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| Status |
Public on May 15, 2018 |
| Title |
WT_E10.0_CHD4_ChIP_Rep2 |
| Sample type |
SRA |
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| Source name |
E10.0 cardiac tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
genotype: WT
development stage: Embryonic day 10.0
tissue: cardiac
chip antibody: Anti-CHD4 antibody [3F2/4] - ChIP Grade, Abcam, catalog# ab70469, mouse monoclonal
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic hearts were collected in PBS, fixed and DNA was isolated for ChIP-seq according to methods in [Wilczewski et. Al, 2017].
Libraries were prepared using the Nextera XT DNA Library Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA fastq files were first filtered for reads containing adapter sequences using TagDust (v1.12) with and FDR of 0.001. Reads were then mapped to the mm10 genome using Bowtie (v1.2.0) and options: -m 1, --best, --seed=123, and --nomaqround. Post-alignment, samtools (v1.6) and BedTools (v2.25.0) were used to interconvert and manipulate files. HTSeq (v0.6.2), using the refFlat gtf from UCSC Genome Browser, was run to get read counts over genes and these counts were used in DESeq2 (v1.6.3) to determine differential transcripts.
ChIP fastq files were first filtered for reads containing adapter sequences using TagDust (v1.12) with and FDR of 0.001. In-house scripts were used to ensure TagDust filtered reads were maintained in the proper order for alignment. Reads were then mapped to the mm10 genome using Bowtie (v1.2.0) using options: -m 1, --best, --seed=123, --nomaqround. Aligned fragments were then filtered for any duplicate reads based on alignment position using in-house scripts. Samtools (v1.6) and BedTools (v2.25.0) were used to interconvert and manipulate files. Peaks were called with MACS2, and only high confidence peaks (found in at least two of the three replicates) were used in downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files contain genomic signal tracks, normalized by total read depth per million. Duplicate and unproperly paired (for paired-end) reads have been filtered out. Bed files contain peaks called by MACS2 between the control sample as its relative input sample. The combined bed contains the merged collection of peaks that were found in at least 2 of 3 replicates. DESeq2 files contain the differentially expressed genes between Chd4(flox/flox) and Chd4(Δflox/Δflox) cardiac tissues for each timepoint (E9.5 and E10.5). RPKM files contain a tab-delimited matrix of all calculated RPKMs for each gene in each RNA timepoint.
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| Submission date |
Jan 10, 2018 |
| Last update date |
May 17, 2018 |
| Contact name |
Austin J Hepperla |
| E-mail(s) |
hepperla@unc.edu
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Genetics
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| Street address |
7018B Mary Ellen Jones Building
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE109012 |
CHD4 and the NuRD complex directly control cardiac sarcomere formation |
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| Relations |
| BioSample |
SAMN08345882 |
| SRA |
SRX3548188 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2927993_CHD4_Rep2_clean_sync_filt_nameSorted_dupsRemoved_normalized.bw |
964.6 Mb |
(ftp)(http) |
BW |
| GSM2927993_CHD4_Rep2_clean_sync_filt_peaks.bed.gz |
741.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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