5e837900-9338-44f3-b664-c09ad24f9ec7 - samples
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ABSTRACT:
PROVIDER: EGAD00001005225 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format
2016-03-31 | GSE67441 | GEO
Project description:Purpose: To compare the transcriptomes of HCC1937 vector and wtBRCA1 cells which were treated with OTX-015. Methods: HCC1937 vector and wtBRCA1 cells were treated with 5 micromolar OTX-015 for 24 hours. Total RNA was extracted and processed with NEBNext Ultra Directional RNA Library Prep Kit for cDNA library preparation. The data are in duplicate and raw data were generated by Illumina 2500 sequencer. The Fastq format data were then processed with Tophat for genome mapping. After getting the bam files, they were further analyzed with cuffdiff for gene expression of different groups. Results: From the transcriotome profiling and analysis, we got gene expression data of DMSO control group and OTX-015 treatment group for the HCC1937 BRCA1 isogenic cell lines. Conclusion: The gene expression data revealed the transcriptome variation by OTX-015 treatment.
2019-01-30 | GSE109809 | GEO
Project description:E15.5 embryos were micro-disscted from Gata4 G295S mutant mice and littermate controls, RNA was isolated using Norgen total RNA isolation, and libraries were generated with the RNA TruSeq Stranded Total RNA kit. 50 base pair paired end reads were obtained on an illumina high seq 2500. Fastq files were aligned to the mouse genome using STAR aligner. QC was performed using RNASeQC and RSeQC. BAM files were processed using cufflinks pipeline.
2019-05-17 | GSE117621 | GEO
Project description:This submission contains the data from https://www.biorxiv.org/content/10.1101/795047v2.full This dataset contains processed data of cell-free reduced representation bisulfite sequencing from 60 pediatric cancer samples, in order to classify them according to histopathological diagnosis. Files are provided in bismark coverage format. Samples were sequenced on a NextSeq 500.
2020-02-27 | E-MTAB-8770 | biostudies-arrayexpress
Project description:This is a Phase II study of combined surgical resection for patients with both intra- and extra-hepatic metastases from colorectal cancer. The primary objective is to determine the two-year disease free survival (DFS) of patients who undergo surgical resection of both intra- and extra-hepatic metastases from colorectal cancer. The secondary objectives are to determine the overall survival rate (OS), patterns of treatment failure, treatment efficacy (R0 resection rate), peri-operative morbidity and mortality rates, health related quality of life, and hospital length of stay.
| 2049976 | ecrin-mdr-crc
Project description:This dataset contains microarray data from normal controls (aged 20-99 yrs) and Alzheimer's disease cases, from 4 brain regions: hippocampus, entorhinal cortex, superior frontal cortex, post-central gyrus. Changes in expression of synaptic and immune related genes were analyzed, investigating age-related changes and AD-related changes, and region-specific patterns of change. These AD cases were processed simultaneously with the control cases (young and aged) included in GSE11882 (GSE11882 dataset contains data exclusively from normal control brains).
2014-04-21 | GSE48350 | GEO
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:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format Validating an algorithm called SRiD that generates random DNA barcodes that do not match a genome of interest, in this case human genome. 20 DNA barcodes were used for this validation.
2016-03-31 | E-GEOD-67441 | biostudies-arrayexpress
Project description:We report on genetic and functional data from an asymptomatic female with a large deletion on the X-chromosome. Blood RNA samples from individual II.3 and an age and sex-matched control were analyzed by RNA-Seq in Illumina platform. Total RNA was purified using poly-T oligo-attached magnetic beads with rRNA removal. The resulting directional RNA-Seq NEB libraries were sequenced in paired-end format. Image analysis and per-cycle base calling were performed with Illumina Real-Time Analysis software (RTA1.9). Conversion to FastQ read format was obtained by CASAVA-1.8 and sequenced reads were quality-checked with FastQC. Sequence adaptors were removed with cutadapt v1.2.1, and reads were aligned to the human reference genome (GRCh37/hg19) with STAR. BAM files were visualized by using the Integrative Genomics Viewer. The quantification of reads were obtained by HTSeq v0.6.1. Transcriptome-wide analysis in individual II.3 uncovered 1,026 differentially blood-expressed genes, as compared with the matched control sample. From the 598 RefSeq genes mapping within the X-chromosome deletion, 241 genes were expressed on blood. From these, 117 transcripts have more than ten counts in at least in one of the samples (individual II.3 or control). Only three genes within the deletion (GPR112, SLC6A8 and, FUNDC2) showed statically significant adjusted p-values and |log2(FoldChange)|.Our data suggest that a protective gene-by-gene mechanism occurs at the transcriptional level in the active X chromosome to counterbalance detrimental effects of large Xq deletions.
2020-03-09 | GSE141766 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below GSE248280 contains ChIP-Seq input (IN) and IP (IP) data. GSE248281 contains micro-C in the mcool format. N1 and N2 represent repeats 1 and 2. For ChIP, Merged represent the Merged IP Merged mcool files are in supplementary files of the serie GSE248280
2024-08-04 | GSE248282 | GEO