Chao Liu Similar Datasets
Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports
| 2291850 | ecrin-mdr-crc
Project description:The demo datasets available for MSCohort analysis. You can download to inspect their formats and practice using the software tool. This dataset contains raw files of 7 urine QC samples, spectronaut analysis results and MSCohort report results
2024-03-06 | PXD050389 | iProX
Project description:The transcriptional response of E. coli being predated by Bdellovibrio bacteriovorus Keywords: Transcriptional analysis 5 biological replicates with 2 technical replicates each of E. coli cells only and E. coli cells 15 minutes post-infection arrays 4 arrays, with samples swapped for each biological replicate. Gel image files generated by the ImageQuant scanning software. Each raw data txt file has the "control" samples which are the E. coli samples reading on the entire array and thus with the 2 technical replicates, and the "data" samples to which it is compared by Arrayvision. the "data" samples of ec1 to ec5 are Bdellovibrio only controls 2 technical replicates). The "data" samples of t1 to t5 are the test samples. Hence t1 to t5 are the raw data files for samples test1 to test10 and ec1 to ec5 are the raw data files for all of samples ec-1 to ec-10 and bd-1 to bd-10.
2009-12-08 | E-GEOD-9495 | biostudies-arrayexpress
Project description:Copy number status of 39 human AML samples was analyzed using CytoChip Cancer 4x180K v2.0 microarray chips from BlueGnome. Half the samples represent de novo AMLs while the other half represents secondary AMLs. Sample material consisted of cryopreserved bone marrow or blood aspirates. DNA was purified using the Gentra Puregene Blood Kit (Qiagen Nordic, Solna, Sweden) according to protocol. The test samples were labelled with Cy3 and the reference samples, consisting of sex-matched genomic DNA (Promega, Madison, WI, USA), were labelled with Cy5. The arrays were processed according to the manufacture’s recommendations using 0.5-1.0 µg of DNA as input material for each labelling reaction. The processed microarrays were scanned at 532 and 635 nm using a GenePix 4400A laserscanner (Molecular Devices, Winnersh, UK) at a resolution of 2.5 µm and GenePix Pro 7.0 software (Molecular Devices). The resultant image files were analyzed in BlueFuse Multi 3.1. using the Cytochip v2 algorithm. This software does not provide raw data files but only the processed data for each hybridization. Therefore, no raw data files are attached to this experiment.
2020-12-31 | E-MTAB-3663 | biostudies-arrayexpress
Project description:Normal human hepatocytes and 3 different HCC cell lines have been analyzed for the global expression of long non coding RNA (lncRNA). Total RNA was extracted from each sample using RNeasy Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed by Nanodrop ND-1000 and Bioanalyser2100. DNA microarray The Human Long Non-coding RNA Array was manufactured by Roche NimbleGen. Each array represents all long transcripts, both protein coding mRNAs and lncRNAs (long non-coding RNAs) in the human genome. More than 22000 lncRNAs are collected from the authoritative data sources including NCBI RefSeq, UCSC, RNAdb, lncRNAs from literatures and UCRs. Fluorescent cDNA targets were prepared using NimbleGen One-Color DNA Labeling Kit. Microarray hybridization was performed at 42°C for 16-20 hours in NimbleGen Hybridization System. After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner. Data Analysis Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The Probe level (*_norm_RMA.pair) files and Gene summary (*_RMA.calls) files were produced. The gene summary files were imported into Agilent GeneSpring Software (version 10.0) for further analysis. Differentially expressed genes and non-coding RNA were identified through Fold-change screening. Unsupervised hierarchical clustering, GO analysis and Pathway analysis was performed using the Agilent GeneSpring GX software (version 10.0).
2013-12-01 | GSE25859 | GEO
Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46607 | GEO
Project description:A collection of HEK293 SWATH-MS raw data files generated as part of the routine operation of the ProCan experimental facility. These files represent technical replicates each being an aliquot from the same pooled digest, with fifteen runs collected from each of the six Sciex Triple TOF 6600 mass spectrometers, giving a total of 90 raw data files.
2019-04-11 | PXD011093 | Pride
Project description:The transcription factor IRF4 regulates immunoglobulin class switch recombination and plasma cell differentiation. Its differing concentrations appear to regulate mutually antagonistic programs of B and plasma cell gene expression. We show IRF4 to be also required for generation of germinal center (GC) B cells. Its transient expression in vivo induced the expression of key GC genes including Bcl6 and Aicda. In contrast, sustained and higher concentrations of IRF4 promoted the generation of plasma cells while antagonizing the GC fate. IRF4 cobound with the transcription factors PU.1 or BATF to Ets or AP-1 composite motifs, associated with genes involved in B cell activation and the GC response. At higher concentrations, IRF4 binding shifted to interferon sequence response motifs; these enriched for genes involved in plasma cell differentiation. Our results support a model of "kinetic control" in which signaling-induced dynamics of IRF4 in activated B cells control their cell-fate outcomes. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46608 | GEO
Project description:Controlled dataset covering multiple passage conditions, from the genome-reduced bacterium Mycoplasma pneumoniae, to test and validate two new software tools: FASTQINS and ANUBIS. These computational tools allow the generation of insertion profile datasets from raw transposon sequencing data, detection of artifacts and to test different methodologies for essentiality estimation.
2020-08-28 | E-MTAB-8918 | biostudies-arrayexpress