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Sample GSM4138668 Query DataSets for GSM4138668
Status Public on Dec 20, 2019
Title ChIPseq_B2B_Ni_washout_input
Sample type SRA
 
Source name BEAS-2B
Organism Homo sapiens
Characteristics cell line: BEAS-2B
tissue: Human lung epithelial cell line
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.
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.
Extracted molecule genomic DNA
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Oct 24, 2019
Last update date Dec 20, 2019
Contact name Zhenjia Wang
Organization name University of Virginia
Department Center for Public Health Genomics
Street address 1300 Jefferson Park Avenue
City Charlottesville
State/province VIRGINIA
ZIP/Postal code 22908
Country USA
 
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
Relations
BioSample SAMN13110790
SRA SRX7052916

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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