title: Dapagliflozin protects against chronic heart failure in mice via inhibiting macrophage-mediated inflammation, independent of SGLT2 [RNA-Seq]

first: Qing

last: Wu

summary: The specific mechanism of sodium-glucose cotransporter 2 (SGLT2) inhibitor in heart failure (HF) needs to be elucidated. In this study, we use SGLT2 global knockout (SGLT2-KO) mice to assess the mechanism of SGLT2 inhibitor on HF. Dapagliflozin ameliorates both myocardial infarction (MI)-and transverse aortic constriction (TAC) -induced HF. Global SGLT2-deficiency doesn’t exert protection against adverse remodeling in both MI- and TAC-induced HF models.  Dapagliflozin blurs MI- and TAC-induced HF phenotypes in SGLT2-KO mice.  Dapagliflozin causes major changes in cardiac fibrosis and inflammation. Based on single-cell RNA sequencing dapagliflozin causes significant differences in the gene expression profile of macrophages and fibroblasts. Moreover, dapagliflozin directly inhibites macrophage inflammation, thereby suppressing cardiac fibroblasts activation. The cardio-protection of dapagliflozin is blurred in mice treated with a C-C chemokine receptor type 2 (CCR2) antagonist. Taken together the protective effects of dapagliflozin against HF are independent of SGLT2, macrophage inhibition is the main target of dapagliflozin against HF.

overall_design: RNA-seq was performed in HF-heart tissue to confirm the precise effect of dapagliflozin on myocardial infarction(MI)-induced HFrEF.Group：MI + NS (MI-NS),and MI + dapagliflozin (MI-DAPA).

first: Qizhu

last: Tang

first: Qingqing


title: Single-cell chromatin accessibility profiling of mouse cardio-pharyngeal development under maternal diabetes mellitus

status: Public on Oct 16 2023

city: San Francisco

first: Tomohiro

last: Nishino

state: California

address: 1650 Owens Street

department: Cardiovascular Disease Institute

country: USA

institute: Gladstone Institutes (UCSF)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We employed single cell ATAC sequencing to interrogate the consequence of maternal diabetes in cardiac and craniopharyngeal development

overall_design: Examination of single cell chromatin accessibility from craniopharyngeal and cardiac cells captured at E10.5 fetues from vehicle pre-treated or streptozoticine pre-treated females.  At least 3 biological replicate embryos were analyzed per genotype.

first: Angelo

last: Pelonero

first: Deepak

last: Srivastava


title: VMP1 restricts NLRP3 inflammasome activation through its modulation of SERCA activity and autophagy

status: Public on Oct 12 2023

city: Maywood

first: Edward

middle: M

last: Campbell

state: IL

address: 2160 S 1st Ave

institute: Loyola University Chicago

type: Expression profiling by high throughput sequencing

summary: To investigate the effect of VMP1 deletion on gene expression in either untreated or LPS and ATP treated human differentiated THP-1 cells. CRISPR-Cas9 technology was used to generate stable knockout cell lines. We then performed an RNA-Seq experiment to assess gene expression changes between untreated and treated VMP1 KO or control macrophages.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cells and its KO derivatives (VMP1 KO). Three replicates were included for each condition: untreated differentiated control THP-1s, LPS and ATP treated differentiated control THP-1s, untreated differentiated VMP1 KO THP-1s, and LPS and ATP treated differentiated VMP1 KO THP-1s.

first: Stephanie

middle: R

last: Zack


title: EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors [Hi-C]

status: Public on Oct 04 2023

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

summary: EWS fusion oncoproteins underlie the pathogenesis of several human malignancies including Desmoplastic Small Round Cell Tumor (DSRCT), an aggressive mesenchymal tumor driven by fusions between the disordered domain of EWS and the developmental transcription factor WT1. Here we combined chromatin occupancy and long-range interaction profiles to identify EWS-WT1-dependent gene regulation networks and directly controlled target genes. We show that EWS-WT1 operates primarily as a powerful activator of distal regulatory elements and controls an oncogenic gene expression program that characterize primary DSRCTs. Moreover, EWS-WT1 has two isoforms that differ by three amino acids in their DNA binding domain (+/- KTS), as observed for wild type WT1, and we show that each fusion isoform has a specific DNA binding profile that is distinct from its wild type counterparts and requires a functional EWSR1 prion like domain. Remarkably, xenograft experiments using human mesothelial cells, candidate cells of origin of DSRCT, reveal that both isoforms are required to generate viable tumors that resemble DSRCT. Finally, we identify new candidate EWS-WT1 target genes with potential therapeutic implications, including CCND1, whose inhibition by the clinically-approved drug Palbociclib leads to marked tumor burden decrease in DSRCT PDXs in vivo. Taken together, our studies identify gene regulation programs and therapeutic vulnerabilities in DSRCT and provide a mechanistic understanding of the complex isoform-dependent oncogenic activity of EWS-WT1.

overall_design: Using in-situ HiC, we characterized the TAD boundary regions and profiled the organization of EWS-WT1 mediated enhancer connectome in DSRCT model cell.

first: Gaylor

last: Boulay

first: Liliane

middle: C

last: Broye

first: Rajendran

last: Sanalkumar

first: Miguel

middle: N

last: Rivera

first: Nicolò

last: Riggi


title: Expression data from macrophages sorted from the heart tissue of WT mice post-IR

status: Public on Oct 31 2023

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Cardiac resident MerTK+ macrophages exert multiple protective roles post-ischemic injury. To determine the potential reason for the protective role of MerTK+ cardiac macrophages, microarray was performed to identify gene expression profiles on isolated Trem2+, MHCII+, Lyve1+, and MerTK- macrophages from the heart tissue of WT mice post-IR.
We investigated the potential reason for the protective role of MerTK+ cardiac macrophages in myocardial Ischemia reperfusion injuryby microarray.

overall_design: Trem2+, MHCII+, Lyve1+, and MerTK- macrophages were isolated from the heart tissue of WT mice post-IR. Total RNA was isolated with TRIzol (Invitrogen) from macrophages according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.

first: Yulin

last: Li

first: Yihui

last: Shao


title: EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors [RNA-seq]

overall_design:
DSRCT cell line JN-DSRCT1 was analyzed by RNA-seq. EWS-WT1 was depleted by infection with lentiviral shRNAs (shWT1 and shGFP control).
MeT-5a cells were analyzed by RNA-seq. EWS-WT1, WT1 and the mutant proteins EWS(YS37)-WT1 isoforms were expressed in MeT-5a with lentiviral expression vectors.

first: Nicolo


title: EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors [ChIP-seq]

overall_design:
ChIP-seq for histone marks in DSRCT.
ChIP-seq for EWS-WT1 and histone marks in untreated JN-DRCT1 cells and upon EWS-WT1 knock-down using a lentiviral shRNA.
HA-tagged or V5-tagged EWS-WT1, WT1 and the mutant proteins EWS(YS37)-WT1 isoforms were expressed in MeT-5A cells using a lentiviral expression vector and ChIP-seq were performed.

**Submitter declares that the raw data for the DSRCT1 and DSRCT2 Samples could not be submitted due to patient privacy concerns and instead will be submitted to Zenodo**

NOTE: On June 25, 2024, the DSCRT3 and DSCRT4 samples were moved to GSE248842.


title: ATF3 coordinates the survival/proliferation of cardiac macrophages to protect against ischemia-reperfusion injury

status: Public on Nov 07 2023

city: beijing

first: zhu

last: shuolin

state: 北京市

address: Anzhen Street

institute: capital medical university

summary: Cardiac resident MerTK+ macrophages exert multiple protective roles post-ischemic injury, however, the mechanisms regulating their fate are not fully understood. Here we show that GAS6-inducible transcription factor ATF3 prevents apoptosis of MerTK+ macrophages after ischemia-reperfusion (IR) injury, by repressing the transcription of multiple genes involved in type I interferon expression (Ifih1 and Infb1) and apoptosis (Apaf1). Mice lacking ATF3 in cardiac macrophages or myeloid cells showed excessive loss of MerTK+ cardiac macrophages, poor angiogenesis, and worse heart dysfunction post-IR, which were rescued by the transfer of MerTK+ cardiac macrophages. GAS6 administration improved cardiac repair in an ATF3-dependent manner. Finally, we showed a negative association of GAS6 and ATF3 expression with the risk of major adverse cardiac events in patients with ischemic heart disease. These results indicate that the GAS6-ATF3 axis has a protective role against IR injury by regulating MerTK+ cardiac macrophage survival/proliferation.

