IV NSCLC (non-small cell lung cancer). Then the isolated single cells were used for single-cell RNA-seq analysis. In parallel, the remaining cells from different tissues were subsequently used for bulk-cell whole genome sequencing. ***Authors state: 'According to our national policy on the protection of human genetic information, data related to human genetic information cannot be put on the international website'.

first: Li

last: Qingqing

last: Wang


title: Integrative Analysis of Spatial Transcriptome with Single-cell Transcriptome and Single-cell Epigenome in Mouse Lungs after Immunization

status: Public on Aug 15 2022

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

summary: Immunological memory is key to productive adaptive immunity. An unbiased, high through-put gene expression profiling of tissue-resident memory T cells residing in various anatomical location within the lung is fundamental to understand lung immunity but still lacking. In this study, using a well-established model on Klebsiella pneumoniae, we performed an integrative analysis of spatial transcriptome with single-cell RNA-seq and single-cell ATAC-seq on lung cells from mice after Immunization using the 10x Genomics Chromium and Visium platform. We employed several deconvolution algorithms and established an optimized deconvolution pipeline to accurately decipher specific cell-type composition by location. We identified and located 12 major cell types by scRNA-seq and spatial transcriptomic analysis.  Integrating scATAC-seq data from the same cells processed in parallel with scRNA-seq, we found epigenomic profiles provide more robust cell type identification, especially for lineage-specific T helper cells. When combining all three data modalities, we observed a dynamic change in the location of T helper cells as well as their corresponding chemokines for chemotaxis. Furthermore, cell-cell communication analysis of spatial transcriptome provided evidence of lineage-specific T helper cells receiving designated cytokine signaling. In summary, our first-in-class study demonstrated the power of multi-omics analysis to uncover intrinsic spatial- and cell-type-dependent molecular mechanisms of lung immunity. Our data provides a rich research resource of single cell multi-omics data as a reference for understanding spatial dynamics of lung immunization.

overall_design: In this study, we inoculated mice with heat-killed K. pneumoniae and assigned them into two groups, the immunized and the re-challenged group. The immunized group was inoculated twice on day 0 and day 7, whereas the re-challenged group was additionally inoculated on day 13. On day 14, both groups of mice were sacrificed for tissue harvesting. Slices A1 and A2 were sectioned from the fresh frozen lung of the immunized mouse, whereas slices A3 and A4 were from the re-challenged mouse. In a separate cohort, lung tissue from the re-challenged mouse were harvested and single-cell suspension was obtained after enzymatic digestion. The four lung slices were used for spatial transcriptomics, and the single-cell suspension from the re-challenged mouse were subjected to scRNA-seq and scATAC-seq analysis.

first: Zhongli

last: Xu

first: Kong


title: An emerging epithelial to mesenchymal transition inducer: extracellular ATP activates and modulates EMT at levels of transcription, translation, and cell function independent of TGF-b

status: Public on Jul 20 2022

city: Athens

first: Jingwen

last: Song

state: Ohio

address: 172 Water Tower Drive, 101 Konner Bldg.25, The Rideges

department: biological Sciences

institute: Ohio university

summary: EMT is an early process in metastasis that is associated with up to 90% of cancer-related death. ATP has been known to play some roles in EMT. We previously described that internalization of extracellular ATP (eATP) by cancer cells in vitro and in vivo via macropinocytosis increases intracellular ATP levels, cell proliferation and resistance to anticancer drugs. Recently, we reported eATP also induces EMT and other early metastatic activities independent of TGF-b, a well-known inducer of EMT, in human lung cancer cells. However, exactly how eATP induces EMT at gene expression level is far from understood. In this study, we hypothesize that eATP acts as an inducer and regulator of EMT alternative to TGF-b. Transwell assays revealed that eATP treatment, alone, induced human lung cancer A549 and H1299 cells to invade at rates faster than TGF-b. eATP also induced formation of filopodia-like protrusions faster than TGF-b, and it restored viability of cancer cells treated with TGF-b-neutralizing antibodies. eATP significantly elevated intracellular ATP levels while TGF-b did not. RNA sequencing / western blots revealed that eATP induced changes in expression of genes/proteins involved in EMT similar to but with differences in number and induction time compared with those induced by TGF-b. Metabolomics analysis shows that eATP-induced major metabolic changes are consistent/correlated with those identified at the gene expression level.  These differences could be accounted for by the multi-functional and multi-localization properties of eATP and macropinocytosis-internalized eATP, strongly suggesting that eATP is a previously unrecognized master inducer and regulator of EMT.

overall_design: Total 5 conditions are included, they are 2h ATP treatment, 2h TGF-β treatment, 6h ATP treatment, 6h TGF-β treatment and control. For each treatment conditions, four replicates are performed.

first: Maria

last: Evers

first: Xiaozhuo


title: RNA sequencing in POLG-iPSC derived brain cells

status: Public on Jun 28 2022

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary: The pupose of this study is to explore tanalysis to investigate the different phenotypes between homozygous and compound heterozygous genotypes in different brain cell types, including patient-specific fibroblasts, iPSCs and iPSCs-derived neural stem cells (NSCs), and astrocytes.

overall_design:
Examination of mRNA profile in iPSC, ESC and their-derived NSCs and astrocytes.
***Raw data for human samples not available due to patient privacy concerns***

first: Yu

last: Hong

first: Kristina


title: Molecular Neurobiology of Loss

status: Public on Jul 15 2022

city: Cincinnati

first: Marissa

middle: Ann

last: Smail

address: 4227 Allendorf Drive, Apt 1

department: Pharmacology and Systems Physiology

institute: University of Cincinnati


title: Tumor-infiltrating lymphocytes, prognosis and trastuzumab benefit in early-stage breast cancer patients from the FinHER trial

status: Public on Jul 16 2022

city: Brussels

first: Christos

last: Sotiriou

address: Rue Meylemeersch 90

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

summary: The clinical relevance of tumor infiltrating lymphocytes (TILs) in breast cancer (BC) is not firmly established. We aimed to validate previous prognostic findings in triple negative breast cancer (TNBC) and investigate predictive associations with trastuzumab benefit in HER2 overexpressing disease (HER2+).

overall_design: The Finland Herceptin (FinHER) trial (doi.org/10.1186/ISRCTN76560285) was an adjuvant, phase III study enrolling 1010 early-stage BC patients. Those with HER2+ disease (n=232) were randomized to 9 weeks of trastuzumab or no trastuzumab in addition to chemotherapy. Two pathologists independently quantified TILs from the 935 (92.6%) available slides. Distant disease-free survival (DDFS), overall survival (OS), and interactions with trastuzumab were studied.   During the FinHER trial, primary breast cancer specimens were collected from women who had undergone mastectomy or breast-conserving surgery and preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks. RNA extracted from FFPE specimens with Qiagen's miRNeasy FFPE Kit was processed with SensationPlusTM FFPE Amplification and 3'IVT Labeling Kit. Gene expression profiles were derived from the processed RNA using the PrimeView Human Genome U219 Array Plate on the GeneTitanTM instrument.

first: Sherene

last: Loi

first: Stefan

last: Michiels

first: Roberto

last: Salgado

first: Nicolas

last: Sirtaine

first: Vinu

last: Jose

first: Debora

last: Fumagalli

first: David

last: Brown

first: Pirkko-Liisa

last: Kellokumpu-Lehtinen

first: Petri

last: Bono

first: Vesa

last: Kataja

first: Christine

last: Desmedt

first: Martine

last: Piccart

first: Sibylle

last: Loibl

first: Michael

last: Untch

first: Carsten

last: Denkert

first: Mark

last: Smyth

first: Heikki

last: Joensuu


title: Molecular Neurobiology of Loss Part 2

first: Marissa

last: Smail

summary: Psychological loss is a common experience that erodes well-being and negatively impacts quality of life.  The molecular underpinnings of loss are poorly understood, making it challenging to develop treatment strategies.  Here, we investigate the mechanisms of loss using an enrichment removal (ER) paradigm in rats.  RNA-seq was used to investigate the molecular landscape of the basolateral amygdala (BLA), a region previously implicated in loss, in adult male Sprague-Dawley rats following ER.  Rats were subjected to standard housing (SH) for 6 weeks, environmental enrichment (EE) for 6 weeks, or enrichment removal (ER), consisting of 4 weeks of EE followed by 2 weeks of removal into impoverished conditions (n=10/pool/group).  Rats were then perfused and micropunches were collected from the basolateral amygdala (BLA) for bulk RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data collected from the basolateral amygdala of rats subjected to standard housing conditions, environmental enrichment, or enrichment removal (10 rats pooled into 1 biological replicate/group).

first: James

last: Herman

first: Robert

last: McCullumsmith

first: Rammohan

last: Shukla


title: RNAseq anaysis of RTF2 MEF cells

status: Public on Jun 08 2022

city: New York

first: Agata

last: Smogorzewska

state: NY

address: 1230 York Ave

department: Genome Maintenance

institute: The Rockefeller University

summary: Purpose: To identify gene expression in RTF2 null cells compared to WT cells   Method: Total RNA for mRNA Seq, NextSeq High Output 75 SR  Results:  57 genes significantly downregulated and 7 genes significantly upregulated in RTF2 deficient MEFs

overall_design: WT MEFs were compared to RTF2 null MEFs for transcriptional changes. RTF2 Null (Rtf2-/lox + Cre) MEFs are compared to WT (Rtf2+/+ + Cre) littermate controls in triplicate. Two different sets of MEFs (isolated from different mothers) were used. Cre was retrovirally induced in cell 72 hours prior to cell collection and RNA extraction.

