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Sample GSM3110053

Query DataSets for GSM3110053

Status

Public on Apr 24, 2019

Title

NMuMG ATAC-seq shPBRM1 replicate 2

Sample type

SRA

Source name

NMuMG cells

Organism

Mus musculus

Characteristics

treatment: Lentiviral transfection of shPBRM1

Growth protocol

Caki1 and Caki2 cells were cultured in McCoy’s 5A supplemented with 10% FBS, 1% nonessential amino acids, and 1% L-glutamine. HK-2 cells were cultured in RPMI supplemented with 10% FBS and 1% L -glutamine. NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10 µM/mL insulin, 1% L -glutamine, and 1% sodium pyruvate. All cell lines were grown at 37°C in a humidified atmosphere in a 5% CO2 incubator.

Extracted molecule

genomic DNA

Extraction protocol

RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA for ATAC-seq was obtained according to the ENCODE ATAC-seq pipeline.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols.

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2500

Description

ATAC_NMuMG_inc_HOMER.txt
ATAC_NMuMG_dec_HOMER.txt

Data processing

RNA-seq reads were trimmed using Trimmomatic and aligned to the appropriate reference genome using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical. ATAC-seq reads were trimmed using Trimmomatic and mapped to the appropriate reference genome using Bowtie2 in very sensitive end-to-end mode.
For RNA-seq, gene expression levels were computed using htseq-count using default parameters. For ATAC-seq, BAM files were converted to BED files using BEDtools.
For RNA-seq, differential expression analysis was performed with DESeq2 using default parameters. For ATAC-seq, peaks of differential enrichment were identified using SICER-df with a false discovery rate threshold of 0.05. The annotatePeaks utility of HOMER was used to annotate statistically significant peaks.
Genome_build: hg19 for Caki1, Caki2, and HK2. mm10 for NMuMG.
Supplementary_files_format_and_content: For RNA-seq, files are tab-delimted text with the differential expression output from DESeq2. For ATAC-seq, files are tab-delimited text containing the annotated peaks obtained from HOMER.

Submission date

Apr 24, 2018

Last update date

Apr 24, 2019

Contact name

Benjamin Carter

E-mail(s)

beccarte@gmail.com

Organization name

National Institutes of Health

Department

NHLBI