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Status |
Public on Dec 20, 2019 |
Title |
RNAseq_RT4_Untreated |
Sample type |
SRA |
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Source name |
RT4
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Organism |
Homo sapiens |
Characteristics |
cell line: RT4 tissue: Human urinary bladder
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Treatment protocol |
Both BEAS-2B and RT4 cells cells were exposed to 100 μM NiCl2 for 6 weeks. Following exposure, the cells were washed and cultured in Ni‐free medium for 2 weeks to obtain Ni‐washed‐out cells. For BEAS-2B cells, following 6-week exposure, a homogenous populations of Ni-exposed cells was isolated as described. Briefly, the Ni-exposed cells were then plated in 15 cm plates at the rate of 1000, 500, 100 and 50 cells per plate in Ni-free medium. Nicely separated single colonies were randomly isolated and the populations were expanded in Ni-free medium. A randomly selected homogenous population of Ni-washed-out cells (Ni-W) in culture for >6 months post Ni exposure was used for a detailed examination.
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Growth protocol |
Human lung epithelial BEAS-2B cells (ATCC, CRL-9609) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Cellgro) supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum (FBS, Atlanta Biologicals) at 37°C and 5 % CO2. Human urinary bladder epithelial RT4 cells were cultured in McCoy's 5A Modified Medium (Life Technologies, Carlsbad, CA), supplemented with 10% FBS (Atlanta Biologicals) and 0.5% Penicillin‐Streptomycin at 37°C and 5% CO2. Human urinary bladder epithelial RT4 cells (a generous gift from Dr. Tang, New York University School of Medicine, NY) were cultured in McCoy's 5A Modified Medium (Life Technologies, Carlsbad, CA), supplemented with 10% FBS (Atlanta Biologicals) and 0.5% Penicillin‐Streptomycin at 37°C and 5% CO2. The cells were exposed to 100 μM NiCl2 for 6 weeks. Following exposure, the cells were washed and cultured in Ni‐free medium for 2 weeks to obtain Ni‐washed‐out cells.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using RNeasy Kit (Qiagen 74104). ChIP was performed using samples isolated from two biological replicates. The cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500bp fragments. ChIP was performed as described earlier using ChIP grade antibodies against H3K4me3 (Millipore, 07-473). RNA-Seq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002) according to manufacturer’s protocol. ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP -202-1024), according to manufacturer’s protocol.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
ChIP-Seq reads were aligned to the human reference genome (GRCH38/hg38) using BWA. SAM files were then converted into BAM format using samtools. Bedtools was used to convert BAM files into BED format. Only 1 copy of the redundant reads that were mapped to the exact same location in the genome was retained. All non-redundant reads from H3K4me3 ChIP-Seq datasets were included for downstream analyses without peak calling. RNA-Seq raw sequence were mapped to human genome using STAR ; multi hits removed. Gene expression levels were quantified as count, TPM and FPKM. Differential gene expression was calculated using DESeq2. Genome_build: GRCh38/hg38 Supplementary_files_format_and_content: ChIP-seq: promoter (TSS +/-2kb) RPKM, RNA-seq: gene level count, TPM, FPKM
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Submission date |
Oct 24, 2019 |
Last update date |
Dec 20, 2019 |
Contact name |
Zhenjia Wang |
Organization name |
University of Virginia
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Department |
Center for Public Health Genomics
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Street address |
1300 Jefferson Park Avenue
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City |
Charlottesville |
State/province |
VIRGINIA |
ZIP/Postal code |
22908 |
Country |
USA |
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Platform ID |
GPL16791 |
Series (2) |
GSE139355 |
Nickel induced transcriptional changes persist post exposure through epigenetic reprograming (ChIP-seq & RNA-seq datasets) |
GSE139356 |
Nickel induced transcriptional changes persist post exposure through epigenetic reprograming |
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Relations |
BioSample |
SAMN13110789 |
SRA |
SRX7052917 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4138669_Control6W_rep1_rsem.genes.results.txt.gz |
653.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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