4fa21a66-e3fb-487b-9260-7b80be7ba06b - samples
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ABSTRACT:
PROVIDER: EGAD00001005947 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This study aims to investigate the microRNA profile in human medullary carcinoma tissue by microarray analysis and RT-qPCR. Matched tumor and adjacent normal tissue were obtained from 24 patients and analysed using human microRNA Microarray Kit Agilent, Differentially expressed miRNAs were validated by RT-qPCR using 37 other tumors samples (validation set), Associations of microRNA expression with clinicopathological items were studied Matched tumor and adjacent normal frozen tissues were obtained from thyroid of 40 patients. Normal tissue (name with suffix S) and lesionnal tissue (name with suffix L) were hybridized on microarray.
2014-12-15 | E-GEOD-40807 | biostudies-arrayexpress
Project description:Purpose: Investigate transcriptional changes by genetic perturbation of specific transcription factors under sufficient and limiting nitrate conditions. Methods: 9 day old roots were harvested between 1-2pm (get hours after “sunrise”) and frozen in liquid N2. RNA-seq libraries were prepared following the BRAD-Seq DGE protocol (four biological replicates per genotype and treatment). Libraries were sequenced using the Ilummina HiSeq 3000 in SR50 mode. Two technical replicates libraries were created from each RNA sample; after assessing sufficient reproducibility, counts across technical replicates were pooled together. Reads were processed with fastx_trimmer for barcode removal (-f 9 -v -Q 33) and trimmed by quality with reaper (paremeters: -geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late), then mapped to the reference genome of Arabidopsis thaliana (TAIR v10) using bowtie (-a --best --strata -n 1 -m 1 -p 4 --sam --tryhard) with subsequent conversion to BAM format using samtools and counts were obtained with HTSeq-count.
2018-07-30 | GSE107988 | GEO
Project description:Multi-regional and pooled tumor biopsy specimens
| PRJNA301663 | ENA
Project description:Genome-wide analysis of single nucleotide polymorphisms in 64 acute myeloid leukemias has revealed that 20% exhibited large regions of homozygosity that could not be accounted for by visible chromosomal abnormalities in the karyotype. Further analysis confirmed that these patterns were due to partial uniparental disomy (UPD). Remission bone marrow was available from five patients showing UPD in their leukemias, and in all cases the homozygosity was found to be restricted to the leukemic clone. Two examples of UPD11p were shown to be of different parental origin as indicated by the methylation pattern of the H19 gene. Furthermore, a previously identified homozygous mutation in the CEBPA gene coincided with a large-scale UPD on chromosome 19. These cryptic chromosomal abnormalities, which seem to be nonrandom, have the characteristics of somatic recombination events and may define an important new subclass of leukemia. Patient No. from Table 1 of Raghavan et al 2005 and Sample name Patient No: 1 = Sample name: AML sample 35 diagnosis Patient No: 1 = Sample name: AML sample 107 remission Patient No: 2 = Sample name: AML sample 37 diagnosis Patient No: 3 = Sample name: AML sample 10 diagnosis Patient No: 3 = Sample name: AML sample 44 remission Patient No: 4 = Sample name: AML sample 20 diagnosis Patient No: 5 = Sample name: AML sample 65 diagnosis Patient No: 6 = Sample name: AML sample 69 diagnosis Patient No: 6 = Sample name: AML sample 94 remission Patient No: 7 = Sample name: AML sample 40 diagnosis Patient No: 7 = Sample name: AML sample 41 remission Patient No: 8 = Sample name: AML sample 64 diagnosis Patient No: 9 = Sample name: AML sample 7 diagnosis Patient No: 10 = Sample name: AML sample 49 diagnosis Patient No: 10 = Sample name: AML sample 106 remission Patient No: 11 = Sample name: AML sample 76 diagnosis Patient No: 12 = Sample name: AML sample 79 diagnosis Keywords: DNA copy number, loss of heterozygosity
