Single cell RNA-sequencing of gonadal and inguinal adipose tissue Pdgfrβ+ cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE144299 | GEO | 2020/01/27
REPOSITORIES: GEO
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Project description:Illumina bodyMap2 transcriptome Transcription profiling by high throughput sequencing of individual and mixture of 16 human tissues RNA. Additional supplementary files available at foot of this record. Additional information available as supplementary files at the foot of this record. ArrayExpress Release Date: 2011-03-17 Person Roles: submitter Person Last Name: Khrebtukova Person First Name: Irina Person Mid Initials: Person Email: ikhrebtukova@illumina.com Person Phone: 1-510-723-9219 Person Address: 25861 Industrial Blvd, Hayward CA 94545, USA Person Affiliation: Illumina
2011-07-14 | GSE30611 | GEO
Project description:We previously derived a doxycycline-inducible (Tet-On) lineage-tracing model that allows for the indelible labeling of Pdgfrb-expressing perivascular cells in adipose tissue of adult mice (PdgfrbrtTA; TRE-Cre; Rosa26RmT/mG; herein, MuralChaser mice). Prior to exposing animals to doxycyline, all cells within the stromal-vascular fraction (SVF) of adult inguinal WAT (iWAT) express membrane tdTomato from the Rosa26 locus. Following 9 days of exposure to doxycycline-containing chow diet, Cre-mediated excision of the loxP-flanked tdTomato cassette occurs in Pdgfrb-expressing cells, and membrane-bound GFP (mGFP) expression is constitutively activated. We set out to test the hypothesis that Pdgfrb-expressing perivascular cells in inguinal WAT of adult mice are heterogeneous, with subpopulations harboring functionally distinct phenotypes. To this end, we performed single cell RNA-sequencing of mGFP+ cells isolated from iWAT of lean (chow fed) 8 weeks-old male MuralChaser mice following 9 days of doxycycline exposure.
2020-09-01 | GSE144090 | GEO
Project description:Single cell RNA-sequencing of gonadal and inguinal adipose tissue Pdgfrβ+ cells
| PRJNA603328 | ENA
Project description:Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the relations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides and whole-cell RNAs less than 200 nt are investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three novel potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome. Processed data files: Graph files at ftp://ftp.ncbi.nih.gov/pub/geo/DATA/projects/GSE7576/graphs/ Transfrag files at ftp://ftp.ncbi.nih.gov/pub/geo/DATA/projects/GSE7576/transfrags/ CEL files available on each Sample record tpmap files available on each Platform record Keywords: tiling, RNA population complexity profiling
2007-05-25 | GSE7576 | GEO
Project description:Single cell RNA-sequencing of inguinal adipose tissue Pdgfrβ+ cells
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Project description:Remarkably, tens of thousands of piwi-interacting RNAs (piRNAs) arise from a minimal number of discrete clustered regions in many organisms. However, it remains unclear if organization into these domains contributes to the highly coordinated, germline-specific expression of these small RNAs. Here, we show that SNPC-4, the DNA-binding subunit of the small nuclear RNA activating protein complex (SNAPc), binds piRNA clusters in a germline-specific manner and is required for global piRNA expression in C. elegans. Within piRNA domains, SNPC-4 not only binds at discrete sites through its established sequence motif, but also exhibits widely distributed binding across the region. Intriguingly, discrete peaks are not found at every piRNA, but instead occur frequently at Pol III-occupied tRNA genes, which have been previously implicated in chromatin organization. Given its unique binding pattern, we suggest that SNPC-4 promotes robust piRNA expression by establishing a permissive chromatin environment at clusters specifically in the germ line. This data submission includes a total of 11 ChIP-seq samples and 2 RNA-seq samples. The ChIP-seq samples include six timecourse samples (Emb-YA) and three tissue-specific samples (WA, GL, SO) for one factor called SNPC-4 (previously called GEI-11). The remaining two ChIP-seq samples are for pol II (AMA-1) and pol III (RPC-1) at one developmental stage. All of these samples were done in replicate, with inputs, yielding at least four sequencing files per sample. Some of the ChIP-seq samples already have fastq files submitted to GEO: (SNPC-4 EMB _GSE48744: GSM1183805, GSM1183806, GSM1183807, GSM1183808), (SNPC-4 L1_GSE48702: GSM1183629, GSM1183630, GSM1183631, GSM1183632), (SNPC-4 L2_GSE37809: GSM928364, GSM928365, GSM928366, GSM928367), (SNPC-4 L3_GSE35276: GSM864851, GSM864852, GSM864853, GSM864854), and (AMA-1_GSE15535: GSM389309, GSM389310, GSM389312, GSM389313). We are submitting fastq files for the remaining ChIP-seq datasets: SNPC-4 L4 - 4 files, SNPC-4 YA - 5 files, SNPC-4 WA - 4 files, SNPC-4 GL - 4 files, SNPC-4 SO - 4 files, and RPC-1 WA - 5 files. Thus we are submitting an additional 26 fastq files. Additionally, we are submitting processed files for all 11 datasets, consisting of one normalized file for the combined duplicate IP and one normalized file for the input sequence. In the case of the three tissue-specific samples for SNPC-4, we are submitting an additional processed (but not normalized) file that represents the IP data with input-subtracted. Thus, we are submitting a total of 25 processed files. NOTE: The processed files for the ChIP-seq samples that already have fastq files submitted to GEO (SNPC-4 EMB _GSE48744, etc.) are linked below as supplementary files at the foot of the Series record. The RNA-seq samples represent one control (control_RNAseq) and one treatment (SNPC-4(RNAi)_RNA-seq)and were not duplicated. We are submitting one fastq file for each, as well as one processed data file for each, for a total of 2 fastq and 2 processed data files.
2014-11-17 | E-GEOD-53412 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-04-03 | GSE103587 | GEO
Project description:Comparison of WT, xrn1 delta and upf1 delta strains were used in a tiling array to yield genomic regions regulated by these proteins The supplementary CHP files record either the signal in log2 space or the p-values in linear space, per TAS output. The CHP files are further divided between UPF1 delta vs. WT and XRN1 delta vs. WT.
2008-08-21 | GSE11621 | GEO
Project description:Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.
2010-04-15 | E-GEOD-19824 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE25323: Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver (Nov 2009 dataset) GSE25324: Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver (Jan 2010 dataset) Refer to individual Series
2012-03-15 | E-GEOD-25325 | biostudies-arrayexpress