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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 06, 2020 |
| Title |
RNAseq, D0, Replicate 4 |
| Sample type |
SRA |
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| Source name |
CD8+ T cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
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 |
total RNA |
| 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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 |
SAMN13581732 |
| SRA |
SRX7389147 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4221545_cDNA2412_D0-WT4_bin10_BPM.bw |
170.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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