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The effects of broflanilide on developing zebrafish

ABSTRACT: For RNA-seq experiments, 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10-minute window. (N=5 beakers per treatment). On 7 days post fertilization (dpf), fish were transferred to a labeled and pre-weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA-seq analysis.

ORGANISM(S): Danio rerio

PROVIDER: GSE236484 | GEO | 2023/07/15

REPOSITORIES: GEO

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The effects of atorvastatin (AVS) and afidopyropen on developing zebrafish

Project description:For RNA-seq experiments, 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10-minute window. Exposure groups included ERM, [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] (N=5 beakers per treatment). On 7 days post fertilization (dpf), fish were transferred to a labeled and pre-weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA-seq analysis.

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The effects of ifosfamide and citalopram on developing zebrafish

Project description:For RNA-seq experiments, 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10-minute window. Exposure groups included ERM, 1 µg/L, and 100 µg/L ifosfamide or 10 and 1000 µg/L citalopram (N=5 beakers per treatment). On 7 days post fertilization (dpf), fish were transferred to a labeled and pre-weighed 1.7 mL tube using a p1000 with the tip cut off, then water was completely removed using a p200. The tube was then immediately flash frozen in liquid nitrogen prior to RNA-seq analysis.

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Comparison of conventional and germ-free gastrointestinal tract

Project description:Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum. Keywords: other

2004-06-24 | GSE1392 | GEO

NET-seq analysis of pSer2-Pol II profile in shCTRL, shMETTL3 and shDDX21 HeLa cells

Project description:The chromatin fraction was isolated from 5x107 HeLa cells. Chromatin was digested in 100 mL of MNase (40 units/ mL ) reaction buffer for 3 min at 37 °C in a thermomixer (1,400 rpm). After addition of 10 L EGTA (25mM) to inactivate MNase, soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min. 10 mg of Pol II antibody was conjugated to magnetic protein A beads. The supernatant was diluted with 400 mL of NET-2 buffer and pSer2-Pol II antibody-conjugated beads were added. Incubated the IP reaction at 4 °C for 1 hr. The beads were washed with 1 mL of NET-2 buffer six times and 100 mL of 1xPNKT (1xPNK buffer and 0.05% Triton X-100) buffer once. Washed beads were incubated in 50 mL PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK (NEB)) in Thermomixer at 37 °C, 1,400 rpm for 6 min. Beads were washed with 1 mL of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was suspended in urea Dye (7M Urea, 1xTBE, 0.1% BPB and 0.1% XC) and resolved on 6% TBU gel (Invitrogen) at 200 V for 5 min. Gels with 30-160 nt RNAs were collected. 0.2 mL tube was prepared with holes made with 25G needle and placed in a 1.5 mL tube. Gel fragments were placed in the layered tube and broken down by centrifugation at 12,000 rpm for 1 min. The small RNAs were eluted from gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) at 25 °C for 1 hr in Thermomixer (900 rpm). Eluted RNA was puriﬁed with SpinX column (Coster) with 2 glass ﬁlters (Millipore) and the ﬂow-through RNA was ethanol precipitated.

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Transcriptional profiles in rat hair follicles after single wave blasting impact

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Transcription profiling of mouse gastro intestinal tract after conventional and germ free treatments

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T cell metabolism during graft-versus-host disease(CAB 311)

Project description:T cells were injected into mice to model graft-versus-host disease. On day 7 after bone marrow transplantation (BMT), cells were recovered and CD8 T cells were purified to > 90% purity over magnetic columns. Naïve T cells were used as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they were removed from the plates, counted, and an equal number (2.5x10^6) were placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed once with ammonium chloride, residual volume was removed by a second brief spin, cell pellets were flash frozen in liquid nitrogen and stored at -80oC until analysis.

2015-06-07 | ST000181 | MetabolomicsWorkbench

scRNA-seq on C57BL/6J mice retina

Project description:Fresh retinatissues were harvested from 30 day old C57BL/6J mice according to published protocols. 3 retinas were pooled together to form one biological sample. Under a dissecting microscope, spring scissors were used to puncture the eye and remove the cornea, iris, and lens. The remaining eyecup had 4 radial incisions made every 90 degrees, resulting in a flat and open eye cup. The retina was then gently removed using curved tweezers and placed in a 1.5 ml microcentrifuge tube.

2020-09-29 | GSE153818 | GEO

Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La

Project description:shock treatment<br>Differential gene expression between the alternate 2La arrangements was examined for heat shock treated and control fourth instar larvae at three discrete time points to examine temporal variation in thermal stress response. One week after egg hatching, 72 fourth instar larvae of each 2La inversion polmorphism were randomly selected from multiple pans and placed into individual 13x100 mm glass culture tubes containing 2 mL of water. Heat shock treatment was carried out by placing tube racks containing larvae into a 38?C water bath for 60 min. After heat shock, larvae were placed back into 27?C water until collection, which took place 0.25 h, 2 h, and 8 h later by pooling 24 individuals into a 1.5 mL microcentrifuge tube and snap-freezing them in liquid nitrogen. Samples were stored at -80 ?C until RNA isolation. Control groups were treated identically for each time point with the only difference being that they were not exposed to the 60 min heat shock but rather placed into 27?C water<br>

2011-12-02 | E-MEXP-3078 | biostudies-arrayexpress

Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site

Project description:This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle. At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation.

2011-06-06 | GSE25245 | GEO

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