Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11816933.fastq.gz | Fastqsanger.gz | |||
| SRR11816934.fastq.gz | Fastqsanger.gz | |||
| SRR11816935.fastq.gz | Fastqsanger.gz | |||
| SRR11816936.fastq.gz | Fastqsanger.gz | |||
| SRR11816937.fastq.gz | Fastqsanger.gz |
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Project description:We compared the relative abundance of RNAs in the UV- cross-linked (CL) and non-cross-linked (NC) samples using total RNA-seq of both promastigotes and axenic amastigotes of L. mexicana parasites. Irradiation of the Leishmania parasites with UV-dose of 525 mJ/cm2 followed by sequential AGPC phase partitioning and proteinase-treatment of the final interface provided the CL samples for the RNA-seq analyses. The abundance of RNA species in CL and NC samples were different; ncRNAs and protein coding RNAs respectively predominate the NC samples and CL samples in both promastigotes and amastigotes. Similarly, the CL samples of the two life cycle stages showed a higher Pearson correlation (median correlation 0.86) as compared to the correlation between the CL and NC samples in promastigotes (median correlation 0.69) and amastigotes (median correlation 0.84). Crucially, in addition to the similar distribution of RNA species in the CL samples of both life cycle stages, the abundance of the RNAs at the interface after CL was unaffected by the size of RNAs, suggesting that the orthogonal organic phase separation method recovered all CL Leishmania RNAs above 60bp without any systematic bias.
2022-01-14 | GSE188357 | GEO
Project description:The standard treatment for canine lymphoma (cL) is the CHOP chemotherapy protocol. Most cL patients treated with CHOP initially achieve remission but the duration varies and the majority of dogs eventually relapse with a multidrug resistant phenotype. This study assesses changes in gene expression occurring in cL tumor cell populations over the course of CHOP treatment. We measured gene expression using RNA-Seq on 15 cL patient samples taken prior to treatment and again 6 weeks into treatment.
2021-07-14 | GSE179920 | GEO
Project description:Corpus luteum (CL) is an ephemeral gland whose main function is to secrete progesterone required for the establishment and maintenance of pregnancy. It is very well established that development and maintenance of CL function in primates requires action of luteinizing hormone (LH) but the extent and mechanism by which LH contributes to the maintenance of CL function through out the luteal phase is not known. To study the nuclear actions mediated by LH, we evaluated global genomic changes in CL of monkeys treated with GnRH receptor antagonist to inhibit pituitary LH secretion. Affymetrix microarray analysis was performed on RNA samples from CL obtained from VEH or CET treated monkeys. Results demonstrate that LH regulates expression of a number of genes which might be important for maintenance of CL structure and function. Keywords: CL, LH, CET, gene expression
2007-06-07 | GSE7827 | GEO
Project description:Cellular plasticity is a hallmark of rare Claudin-low (CL) and metaplastic (MBC) breast cancer subtypes, with a documented overlap whose exact extent is yet unknown, and which are associated to resistance and poor survival. We used spatial transcriptomics to further characterise these plastic subtypes, respectively defined molecularly and histopathologically. We identified 3 putative CL tumours (CL-like) and 4 genomically unstable TNBC samples via molecular analyses, combined with 4 MBCs identified by a breast pathologist.
2023-10-16 | GSE213688 | GEO
Project description:To explore chorionic gonadotropin (CG)-regulated gene expression in the primate corpus luteum (CL), adult female rhesus macaques were treated with a model of simulated early pregnancy (SEP). Total RNA was isolated from individual CL and hybridized to Affymetrix™ GeneChip Rhesus Macaque Genome Arrays The level of 1192 transcripts changed expression > 2-fold (one-way ANOVA, FDR correction; P<0.05) during SEP when compared to Day 10 untreated controls, and the majority of changes occurred between Days 10 and 12 of SEP. To compare transcript levels between SEP rescued and regressing CL, previously banked rhesus GeneChip array data from the mid- to late and very late luteal phase were analyzed with time-matched intervals in SEP. Comparing RMA-normalized transcripts from the natural cycle with those from luteal rescue revealed 7677 transcripts changing in expression pattern >2 fold (one-way ANOVA, FDR correction; P<0.05) between the two groups. Clustering of samples revealed that the SEP samples possessed the most related transcript expression profiles. Regressed CL (days 18-19, around menses) were the most unlike all other CL. The most affected KEGG pathway was Steroid Biosynthesis, and most significantly absent pathways following SEP treatment includes groups of genes whose products promote cell-death. By further comparing the genome-wide changes in luteal gene expression during rescue in SEP, with those in CL during luteolysis in the natural menstrual cycle, it is possible to identify key regulatory pathways promoting fertility.