overall_design: Six hours after IR or sham operation, single-cell suspension of left ventricle tissues were prepared and loaded into a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed, and sequencing libraries were constructed with reagents from a 10× Chromium Single Cell 30 v2 reagent kit (10X Genomics) according to the manufacturer’s protocol. The resulting libraries were sequenced on an Illumina NovaSeq6000 platform.


title: EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors [HiChIP]

overall_design: Using H3K27ac Hi-ChIP, we profiled the organization and establishment of EWS-WT1 mediated connectome in JN-DSRCT1 cell.


title: Activation and partial inactivation of NF-κB signaling lead to hypertension and chronic kidney disease

status: Public on Sep 30 2023

city: Guangzhou

first: Tan

middle: xiao

last: Zhang

address: Huang pu street

institute: First Affiliated Hospital of Jinan University

summary: Activation of NF-κB-signalling is key in the pathogenesis of chronic kidney diseases (CKD). However, a certain level of NF-κB activity is necessary to enable tissue repair and hence maintain a healthy kidney. To investigate the relationship between activated and inactivated NF-κB signaling on the pathogenesis of CKD, mouse models of NF-κB partial inactivation (mutating cysteine at position 59 of the sixth exon on the NF-κB gene into alanine) and activation (mutating cysteine at position 59 of the sixth exon on the NF-κB gene into serine) were used. Blood pressure, serum creatinine and urinary albumin-to-creatinine-ratio markedly increased in NF-κB activated and inactivated mice compared to controls. PAS-, Masson trichrome-, and Sirius-Red-staining, as well as α-SMA immunofluorescence staining in kidneys of NF-κBC59A, and NF-κBC59S mice demonstrated kidney fibrosis in both models. Transmission electron microscopy indicated that the glomerular basement membrane was thicker in both NF-κBC59A and NF-κBC59S mice compared to wild-type mice. KEGG enrichment analysis of RNA sequencing data revealed that the PPAR pathway was most markedly upregulated in both mouse models. However, there were also differences such as fatty acid degradation, peroxisome and glutathione metabolism, and downregulation of retinol metabolism in NF-κBC59A mice with decreased NF-κB signaling, whereas cell adhesion molecules, fat digestion, and absorption were upregulated in mice with activated NF-κB signaling (NF-κBC59S mice). In conclusion, using mice models with primarily activated and partially inactivated NF-κB pathways suggests that there is an apparently U-shaped relationship between kidney function as well as morphology and the activation of the NF-κB pathway.

overall_design: For active and inactive transgenic NF-κB mice, knock-in mice of NF-κB1C59A and NF-κB1C59S (NF-κB activated and inactivated) were obtained from the Modern Animal Research Center of Nanjing University. Exon 6 of the NF-κB1 (p50) gene, codon TGT for Cys-59 was mutated to either GCT or TCA (encoding Ala) by site-directed mutagenesis, in which the substitution of p50 either reduces or increases DNA binding activity respectively. This means that the NF-κB signal is either inactivated or activated to some extent in the transgenic mice5-7. A PGK-neo cassette was inserted in an intron near the mutation point as a selective marker. Standard cloning techniques were used to construct targeting vectors. The fragment containing the 5 kb 5′arm, the mutation point, PGK-neo, and the 5 kb 3′arm. The targeting vector was linearized and transferred to the C57BL/6NTac-derived ES cell line. The target clone was screened by long-range polymerase chain reaction (PCR) and southern blot. ES cell clones carrying the expected NF-κB1 (p50) mutation were injected into E3.5 C57BL/6 blastocysts that were subsequently transferred into foster mothers. Knock-in mutation was confirmed by sequencing tail DNA samples from offspring mice. Multiplex PCR genotyping used four primers to detect the knock-in alleles (Primer 1, Primer 2, Primer 3, and Primer 4). The following conditions for PCR were used to detect wild-type,NF-κB1C59A and NF-κB1C59S alleles: 94°C, 5 min; 41 cycles of 94°C, 30 s; 58°C, 30 s; 72°C, 45 s; 72°C, 5 min. Primers were obtained from Sangon Biotech (Shanghai, China), and the sequences are listed in Supplementary Table 1. All of the offspring mice were maintained under a 12:12 light/dark cycle at a constant temperature of approximately 25°C and humidity between 35% and 75%. This study was carried out in strict accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocol was approved by the Committee on the Ethics of Animal Experiments of Jinan University. All surgeries were performed under pentobarbital anesthesia, and all efforts were made to minimize mouse suffering.

first: Xiaotan

first: Guang

last: Wang

first: Berthold

last: Hocher

first: Xuesong

last: Yang


title: RIP-seq of MSTR-1::FLAG and N2

status: Public on Oct 01 2023

city: Toronto

first: Matthew

last: Eroglu

state: ON

address: 686 Bay St

department: DSCB

country: Canada

institute: Hospital for Sick Children

summary: Worms expressing 3xFLAG-tagged MSTR-1 (F22D6.2) were grown to young adult stage, crosslinked with 2% formaldehyde, and RIP-seq was performed to identify binding regions on target RNAs

overall_design: Two biological replicates of MSTR-1::FLAG expressing (WD656) and WT (N2) control worms not expressing FLAG, and respective inputs

first: W

middle: B

last: Derry


title: Bulk RNA-Seq analysis of adoptively co-transferred PKM2 wildtype and PKM2 knockout CD8+ T cells into tumor-bearing mice subsequently treated with and without PD-1 checkpoint blockade

status: Public on Oct 19 2023

city: New York

first: Vivek

last: Mittal

state: NY

address: 525 East 68th Street, W412

department: Cardiothoracic Surgery

institute: Weill Cornell Medicine

summary: In this study we investigated how manipulation of the glycolytic enzyme pyruvate kinase muscle 2 (PKM2) alters CD8+ T cell gene expression and responsiveness to PD-1 checkpoint blockade in orthotopic mouse lung adenocarcinoma. In this dataset, we performed adoptive co-transfers of antigen-specific OT-I+ Thy1.1+ CD8+ T cells genetically modified by CRISPR/Cas9 ribonucleoproteins to become PKM2 knockout (in Thy1.1+/- cells) or PKM2 wildtype (in Thy1.1+/+ cells). T cells were transferred into orthotopic mouse lung adenocarcinoma HKP1-ova-GFP tumor-bearing syngeneic C57BL/6 mice, and subsequently mice were treated with either IgG or anti-PD-1. Adoptively-transferred T cells were sorted based on Thy1.1 zygosity from tumors at two different time points and bulk RNA sequenced.

overall_design: Comparative gene expression profiling of three biological replicates of adoptively co-transferred PKM2 wild-type or PKM2 knockout OT-I+ CD8+ T cells, distinguished by Thy1.1 zygosity, into Thy1.2+/+ C57BL/6 mice bearing HKP1-ova-GFP orthotopic lung tumors and subsequently treated with either IgG or anti-PD-1, harvested at two timepoints.

first: Geoffrey

middle: J

last: Markowitz


title: Single-cell chromatin state transitions during epigenetic memory formation

status: Public on Sep 21 2023

city: Stanford

first: Taihei

last: Fujimori

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

summary: Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for the histone modifications H3K9me3, H3K9me2, H3K27me3, H3K9ac, H3K27ac in HEK293T cells with synthetic reporter system (B9 clone)

first: Lacramioara

last: Bintu


title: First-in-human clinical trial of personalized neoantigen vaccines as early intervention in untreated patients with lymphoplasmacytic lymphoma

status: Public on Sep 20 2023

city: Duarte

first: Szymon

last: Szymura

state: CA

address: 1500 E Duarte Rd

department: Toni Stephenson Lymphoma Center

institute: City of Hope

summary: We performed single cell RNA-seq gene expression analysis on bone marrow of 9 lymphoplasmacytic lymphoma patients before and after vaccination with personalized idiotype DNA vaccine to study changes in tumor microenvironment

overall_design:
Bone marrow samples before and after vaccination of 8 patients and one sample of pre vaccination sample for one patient were processed for single cell RNA seq using 10x genomics 5' chromium kit. For all except one patient samples of pre and post for a given patient were processed together on the same day and loaded separately into a well of 10x Genomics chip. For one patient (LPL008) samples of pre and post were first stained with two hashing antibodies, and then samples were mixed together at 1:1 ratio and loaded into a single well of 10x Genomics chip (additional data files are included for that patient for cell surface barcode sequencing).
Bone marrow samples before and after vaccination of 9 patients were processed for single cell RNA seq paired with single cell TCR and single cell BCR seq using 10x genomics 5' chromium kit.

first: Larry

middle: W

last: Kwak

first: Soungchul

last: Cha

first: Lin


title: MoTrPAC - Endurance Exercise Training Study In 6 Months Old Rats [ATAC-seq]

first: Euan

last: Ashley

address: 870 Quarry Road

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.

overall_design:
Regular exercise promotes whole-body health and prevents disease, yet the underlying molecular mechanisms throughout a whole organism are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome, and immunome in whole blood, plasma, and 18 solid tissues in Rattus norvegicus over 8 weeks of endurance exercise training. The resulting data compendium encompasses 9466 assays across 19 tissues, 25 molecular platforms, and 4 training time points in young adult male and female rats.