first: Smogorzewska

last: Agata

first: Conti

last: Brooke


title: Regulation of 27-hydroxycholesterol metabolism by ZMYND8 in mammospheres

status: Public on Jun 02 2022

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

summary: ZMYND8 is a master regulator of 27-hydroxycholesterol metabolism in breast cancer stem cells.

overall_design: Parental and ZMYND8 knockout MDA-MB-231 mammospheres were subjected to ZMYND8 ChIP-seq.

first: Lei

last: Bao

first: Maowu


title: Regulation of 27-hydroxycholesterol metabolism by ZMYND8

overall_design: MDA-MB-231 monolayer cells and mammospheres were subjected to mRNA-seq. MDA-MB-231 cells were subjected to ChIP-seq.


title: mTORC1 couples SREBP-dependent transcription and splicing of de novo lipid synthesis enzymes via FAM120A  de novo lipid synthesis enzymes via FAM120A

status: Public on Jul 02 2022

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

institute: Korea University College of Medicine

summary:
FAM120A as a transcriptional co-activator that couples transcription and splicing of lipid synthesis enzymes downstream of mTORC1-SRPK2 signaling.
Mechanistically, the mTORC1-activated SRPK2 phosphorylates a splicing factor SRSF1, enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging newly transcribed lipogenic genes to the RNA splicing machinery.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LAM 621-101 cells and its KD derivatives (siNTC or siFAM120A).

first: Sungyun

last: Cho

first: John

last: Blenis


title: Molecular Neurobiology of Loss Part 1

summary: Psychological loss is a common experience that erodes well-being and negatively impacts quality of life.  The molecular underpinnings of loss are poorly understood, making it challenging to develop treatment strategies.  Here, we investigate the mechanisms of loss using an enrichment removal (ER) paradigm in rats.  RNA-seq was used to investigate the molecular landscape of the basolateral amygdala (BLA), a region previously implicated in loss, in adult male Sprague-Dawley rats following ER.  Rats were subjected to standard housing (SH) for 6 weeks, environmental enrichment (EE) for 6 weeks, or enrichment removal (ER), consisting of 4 weeks of EE followed by 2 weeks of removal into impoverished conditions (n=6/group).  Rats were then perfused and micropunches were collected from the basolateral amygdala (BLA) for bulk RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data collected from the basolateral amygdala of rats subjected to standard housing conditions, environmental enrichment, or enrichment removal (n=6 biological replicates/group).

first: Brittany

last: Smith


title: Tumor-associated Tregs obstruct anti-tumor immunity by promoting T cell dysfunction and restricting clonal diversity in tumor-infiltrating CD8+ T cells

status: Public on Jun 01 2022

city: Tampa

first: Dennis

last: Adeegbe

state: FL

address: 13131 USF Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center

summary: We investigated how accumulation of Tregs contributes to T cell dysfunction and clonal constriction of tumor-infiltrating CD8+ T cells. Resected melanoma atissues from tumor-bearing mice were analyzed. The clonal diversity of tumor-associated CD8+ T cells were evaluated by single-cell TCR sequencing respectively, at early or advanced tumor stages or under Treg depletion conditions. TCR-sequencing revealed a clonal shrinkage of tumor-infiltrating CD8+ T cells as tumor progressed, which was associated with reduced survival profile concomitant to increasing Treg proportions.

overall_design: CD8+ T cells sorted from melanoma tissues in B16-F10 incoculated mice were processed for single-cell TCR sequencing

first: David

last: Noyes

first: Jon

last: Semidey-Hurtado


title: The SWI/SNF ATPase BRG1 facilitates multiple pro-tumorigenic gene expression programs in SMARCB1-deficient cancer cells

status: Public on May 31 2022

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: Here, we expose the connection between rSWI/SNF and oncogenic processes using a well-characterized chemical degrader to deplete the SWI/SNF ATPase, BRG1. Using a combination of gene expression and chromatin accessibility assays we show that rSWI/SNF complexes facilitate MYC target gene expression. We also find that rSWI/SNF maintains open chromatin at sites associated with hallmark cancer genes linked to the AP-1 transcription factor, suggesting that AP-1 may drive oncogenesis in MRT.

overall_design: We used a well-characterized chemical degrader targeted against the SWI/SNF ATPase, BRG1 to deplete BRG1 in the G401 MRT cell line. For RNA-seq and ATAC-seq, G401 cells were treated for 24 hours with 250 nM ACBI1 or matched DMSO control.

first: William

last: Tansey

first: April

middle: M

last: Weissmiller

first: Qi

last: Liu


title: Divergent transcriptional regulation of astrocyte reactivity across disorders [TR_ATAC_SCI]

status: Public on May 26 2022

city: Los Angeles

first: Joshua

middle: Evan

last: Burda

state: CA

address: 127 S San Vicente Blvd

department: Biomedical Sciences, Center for Neural Science and Medicine

institute: Cedars Sinai Medical Center

summary: Single-nuclei Assay for Transposase-Accessible Chromatin with sequencing (snATACseq) was applied to examine chromatin landscape changes and transcriptional regulator (TR) DNA motif accessibility in reactive astrocytes following traumatic spinal cord injury (SCI). Astrocyte nuclei were isolated from the spinal cord of wild type mice and mice with astrocyte-specific conditional gene deletion (cKO) of test-case TRs, SMARCA4 (Smarca4-astro-cKO) or STAT3 knockout (Stat3-astro-cKO). Comparison of differential chromatin accessibility revealed substantial remodeling during astrocyte reactivity, with more chromatin opening than closing. Marked alterations in access to SCI reactivity-associated TR motifs were also detected.

overall_design: Astrocyte nuclei were isolated from the spinal cord of wild type, Smarca4-astro-cKO, and Stat3-astro-cKO mice 14 days following SCI. Equivalent spinal cord tissues were examined from healthy (uninjured) control mice.

first: Michael

middle: V

last: Sofroniew


title: Divergent transcriptional regulation of astrocyte reactivity across disorders

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

overall_design: Refer to individual Series


title: Divergent transcriptional regulation of astrocyte reactivity across disorders [TR_ATAC_LPS]

summary: Single-nuclei Assay for Transposase-Accessible Chromatin with sequencing (snATACseq) was applied to examine chromatin landscape changes and transcriptional regulator (TR) DNA motif accessibility in reactive astrocytes following neuroinflammatory insult by systemic administration of lipopolysaccharide (LPS).  Astrocyte nuclei were isolated from the spinal cord of wild type mice and mice with astrocyte-specific conditional gene deletion (cKO) of test-case TRs, SMARCA4 (Smarca4-astro-cKO) or STAT3 knockout (Stat3-astro-cKO). Comparison of differential chromatin accessibility revealed substantial remodeling during astrocyte reactivity, with more chromatin opening than closing. Marked alterations in access to LPS reactivity-associated TR motifs were also detected.

overall_design: Astrocyte nuclei were isolated from the spinal cord of wild type, Smarca4-astro-cKO, and Stat3-astro-cKO mice 24 hours following intraperitoneal injection of 5 mg/Kg LPS. Equivalent spinal cord tissues were examined from genotype matched healthy control mice.


title: Divergent transcriptional regulation of astrocyte reactivity across disorders [RNA-seq]

summary: RNA sequencing was applied to examine changes in gene expression in reactive astrocytes following traumatic spinal cord injury (SCI) or neuroinflammatory insult by systemic administration of lipopolysaccharide (LPS). Transgenic Ribotag technology was used to isolate astrocyte ribosome-associated mRNAs from the spinal cord of wild type mice and mice with astrocyte-specific conditional gene deletion (cKO) of test-case transcriptional regulators of reactivity, SMARCA4 (Smarca4-astro-cKO) or STAT3 knockout (Stat3-astro-cKO). Examination of differentially expressed gene (DEG) profiles by upstream transcriptional regulator enrichment analysis (TREA) was used identify transcriptional regulators of reactivity in each condition. Together, findings from this study show that transcriptional changes associated with astrocyte reactivity are exquisitely heterogeneous and are customized from vast numbers of potential DEGs via context-specific combinatorial TR interactions. These data have also been made accessible in a open-access, searchable database: http://tr.astrocytereactivity.com

overall_design: Astrocyte ribosome-associated mRNAs were isolated from the spinal cord of wild type, Smarca4-astro-cKO, and Stat3-astro-cKO Ribotag mice at 14 days post-SCI or 24 hours following  intraperitoneal injection of 5 mg/Kg LPS administration. Equivalent spinal cord tissues were examined from genotype matched healthy (uninjured) control mice.


title: Identification of DDX3X-dependent translation targets in the E11.5 mouse cortex

status: Public on May 18 2022

city: Durham

first: Debra

last: Silver

state: North Carolina

address: 224 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: To identify DDX3X-dependent translation targets in the developing mouse cortex, we used E11.5 cortices from both sexes of wildtype and conditional Ddx3x knockout mice (driven by Emx1-Cre). We performed RNAseq and Riboseq on these samples in parallel.

overall_design: Comparative gene expression profiling analysis of RNA-seq and Ribo-seq data for wildtype and Ddx3x conditional knockout mouse E11.5 cortex. The following are biological replicates: Female controls: F2, F3; Male controls: M1, M2, M3; cKO females: F1, F2, F3; cKO mals: M1, M2, M3

first: Mariah

last: Hoye

first: Lorenzo

last: Calviello


title: Identification of differentially expressed genes in OVISE cells treated gamma irradation with either paclitaxol  or bevacizumab

status: Public on May 17 2022

city: Tokyo

first: Nozomu

last: Yanaihara

address: 3-25-8, Nishi-shinbashi, Minato-ku

country: Japan

institute: The Jikei Univ.

