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Sample GSM3534523

Query DataSets for GSM3534523

Status

Public on Jan 01, 2020

Title

HFD_RNAseq_replicate4

Sample type

SRA

Source name

liver tissue

Organism

Mus musculus

Characteristics

strain: C57BL/6
Sex: male
library type: RNA-seq,ribozero
diet: high fat diet

Treatment protocol

liver tissue was isolated from mice on the low fat diet and high fat diet

Extracted molecule

total RNA

Extraction protocol

Chip-seq libraries were prepared by Bioo NEXTflex Rapid DNA-seq Kit (cat# 514402).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

RNAseq_TPM_per_gene_DEseq2.txt.gz, RNAseq_counts_per_gene.txt.gz

Data processing

ChIP-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered reads were mapped to mm9 via Bowtie (v0.12.8) with parameters -m 1 -X 2000 --chunkmbs 1024.
Duplicate read pairs were removed via MarkDuplicates.jar from the Picard tools suite v1.110.
Uniquely-mapped non-duplicate reads were downsampled to 10 million prior to peak-calling with SICER. SICER parameters were window size 200, gap size 200, FDR 0.001 for H3K27ac.
For HNF4a and C/EBPa, peak calls was done by Homer with "- factor"
Mapped read depth files were generated by BEDtools genomeCoverageBed then by UCSC utility bedGraphToBigWig, after read pairs were converted to a single fragment by filling in region between read ends with Ns. Mapped depths are normalized to 10M uniquely-mapped non-duplicate read pairs per sample.
RNA-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered read pairs were mapped to mm9 via STAR v2.5 with the following paramters: --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000.
For each sample, counts per gene were extracted by subread featureCounts v1.5.0-p1 with parameters -s2 -Sfr -p.
HiC and capture HiC reads were processed by HiCUP (v0.6.1) to generate genomic alignments.
HiCExplorer was used to generate contact matrices (hicBuildMatrix with parameters --binSize 10000 --restrictionSequence AAGCTT --inputBufferSize 100000; then hicSumMatrices to combine replicates), normalize (hicCorrectMatrix), and call TADs (hicFindTADs).
CHiCAGO (v1.2.0) was used to process the capture HiC data and generate interaction calls; filtering was applied to require a minimum score of a 5 and maximum distance of 1Mb.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq normalized mapped read depth in bigWig format.
Supplementary_files_format_and_content: ChIP-seq peak calls in BED or txt format.
Supplementary_files_format_and_content: RNA-seq raw counts per gene per sample in tab-delimited text format.
Supplementary_files_format_and_content: HiC TADs in tab-delimited text format.
Supplementary_files_format_and_content: PCHiC interactions in tab-delimited text format.

Submission date

Dec 28, 2018

Last update date

Jan 01, 2020

Contact name

Paul A Wade

E-mail(s)

wadep2@niehs.nih.gov

Phone

919-541-3392

Organization name

NIEHS