Contributor: Molecular Transducers of Physical Activity Consortium (MoTrPAC)


title: Transcriptomes alteration of lentoid body induction on LN511-coated culture

status: Public on Sep 08 2023

first: Jinyan

last: Li

address: 7th Jinsui Road

institute: Zhongshan Ophthalmic Centre

summary: In order to examine the transcriptomes alteration of LN511-based lens epithelial stem cells induction, human embryonic stem cells (hESCs) were induced into lentoid body followed the protocol from Yang et al (FASEB J. 2010), on Matrigel-coated or LN511-coated culture. Each group of cells were collected at day 12 and day 18, during the time when lens epithelial stem cells were generated. The samples were named as Ctrl-d12, Ctrl-d18, LN-511-d12 and LN-511-d18, respectively, (3 replicates, -1/2/3) and sent for RNA-sequence using Illumina HiSeq2500. It turned out that LN511 acted as a robust signaling factor for lens epithelial stem cells induction via enhancing the expression of lens specification related transcription factor, promoting cell proliferation, and suppressing Hippo/Yap signaling. These results provided a valuable resource for studying the mechanisms regulating in vitro lens epithelial stem cells induction.

overall_design:
To examine the transcriptomes alteration, each group of cells, on either Matrigel-coated or LN511-coated culture, were collected at day 12 and day 18, respectively.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at two time points (3 replicates, -1/2/3).
Comparative gene expression profiling analysis of RNA-seq for cells on Matrigel-coated culture and that on LN511-coated culture.

first: Jingyu

last: Ma


title: Effect of CuCl2 on transcriptional expression profile of A549 cells

city: Chicago

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

institute: University of Chicago

summary: To investigate the effects of disrupting Cu homeostasis on A549 cells in vitro, we treated cells with sDMEM supplemented with 0µM(control), 30µM, or 200µM CuCl2 for 2 or 4 hours

overall_design: Following RNA extraction, poly(A) enrichment library generation, and sequencing, we then performed differential expression analysis of extracted RNA, comparing 30µM or 200µM-CuCl2-treated cells to 0µM-CuCl2-treated cells at 2 hours and 4 hours

first: Ross

last: Matthew

first: Owyang

last: Ryan

first: Ye

last: Chang

first: He

last: Chuan


title: nascent RNA sequencing during embryonic development of tinWT and tinmDPE embryos

status: Public on Sep 11 2023

city: Ramat Gan

first: Tamar

last: Juven-Gershon

address: Life Sciences Building (212) Room 102

country: Israel

institute: Bar-Ilan University

type: Non-coding RNA profiling by high throughput sequencing

overall_design: capped short RNA-seq (csRNA-seq) and small RNA-seq

first: Sascha

middle: H

last: Duttke

first: Anna

last: Sloutskin


title: High-throughput sequencing in HNRNPD knock-out and knock-in HEK293T cell lines

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: As HNRNPD regulates the alternative splicing of hundreds of genes, we sought to investigate whether HNRNPD could regulate the biogenesis of circRNAs. To identify the effect of HNRNPD on circRNAs and linear RNAs, we performed circRNA and linear RNAs (ployA enrichment RNA and lncRNA) sequencing in HNRNPD knockout and wild-type HEK293T cells. We also inserted 3FHBH (3xFLAG, Histidine, Biotin, and Histidine) into the HNRNPD genome to obtain HEK293T_HNRNPD_3FHBH cells by using CRISPR-Cas9 technology, which was used to ascertain the direct HNRNPD targeting RNA sequence with the help of FLASH sequencing (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing). To evaluate the impacts of HNRNPD deficiency on circRNA formation, we captured nascent RNA in HEK293T and HNRNPD knock-out HEK293T cells by immunoprecipitation of 5-ethyluridine (EU) labeling. Comparative analysis of these data, we found the higher propensity of binding to introns of HNRNPD was related to inhibiting circRNA biogenesis.

overall_design: We used CRISPR-Cas9 technology to generate HNRNPD knock-out and knock-in HEK293T cell lines. We extracted total RNA and digested it with RNase R in HNRNPD knock-out and wild-type HEK293T cell lines for circRNA sequencing; In the HEK293T_HNRNPD_3FHBH cell, we followed the entire FLASH protocol to collect the RNA that was bound by HNRNPD. Next, the RNA was performed for FLASH sequencing; Culturing to 80% confluence, the cell transcription was terminated with 5,6-dichloro-1-β-D- ribofuranosylbenzimidazole (DRB, final concentration 0.5 mM) for 3 hours in HNRNPD knock-out and wild-type HEK293T cell lines. Subsequently, the culture media was changed with fresh DMEM medium adding 5-ethyluridine (EU, final concentration 0.25 mM) for another 1 hour. Then the nascent RNA was immunoprecipitated with streptavidin-conjugated magnetic beads and extracted with Trizol reagent. The nascent RNAs were to conduct RIP-sequencing.

first: Shuhui

first: Liang

last: Chen


title: Comparative analysis of nascent transcription among plant species

status: Public on Sep 28 2023

city: Pullman

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

sample_organism:
Chlamydomonas reinhardtii
Physcomitrium patens
Carica papaya
Arabidopsis thaliana
Hordeum vulgare
Zea mays
Drosophila melanogaster
Selaginella moellendorffii

overall_design: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

first: Bayley

last: McDonald

first: Ian

last: Brabb


title: A high-resolution map of functional  miR-181 target sites in the thymus reveals the role of coding sequence targeting and alternative seed binding

status: Public on Sep 06 2023

city: Gießen

first: Andreas

last: Krueger

address: Schubertstr. 81

country: Germany

institute: Justus Liebig University

summary: MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNA, resulting in translational inhibition and/or mRNA degradation. Efficient targeting depends on a combination of biochemically established targeting rules and contextual factors of a given miRNA and cell type. Here, we generated a high-resolution map of miR-181 MREs to define the targeting rules of miRNA miR-181a/b-1 in murine T-cell development. We uncovered a broad array of novel functional targets of miR-181 and demonstrated that miR-181 acts predominantly through RNA destabilization. High-resolution analysis validated the dominance of seed matches. Critically, we also discovered a unique alternative seed match for miR-181 and identified a distinct group of targets controlled by translational inhibition. In conclusion, deep profiling of miRNA MREs in primary cells is critical to expand physiologically relevant miRNA targetomes and helps to establish context-dependent miRNA targeting rules.

overall_design: Ribosome footprinting and RNAseq were performed with mouse thymocytes isolated from 3 WT and 3 miR-181a/b-1 KO mice.

first: Nikita

middle: A

last: Verheyden

first: Melina

last: Klostermann

first: Mirko

last: Brüggemann

first: Anica

last: Scholz

first: Shady

last: Amr

first: Chiara

last: Lichtenthäler

first: Christian

last: Münch

first: Tobias

last: Schmid

first: Kathi

last: Zarnack


title: miR-eCLIP of miR181-5p in mouse thymocytes.

status: Public on Sep 04 2023

summary: Enriched eCLIP combined with miR-181a/b-1 deficiency allows for the stringent identification of 6,729 miR-181 MREs in murine thymocytes.

overall_design: miR-eCLIP experiment was setup and perforemd by Eclisebio. The experiment consists of four conditions: an Ago2 IP, an Ago2 IP with miR181 knockout, an miR181 IP on top of the Ago2 IP also without and with miR181 knockout.