summary: To ideintify differentially expressed genes in OVISE cells after treatment by gamma irradiation with either paclitaxol  or bevacizumab.

overall_design: OVISE cells were treated with wither paclitaxol or bevacizumab and incubated for 192 h and then total RNA, which was used for RNA sequencing, was extracted from these cells 2 h after treatment with 2 Gy of gamma irradiation.

first: Yasushi

last: Iida


title: Core Transcription Programs Controlling Injury-Induced Neurodegeneration of Retinal Ganglion Cells

status: Public on May 06 2022

first: Yuyan

last: Cheng

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

institute: UCLA

summary: In this study, we performed RNA-seq of injured and FACS-purified RGCs receiving CRISPR-mediated knockout of ATF3, ATF4, CEBPγ or CHOP

overall_design: We generated RNA-seq data on mouse RGCs receiving control or sgRNA targeting ATF3, ATF4, CEBPγ or CHOP at 3 days following optic nerve injury, with 2-6 replicates in each condition.

first: Feng

last: Tian

first: Daniel

last: Geschwind

first: Zhigang

last: He


title: lncRNA related studies in MAPK-driven melanoma

status: Public on May 01 2022

city: San Francisco

first: Valentin

last: Feichtenschlager

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

type: Non-coding RNA profiling by high throughput sequencing

summary: RNAseq data of 2 NRAS mutant melanoma cell lines (D04, mm415), melanocytes with NRAS mutation (PHMq61), melanocytes harboring an empty vector (PHMe) and untreated melanocytes (PHM). D04 cells (samples 6-11) treated with non targeting control ASOs, or ASOs that target the lncRNA 'TRASH'

overall_design: D04, mm415, PHMe, PHMq61 and PHM data was generated to identify lncRNAs that respond with differential expression to MAPK pathway activation. D04 cells then were anlayzed for transcriptomic changes in response to knockdown of the MAPK-pathway responsive lncRNA 'TRASH'

first: Susana

last: Ortiz-Urda

first: Igor

last: Vujic

first: Martina

last: Sanlorenzo

first: Kevin

last: Lin


title: Expression data from liver samples overexpressing either GFP or ChREBP

status: Public on Apr 15 2022

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: The GFP or ChREBP were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later.  We used microarray analysis to detail the global program of gene expression underlying ChREBP overexpression and identified distinct classes of up and down regulated genes.

overall_design: RNA extraction and hybridization on Affymetrix microarrays.

first: R

last: Dentin

first: E

last: Benichou


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [RNAseq]

status: Public on Nov 01 2022

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

summary: Genome-wide association studies (GWAS) have discovered thousands of risk loci for common, complex diseases, each of which could point to genes and gene programs that influence disease. For some diseases, it has been observed that GWAS signals converge on a smaller number of biological programs, and that this convergence can help to identify causal genes. However, identifying such convergence remains challenging: each GWAS locus can have 2-20 candidate genes, the cellular programs a gene participates in are difficult to define in an unbiased fashion, and it remains unclear which genes and programs would be likely to influence disease risk. Here, we explored a new approach to address this challenge, by creating an unbiased catalog of gene programs and their regulators in endothelial cells to link variants to functions for coronary artery disease (CAD). To do so, we applied CRISPRi-Perturb-seq to knock down all expressed genes within 500 Kb of all CAD GWAS loci (2,285 genes in total) and measure their effects on the transcriptome using single-cell RNA-seq. We used consensus non-negative matrix factorization to define 60 gene expression programs—including core cellular programs, such as ribosome biogenesis, and endothelial cell-specific programs, such as flow response and angiogenesis—and link these programs to upstream regulators including transcription factors, chromatin regulators, metabolic enzymes, and signaling cascades. By combining this gene-to-program catalog with variant-to-gene maps, we find that candidate CAD genes converge onto 6 interrelated gene programs, together involving known and novel genes in 39 of 229 CAD GWAS loci. Analysis of these programs revealed that the cerebral cavernous malformations (CCM) complex—whose potential connection to CAD has not been previously explored—acts upstream to regulate other CAD genes involved in cytoskeletal organization, extracellular matrix remodeling, and cell migration. The strongest regulator of these programs is TLNRD1, a highly conserved but poorly studied gene that we show acts in the CCM pathway and regulates actin organization and endothelial cell barrier function. Together, our study nominates new genes that likely influence risk for CAD, identifies convergence of CAD risk loci into certain gene programs in endothelial cells, and demonstrates a generalizable strategy to catalog gene programs to connect disease variants to functions.

overall_design: RNA was collected from parental human endothelial cell lines (TeloHAEC and Eahy926) grown in normal growth media, or media supplemented with 10ng/ml interleukin 1 beta (IL1b) or tumor necrosis factor alpha (TNFa) for 24 hours, and RNA-seq libraries made from poly-A+ mRNA using kits from NEB. RNA-seq libraries were also made from CRISPRi TeloHAEC (TeloHAEC with doxycycline-inducible KRAB-dCAS9-BFP) that were transduced with lentiviral single guide RNA vectors, selected for blast resistance, and treated with doxycycline to induce CRISPRi machinery and silence the sgRNA-targeted promoters.

first: Gavin

middle: R

last: Schnitzler

first: Helen

last: Kang

first: Vivian

last: Lee-Kim

first: X

last: Ma

first: Tony

last: Zeng

first: Shamsudheen

last: Vellarikkal

first: Ronghao

last: Zhou

first: Katherine

last: Guo

first: Oscar

last: Sias-Garcia

first: Alex

last: Bloemendal

first: Glen

last: Munson

first: Philine

last: Guckelberger

first: Tung

middle: H

last: Nguyen

first: Drew

middle: T

last: Bergman

first: Deepak

last: Atri

first: Nathan

first: Brian

last: Cleary

first: Eric

last: Lander

first: Hilary

last: Finucane

first: Rajat

last: Gupta


title: Expression data from ChREBP overexpressing HCC tumors compared to non-tumoral adjacent liver tissue

first: Franck

last: Letourneur

summary:
ChREBP was stably overexpressed in the  liver of C57BL/6J mice through the use of the sleeping beauty transposon system. ChREBP overexpression resulted in HCC tumor development in 12 months.
We used microarray analysis to detail the global program of gene expression in ChREBP overexpressing tumors compared to non-tumoral adjacent tissue or compared with normal liver samples from C57BL/6J mice. WE then identified distinct classes of up and down regulated genes.

first: R

last: Dentin

first: E

last: Benichou


title: Glomerular RNAseq counts from the Neptune Cohort and healthy living donors

status: Public on Apr 13 2022

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

summary: Glomerular Transcriptome in the Neptune Cohort

overall_design:
Glomerular RNAseq count
***Please note that updated count matrix and voom transformed data is available in the GSE254957 records***
----------------------------
Authors state "Raw data (fastq) files are available upon approved ancillary study request from the NEPTUNE consortium (please see https://www.neptune-study.org/ancillary-studies; email contact: NEPTUNE-STUDY@umich.edu"

first: Felix

last: Eichinger

first: Laura

last: Mariani

first: Raji

last: Menon

first: Brad

last: Godfrey

first: Matthias

last: Kretzler


title: RNA-Seq analysis of switchgrass  transcriptome in response to single drought and combinations of drought and heat stress

status: Public on Mar 31 2022

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

summary:
Purpose: Increasing biomass yield and quality of feedstock have been a recent interest in switchgrass research.  Despite the economic importance of switchgrass, increasing temperature and water deficit are  limiting factors to the cultivation of bioenergy crops in the semi-arid areas. The effect of individual drought or heat stress has been studied separately in switchgrass. However, there is relatively limited or no report on the molecular basis of combined abiotic stress tolerance in switchgrass particularly the combination of drought and heat stress. We used RNA-Seq approaches to elucidate the transcriptome changes of switchgrass in response to drought and high temperatures simultaneously.
Method: We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted.
Results:Out of total 32,190 genes, we identified 3,912, as DT responsive genes, 2,339 and 4,635 as , heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively
Conclusion: Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.

overall_design: Leaf mRNA profiling of AP13 genotype, a selection from lowland cultivar ‘Alamo’ during drought and heat stress at time points, 0h, 72h, 96h, 120h, 144h and 168h.

first: Rita

last: Hayford

first: Desalegn

middle: D

last: Serba

first: Vasudevan

last: Ayyappan

first: Jyothi

last: Thimmapuram

first: Malay

middle: C

last: Saha

first: Cathy

last: Wu

first: Venu

last: Kalavacharla


title: Analysis of the DNA topology upon multiple histone H1 variants depletion by Hi-C experiments

status: Public on Mar 23 2022

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

summary: The combined depletion of histones H1.2 and H1.4 in T47D-MTVL human breast cancer cells has a strong deleterious effect, deregulates gene expression, promotes the appearance of genome-wide accessibility sites, and triggers the interferon response. We have further analyzed the consequences of multiple H1 variants depletion at the topological level by performing Hi-C experiments on T47D-MTVL cancer cells expressing a Dox-inducible shRNA against multiple H1 variants.

overall_design: Stable breast cancer-derived cell lines expressing an shRNA against different histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox. Three Hi-C libraries were subsequently prepared and high-throughput sequenced.