2007-04-11 | GSE7490 | GEO
Project description:This dataset was created to (i) compare the protein expression of E. coli DSM613 cells infected and uninfected with phage vB_EcoS-EE09 and (ii) detect structural proteins of phage vB_EcoS-EE09. Thus, this set provides proteomic data of three setups: 1. Uninfected E. coli DSM613 (file names [file ID]: 04_22A [F40]; 13_ecolicontrol_01 [F13]; 14_ecolicontrol_02 [F14]) 2. E. coli DSM613 infected with phage vB_EcoS-EE09 (file names [file ID]: 02_13A [F39]; 27_ecoliinfected_01 [F27]; 28_ecoliinfected_02 [F28]) 3. Cell-free phage lysate of phage vB_EcoS-EE09 (sample name: 01_EE09)
2023-11-13 | PXD046455 | Pride
Project description:Three related datasets are included, all from immunoprecipitations of FLAG-tagged DCBLD1 and DCBLD2 (human) from 293 cells. Letters at the end of file names denote regions of each gel lave from highest (“A”) to lowest (“B”-X) molecular weight. File names containing “SILAC” are part of a dataset composed of 3 biological replicates (“T1”,”T2”,”T3” in file name) run of 10% or 15% gels (“10” or “15” in file name). DCBLD1 or DCBLD2 were immunoprecipitated from cells alone (light SILAC condition) or with Fyn/Abl (heavy SILAC condition). “Mock”, “Fyn” alone, or “Abl” alone in file names denote control immunoprecipitates, in which the light condition was a mock transfection and the heavy was either a mock or had Fyn/Abl expressed alone. Trypsin was used as the proteolytic enzyme. File names beginning with “Label_free” are part of datasets from LC-MS/MS analysis of DCBLD1 or DCBLD2 immunoprecipitates from 293 lysates. Prior to LC-MS/MS analysis, immunoprecipitates were digested with trypsin and GluC. Only DCBLD1 and DCBLD2 protein bands were analyzed via LC-MS/MS. File names containing “zebrafish” are part of datasets from LC-MS/MS analysis of DCBLD2 immunoprecipitates from 293 extracts that were then incubated with zebrafish extracts. These datasets include tryptic peptides from both human and zebrafish proteins.
2020-08-07 | PXD017723 | Pride
Project description:<p>The purpose of this study is to ascertain the locations of somatic LINE-1 retrotransposition events in human colon tumor samples by pooling multiple tumor samples from different patients and performing a targeted resequencing assay (Ewing and Kazazian, Genome Research 2010) to sequence the 3' flanking regions of all insertions in the pooled sample. The result is compared to the result of applying the same method to pooled normal samples from the same patients as were used in the pooled tumor sample and selecting sites that show an insertion in the tumor but not in the normaltissue and do not correspond to any known non-reference LINE-1 insertion allele. The selected sites are then validated by site-specific PCR and capillary sequencing to confirm that they represent LINE-1 insertions and to obtain breakpoint sequences.</p>
| phs000536 | dbGaP
Project description:This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages (34 dph (days post-hatching) alevin; 109 dph; fry and 162 dph parr;) and secondly, whether phenotypic differences at these stages were reflected in protein samples collected from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n = 3) were first fed at 35 dph and then maintained by feeding to satiation on commercial feeds. NOTE on file nomenclature - T/D refer to triploid/diploid; E* refers to sequential protein extract (1 or 2) and S3 refers to sampling time point #3 (all other files with either no suffix or long suffix are sampling time point #2)
2017-12-14 | PXD005451 | Pride
