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| Status |
Public on Nov 30, 2015 |
| Title |
WT_ESC_DNaseI_R2 |
| Sample type |
SRA |
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| Source name |
WT embryonic stem cells, DNaseI
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell type: embryonic stem cell line
genotype/variation: WT
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| Growth protocol |
Wild-type ES cell line was derived from littermate male blastocysts produced from matings of N7 backcrossed C57BL/6 triple heterozygous H1 mutant parents. The transgenic lines are further described in Fan et al. Cell 2005 (PMID 16377562).
WT and H1 TKO ES cells were grown on irradiated mouse embryonic fibroblasts in DMEM (high glucose, Gibco) with 15% FBS, 1x non-essential amino acids (NEAA; Gibco), 1x penicillin–streptomycin (Gibco), 1:1,000 b-mercaptoethanol (Invitrogen), 1x L-glutamine (Gibco) and 1,000 U/ml leukaemia inhibitory factor (LIF; Gibco).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
TruSeq DNA sample preparation kit (Illumina).
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Hi-C : Reads from both ends were mapped separately single end with bwa aln with default parameters. Uniquely mapped reads were sorted and paired by read ID using samtools. Mapped pairs were filtered to remove reads coming from the same or neighboring restriction fragments. Filtered pairs were deduplicated to remove PCR duplicates and valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files.
DNase Hypersensitivity : Aligned reads in bam files are those 36bp reads that aligned uniquely (Bowtie) to the reference (NCBI37/mm9) and contain no more than 2 mismatches. DNaseI-sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004).
DNA methylation HELP tagging data was processed with the WASP pipeline (version 3.0.31 (rev. 3822). Reads were aligned with Illumina's CASAVA and ELAND v. 1.7.0 allowing 2 mismatches in the first 32bp and no more than 10 alignments for each read. HELP angles were computed as described in (Suzuki et al. 2010).
RNA-Seq : We aligned 2x100 paired-end reads of 2 replicate WT ESC RNA-seq libraries and 3 replicate H1 TKO ESC RNA-seq libraries to the reference genome (NCBI37/mm9) with TopHat and used Cufflinks and CuffDiff for differential expression analysis of RNA-seq expression for a non-redundant collection of 20876 known RefSeq transcripts. We considered genes with a marginal p-value smaller than 0.05 and an absolute log2 fold-change bigger than 1 to be differentially expressed.
ChIP-Seq : Reads from all different libraries were aligned to the reference genome (NCBI37/mm9) with bowtie2 with default settings and the --qc-filter switch. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/) and were removed from the data for subsequent analyses. Regions significantly enriched for H3K4me1, H3K4me3, H3K27me3 and H3K9me3 compared to matched input samples were identified using the MACS2 peak caller with default settings. For the H3K9me3 and H3K27me3 histone marks, the parameter - - broad was set. Analysis of differential ChIP enrichment was done using diffReps with parameters -me gt –pval 0.001 --frag 150.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files; ChIP-Seq peaks called by MACS2 are in peaks.bed.gz files; DNaseI-hypersensitive sites called with the HOTSPOT algorithm in mm9.bed.gz files; DNA methylation HELP angles are in HELP.txt.gz file; RNA-Seq FPKM values are in FPKM.txt.gz file.
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| Submission date |
Nov 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Geert Geeven |
| E-mail(s) |
geertgeeven@yahoo.com
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| Organization name |
Hubrecht Institute
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| Department |
Biomedical Genomics
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| Lab |
Wouter de Laat
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE75426 |
Local compartment changes and regulatory landscape alterations in histone H1-depleted cells |
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| Relations |
| BioSample |
SAMN04296655 |
| SRA |
SRX1452764 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1954932_WT_ESC_DNaseI_R2_hotspot.twopass.mm9.bed.gz |
3.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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