first: A

first: N

last: Serna

first: M

last: Salinas


title: Effect of deletion of AZF1 on gene expression under the SEF1-deleted background in yeast Lachancea kluyveri

status: Public on Apr 12 2022

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: The investigate the loss-of fucntion azf1 suppressive mutations to the sef1-deleted transcriptional netwrok in L. kluyveri, we analyzed the gene expression profiles in response to azf1 deletion under fermentative and respiratory conditions and foucsed on the compensatory effects on gene expression to sef1 deletion.

overall_design: Comparative analyses between the wild type, sef1-deleted, azf1-deleted, and sef1azf1 double-deleted strains under the YPD and YPGly conditions were performed. Each sample contains three technical repeats.

first: Jun-Yi

last: Leu


title: Single-nuclei profiling of aged skeletal muscle

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Aging is accompanied by a loss of muscle mass and function, termed sarcopenia, causing numerous morbidities and economic burdens in human populations. Mechanisms implicated in age-related sarcopenia include inflammation, muscle stem cell depletion, mitochondrial dysfunction and loss of motor neurons, but whether there are key drivers of sarcopenia is not yet known. To gain deeper insights into age-related sarcopenia, we performed transcriptome profiling on lower limb muscle biopsies from 72 young, old and sarcopenic subjects using bulk RNA-seq (N = 72) and single-nuclei RNA-seq (N = 17). Using this combined approach, we discovered novel changes in gene expression that occur with age and sarcopenia in multiple cell types comprising mature skeletal muscle. Notably, we found increased expression of the genes MYH8 and PDK4, and decreased expression of the gene IGFN1, in old muscle. We also identified a small population of nuclei that express CDKN1A, present only in aged samples, consistent with P21CIP1 senescence in this subpopulation. Our findings identify unique cellular sub-populations populations in aged and sarcopenic skeletal muscle, which will facilitate the development of new therapeutic strategies to combat age-related sarcopenia.

overall_design: We performed transcriptome profiling on lower limb muscle biopsies from 72 young, old and sarcopenic subjects using bulk RNA-seq (N = 72) and single-nuclei RNA-seq (N = 17).

first: Kevin

last: Perez

first: Serban

last: Ciotlos


title: Profiling of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer tissues and adjacent normal tissues

status: Public on Mar 15 2022

city: Guangzhou

first: Yongxin

last: Zhang

address: 58 Zhongshan  9 2nd Road

institute: the First Affiliated Hospital, Sun Yat-sen University

summary:
Purpose: To investigate the role and mechanism of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer.
Methods: RNA-seq of ribosomal RNA-depleted total RNA were performed to screen differential expressed mRNAs, long chain non-coding RNAs  between paired gastric cancer tissues and adjacent normal tissues.For the linear RNA was digested with 3 U of RNase R per µg of RNA.
Results: A total of 83672 mRNAs, 105998 long chain non-coding RNAs, 25441 distinct circRNAs were identified in these samples, and 13929 of these circRNAs were identified as novel circRNAs.

overall_design: Gastric mRNAs, long chain non-coding RNAs and circular RNAs profiles of paired gastric cancer tissues and adjacent normal tissues were generated by deep sequencing, using an Illumina Hiseq 4000 platform.

first: Wei

last: Feng

first: Wenwei

last: Liu


title: Severe COVID-19 is associated with molecular signatures of aging in the human brain

status: Public on Mar 22 2022

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: As coronavirus disease 2019 (COVID-19) and aging are both accompanied by cognitive decline, we hypothesized that COVID-19 might lead to molecular signatures similar to aging. We performed whole-transcriptome analysis of the frontal cortex, a critical area for cognitive function, in individuals with COVID-19, age-matched and sex-matched uninfected controls, and uninfected individuals with intensive care unit/ventilator treatment. Our findings indicate that COVID-19 is associated with molecular signatures of brain aging and emphasize the value of neurological follow-up in recovered individuals.

overall_design: RNA-seq profiling of human frontal cortex in severe COVID-19 or unaffected patients

first: Maria

last: Mavrikaki

first: Frank

middle: J

last: Slack


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [scRNAseq]

first: Jesse

last: Engreitz

overall_design: Human immortalized endothelial cells engineered to contain doxycycline inducible CRISPR interference machinery (CRISPRi TeloHAEC), were transduced with a library of 36,880 guide RNAs targeting gene promoters, in a CROP-seq vector. After 5 days of doxycycline treatment, cells were run on 20 lanes of a 10X Chromium Controller and scRNA-seq libraries generated. polyA+ cDNA surrounding the guide sequences was amplified to make "dialout" libraries, used to link guide RNA sequences to scRNAseq cell barcodes.

first: Gavin

last: Schnitzler

first: Helen

last: Kang

first: Vivian

last: Lee-Kim

first: X

last: Ma

first: Tony

last: Zeng

first: Shamsudheen

last: Vellarikkal

first: Ronghao

last: Zhou

first: Katherine

last: Guo

first: Oscar

last: Sias-Garcia

first: Alex

last: Bloemendal

first: Glen

last: Munson

first: Philine

last: Guckelberger

first: Tung

last: Nguyen

first: Drew

last: Bergman

first: Deepak

last: Atri

first: Nathan

last: Cheng

first: Brian

last: Cleary

first: Eric

middle: S

last: Lander

first: Hilary

last: Finucane

first: Rajat

last: Gupta


title: RNA-seq for J-gammal cell line in either the absence or presence of FYB1

status: Public on May 23 2022

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for J-gammal cell line in either the absence or presence of FYB1

overall_design: 2 J-gammal samples with no treatment and 2 J-gammal samples with FYB1 knockdown

first: Pan

last: Jian

first: Zhuang

middle: K

last: Long


title: Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy

status: Public on Mar 10 2022

city: Houston

first: Hussein

middle: A.

last: Abbas

state: TX

address: 1400 Holcombe Blvd

department: Leukemia and Genomic Medicine

institute: MD Anderson Cancer Center

summary: We report the application of single cell RNA and TCR sequencing technology on 22 bone marrow aspirates from 8 AML patients. By exploring 60753 AML cells and 52641 tumor microenvironment cells, we show that TCR repertoires expand and primarily emerge from CD8+ cells in responsive patients, but contract in therapy-resistant patients.Tractory analysis reveals that CD8 + T cells in AML are on continuum with GZMK expression being enriched in a memory subset of CD8 + T cells. Also, Chromosome 7/7q loss s an intrinsic AML biomarker of resistance to ICB-therapy.

overall_design:
Examination of 22 bone marrow samples from 8 relapsed/refractory AML patients.
Raw data have been deposited at EGA (https://ega-archive.org/studies/EGAS00001004894).


title: Tumor infiltrating CD8+ Tex cells dictate divergent survival outcomes in pre- vs post-menopausal ER+ breast cancer

status: Public on Feb 23 2022

city: Duarte

first: Peter

middle: P

last: Lee

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

summary: We identify subsets of BC tumors infiltrated by CD8+ T cells with characteristic features of exhausted T cells (TEX). Tumors with abundant CD8+ TEX exhibit a distinct tumor microenvironment marked by amplified interferon-γ signaling related pathways and higher PD-L1 expression.

overall_design: ER+ tumors were segregated into TEX ‘high’ (TEXhi) and TEX ‘low’ (TEXlo) tumors as defined by above and below 5% TEX of CD8+ TILs based on FACS.

first: Weihua

last: Guo

first: Colt

middle: A

last: Egelston


title: Defining Giardia lamblia cleavage sites

status: Public on Mar 09 2022

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

summary: 3'-end sequencing and Oxford Nanopore Technologies long-read sequencing of trophozoite RNA to define mRNA cleavage sites

overall_design: RNA Sequencing of G. lamblia trophozoites

first: Danielle

middle: Y

last: Bilodeau

first: Ryan

last: Sheridan

first: Balu

last: Balan

first: Aaron

last: Jex


title: RNAi components regulate the microparasitism in Trichoderma atroviride

status: Public on Feb 28 2022

city: Irapuato

first: Alfredo

last: Herrera Estrella

state: Guanajuato

address: Libr. Norte carr. León, Km 9.6

department: LANGEBIO

country: Mexico

institute: CINVESTAV

summary: Trichoderma atroviride is a fungus capable of establishing symbiotic relationships with plants, however, its main lifestyle is a saprophyte. Due to these characteristics, it must face a great quantity of microorganisms, and be able to compete for nutrients. T. atroviride is considered a necrotrophic mycoparasite and has developed the ability to kill other organisms and obtain nutrients from them. The object of this work is to explore the role of small RNAs in mycoparasitism. To this end, we obtained small RNA-Seq libraries from the interactions of T. atroviride against Alternaria alternata. The libraries were obtained from three stages during mycoparasitsm: before contact (BC), contact (C), and after contact (AC).

overall_design: T. atroviride Wild type strain and dcr-2 mutant co-cultured with Alternaria alternata and collected at three stages: Before contact (BC), Contact (C) and After Contact (AC). The controls of T. atroviride were strains growing alone. Three replicates per condition. Total number of samples: 24

first: Eli

middle: E

last: Felix

first: Camilo

last: Salazar

first: Guillermo

last: Rico

first: Jose

last: Villalobos

last: Estrella


title: Genome-wide DNA methylation profiling identifies epigenetic changes in CD4+ and CD14+ cells of multiple sclerosis patients [CD4]

city: Moscow

first: Ivan

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

summary: Multiple sclerosis (MS) is a chronic autoimmune and degenerative disease of the central nervous system, which develops in genetically predisposed individuals upon exposure to environmental influences. Environmental triggers of MS, such as viral infections or smoking, were demonstrated to affect DNA methylation, and thus to involve this important epigenetic mechanism  in the development of pathological processes. To identify DNA methylation hallmarks, associated with MS, we performed genome-wide DNA methylation profiling of two cell populations (CD4+ T-lymphocytes and CD14+ monocytes), collected from the same individuals (relapsing-remitting MS patients and healthy subjects), using Illumina 450K methylation arrays. We revealed significant changes in DNA methylation for both cell populations of studied groups. In CD4+ cells the majority of differentially methylated positions (DMPs) were shown to be hypomethylated, while in CD14+ cells – hypermethylated in MS patients. Noteworthy, in CD4+, but not in CD14+ cells, we found differential methylation of HLA-DRB6 gene from HLA locus, which is known to have the strongest genetic association with MS. Besides, about 20% of DMPs identified in studied cells were identical; they all had the same direction of methylation changes in both cell populations and may be involved in basic epigenetic processes occuring in MS. These findings suggest that the epigenetic mechanism of DNA methylation in immune cells contributes to MS; further studies are now required to validate these results and understand their functional significance.

