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Sample GSM2187266 Query DataSets for GSM2187266
Status Public on Jul 28, 2016
Title shJARID1D_RNA-Seq_rep2
Sample type SRA
Source name DU145 cells, shJARID1D
Organism Homo sapiens
Characteristics cell line: DU145
cell type: prostate cancer cell line
tissue derivation: prostate; derived from brain metastatic site
treatment: shJARID1D
chip antibody: None
Treatment protocol JARID1D knockdown DU145 cells.
Growth protocol DU145 were cultured in High Glucose Dulbecco's Modified Eagle's Medium supplemented with L-glutamine, sodium bicarbonate, pyridoxine.HCI, sodium pyruvate and 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using RNeasy kits (Qiagen), which were used for RNA-seq experiments.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Processed data file: genes.count_tracking.txt
Data processing Illumina Casava1.7 software used for basecalling.
Total read numbers of ChIP-Seq samples without spike-in control are normalized to be 25 million, and ChIP-Seq samples with spiked-in Control are normalized according to the number of spiked-in Drosophila melanogaster chromatin.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with parameters -p 8 -m 1 --chunkmbs 512 --best
ChIP-Seq peaks were called using DANPOS2 v2.2.2 with the following parameters: --smooth_width 0 -e 1 --frsz 200 --extend 200 --pheight 1e-50 --extend_pheight 1e-20
RNA-Seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome assembly using tophat v2.0.12 with parameters --mate-std-dev 200 -p 8 -r 203
The number of fragments that originated from each gene in each sample is estimated using cuffdiff with default parameters. Then, the differentially expressed genes based on read counts are inferred using edgeR R package v3.12.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text file (genes.count_tracking.txt) includes raw counts of reads, RPKM values for each gene of each sample.
Supplementary_files_format_and_content: For ChIP-Seq data, wig files showing the average signal density across genome are generated using DANPOS2 v2.2.2.
Submission date Jun 03, 2016
Last update date May 15, 2019
Contact name JIE Lv
Organization name St Jude Children's Research Hospital
Department Department of Computational Biology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
Platform ID GPL21290
Series (1)
GSE82260 ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes
BioSample SAMN05204096
SRA SRX1819634

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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