title: NPAS4 controls cell type-specific circuit adaptations underlying drug-seeking behavior

status: Public on Aug 31 2023

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Use of addictive substances often creates powerful and enduring associations with external cues that act as relapse triggers in individuals recovering from a substance use disorder (SUD). In the reward-associated brain region, the nucleus accumbens (NAc), drug use or drug-associated cue exposure activates a subset of D1 dopamine receptor-expressing medium spiny neurons (D1-MSNs), which typically promotes drug seeking, and a smaller subset of D2 dopamine receptor-expressing MSNs (D2-MSNs), which typically opposes drug seeking. The activity-regulated transcription factor, Neuronal PAS Domain Protein 4 (NPAS4), is activated in a small subset of NAc neurons during cocaine conditioning, and NAc NPAS4 is required for drug-context memories. Using a new Npas4-TRAP mouse combined with chemogenetics, we found that the during cocaine conditioning, the NPAS4-positive ensemble is required for drug-context associations. Single-cell transcriptomic analyses and in situ hybridization of NAc tissues from drug-conditioned mice revealed that NPAS4 is expressed predominantly in MSNs, and using cell type-specific molecular genetic approaches, we found that NPAS4 in D2-MSNs, but not D1-MSNs, was required for both drug-context associations and cue-reinstated cocaine seeking. Similarly, NPAS4 in NAc D2-MSNs, but not D1-MSNs, blocked cocaine experience-dependent strengthening of glutamatergic prefrontal cortical (PFC) inputs onto D2-MSNs. Analysis of differential gene expression in D2-MSNs revealed that NPAS4 and cocaine conditioning influence a gene expression program associated with synapses, dendrites, neuronal projections, dopamine, and cocaine. Together, our data reveal that NPAS4 functions during active cocaine use to maintain the imbalance of D1-MSN:D2-MSN activation and cue-induced drug seeking by suppressing excitatory drive onto relapse-opposing NAc D2-MSN circuits.

overall_design: We performed single nuclei RNA sequencing (snRNA-Seq) from NAc tissues isolated from mice expressing either AAV2-shNpas4 or AAV2-shScram virus. Mice were subjected to either cocaine or saline conditioning, and 24-hrs later (CPP test day), NAc tissues were rapidly extracted and processed for single nuclei RNA-sequencing (snRNA-seq)

first: Brandon

last: Hughes

first: Makoto

last: Taniguchi

first: Chirstopher

last: Cowan


title: New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile

status: Public on Aug 29 2023

city: Greenville

first: Edson

last: Rocha

state: NC

address: 600 Moye Blvd.

department: M

institute: East Carolina University Brody School of Medicine

summary:
Genome expression study of Bacteroides fragilis strain 638R comparing a fur deletion mutant with the wild-type strain grown in minimal defined media with iron-replete or iron-limiting conditions following  oxygen exposure.
The construction of the fur mutant analyzed in this study was described in Robertson KP, Smith CJ, Gough AM, Rocha ER. Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. Infect Immun. 2006 74:2304-2316.

overall_design: 10 chip study with 8 technical replicate on each chip comparing iron and oxygen regulated genes in the wild-type strain and fur deletion mutant.

first: C

last: Smith


title: An Anabolic Hormone to Promote Skeletal Stem Cell Bone Formation

status: Public on Aug 28 2023

city: Sacramento

first: Thomas

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

summary: During lactation, mothers initiate cycles of bone formation followed by significant bone loss to meet the high calcium (Ca2+) demand by progeny. While estrogen functions typically as an anabolic driver of bone remodeling, this sex steroid is absent in postpartum females. Here, we report that a brain-derived secreted from neurons of the arcuate nucleus (ARC) fills this void and functions as a potent osteogenic factor to promote bone mass in lactating females. We previously reported an extraordinarily sex-specific high bone mass phenotype in female mice that persists with aging and is central in origin after eliminating estrogen receptor alpha signaling in ARCKISS1 neurons. Parabiosis and bone transplant studies established that a humoral factor in mutant females accounts for this unusual skeletal phenotype. High bone mass in mutant females could be traced back to the skeletal stem cell (SSC) level, reflected by their increased frequency and osteochondrogenic potential. Based on ex-vivo, in vivo, and in vitro assays, one protein emerged as the most promising secreted pro-osteogenic factor from the ARC, acting in mice and human SSCs at low concentrations (<nM) independent of age and sex. The role of this brain-derived factor in bone formation was confirmed by in vivo gain and loss of function studies. Unexpectedly, in wild-type females, a transient spike of this protein appears in ARCKISS1 neurons coincident with lactation when bone remodeling and high calcium demand intensify in estrogen-depleted mothers. Our findings establish a potentially new therapeutic anabolic bone hormone that functions in a novel female-specific brain-bone axis to ensure mammalian species survival.

overall_design: SmartSeq2 single cell RNA sequencing of freshly, prospectively, flow cytometrically purified single skeletal stem cell isolated based on their previously reported surface marker profile CD45-Ter119-Tie2-CD105-6C3-Thy1-CD51+CD200+ from 7-week-old Esr1fl/fl with normal bone mass and Esr1Nkx2.1-Cre female mice with high bone mass.

first: Charles

middle: K

last: Chan

first: Holly

last: Ingraham

first: Candice

last: Herber

first: Muriel

last: Babey

first: William

last: Krause


title: Single-cell transcriptional analysis of CD45+ cells in the rhesus brain during acute SIV infection.

status: Public on Aug 26 2023

city: Davis

first: Chase

middle: Elliott

last: Hawes

address: 2005, CIID, County Rd 98 & Hutchinson Drive

department: Center for Immunology and Infectious Diseases

institute: University of California, Davis

summary: People living with HIV are particularly vulnerable to developing a spectrum of neurocognitive abnormalities referred to as HIV-associated neurocognitive disorders. These disorders have been linked to neurological impairment driven by inflammation within areas of the brain controlling cognition. Current data suggest that HIV establishment within the central nervous system (CNS) occurs within the first weeks following infection and drives subsequent neuroinflammatory processes. Various studies have implicated HIV-target cells (i.e., monocytes, macrophages, and CD4 T cells) as key facilitators of HIV CNS establishment via a “trojan horse” mechanism, in which infected cells cross CNS barrier tissues and contribute to viral seeding.   Cellular entry is mediated by integrins, specifically α4 integrins, which are expressed at the blood brain barrier and blood cerebrospinal fluid barrier and allow circulating immune cells to enter the CNS. To investigate the contribution of CNS infiltrating cells to early neurological disease, we utilized an acute rhesus macaque SIVmac251 infection model, where animals were treated with an anti-a4 integrin monoclonal antibody to inhibit immune cell trafficking to the CNS.     To gain insights into neuro inflammatory transcriptional programs induced following SIV infection and how this might be modulated by a4 integrin blockade, we utilized single cell (sc) RNA sequencing of FACS sorted CD45+ cells isolated from brain and spleen.

overall_design: Rhesus macaques were infected intravenously with (10^4 TCID50) SIVmac251 and euthanized at three weeks post-infection. Infected animals were divided into two cohorts and treated with either: (1) 25mg/kg rhesus IgG1 anti-a4 integrin blocking monoclonal antibody or (2) 25mg/kg rhesus IgG1 control antibody (specific for Desipramine). The antibody course was initiated 1 week prior to infection and approximately every 10 days subsequently over the course of the study. Furthermore, a cohort of age matched, untreated, uninfected animals were included as additional controls. At three weeks post-infection, animals were euthanized, and mononuclear cells were collected from the spleen and the right brain hemisphere. Once mononuclear cells were isolated, they were cryopreserved in DMSO and 10% FBS. Cells were subsequently thawed and CD45+ cells enriched using Miltenyi Biotec CD45 Microbeads for non-human primates. Live CD45+ cells were further enriched by fluorescent activated cell sorting for subsequent single cell RNA-seq analyses.

first: Smita

middle: S

last: Iyer


title: EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors

status: Public on Oct 04 2023

city: Charlestown

first: Rui

last: Dong

address: 149 13th Street

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: In vivo analysis of gene expression changes in mouse astrocytes after traumatic spinal cord injury

city: Boston

first: Timothy

last: O'Shea

address: 44 Cummington Mall, ERB Room 521

department: Biomedical Engineering

institute: Boston University

summary: Central nervous system (CNS) lesions become surrounded by neuroprotective borders of newly proliferated reactive astrocytes. Fundamental features of these cells are poorly understood. Here, using temporal transcriptome analysis of Aldh1l1-expressing local astrocytes we showed that after CNS injury, local mature astrocytes dedifferentiated, proliferated, and become transcriptionally reprogrammed to permanently altered new functional states, with persisting downregulation of molecules associated with astrocyte-neuron interactions, and upregulation of molecules associated with wound healing, microbial defence, and interactions with stromal and immune cells. Our findings show that at CNS injury sites, local mature astrocytes proliferate and adopt canonical features of essential wound repair cells that persist in adaptive states and are the predominant source of neuroprotective borders that re-establish CNS integrity by separating neural parenchyma from stromal and immune cells as occurs throughout the healthy CNS.