overall_design: We performed a genome-wide DNA methylation analysis in CD4+ T lymphocytes of 6 treatment-naïve patients with relapsing-remitting multiple sclerosis in stable remission (MS) and 8 healthy controls (HC).

first: Ludmila

last: Danilova


title: Systematic reconstruction of the cellular trajectories of mammalian embryogenesis (E8.5)

status: Public on Mar 11 2022

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary:
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single cell zygote gives rise to millions of cells expressing a panoply of molecular programs, including much of the diversity that will subsequently be present in adult tissues. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive.
For mouse embryogenesis in particular, we and others have performed single cell or single nucleus RNA-seq data (scRNA-seq) during implantation, gastrulation and organogenesis. Here we set out to integrate several single cell RNA-seq datasets (scRNA-seq) that collectively span mouse gastrulation and organogenesis. However, a technical challenge that we faced is that the datasets that we sought to integrate were generated by different groups at different times using different scRNA-seq technologies. In particular, probably because there was no overlapping timepoint, the integration of scRNA-seq data generated at E8.5 (cells, 10X Genomics) and E9.5 (nuclei, sci-RNA-seq3) was challenging (Cao et al. 2019; Pijuan-Sala et al. 2019).
To address this, we set out to generate new data at E8.5 that might serve to “bridge” these two datasets. Because of how quickly changes are occurring during this window of development, we focused on individual, somite-resolved E8.5 embryos using a simplified, optimized version of sci-RNA-seq3. We selected 12 embryos from 2 separate litters harvested at E8.5, including a single primitive streak stage embryo (prior to somitogenesis) and 11 embryos staged in 1-somite increments from 2 to 12 somites. The optimized sci-RNA-seq3 method markedly improved data quality, with 9-fold higher UMIs and 6-fold higher gene detection per nucleus, relative to (Cao et al. 2019).
Overall, we collected published data (Cheng et al. 2019; Mohammed et al. 2017; Pijuan-Sala et al. 2019), the new E8.5 data, and published data from one study spanning E9.5 to E13.5 but with deeper sequencing of those libraries (Cao et al. 2019). Altogether, we define cell states at each of 19 successive stages spanning E3.5 to E13.5, heuristically connect them to their pseudo-ancestors and pseudo-descendants. Despite being constructed through automated procedures, the resulting trajectories of mammalian embryogenesis (TOME) are largely consistent with our contemporary understanding of mammalian development.
In addition, the new E8.5 data itself comprises a foundational resource for mammalian developmental biology (especially for the early somitogenesis), and are made available in a way that will facilitate their ongoing annotation by the research community.

overall_design: Around 240 thousand cells derived from 12 individual, somite-resolved E8.5 mouse embryos. The 12 samples are from 2 separate litters harvested at E8.5, including a single primitive streak stage embryo (prior to somitogenesis) and 11 embryos staged in 1-somite increments from 2 to 12 somites.

first: Junyue

last: Cao

first: Beth

last: Martin

first: Tony

last: Li

first: Ian

last: Welsh

first: Sanjay

last: Srivatsan

first: Xingfan

last: Huang

first: Diego

last: Calderon

first: William

last: Noble

first: Christine

middle: M

last: Disteche

first: Stephen

last: Murray

first: Malte

last: Spielmann

first: Cecilia

middle: B

last: Moens

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: Systematic reconstruction of the cellular trajectories of mammalian embryogenesis (deeper sequencing of E9.5-E13.5)

summary:
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single cell zygote gives rise to millions of cells expressing a panoply of molecular programs, including much of the diversity that will subsequently be present in adult tissues. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive.
For mouse embryogenesis in particular, we and others have performed single cell or single nucleus RNA-seq data (scRNA-seq) during implantation, gastrulation and organogenesis. Here we set out to integrate several single cell RNA-seq datasets (scRNA-seq) that collectively span mouse gastrulation and organogenesis. However, a technical challenge that we faced is that the datasets that we sought to integrate were generated by different groups at different times using different scRNA-seq technologies. In particular, probably because there was no overlapping timepoint, the integration of scRNA-seq data generated at E8.5 (cells, 10X Genomics) and E9.5 (nuclei, sci-RNA-seq3) was challenging (Cao et al. 2019; Pijuan-Sala et al. 2019).
To address this, we set out to generate new data at E8.5 that might serve to “bridge” these two datasets. Because of how quickly changes are occurring during this window of development, we focused on individual, somite-resolved E8.5 embryos using a simplified, optimized version of sci-RNA-seq3. At the same time, to obtain higher quality data across E9.5-E13.5, we performed a deeper sequencing (specifically, three additional Novaseq runs) of previously reported libraries (Cao et al. 2019). Compared to the previous data (Cao et al. 2019), the median UMI count per cell improved from 671 to 1,434, while the median genes detected per cell improved from 518 to 735.
Overall, we collected published data (Cheng et al. 2019; Mohammed et al. 2017; Pijuan-Sala et al. 2019), the new E8.5 data, and the deeper sequencing of previous libraries (Cao et al. 2019). Altogether, we define cell states at each of 19 successive stages spanning E3.5 to E13.5, heuristically connect them to their pseudo-ancestors and pseudo-descendants. Despite being constructed through automated procedures, the resulting trajectories of mammalian embryogenesis (TOME) are largely consistent with our contemporary understanding of mammalian development.
In addition, the data of deeper sequencing of previously reported libraries itself comprises a foundational resource for mammalian developmental biology, and are made available in a way that will facilitate their ongoing annotation by the research community.

overall_design: 2 million cells derived from 61 mouse embryos staged between 9.5 and 13.5 days of gestation (E9.5 to E13.5; 10 to 15 replicates per timepoint)


title: CD38 enzymatic activity promotes hematopoietic stem cell dormancy

status: Public on Feb 18 2022

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

country: Germany

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

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

overall_design: Refer to individual Series


title: CD38 enzymatic activity promotes hematopoietic stem cell dormancy [scRNA-Seq]

summary: Quiescence is a fundamental property that protects hematopoietic stem cells’ (HSCs) function throughout life. A subpopulation of deeply quiescent, so-called dormant HSCs (dHSCs) harbors the highest long-term blood repopulation capacity and resides at the top of the hematopoietic hierarchy. However, the mechanisms of HSC dormancy remain elusive, mainly due to the absence of surface markers for dHSCs’ prompt isolation. We identified CD38 nicotinamide adenine dinucleotide (NAD+) catabolic ecto-enzyme as a novel surface marker for murine dHSCs. The product of CD38 cyclase activity – cyclic adenosine diphosphate ribose (cADPR), regulates the expression of the transcription factor and cell cycle regulator c-Fos via an increase of cytoplasmic Ca2+ concentration. Strikingly, we uncovered that c-Fos drives HSCs quiescence through the induction of the cell cycle inhibitor p57Kip2 expression. Moreover, we found a similar CD38-dependent mechanism of quiescence regulation for human HSCs, which are CD38 negative. Specifically, we found that CD38 ecto-enzymatic activity at the neighboring CD38-positive cells promote human HSCs’ dormancy. Together, our work reveals how extracellular metabolic cues trigger a signaling cascade blocking HSC cell cycle entrance. Pharmacological manipulations of defined pathway will provide new strategies to modulate HSCs activation upon infections, blood loss or transplantation in clinical practice.

overall_design: We sorted HSCs, Lin-, kit+ Sca1+ CD48- CD150+ from 8 w and 24w old mice separately ( 2 mice per samples, pooled). Cells from both samples were included to the subsequent analysis.

first: Liliia

last: Ibaneeva

first: Anupam

last: Sinha

first: Tatyana

last: Grinenko


title: Coenzyme Q regulates UCP1 expression and thermogenesis through the integrated stress responses

status: Public on Feb 01 2022

city: Berkeley

first: Greg

last: Timblin

department: MCB

institute: UC Berkeley

summary: Coenzyme Q is an essential component of mitochondrial function and required for thermogenic activity in brown adipose tissues (BAT). BAT CoQ deficiency (50-75%) by genetic or pharmacological means does not interfere with basal or maximal mitochondrial respiration in brown adipocytes but increases mitochondrial oxidants and induces UPRmt, ISR, and repression of UCP1 expression. ATF4, the master regulator of ISR, is required for UCP1 suppression in BAT CoQ deficiency. In animals, BAT CoQ deficiency causes cold intolerance but activates compensatory thermogenic mechanisms in BAT and other tissues via greatly induced BAT FGF21 expression resulting in paradoxically upregulated whole-body respiration rates and protection from obesity at room temperature and thermoneutrality. BAT-specific loss of either ATF4 or FGF21 abolishes these metabolic benefits demonstrating a central role for CoQ in the modulation of whole-body energy expenditure and thus for the etiology of primary and secondary CoQ deficiencies.