Project description:Obesity-induced inflammation causes metabolic dysfunction, but the mechanisms remain elusive. Here we show that the innate immune transcription factor interferon regulatory factor (IRF3) adversely affects glucose homeostasis through induction of the endogenous FAHFA hydrolase androgen induced gene 1 (AIG1) in adipocytes. Adipocyte-specific knockout of IRF3 protects mice against high-fat diet-induced insulin resistance, whereas overexpression of IRF3 or AIG1 in adipocytes promotes insulin resistance on a high-fat diet. Furthermore, pharmacological inhibition of AIG1 reversed obesity-induced insulin resistance and restored glucose homeostasis in the setting of adipocyte IRF3 overexpression. We, therefore, identify the adipocyte IRF3/AIG1 axis as a crucial link between obesity-induced inflammation and insulin resistance and suggest an approach for limiting the metabolic dysfunction accompanying obesity. ## File Key ### MS-ABPP The following raw files were acquired on an Eclipse instrument in triplicate with two concentrations of inhibitor in both brain and kidney. These variables are encoded in the file names. Associated analysis pipeline files from CIMAGE are provided for each raw file (same file name, with a .raw_output_rt_10_sn_2.5.to_excel extension). - brain_conc1.0_rep1.raw - brain_conc1.0_rep2.raw - brain_conc1.0_rep3.raw - brain_conc10.0_rep1.raw - brain_conc10.0_rep2.raw - brain_conc10.0_rep3.raw - kidney_conc1.0_rep1.raw - kidney_conc1.0_rep2.raw - kidney_conc1.0_rep3.raw - kidney_conc10.0_rep1.raw - kidney_conc10.0_rep2.raw - kidney_conc10.0_rep3.raw ### TMT Dose Response The following raw files were acquired on an Eclipse instrument instrument in both brain and white adipose tissues: - brain_dose_response.raw - wat_dose_response.raw The TMT channels were organized as follows: - DMSO channels: 1, 3, 5 - ABD-110 @ 0.001 μM: 7, 9, 11 - ABD-110 @ 0.01 μM: 2, 4, 6 - ABD-110 @ 0.1 μM: 13, 15, 17 - ABD-110 @ 1 μM: 8, 10, 12 - ABD-110 @ 10 μM: 14, 16, 18 Associated analysis pipeline files after IDFilter run are provided for each file (same file name, with a _filtered_matches suffix and an .idXML extension). ### PRM AIG1 In Vivo Target Engagement The A prefix before the replicate number refers to treatment with ABD-110, whereas the V prefix refers to vehicle treatment. Diet and tissue type are also encoded in the filename. The following files were acquired on a Lumos instrument, with 5 replicates for each condition (as noted in square brackets). Associated pipeline analysis files are Skyline exports and are provided as two .csv files having names beginning with Skyline_PRM_export and ending with the tissue types contained. - Brain_Chow_A[1-5].raw - Brain_Chow_V[1-5].raw - Brain_HVD_A[1-5].raw - Brain_HVD_V[1-5].raw - eWAT_Chow_A[1-5].raw - eWAT_Chow_V[1-5].raw - eWAT_HVD_A[1-5].raw - eWAT_HVD_V[1-5].raw - iWAT_Chow_A[1-5].raw - iWAT_Chow_V[1-5].raw - iWAT_HVD_A[1-5].raw - iWAT_HVD_V[1-5].raw - Kindey_Chow_A[1-5].raw - Kindey_Chow_V[1-5].raw - Kindey_HVD_A[1-5].raw - Kindey_HVD_V[1-5].raw
2024-03-14 | PXD047864 | Pride
Project description:In this study, we compared the proteomes of mouse CD4+Foxp3+ regulatory T cells (Treg) and CD4+Foxp3- conventional T cells (Tconv) in order to build a data set of proteins differentially regulated in these two cell populations. The data set contains mass spectrometry results from the analysis of 7 biological replicates of Treg/Tconv cell samples purified by flow cytometry, each experiment performed from a pool of 4-5 mice. Global proteomic analysis of each sample was performed by single-run nanoLC-MS/MS, using chromatographic separation of peptides on 50cm C18 reverse-phase columns, with either a 480min gradient on LTQ-Velos orbitrap mass spectrometer (replicates 1 and 2) or a 300min gradient on Q-Exactive orbitrap mass spectrometer (replicates 3-7). Several MS injection replicates were performed for some experiments, leading to 27 raw files composing the data set. The detailed description of each analysis (file name, sample type, biological replicate number, MS technical replicate number, MS instrument used, sample name in MaxQuant ouput) is given in the table “Files list.txt”.
2017-04-10 | PXD004436 | Pride