overall_design:
We conducted genome-wide RNA sequencing of spinal cord astrocyte specific ribosome-associated mRNA using RiboTag methods. To generate the mice for this study, mice expressing RiboTag (JAX: 029977) were crossed either with Aldh1l1-CreERT2 (JAX: 031008) or with mGfap-Cre-73.12 (JAX: 012886). Astrocyte specific mRNA as well as non-enriched flow through samples were collected and analyzed from Aldh1l1 CreERT2-RiboTag mice at 2, 5, 14, 28, 42, and 70 days after crush spinal cord injury. Astrocyte specific mRNA as well as non-enriched flow through samples were collected and analyzed from mGfap-Cre-73.12 RiboTag mice at 14 days after crush spinal cord injury. Healthy uninjured astrocyte specific mRNA as well as non-enriched flow through samples were collected and analyzed from Aldh1l1 CreERT2-RiboTag and mGfap-Cre-73.12 RiboTag mice. Astrocyte specific mRNA was also collected and analyzed from healthy uninjured mGfap-RiboTag mice at postnatal days P0, P3, P7, P14, P21, P35, P63. RiboTag transgene expression for each sample was confirmed by genotyping of collected tail samples prior to processing for astrocyte specific RNA.
For SCI surgery, a laminectomy of a single vertebra was performed at spinal cord level T10. A timed (5 second) lateral compression, complete crush SCI was made using No. 5 Dumont forceps with a tip width of 0.5 mm. Uninjured mice, or mice at various time points after complete crush SCI, were perfused with ice cold heparinized saline that was prepared using RNAse- and DNAse- free water and 10X PBS for 2 minutes at 7ml/min for blood clearance. Spinal cords were rapidly dissected on ice chilled blocks. For SCI samples, the lesion core center was identified and a tissue block of 1 mm rostral and caudal was then rapidly removed. Anatomically equivalent regions of spinal cord were taken from uninjured mice including from postnatal samples. Tissue samples were rapidly snap frozen in microcentrifuge tubes maintained in a dry ice bath and stored at -80°C until further processing. Frozen spinal cord tissue was processed by RiboTag Immunoprecipitation (IP). For specific animals, two RNA samples were generated: (i) Sample A (RiboTag) = RiboTag immunoprecipitation (IP) using Anti-HA.11 Epitope Tag Antibody to enrich for border astrocyte Ribosomes with mRNA extracted from those ribosomes; (ii) Sample B (Flow through samples) = mRNA extracted from the supernatant solution remaining after RiboTag IP to provide a characterization of the other cells in the tissue and enable astrocyte gene enrichment analysis. For the RiboTag procedure, dounce homogenization was used to generate tissue lysates from frozen spinal cord segments and centrifuged to remove tissue debris. IP of HA-positive ribosomes was performed by incubating with Anti-HA.11 Epitope Tag Antibody (Biolegend, Cat# 901515) for 4 hours in a microcentrifuge tube on a microtube rotator kept at 4°C. IP solutions were combined with Pierce A/G Magnetic Beads (Thermofisher, #PI88803) and incubated overnight on a microtube rotator at 4°C. On the second day, the solution was separated from the magnetic beads and processed as the “flow through” sample representing mRNA of other cells not from RiboTag-positive cells. Magnetic beads were washed three times with high salt solution (50 mM Tris pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 100 mg/ml Cyclohexamide). Unpurified RNA was collected from the magnetic beads by addition of RLT Plus buffer with BME and vigorous vortexing. RNA was then purified using RNeasy Plus Mini (for in vitro cell pellets) or Micro Kits (for spinal cord tissue) (QIAGEN Cat# 74134 and 74034). Total mRNA derived from the RiboTag IP was quantified using a 2100 Bioanalyzer (Agilent) with RNA samples having an RNA integrity numbers (RIN) greater than seven being processed for RNA-Sequencing. Sequencing was performed on poly-A selected libraries using Illumina NovaSeq S2 (UCLA Technology Center for Genomics & Bioinformatics) using pair end reads (2x50 – 50bp length) with an average of 50-100M reads per sample split over two lanes of the S2 flow cell.

first: Michael

middle: V

last: Sofroniew


title: Cooperative armoring of CAR and TCR T-cells by T cell-restricted IL-15 and IL-21 universally enhances solid tumor efficacy

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

summary: Chimeric antigen receptor (CAR) and T-cell receptor (TCR) T-cell therapies are effective in a subset of patients with solid tumors, but new approaches are needed to enhance efficacy and universally improve patient outcomes. IL-15 and IL-21 are common cytokine-receptor gamma chain family members with distinct, pleiotropic effects on T-cells and other lymphocytes. We found that self-delivery of these cytokines by CAR or TCR T-cells prevents functional exhaustion by repeated stimulation and limits the emergence of dysfunctional natural killer (NK)-like T-cells. Across different preclinical murine solid tumor models, we observe enhanced regression with each individual cytokine but the greatest anti-tumor efficacy when T-cells are armored with both. Thus, the co-expression of membrane-tethered IL-15 and IL-21 represents a technology to enhance the resilience and function of engineered T-cells against solid tumors and could be applicable to multiple therapy platforms and diseases.

overall_design: T cells from a 28-year-old donor were transduced to express E7-TCR (E7-TCR T cells). We compare E7-TCR T cells with either 1. Tethered IL15 or 2. Tethered IL15/IL21. These T cells were then exposed to continuous antigen (CAE) via CaSki cancer cells in vitro. Cancer cells were replenished Q2-4 days for a total of 14 tumor rechallenges. The samples were analyzed after manufacturing (no tumor exposure, Day0), after 5 exposures (Day12), and after 14 exposured (Day26) using single-cell sequencing. In each sample, we labeled the IL15 cells with TotalSeq-C0251, cat. no. 394661, barcode seq. GTCAACTCTTTAGCG; - IL15/21 cells TotalSeq-C0252, cat. no. 394663, barcode seq. TGATGGCCTATTGGG

first: Rosa

last: Nguyen


title: MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling

status: Public on Aug 25 2023

city: Guangzhou

first: Wei

last: Zhu

address: No.1 Kangda Road, Haizhu District, Guangzhou City, Guangdong Province

institute: The First Affiliated Hospital of Guangzhou Medical University

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling [RIP-seq]

summary: To investigate the potential role of miRNA-148b-5p in the pathogenesis of kidney stones, we conducted RIP-seq of rat's kidney tissue.

overall_design: In order to screen the downstream target genes regulated by mi-148b-5p, we carried out RIP experiments on the corresponding Ago2 proteins and sequenced them.


title: Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex [spatial transcriptomics]

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

address: Großhaderner Straße 9

department: Department of Cell Biology and Anatomy III

institute: Biomedical Center (BMC),LMU - Munich

summary: Traumatic brain injury leads to a highly orchestrated immune- and glial cell response partially responsible for long-lasting disability and the development of secondary neurodegenerative diseases. A holistic understanding of the mechanisms controlling the responses of specific cell types and their crosstalk is required to develop an efficient strategy for better regeneration. Here, we combined spatial and single-cell transcriptomics to chart the transcriptomic signature of the injured murine cerebral cortex, and identified specific states of astrocytes, microglia, and oligodendrocyte precursor cells contributing to this signature. Interestingly, these cellular populations share a large fraction of injury-regulated genes, including inflammatory programs downstream of the innate immune-associated pathways Cxcr3 and Tlr1/2. Systemic manipulation of these pathways decreased the reactivity state of glial cells associated with poor regeneration. The functional relevance of the newly discovered shared signature of glial cells highlights the importance of our resource enabling comprehensive analysis of early events after brain injury.

overall_design: Spatial transcriptomics of the intact and injured mouse cerebral cortex at 3 days post injury (dpi).

first: Christina

last: Koupourtidou

first: Veronika

last: Schwarz

first: Hananeh

last: Aliee

first: Simon

last: Frerich

first: Judith

last: Fischer-Sternjak

first: Riccardo

last: Bocchi

first: Tatiana

last: Simon-Ebert

first: Martin

last: Dichgans

first: Magdalena

last: Götz

first: Fabian

last: Theis


title: Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex [scRNA-Seq]

overall_design: Single cell transcriptomics of all cells of the intact and injured mouse cerebral cortex at 3 and 5 days post injury (dpi), in control condition and upon inhibition of the Tlr1/2 and Cxcr3 pathways.