overall_design: RNAseq was used to compare gene expression in a brown adipocyte cell line treatde with vehicle control or 4CBA for 48 hours.(3 replicates per group). All data was generated using Illumina HiSeq4000.


title: CD38 enzymatic activity promotes hematopoietic stem cell dormancy [bulk RNA-Seq]

overall_design: 6 samples were analysed, HSCs from 10 mice were sorted for each sample (CD38pos vs CD38neg: S1+S2, S3+S4, S5+S6)


title: Transcriptome analysis of childhood acute lymphoblastic leukemia cell lines

status: Public on Feb 16 2022

city: Solna

first: Rozbeh

last: Jafari

address: Tomtebodavägen 23B

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome profiling of 49 childhood acute lymphoblastic leukemia cell lines and 2 EBV transformed B-cell lines.

overall_design: RNA-sequencing of ribosomal depleted total RNA extracted from 51 untreated ALL cell lines

first: Luay

last: Aswad

first: Matthias

last: Stahl


title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by LIGHT.

status: Public on Feb 20 2022

city: Kobe

first: Koji

last: Fukuda

address: 7-5-1 Kusunoki, Chuo

department: Department of Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

summary:
LIGHT/TNFSF6, a member of the tumor necrosis factor (TNF) superfamily, can promote apoptosis in activated primary B cells, T cells, dendritic cells, and synovial fibroblasts through Fas and  is involved in the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA). Meanwhile, decoy receptor 3 (DcR3) competitively binds soluble LIGHT in addition to TL1A and FasL and inhibits the signaling of LIGHT via HEVN and. Therefore, LIGHT-DcR3/HEVN/ signaling may be involved in the pathogenesis of RA.
We hypothesized that LIGHT regulates the gene expression in RA-FLS. We used to search for genes in which expression in RA-FLS is regulated by LIGHT.

overall_design: RA-FLS were obtained from 4 RA patients (sample1-4). Each sample was incubated with either 1.0 μg/ml recombinant human LIGHT protein or phosphate buffered saline diluted with serum-free Opti-MEM medium as non-stimulated control. Gene expression in RA-FLS stimulated by LIGHT was compared with that of their respective non-stimulated controls.

first: Yasushi

last: Miura

first: Toshihisa

last: Maeda

first: Kenichi

last: Kikuchi

first: Yoshinori

last: Takashima

first: Shinya

last: Hayashi

first: Tomoyuki

last: Matsumoto

first: Ryosuke

last: Kuroda


title: Systematic reconstruction of the cellular trajectories of mammalian embryogenesis

first: Chengxiang

last: Qiu


title: lncRNA-seq in human lung cancer tissues

status: Public on Jan 27 2022

city: 上海

first: Yani

last: Kang

address: 东川路800号

institute: Shanghai Jiaotong University

summary: We conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). Function analysis on DEM-target genes can explain the regulatory roles of miRNAs in LC. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified, which were then combined to construct the interplay of lncRNAs/miRNAs/mRNAs. And we used the online databases to verify the selected DEMs, DELs, and DEGs.  Our study identified 2509 DEGs, 34 DEMs, and 432 DELs in LC patients. miRNA-mRNA pairs, including 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG), were figured out. We finally found the hub subnetwork (LINC00632/has-miR-21-5p/TIMP3) by combining lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs.

overall_design: miRNA-seq combined with lnRNA-seq analysis to find the regulation network in lung cancer

first: Baiqing

last: Wen

first: Mengju

last: He

first: Hui

last: Zhang

last: Zhao


title: lncRNA-seq and miRNA-seq in human lung cancer tissues


title: Hematopoietic Transcription Factors Bind rDNA and Regulate rRNA Transcription

status: Public on Jan 15 2022

city: Philadelphia

first: Vikram

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine


title: Assessing effect of CEBPA degradation on rRNA transcription machinery

summary: We report the effect of degradation of CEBPA (a critical myeloid lineage transcription factor) on the occupancy of core rRNA transcription machinery on rDNA in mouse GMP cells. We generated a CEBPA-Degron line by tagging endogenous alleles of the Cebpa gene with the FKBPV degron domain, and degraded CEBPA-FKBPV-FLAG fusion protein using dTAGV-1 ligand. We used anti-FLAG pulldown to demonstrate binding of CEBPA protein to rDNA at a conserved motif within the 18S transcribed region. On degradation of CEBPA, we found that RPA194 (component of Pol I) and RRN3 occupancy on rDNA were reduced, while the occupancy of upstream factors TAF1B (component of SL-1) and UBTF were unchanged. In parallel, we also found that CEBPA degradation reduced nascent rRNA transcription, cellular ribosome abundance, and cell growth. Our work indicates that the cell-type-specific transcription factor CEBPA recruits the Pol I-RRN3 complex to ribosomal DNA to promote rRNA transcription.

overall_design: Examination of the effect of CEBPA degradation on rRNA transcription machinery using timecourse ChIP-Seq (2 replicates per timepoint) of RPA194 (component of Pol I), RRN3, TAF1B (component of SL-1), and UBTF.

first: Subin

last: George


title: Next Generation Sequencing Facilitates Quantitative Analysis of hippocampus transcriptomes from WT and miR-301a-/- mice

status: Public on Jan 28 2022

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

summary: Purpose: we used next generation sequencing to analyze gene expression profiles of hippocampus from WT and miR-301a-/- mice. The goals of this study are to compare the different gene expression profiles of hippocampus between WT and miR-301a-/- mice.

overall_design: WT and miR-301a-/- mice (6-8 weeks) were sacrificed and hippocampus were isolated from brain. Total RNA was extracted and mRNA profiles were generated by deep sequencing by using novaseq 6000 sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan or SYBR Green assays.


title: Hematopoiesis in Murine Fancd2-/- vs WT Fetal Liver

status: Public on Dec 31 2021

first: Peter

last: Kurre

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary:
Fanconi anemia (FA) is a rare inherited bone marrow failure (BMF) syndrome, caused by mutation in one of at least 23 proteins in the FA complementation group. The mechanism of BMF in FA is currently unknown.
Previous studies have shown that functional defects in hematopoeitic stem and progenitor cells (HSPC) arise spontaneously in response to developmental replication stress in murine FA fetal livers (FL) as early as 13.5 dpc.
In this study, we harvested E13.5 wild-type (WT) and Fancd2-/- FL from three pregnancies, depleted samples of erythroid progenitors via FACS against Ter-119, and performed single-cell RNA sequencing.
Our goal was to identify which popoulations in the fetal liver at this time point show severe transcriptional dysregulation, as well as to identify what cellular processes in these populations are most affected, in order to gain insight into the mechanism of BMF in FA and guide future studies.

overall_design:
single-cell RNA sequencing of live TER119- E13.5 WT and Fancd2-/- FL cells
libraries generated from freshly isolated cells (same day) of sex-matched littermates from three pregnancies
pregnancy #1: male WT (1.1), male Fancd2-/- (1.1)
pregnancy #2: female WT (2.1), female Fancd2-/- (2.1)
pregnancy #3: male WT (3.1), male WT (3.2), female Fancd2-/- (3.1), female Fancd2-/- (3.2)

first: Theresa

middle: N

last: Menna

first: Zhe

first: Jacqueline

last: Smiler

first: Michael

middle: V

last: Gonzalez

first: James

last: Garifallou

first: Fernanda

last: Thompson


title: miRNA-seq in human lung cancer tissues

summary: we conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). Function analysis on DEM-target genes can explain the regulatory roles of miRNAs in LC. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified, which were then combined to construct the interplay of lncRNAs/miRNAs/mRNAs. And we used the online databases to verify the selected DEMs, DELs, and DEGs.  Our study identified 2509 DEGs, 34 DEMs, and 432 DELs in LC patients. miRNA-mRNA pairs, including 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG), were figured out. We finally found the hub subnetwork (LINC00632/has-miR-21-5p/TIMP3) by combining lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs.

overall_design: miRNA-seq combined with lncRNA-seq analysis to find the regulation network in lung cancer


title: Generation of Hematopoietic TF-rDNA Atlas in Human and Mouse

middle: R

summary:
Over 2000 publicly accessible human and mouse ChIP-Seq datasets for about 250 Transcription Factors and chromatin complexes from various databases (ENCODE, GEO) were mapped to custom-made human and mouse genomes containing a reference rDNA sequence of the appropriate species (Genbank U13369.1 for human, BK000964.3 for mouse). The read mapping density across the rDNA sequence was then extracted and normalized to the median in that dataset. Unbiased clustering and analysis, followed by curation, was performed to identify high-confidence patterns of rDNA occupancy for numerous hematopoietic TFs and TF families at canonical TF motif sequences.

************************
Data processing steps:
FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
Reads were mapped to customized genomes (containing additional rDNA sequence) using Bowtie2 using the following parameter: -X 2000
Read density across the rDNA sequence was extracted using igvtools
************************

sample_organism:
Homo sapiens
Mus musculus

overall_design: Identification of robust, high-confidence rDNA occupancy of numerous hematopoietic TFs and TF families at canonical TF motif sequences


title: A novel anti-influenza combined therapy assessed by single cell RNA-sequencing

status: Public on Dec 19 2021

city: Geneva

first: Ilya

last: Kolpakov

state: GE

address: 9 Ch. des MInes

department: Health 2030 Genome Center`

country: Switzerland

institute: Fondation Campus Biotech Geneva

summary: To develop a novel treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We also showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assess the ability of the treatments to restore them.

overall_design:
Reconstituted human airway epithelia infected with Influenza A and treated with cyclodextrins, interferon lambda or both.

