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Status |
Public on Mar 06, 2020 |
Title |
H3K4me3 ChIPseq, D0, Replicate 1 |
Sample type |
SRA |
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Source name |
CD8+ T cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 antibody: H3K4me3 time point: D0
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Growth protocol |
Naive T cells were isolated from C57BL/6J TCR transgenic mice (OT-I) and either used non-activated (D0) or seeded in plates coated with 10μg/mL of CD3e, in the RPMI medium supplemented with 10% of FCS, rhIL-2 (40UmL), 2-mercaptoethanol, Pen-Strep, L-glutamine, non-essential amino acids and 1μg/mL of anti-CD28 antibodies
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Extracted molecule |
genomic DNA |
Extraction protocol |
For ATAC-Seq, 50 000 cells were lysed and treated with Tn Transposase, then purified using MinElute PCR purification kit (Qiagen). For ChIP-Seq, histone-DNA complexes were isolated from sonicated nuclei using bead-immobilized antibody. DNA was isolated by phenol/chloroform extraction. For RNAseq, cells were lysed in Trizol, and total RNA was isolated using Qiagen columns. RNA was treated with DNAse once on-column and once in-tube using Turbo DNAse kit (Thermo FIsher). ATAC-Seq libraries were prepared using Nextera PCR primers (Illumina). ChIP-Seq libraries were prepared using TruSeq ChIP Libary Preparation Kit (Illumina). RNAseq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase Kit (Roche/KAPA Biosystems)
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
RNAseq were aligned to the unique locations of the mouse reference genome mm10 using Tophat v2.0.6. ATAC-seq and ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.1.0 with the following configurations : Method: Global alignment - 1 mismatch in seed alignment ; Algorithm used: Choose uniquely the alignment with the best score; ATAC data were filtered using the following specifications : MAPQ30 ; ChIP data were filtered using the following specifications : MAPQ20 H3K4me3-normalized.wig files were generated using SICER version 1.1 (each with its own Input) with the following setting: windows size w = 500, gap size g = 1500, FDR = 0.05 Genome_build: mm10 Supplementary_files_format_and_content: Bigwig files were generated using Deeptools v3.1.1 : bamCoverage –normalizeUsing BPM, --binSize 10 Supplementary_files_format_and_content: H3K4me3-normalized.wig files were generated using SICER version 1.1
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Submission date |
Dec 16, 2019 |
Last update date |
Mar 07, 2020 |
Contact name |
Mengliang YE |
E-mail(s) |
mengliang.ye@curie.fr
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Organization name |
Institut Curie
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Street address |
26 Rue d'ULM
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City |
PARIS |
ZIP/Postal code |
75005 |
Country |
France |
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Platform ID |
GPL17021 |
Series (1) |
GSE142151 |
Chromatin states and transcriptome of CD8+ T cells over the course of differentiation |
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Relations |
BioSample |
SAMN13581650 |
SRA |
SRX7389135 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4221534_D0_H3K4me3_rep1-W500-normalized.wig.gz |
16.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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