title: Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex


title: Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition

city: York

first: Ethan

middle: James

last: Redmond

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: University of York

type: Genome variation profiling by high throughput sequencing

summary: A population of wild type plants can contain individuals with drastically different flowering times, due to developmental asynchrony. We performed RNA-seq on individual plants from a large population of wild type (Ws-2) Arabidopsis thaliana, sampling a large number (~70) of replicates at one timepoint during the flowering transition. We have characterised a major transcriptomic switch between plants before and after bolting. Applying methods used in single-cell RNA-seq, we used this data to order the plants by their predicted age – which is referred to as a pseudo-time series. In contrast to a traditional RNA-seq time series, this allows us to view changes in gene expression at a fine temporal scale. Importantly, we can infer the order that transcription factors ‘switch on’ during the vegetative to floral transition.

overall_design:
A population of wild type plants were grown under controlled conditions and physiological traits were measured. 75 plants were chosen for sequencing, to represent a diversity of bolting statuses.
We then performed RNA-seq and quantified the gene expression of each individual set of plant leaves.
In addition, we called variants across the population from the RNA-seq data, to assess the impact of genetic variation on physiology and developmental asynchrony.

first: James

last: Ronald

first: Seth

last: Davis

first: Daphne

last: Ezer


title: Thrombospondin-1 promotes fibro-adipogenic stromal expansion and contractile dysfunction of the diaphragm in obesity

status: Public on Aug 16 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: This study defines the impact of in vivo thrombospondin-1 (THBS1) ablation on diaphram stromal cell profile, histology and contractile funciton in a mosue model of diet-induced obesity

overall_design: Single cell RNA sequencing of mononuclear cell isolates from daiphragms of wild type C57 mice fed either control diet or high fat diet (45% kcal from lipid) for 6 months; as well as thrombospondin-1 knockout mice fed high fat diet for 6 months

first: Eric

last: Buras

first: Tae-Hwa

last: Chun


title: MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling [exosome-miR-seq]

first: Wei

last: Zhu

summary: To investigate the potential role of miRNA-148b-5p in the pathogenesis of kidney stones, we conducted urinary exosomal sequencing.

overall_design:
In order to study the difference of miRNA-148b-5p expression between patients with renal calculi and normal subjects, we sequenced the miRNA in the corresponding exocrine.

Please note that, as the mapping of the 'P11' sample was too low, the 'P11' sample was not included in the further analysis and thus no processed data was provided.


title: Gene expression profile at single cell level of in vitro induced regulatory B cells expressing granzyme B (GZMB+Bregs) and non-Bregs from healthy donors and kidney transplant recipients.

status: Public on Aug 23 2023

city: Nantes

first: Nicolas

last: Sailliet

address: 30 Boulevard Jean Monnet

country: France

institute: Nantes université

summary: Regulatory B cells are considered as a very heterogenous population of different origins and functions. We used single cell RNA sequencing (scRNA-seq) to analyze the regulatory B cells expressing granzyme B (GZMB+Bregs).

overall_design: B cells from 4 healthy individuals and 6 kidney transplant recipients (3 with humoral rejection, 1 with stable function and 2 Spontaneous Operational Tolerants) were isolated from blood uning the comercialized B cell isolation kit II (Miltenyi) and separated in two conditions of non-Bregs (culture medium for 3 days) and GZMB+Bregs (culture medium supplemented with IL-21, IL-2, CpG DNA, CD40L, anti-human IgG/A/M F(ab)’2  for 3 days)

first: Hoa

last: Mai

first: Amandine

last: Dupuy

first: Gaëlle

last: Tilly

first: Cynthia

last: Fougeux

last: Braud

first: Magali

last: Giral

first: Jean-Michel

last: Robert

last: Degauque

first: Richard

last: Danger

first: Jeremie

last: Poschmann

first: Sophie

last: Brouard


title: mouse thymocytes

first: Andreas

last: Krueger


title: Spatial transcriptome reveals disturbance of peri-infundibular immune infiltration in androgenetic alopecia

status: Public on Aug 11 2023

city: Rangsit

first: Sasin

last: Charoensuksira

state: Pathum Thani

address: 99 Moo 18 Klong Luang

country: Thailand

institute: Thammasat University

summary: Several studies have suggested that in addition to androgen-sensitive dermal papilla cells, peri-infundibular immune infiltration is associated with the balding process in androgenetic alopecia (AGA). Nevertheless, investigations into the molecular signatures of this compartments are limited because none of the current techniques enable high-throughput profiling of specific pathological areas.

overall_design: The spatial transcriptome technique was used to capture the transcriptome profiles of CD45+ peri-infundibular immune infiltration (PII) regions to identify molecular perturbations between PII from AGA patients (PII-A) and normal donors (PII-C)

first: Saranyoo

last: Ponnikorn

first: Supasit

last: Tantiwong

first: Sirashat

last: Hanvivattanakul

first: Piyaporn

last: Surinlert

first: Wilai

last: Thanasarnaksorn

first: Aungkana

last: Krajarng

first: Suradej

last: Hongeng

first: Juthapa

last: Pongklaokam


title: Stem cells tightly regulate dead cell clearance to maintain tissue fitness [Bulk RNA-seq]

status: Public on Aug 07 2023

city: New York City

first: Katherine

last: Stewart

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

summary: Macrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial amount of these dying cells are cleared by local tissue cells, so-called ‘non-professional phagocytes’, critical to preserve organismal fitness. How non-professional phagocytes are able to sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying this balancing act.  Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires not only local lipids produced by apoptotic corpses, which are necessary for RXRα activation, but also tissue-specific retinoids able to activate RARg. The dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an attractive mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche.

overall_design: Cultured hair follicle stem cells were FACS-sorted directly into TRI Reagent, and total RNA was purified using the Direct-zol RNA kit (Zymo Research) according to the kit protocol. RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit (non-stranded, poly-A selection) and sequenced on an Illumina HiSeq 4000 or NovaSeq.

first: Elaine

last: Fuchs


title: Effect of CuCl2 on genomic ssDNA regions in A549 cells

city: Chicago

first: Matthew

last: Ross

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

institute: University of Chicago

summary:
To investigate the genomic effects of CuCl2 on A549 cells in vitro, we treated cells with sDMEM (DMEM + 10% FBS + 1% Pen/Strep cocktail) or sDMEM + CuCl2 for various timepoints at various concentrations (or untreated cell control) followed by kethoxal labeling of single stranded DNA (ssDNA)
We then performed differential analysis of ssDNA levels following the KAS-pipe pipeline

overall_design: Comparative ssDNA profiling analysis of KAS-seq data for human A549 cells treated with CuCl2 vs. untreated cells.

first: Chuan

last: He


title: Effect of CuCl2 on transcriptional expression of MDA-MB-468 cells

summary: To investigate the effects of disrupting Cu homeostasis on MDA-MB-468 cells in vitro, we treated cells with DCAC50, tetrathiomolybdate, or DMSO (control) or sDMEM for 24 hours

overall_design: Following RNA extraction, ribo-minus library generation, and sequencing, we then performed differential expression analysis of extracted RNA, comparing DCAC50- or tetrathiomolybdate-treated cells to DMSO-treated

first: Ruitu

last: Lyu

first: Olga

last: Karginova

first: Olufunmilayo

last: Olopade


title: Impact of 5-methylcytosine (5mC) on UV-induced CPD formation

status: Public on Aug 15 2023

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

institute: Washington State University

summary: We used a high-throughput sequencing method known as CPD-seq to map the formation of UV-induced cyclobutane pyrimidine dimers (CPD)  at single nucleotide resolution in UV-irradiated yeast genomic DNA (naked DNA) in the presence or absence of cytosine methylation at CpG sites by the methyltransferase M.SssI.

overall_design: Mapping UV-induced CPDs in isolated yeast genomic DNA in the presence or absence of CpG methylation in vitro by M.SssI methyltransferase and then irradiated with 90J/m2 of UVC or 500 J/m2 of UVB light.

first: Hannah

last: Wilson


title: INFANT AND ADULT HUMAN INTESTINAL ENTEROIDS ARE MORPHOLOGICALLY AND FUNCTIONALLY DISTINCT

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: Intestinal tissues from 3 infants and 3 adults were obtained and the stem cells were isolated to generate  enteroids. Enteroids were differentiated for 5 days prior to RNA extraction and sequencing.