2011-11-21 | GSE25335 | GEO
Project description:Cl-amidine treatment reduces autoantibody responses in CIA. Sera were collected from Cl-amidine and control treated mice, and autoantibodies in these samples were profiled using Synovial Antigen Arrays. Significance Analysis of Microarrays (SAM) was used to analyze the antigen array datasets, and identified 8 antigens with a significant difference in autoantibody reactivity (false discovery rate (q) < 5%). Hierarchical clustering was then performed to elucidate the relationships between the autoantibody profiles. The Cl-amidine treated mice clustered together and exhibited lower autoantibody titers against all of the 8 antigens identified by SAM, including autoantibody reactivity to native epitopes derived from cartilage as well as citrulline-modified filaggrin peptides.
2010-08-21 | GSE23731 | GEO
Project description:The corpus luteum (CL), an ovarian transient gland, develops from the remnants of the ovulatory follicle and produces progesterone, required for maintenance of pregnancy in mammals. The development of the CL is characterized by the differentiation of granulosal and thecal cells into luteal cells, cell hypertrophy and hyperplasia. As the CL matures, growth ceases and the tissue acquires the ability to undergo regression in response to luteolytic signals (prostaglandin F2alpha). The regulators of this transition are poorly understood. MicroRNA, posttranscriptional regulators of tissue development and function, are hypothesized to play a role during these processes. The goal of this study was to profile the expression of microRNA (miRNA) in the corpus luteum (CL) of Holstein cows at two time points of the estrous cycle (early-cycle (Day4) and midcycle (D9-12); day0= day of estrus) in order to investigate their role in regulating CL development and function.
2016-09-03 | GSE72733 | GEO
Project description:The absence of luteolytic signal on non-pregnant bitches leads to the existence of a physiological pseudopregnancy maintained by a long lasting luteal function. During the diestrus, hormonal regulation of the canine CL changes. While in later stages prolactin is the main luteotropic hormone, in earlier stages the CL is independent from hypophysary hormones. At this time, prostaglandins are among the main luteotropic factors. In the present project, the aim was to further understand the effects of prostaglandins withdrawal on luteal function. In the present project, next generation sequencing (NGS), RNA-seq, was applied to explore the modulatory role of prostaglandins in the canine corpus luteum (CL) during the first half of diestrus. For this, transcriptome analysis of genes differently expressed in the CL of bitches treated in vivo with a COX2 inhibitor (Previcox, Merial) was performed. Additionally, by using just control samples, effects dependent on time were also explored and used as primary validation of results. Higher represented differentially expressed genes (DEG, p<0.01, FDR<0.1) in mature CL (days 20 and 30) referred to steroidogenesis, while in early CL (days 5 and 10) to proliferation and immune system. Then, treatment effects were investigated at each time point. No gene was concomitantly affected in all investigated groups. Thus, clearly, the effects were dioestrus stage-dependent. Higher numbers of DEG were found on day 20 (n=1741), mainly related to increased immune function, while on day 30 (n=552) they were related to decreased steroidogenesis and vascularization. Low numbers of DEG were found in early CL. Our results suggest the presence of strong compensatory effects in the early CL and multidirectional effects towards luteal gonadotropin-dependency after COX2-inhibition.
2019-12-01 | GSE130369 | GEO
Project description:Corpus luteum (CL) is an ephemeral gland whose main function is to secrete progesterone required for the establishment and maintenance of pregnancy. It is very well established that development and maintenance of CL function in primates requires action of luteinizing hormone (LH) but the extent and mechanism by which LH contributes to the maintenance of CL function through out the luteal phase is not known. To study the nuclear actions mediated by LH, we evaluated global genomic changes in CL of monkeys treated with GnRH receptor antagonist to inhibit pituitary LH secretion. Affymetrix microarray analysis was performed on RNA samples from CL obtained from VEH or CET treated monkeys. Results demonstrate that LH regulates expression of a number of genes which might be important for maintenance of CL structure and function. Keywords: CL, LH, CET, gene expression A single s.c. injection of GnRH receptor antagonist, Cetrorelix (CET), administered at a dose of 150 µg/kg BW has been shown to induce luteolysis. For the purpose of microarray analysis, VEH (5.25% glucose) or CET (treatment) was injected to female monkeys on day 7 of luteal phase and CL collected at 24 h post treatment (n=3) was cut into small quarters and snap frozen in liquid nitrogen. To minimize between animal variations, CL for both VEH and CET treatments were collected from the same monkeys.
2010-06-11 | E-GEOD-7827 | biostudies-arrayexpress