UPDATE: [Mar-22-2024] The Sample titles and characteristics were corrected. The associations of the raw data and processed data files with the Samples (GSMxxx) did not change.

first: Chiara

last: Medaglia

first: Caroline

last: Tapparel

first: Ioannis

last: Xenarios

first: Arnaud

last: Charles

first: Antoine

last: Zwygart

first: Francesco

last: Stellacci

first: Yong

last: Zhu

first: Samuel

last: Constant

first: Song

last: Huang

first: Valeria

last: Cagno

first: Emmanouil

middle: T

last: Dermitzakis


title: DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq

status: Public on Nov 08 2021

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

type: Methylation profiling by high throughput sequencing

summary: Using hMeDIP-seq we validated the single-base resolution hydroxymethylomes (ACE-seq) of sea urchin, lancelet and zebrafish embryos.

sample_organism:
Strongylocentrotus purpuratus
Branchiostoma lanceolatum
Danio rerio

overall_design: hMeDIP-seq was perfomred on (i) purple sea urchin 72 hpf embryos; (ii) european lancelet 36 hpf embryo; (iii)  zebrafish 24 hpf embryo (in replicates). Input DNA sequencing has been performed in parallel.

first: Ozren

last: Bogdanovic


title: Base-resolution DNA methylation maps of purple sea urchin (Strongylocentrotus purpuratus)

summary: Using MethylC-seq we investigated single-base resolution methylomes of sea urchin during development.

overall_design: MethylC-seq was performed on (i) 24 hpf, 48 hpf, 72 hpf embryos and adult tissue (tube feet) of purple sea urchin in biological replicates.


title: Base-resolution 5-hydroxymethylcytosine maps of sea urchin and lancelet embryos and adult tissues

platform_organism:
Strongylocentrotus purpuratus
Branchiostoma lanceolatum
Danio rerio


title: Base-resolution DNA hydroxymethylation maps of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using ACE-seq

summary: Using ACE-seq we investigated single-base resolution hydroxymethylomes of sea urchin, lancelet and zebrafish during development.

overall_design: ACE-seq was perfomred on (i) 24 hpf, 48 hpf, 72 hpf embryos and adult tissue (tube feet) of purple sea urchin in biological replicates; (ii) 36 hpf, larvae (60-70 hpf), juvenile (3-4mo) and adult tissue (liver) of european lancelet in biological replicates (larvae and juvenile stages); (iii) zebrafish 24 hpf embryo.


title: RNA-seq Analysis of the gene expression regulated by GO6983 in mouse embryonic stem cells

status: Public on Oct 30 2021

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Purpose:The goals of this study is to analyze the candidate genes motified by GO6983 (GO) to promote the mouse embryonic stem cell (ESC) self-renewal through RNA-seq approach.

overall_design: 46C mouse ESCs cultured in serum-containing medium in the presence or absence of 5 μM GO for 24 hr and then were collected by using Trizol. Two repeat groups were set for each treatment group. These samples were sent to GENERGY BIO (Shanghai, China) company to do deep sequencing by using illumina Hiseq.

first: Shoudong

last: Ye


title: In vitro expansion of muscle stem cells derived from pluripotent stem cells

status: Public on Dec 15 2021

city: Minneapolis

first: Sunny

middle: SK

last: Chan

state: MN

institute: University of Minnesota

summary: We have developed a method to generate muscle stem cells from pluripotent stem cells via teratoma formation. We further find these cells are functionally expandable in vitro while retaining their in vivo regenerative potential. The goal of this study is to compare the transcriptome of fresh and expanded teratoma-derived myogenic cells versus satellite cells.

overall_design: RNAs from 4 groups of skeletal myogenic cells: fresh teratoma-derived, expanded teratoma-derived, fresh satellite cells, and expanded satellite cells. In 2 biological replicates.

first: Ning

last: Xie


title: Heterogeneous Gene Expression Patterns of Tuberculosis-Diabetes Interaction in Diverse Cohorts

status: Public on Dec 29 2021

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

summary:
Background. Diabetes mellitus (DM) increases tuberculosis (TB) severity. We previously reported baseline blood microarray data in a South Indian pulmonary TB cohort with or without DM, finding no qualitative or quantitative differences in immune pathway gene expression. To extend those observations, we compared baseline and longitudinal blood gene expression in TB patients from South India and Brazil.
Methods. Adults with pulmonary TB, with or without DM, were enrolled at two sites in India and one site in Brazil. Blood RNA sequencing (RNAseq) was performed at baseline and treatment months 2 and 6. Differentially expressed genes (DEGs) and pathway activation were compared by group and site. Comparison was also made with published RNAseq data from the TANDEM study South African and Romanian cohorts.
Findings. No consistent pattern of DEGs discriminated TB from TBDM in India or Brazil. Pathway analysis also showed little commonality between sites, although a shared profile of complement activation and matrix degradation was identified in TBDM. Indian participants showed marked longitudinal changes in DEGs and pathways at 2 and 6 months of treatment, whereas these were stable in Brazilian participants. High variability in gene expression was observed between sites at baseline and during treatment.
Interpretation. DM exacerbates matrix degradation in TB but is not associated with major immune gene expression or pathway differences compared to TB without DM. Comparison between cohorts in India, Brazil, Romania, and South Africa revealed an unexpectedly high degree of site-specific variation that may reflect population differences in TB pathobiology.

overall_design: Gene expression analysis on subjects TB-infected with and without diabetes from different locations.

first: Hardy

last: Kornfeld

first: Bruno

last: Andrade

first: Amita

last: Gupta

first: Timothy

last: Sterling

first: Caian

middle: L

last: Vinhaes

first: Nathella

last: Kumar

first: Akshay

last: Gupte

first: Kiyoshi

middle: F

last: Fukutani


title: test on prod:  sra9993 - sep22

status: Public on Sep 24 2021

city: qq

first: Pierre

middle: X

last: Ledoux

address: qq

institute: werty

summary: test on prod:  sra9993 - sep22

overall_design: test on prod:  sra9993 - sep22


status: Public on Oct 26 2021

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

summary:
Single pollen precursors were isolated from maize anthers, covering 3 weeks of development from before meiosis through mature pollen. Starting material was staged by anther length and microscopy, and anther stages were densely sampled throughout pollen development. All samples were from an F1 hybrid between A188 and B73 inbred lines, and transcripts were associated with a specific parental allele when possible.

In the "transcript_counts.csv" file, each sample is given 4 columns to separate the allele calls: '_g1' contains counts matching the B73 allele, '_g2' contains counts matching the A188 allele, 'ua' means unassigned (no SNPs were present in the transcript), and '_cf' means conflicting (the transcript had SNPs matching both alleles -- this is most likely sequencing error).

Code to reproduce all figures from the main text of Nelms and Walbot (2022) can be found at https://doi.org/10.5281/zenodo.6620997

overall_design: Allele-specific RNA-seq of single pollen precursors from maize anthers. Libraries were constructed with a modified version of CelSeq2.

first: Virginia

last: Walbot


title: RNAi components regulate the micoparasitism in Trichoderma atroviride

status: Public on Dec 05 2021

first: Alfredo

last: Herrera Estrella

institute: CINVESTAV

summary: Trichoderma atroviride is a fungus capable of establishing symbiotic relationships with plants, however, its main lifestyle is a saprophyte. Due to these characteristics, it must face a great quantity of microorganisms, and be able to compete for nutrients. T. atroviride is considered a necrotrophic mycoparasite and has developed the ability to kill other organisms and obtain nutrients from them. The object of this work is to explore the role of small RNAs in mycoparasitism. To this end, we obtained RNA-Seq libraries from the interactions of T. atroviride against Alternaria alternata and Rhizoctonia solani. The transcriptomes were obtained from three stages during mycoparasitsm: before contact (BC), contact (C), and after contact (AC).

overall_design:
T. atroviride WT vs Rhizoctonia solani AG2; T. atroviride WT vs R. solani AG5; T. atroviride WT vs Alternaria alternata; T. atroviride control
T. atroviride dcr2 mutant vs Rhizoctonia solani AG2;   T. atroviride dcr2 mutant vs Rhizoctonia solani AG5;  T. atroviride dcr2 mutant vs Alternaria alternata;  T. atroviride dcr2 mutant control
T. atroviride ago3 mutant vs Rhizoctonia solani AG2;   T. atroviride ago3 mutant vs Rhizoctonia solani AG5;  T. atroviride ago3 mutant vs Alternaria alternata;  T. atroviride ago3 control
3 replicates per condition, The controls are T. atroviride strains growing alone without any fungal prey

first: Eli

last: Felix

first: Camilo

last: Salazar

first: Guillermo

last: Rico

first: Jose

last: Villalobos

middle: H

last: Estrella


title: Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

status: Public on Oct 24 2021

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

institute: Centro Andaluz de Biología del Desarrollo

summary: We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species

overall_design: ATAC-seq assays in wild-type sea urchin embryos, at 48 hpf developmental stage

middle: S

first: Danila

last: Voronov

first: Maria

middle: I

last: Arnone

first: Igniacio

last: Maeso

first: José

last: Gómez-Skarmeta


title: Loss of Polycomb Repressive Complex 1 activity and chromosomal instability drive uveal melanoma progression

status: Public on Aug 05 2021

city: NEW YORK

first: Ashley

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics, and Systems Biology

institute: Weill Cornell Medicine

summary: Chromosomal instability (CIN) and epigenetic alterations have been implicated in tumor progression and metastasis. Yet, how these two hallmarks of cancer are related remains poorly understood. By integrating genetic, epigenetic, and functional analyses at the single cell level, we show that the progression of uveal melanoma (UM), the most common intraocular primary cancer, is driven by loss of Polycomb Repressive Complex 1 (PRC1) in a subpopulation of tumor cells. This is done by transcriptionally profiling 17,074 single cells obtained from fresh surgical human samples taken from primary tumors (n = 6). These samples were derived from patients spanning various stages of tumour progression without enrichment for a specific cell type, such that the entire tumour and its microenvironment were sampled in an unbiased manner. Data from all patients were merged to create a global cell atlas.