overall_design: RNA-seq

first: Grace

middle: O

last: Adeniyi-Ipadeola

first: Julia

middle: D

last: Hankins

first: Amal

last: Kambal

first: Zeng

last: Xi-Lei

first: Ketki

last: Patil

first: Victoria

last: Poplaski

first: Carolyn

last: Bomidi

first: Hoa

last: Nguyen-Phuc

first: Sandra

middle: L

last: Grimm

first: Cristian

last: Coarfa

first: Sue

middle: E

last: Crawford

first: Sarah

last: Blutt

first: Allison

last: Speer

first: Mark

first: Sasirekha

last: Ramani


title: Single-cell RNA sequencing of Drosophila embryonic heart

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: Single-cell RNA sequencing was performed on embryonic Drosophila heart cells. Analysis of single-cell RNA sequence (scRNA-seq) data at timepoints prior to migration of cardiac progenitor cells through to heart tube closure (embryonic stages 13, 14-early, 14-late, 15 and 16) revealed several interesting findings. We found specification of cardiac cell types takes place early, before stage 13, with biggest changes in transcriptomic profiles detected once cells had settled at the midline for further cardioblast maturation. Throughout development, our data identified multiple cell types, covering cardioblasts and five types of pericardial cells including a neural cardiac cell type. The scRNA-seq data further revealed a combination of first and second heart fields during heart development in fly. Further, we uncovered new cell type-specific markers discerning the different cardiac cell types. And we identified signaling pathways key to heart cell maturation, which are conserved from fly to human.

overall_design: We collected fresh embryonic heart cells from stage 13 to stage16 by FACS and prepared single-cell RNA library according to the manufacturer's protocol (10X Genomics, CA, USA), and samples were sequenced by Illumina HiSeq platform (carried out by Novogene, CA).

first: X

last: Huang

first: Y

last: Fu

first: H

first: P

last: Zhang

first: Z

last: Han


title: Nucleosome-mediated competition of pioneer transcription factors

status: Public on Aug 02 2023

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

summary: Pioneer transcription factors Nanog, Pou5f3 and Sox19b  promote chromatin accessibility on the enhancers of the early zebrafish embryos. It is poorly understood how they act together; it is commonly assumed that they act additively or cooperatively to clear chromatin from the nucleosomes. We investigated this question by comparing chromatin accessibility (Omni ATAC-seq)  in seven mutant genotypes: single, double and triple maternal-zygotic mutants by Pou5f3, Sox19b and Nanog, and the wild-type embryos.  We found, that at most of the directly bound sites, either Pou or Nanog is required for chromatin accessibility; while at the minority of the sites two factors act additively. Further, on  the sites, where Pou5f3 promotes chromatin accessibility, Nanog often suppresses it, and vice versa. To explain this phenomenon,  we suggest a model of nucleosome-mediated competition between pioneer transcription factors: Pou5f3 and Nanog compete for the same binding motif on the DNA, but only one of the factors has a pioneer activity on this site. This entry contains only part fo the Omni-ATAC-seq experiments, the other part is in the previously released entry GSE188364.

overall_design: Omni-ATAC-seq on whole embryos

first: Aileen

last: Riesle


title: Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma [scTCR-seq]

status: Public on Aug 01 2023

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

summary: Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.

overall_design: Expanded TILs profiling in melanoma patients receiving adoptive cell therapy by live cell-sorted single cell RNAseq

first: Johanna

last: Chiffelle

first: Denarda

last: Dangaj

first: Alexandre

last: Harari

first: George

last: Coukos


title: Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma

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

overall_design: Refer to individual Series


title: Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma [scRNA-seq]


title: New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile

status: Public on Aug 18 2023

city: Greenville

first: Edson

middle: R

last: Rocha

address: 600 Moye Blvd.

institute: East Carolina University Brody School of Medicine

summary:
Genome expression study of Bacteroides fragilis strain 638R comparing an fur deletion mutant with the wild-type strain grown in minimal defined media with iron-replete, iron-limiting, heme-replete and heme-limiting conditions.
The construction of the fur mutant analyzed in this study was described in Robertson KP, Smith CJ, Gough AM, Rocha ER. Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. Infect Immun. 2006 74:2304-2316.

overall_design: Twelve chip study with 8 technical replicate on each chip comparing iron and heme regulated genes in the wild-type strain and fur deletion mutant.

first: C

last: Smith


title: Gene expression profile of Fcrls+/CD11b+/Ly6C- microglia from the brain V

status: Public on Jul 31 2023

city: Bonn

first: Rayk

last: Behrendt

address: Venusberg-Campus 1

department: Institute for Clinical Chemistry and Clinical Pharmacology

institute: University Bonn

summary: We used bulk RNA sequencing to investigate the molecular signature of microglia affected by deletion of microglial APOE4 in APP/PS1 mice.

overall_design: Fcrls+/CD11b+/Ly6C- microglia were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using Smartseq2 RNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

middle: N

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

middle: M

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

middle: G

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

middle: J

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Gene expression profile of Fcrls+/CD11b+/Ly6C- microglia from the brain IV

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of microglia affected by administering an Itgb8 blocker in APP/PS1 mice

overall_design: Fcrls+/CD11b+/Ly6C- microglia were isolated from injection sites by Fluorescence-activated cell sorting (FACS) and analyzed using Smartseq2 RNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

middle: A

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao


title: Gene expression profile of Fcrls+/CD11b+/Ly6C- microglia from the brain III

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of microglia isolated from Itgb8 cKO vs. Control mice.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

middle: K

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Gene expression profile of ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes from the brain V

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of astrocytes affected by microglial APOE4 in P301S mice.

overall_design: ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using Smartseq2 RNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao


title: Conservation of primordial ~12-hour ultradian gene programs in humans

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Biological rhythms have important implications for human disease, as evidenced by the effects of disrupting the 24h circadian clock. While circadian rhythms are entrained to the once daily light-dark cycle of the sun, coastal marine organisms are known to exhibit 12h ultradian rhythms, corresponding to the twice daily movement of the tides. Human ancestors emerged from a circa-tidal environment millions of years ago. However, whether 12h ultradian rhythms are conserved in humans remains unknown. Here, we performed prospective, high temporal resolution transcriptome profiling in the peripheral white blood cells of three healthy subjects. Remarkably, all three subjects exhibited a shared transcriptional program demonstrating robust ~12h rhythms. Pathway analysis implicated 12h transcriptional oscillations primarily affected core cellular processes, including RNA and protein metabolism, with strong homology to the 12h gene programs previously identified in cnidarian marine species. These results establish the existence of 12h biological rhythms in humans. Such rhythms appear to have a primordial evolutionary origin dating back at least 700 million years and are likely to have far-reaching implications in human health and disease.

overall_design: Blood samples were collected every two hours for a total of 48-hour period (D1 and D2) from three healthy individuals (S1, S2 and S3).

first: Bokai

last: Zhu

first: Silvia

first: Natalia

last: David

first: William

last: Dion

first: Michelle

last: Sun

first: Nandini

last: Doshi

first: Tristan

last: Pesaresi

first: Rosemary

last: Andrews

first: G

last: Kumar

first: Tânia

last: Amorim

first: Saad

last: Irfan

first: Ankit

middle: X

last: Sharma

first: Lauren

middle: B

last: Siegel

first: Pouneh

last: Fazeli

first: Matthew

last: Steinhauser


title: Gene expression profile of ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes from the brain III

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the astrocytic signature of astrocytes affected by Lgals3 injection in microglia.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Gene expression profile of ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes from the brain IV

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the astrocytic signature isolated from dead-neuron-injected 8-month-old APOE4-cKO mice compared with APOE4-KI mice

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao


title: Gene expression profile of ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes from the brain II

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the astrocytic signature of astrocytes affected the transfer of MGnD microglia

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Gene expression profile at single cell level of CNS cells from the brain

first: Rayk

last: Behrendt

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the subsets of CNS cells affected by deletion of APOE4 in microglia.

overall_design: Total CNS cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao


title: Gene expression profile of either Dead neuron+/Fcrls+/CD11b+/Ly6C- or Dead neuron-/Fcrls+/CD11b+/Ly6C- microglia from the brain

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of both phagocytic microglia and non-phagocytic microglia affected by deletion of Itgb8 in microglia.

overall_design: Dead neuron+/Fcrls+/CD11b+/Ly6C-  and Dead neuron-/Fcrls+/CD11b+/Ly6C- microglia were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using Smartseq2 RNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Gene expression profile of Fcrls+/CD11b+/Ly6C- microglia from the brain I

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of microglia affected by PU.1 inhibitor in APP/PS1:APOE4-KI mice.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao


title: Gene expression profile of Fcrls+/CD11b+/Ly6C- microglia from the brain II

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of microglia affected by microglia-specific APOE isoform (APOE3 vs. APOE4) in both WT and P301S mice

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma [TCR-Seq]

first: David

last: Barras

overall_design: Bulk TCR repertoire of longitudinal blood, tumor and expanded TIL products of melanoma patients receiving TIL-ACT.

first: Johanna

last: Chiffelle

first: Raphael

last: Genolet

first: Alexandre

last: Harari

first: George

last: Coukos


title: Epigenetic profile of Fcrls+/CD11b+/Ly6C- microglia from the brain

first: Rayk

last: Behrendt

summary: Determine the histone modification of microglia expressing different human APOE variants.

overall_design: Microglia from WT mice, expressing either Human APOE3 or APOE4 constituitively, were isolated and H3K9ac was determined as measure for regions of active gene transcription.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu


title: Gene expression profile of either Dead neuron+/Fcrls+/CD11b+/Ly6C-  or Dead neuron-/Fcrls+/CD11b+/Ly6C- microglia from the brain I

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of phagocytic and non-phagocytic microglia affected by APOE isoform (APOE3-KI vs. APOE4-KI)

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: Gene expression profile of Dead neuron+/Fcrls+/CD11b+/Ly6C- microglia from the brain

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of phagocytic microglia affected by deletion of Spi1 in microglia.

overall_design: Dead neuron+/Fcrls+/CD11b+/Ly6C- microglia were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using Smartseq2 RNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Amy

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu


title: APOE4 impairs the microglial response in Alzheimer's disease by inducing TGFbeta-mediated checkpoints

first: Rayk

last: Behrendt

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profile of ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes from the brain I

summary: We used bulk RNA sequencing to investigate the molecular signature of astrocytes affected by PU.1 inhibitor in APP/PS1:APOE4 KI mice.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: IPF and SSc-ILD

status: Public on Jul 26 2023

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech


title: Evaluation of breast cancer PDX tumor heterogeneity

status: Public on Jul 18 2023

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University


title: Evaluation of breast cancer PDX tumor heterogeneity at single cell resolution [scRNA-seq]

summary: Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. One challenge to treatment development is tumor heterogeneity. In this study, we profiled ER+ and triple negative breast cancer PDX models using single-cell RNA-sequencing. This data may help identify populations of cells which are susceptible to certain treatments in order to improve clinical outcomes for breast cancer patients.

overall_design: ER+ and triple-negative mammary tumors were subjected to single-cell RNA sequencing with the goal of identifying and profiling sub-populations within models to improve outcomes of targeted treatments.

first: J

middle: C

last: Harrell

first: Amy

last: Olex

first: Mikhail

last: Dozmorov

first: Julia

last: Altman

first: David

last: Boyd

first: Emily

last: Zboril


title: Gene expression profile of human brain tissue

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of total tissue isolated from AD patients carrying APOE ε3/ε3 and APOEε3/ε4 alleles.

overall_design: mRNA were isolated using mirVana miRNA isolation kit and analyzed using Smartseq2 RNAseq.

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

first: Jen-Li

last: Barry

first: Rajesh

last: Krishnan

first: Sam

last: Wakelin

first: Jared

last: Rhee

first: Anthony

last: Yung

first: Michael

last: Aronchik

first: Chao

last: Wang

first: Nimansha

last: Jain

first: Xin

last: Bao

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

last: Deik

first: Daniel

last: Tenen

first: Tsuneya

last: Ikezu

first: Nicolas

last: Santander

first: Gabriel

last: Mckinsey

first: Caroline

last: Baufeld


title: Gene expression profile of either Dead neuron+/Fcrls+/CD11b+/Ly6C-  or Dead neuron-/Fcrls+/CD11b+/Ly6C- microglia from the brain II

first: Rayk

last: Behrendt

summary: We used bulk RNA sequencing to investigate the molecular signature of phagocytic and non-phagocytic microglia affected by APOE isoform (APOE3-KI vs. APOE3-cKO vs. APOE4-KI vs. APOE4-cKO)

first: Zhuoran

last: Yin

first: Neta

last: Rosenzweig

first: Kilian

last: Kleemann

first: Xiaoming

last: Zhang

first: Wesley

last: Brandao

first: Milica

last: Margeta

first: Caitlin

last: Schroeder

first: Kisha

last: Sivanathan

first: Sebastian

last: Silveira

first: Christian

last: Gauthier

first: Dania

last: Mallah

first: Kristen

last: Pitts

first: Ana

last: Durao

first: Shawn

last: Herron

first: Hannah

last: Shorey

first: Yiran

last: Cheng

last: Barry

first: Amy

first: Dean

last: Sheppard

first: Susanne

last: Krasemann

first: Roni

last: Nowarski

first: Bart

last: Eggen

first: Clary

last: Clish

first: Rudolf

last: Tanzi

first: Charlotte

last: Madore

first: Thomas

last: Arnold


title: The role of stromal and immune cells in atrial disease [II]

status: Public on Jul 13 2023

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: In atrial fibrillation, disturbed electrical conduction disrupts the coordinated contraction of the heart’s antechambers, increasing the risk of stroke and heart failure. The rising prevalence of this disease approaches 9% in patients >65 years. Studying freshly isolated human atrial tissue and a new mouse model, we here decipher how immune and stromal cells contribute to the structural tissue remodeling that underlies atrial fibrillation. Single-cell transcriptomes from control and diseased human atria documented macrophage doubling at the expense of endothelial and mural cells. An inflammatory monocyte and a pro-fibrotic SPP1+ macrophage cluster expanded in patients with atrial fibrillation. To experimentally perturb pathways observed in patients, we matched their risk factors Hypertension, Obesity and Mitral valvE Regurgitation (HOMER) in mice. Atrial single-cell transcriptomes obtained in HOMER mice, which developed enlarged, fibrillation-prone atria, recapitulated human cell composition and transcriptome variations. Recruitment drove the expansion of atrial macrophages; accordingly, inhibition of monocyte migration reduced arrhythmia in Ccr2-/- HOMER mice. Deleting Spp1 established macrophage-derived osteopontin as a pleiotropic signal that promotes atrial fibrillation through pro-fibrotic, inflammatory crosstalk with an arsenal of local immune and stromal cells. Taken together, we identify SPP1+ macrophages as targets for immunomodulatory therapy in atrial fibrillation.

overall_design: Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left atrial tissues collected from 2 C57BL/6 bone marrow transplanted (BMT) and 2 Spp1-/- BMT mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

first: Maarten

last: Hulsmans

first: Maximilian

last: Schloss

first: Kamila

last: Naxerova

first: Matthias

last: Nahrendorf


title: Modulation of profibrotic pathways in systemic sclerosis skin from focuSSced trial with treatment

first: Jason

last: Vander Heiden

summary: Previous microarray analysis of skin biopsies from patients enrolled in the FaSScinate clinical trial revealed pathways modulated by treatment and associated with aggressive disease course. To further our understanding of these pathways, we performed RNA-seq on patients enrolled in the FocuSSced clinical trial to confirm the previous finding and explore new treatment modulated pathways.

overall_design: RNA-seq was performed on a subset of patients that consented for pre- and post-treatment skin biopsies from the FocuSSced study across both arms.

first: Guiquan

last: Jia

first: Margaret

last: Neighbors

last: Hackney

first: Thirumalai

last: Ramalingam


title: The role of stromal and immune cells in atrial disease [III]

overall_design: Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left ventricular tissues collected from 4 sham-operated mice and 4 mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).


title: The role of stromal and immune cells in atrial disease


title: The role of stromal and immune cells in atrial disease [I]

overall_design:
Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left atrial tissues collected from 7 patients with persistent atrial fibrillation undergoing surgical mitral valve repair and from 5 control subjects. We also present single-cell transcriptomic data on FACS-purified, left atrial non-cardiomyocytes from 4 sham-operated mice and 4 mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

**Submitter declares that raw data have not been provided for the human samples due to privacy concerns**

first: I

middle: H

first: George

last: Tolis

first: Serguei

last: Melnitchouk