overall_design: Single-cell RNA sequencing was performed on 6 donors using inDrops protocol.

first: Mathieu

last: Bakhoum

first: Jasmine

last: Francis

first: Albert

last: Agustinus

first: Ethan

last: Earlie

first: David

last: Abramson

first: Mercedes

last: Duran

first: Ignas

last: Masilionis

first: Melody

last: Dibona

first: Alexander

last: Shoushtari

first: Michael

last: Goldbaum

first: Paul

last: Mischel

first: Samuel

first: Elsa

last: Molina


title: scRNAseq of longitidunally acquired samples from a CLL patient

status: Public on Oct 22 2021

city: Salt Lake City

first: Gabor

last: Marth

state: UT

department: Human Genetics

institute: University of Utah

summary: We collected three timepoint blood samples from a CLL patient underwent BTK inhibitor treatment. We performed single cell RNA sequencing on these samples to track expression heterogeneity of malignant B-cell populations over time.

overall_design: Peripheral blood samples across three timepoint (pre-treatment, 1-year after initiating treatment, and 2-years after initiating treatment) were subject to 10X 5’ capture scRNAseq.

first: Yi

last: Qiao

first: Xiaomeng

last: Huang

first: Jennifer

middle: A

last: Woyach

first: Deborah

last: Stephens


title: Indusible hepsin overexpression activates TGFβ signaling in a Wap-Myc model of breast cancer

status: Public on Aug 04 2021

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: To test if ectopic overexpression of hepsin (TMPRSS1) induces TGFβ signaling in the context of tumorigenesis, we made use of a previously published tumor syngraft model of Myc-driven breast cancer (Partanen et al., 2012 PMID: 22308451). Wap-Myc mammary tumor cells, which express high Myc levels, were isolated from donor mice, transduced with the pIND21-HPN lentiviral construct that allows doxycycline (DOX)-induced hepsin overexpression, and subsequentially transplanted into recipient mice. Consistent with the notion that hepsin promotes TGFβ signaling, western blot analysis revealed increased phospho-Smad2/3 and upregulation of the TGFβ signaling downstream target SNAIL in Wap-Myc tumors with DOX-induced hepsin overexpression compared to control (-DOX) tumors. RNAseq analysis of these tumors provided additional evidence for TGFβ pathway upregulation by hepsin as the most significantly upregulated gene signatures corresponded to the TGFβ signaling pathway. The largest cluster of gene signatures affected by hepsin overexpression, however, was related to the ECM and integrins.

overall_design: Isolated Wap-Myc mammary epithelial cells from virgin Wap-Myc mice. Cells were transduced with concentrated pIND21-HPN lentivirus (MOI=10) o/n on the day of cell isolation. Cells were transplanted the next day into the fat pads of recipient mice (105 cells/gland, 3 weeks old). Doxycycline (DOX) was administered in drinking water (2mg/ml 5% sucrose) three days after transplantation. Wap-Myc expression was induced when the mice were 8 weeks old by 2 consecutive pregnancies. Tumor development was monitored once-twice a week after pregnancy. Mice were sacrificed when tumor size reached 1 cm

first: Juha

last: Klefström

first: Denis

last: Belitškin


title: Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer

status: Public on Aug 12 2021

city: Boston

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

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

overall_design: Refer to individual Series


title: Determining the sporophyte-to-gametophyte transition in maize

status: Public on Oct 27 2021

first: Brad

last: Nelms


title: GENERATION OF HEART ORGANOIDS MODELING EARLY HUMAN CARDIAC DEVELOPMENT UNDER DEFINED CONDITIONS

status: Public on Jul 19 2021

city: East Lansing

first: Aitor

last: Aguirre

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

summary: Cardiovascular-related disorders are a significant worldwide health problem. Cardiovascular disease (CVD) is the leading cause of death in developed countries, making up a third of the mortality rate in the US1.  Congenital heart defects (CHD) affect ~1% of all live births2, making it the common birth defect in humans. Current technologies provide some insight into how these disorders originate but are limited in their ability to provide a complete overview of disease pathogenesis and progression due to their lack of physiological complexity. There is a pressing need to develop more faithful organ-like platforms recapitulating complex in vivo phenotypes to study human development and disease in vitro. Here, we report the most faithful in vitro organoid model of human cardiovascular development to date using human pluripotent stem cells (hPSCs). Our protocol is highly efficient, scalable, shows high reproducibility and is compatible with high-throughput approaches. Furthermore, our hHOs showed very high similarity to human fetal hearts, both morphologically and in cell-type complexity. hHOs were differentiated using a two-step manipulation of Wnt signaling using chemical inhibitors and growth factors in completely defined media and culture conditions. Organoids were successfully derived from multiple independent hPSCs lines with very similar efficiency. hHOs started beating at ~6 days, were mostly spherical and grew up to ~1 mm in diameter by day 15 of differentiation. hHOs developed sophisticated, interconnected internal chambers and confocal analysis for cardiac markers revealed the presence of all major cardiac lineages, including cardiomyocytes (TNNT2+), epicardial cells (WT1+, TJP+), cardiac fibroblasts (THY1+, VIM+), endothelial cells (PECAM1+), and endocardial cells (NFATC1+). Morphologically, hHOs developed well-defined epicardial and adjacent myocardial regions and presented a distinct vascular plexus as well as endocardial-lined microchambers. RNA-seq time-course analysis of hHOs, monolayer differentiated iPSCs and fetal human hearts revealed that hHOs recapitulate human fetal heart tissue development better than previously described differentiation protocols.  hHOs allow higher-order interaction of distinct heart tissues for the first time, and display biologically relevant physical and topographical 3D cues that closely resemble the human fetal heart. Our model constitutes a powerful novel tool for discovery and translational studies in human cardiac development and disease.

overall_design: RNA-seq was performed on human iPSC-derived heart organoids and monolayer differentiated cardiomyocytes to determine global gene expression changes and developmental committment

first: Yonatan

last: Lewis-Israeli

first: Mitchell

last: Gabalski

first: Kristen

last: Ball

first: Aaron

last: Wasserman


title: Self-Renewing Tri-Potent Stem/Progenitor-like Cells from Adult Human Pancreas

status: Public on Jul 02 2021

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Stem and progenitor cells in the adult human pancreas provide an under-explored resource for regenerative medicine. Using micro-manipulation and methylcellulose-containing colony/organoid assays, we identified cells within the human cadaveric exocrine pancreas that fulfill the definition of a stem cell: able to self-renew and differentiate. Exocrine tissues were collected after the isolation of endocrine cells, dissociated into single cells, and plated into a 3-dimensional semisolid medium. We found that some pancreatic ductal cells gave rise to cystic colonies/organoids containing pancreatic duct, acinar, and endocrine lineage cells. These cells self-renewed and expanded approximately 300-fold over 9 weeks. When transplanted into diabetic mice, colonies/organoids lowered blood glucose levels and gave rise to insulin-expressing endocrine cells. Thus, stem/progenitor-like cells capable of self-renewal and differentiation either preexist in the adult human pancreas or readily adapt in culture. These human cells have implications for therapy in diabetes patients.

overall_design: Total RNAs were extracted from individual cells obtained following dissociation of freshly obtained human adult islet-depleted pancreas tissue.

first: Janine

middle: C

last: Quijano

first: Heather

last: Zook

first: Min-Hsuan

last: Chen


title: Fever supports CD8+ effector T cell responses by promoting mitochondrial translation

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Fever can provide a survival advantage during infection. Metabolic processes are sensitive to environmental conditions, but the effect of fever on T cell metabolism is not well characterized. We show that in activated CD8+ T cells, exposure to febrile temperature (39°C) augmented metabolic activity and T cell effector functions, despite having a limited effect on proliferation or activation marker expression. Transcriptional profiling revealed an upregulation of mitochondrial pathways, which was consistent with increased mitochondrial metabolism and mass observed in T cells exposed to 39°C. Through in vitro and in vivo models we determined that mitochondrial translation is integral to the enhanced metabolic activity and function of CD8+ T cells exposed to febrile temperature. Transiently exposing donor lymphocytes to 39°C prior to infusion in a myeloid leukemia (ML) mouse model conferred enhanced therapeutic efficacy, raising the possibility that exposure of T cells to febrile temperatures could have clinical potential.

overall_design: Naive CD8+ T cells were isolated from spleen and lymph nodes from 6-12 week old micel. Isolated T cells (1x10^6/ml) were activated using plate bound αCD3 (5 μg/ml) and soluble αCD28 (0.5 μg/ml) in T cell media (TCM; 1640 RPMI with 10% fatal calf serum, 4mM L-glutamine, 1% penicillin/streptomycin, 55μM beta-mercaptoethanol) supplemented with 100 U/ml hrIL-2 (Peprotech). Cells were cultured a 37°C or 39°C as indicated in humidified incubators with 5% CO2 and atmospheric oxygen for 24 or 48 hours following activation. RNA was extracted from 3 independent biological replicates in each treatment and then sequenced.

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