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| Status |
Public on May 15, 2024 |
| Title |
3_LNA_2_24h_rep1_S3_LANE1 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: CD4+ T cells
genotype: LIRIL2R LNA2
treatment: Activated under iTreg condition for 24 hours
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| Treatment protocol |
For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above
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| Growth protocol |
Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D). CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated, and the libraries were prepared using Nextera DNA library preparation kit with i7 and i5 indices (15028212). AMPURE-XP beads (B46053, Beckman Coulter) were used to purify the libraries.
All samples were pooled into one pool and sequenced on two lanes.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Read quality-check and adapter trimming was performed using FastQC (v.0.11.4) (17) and TrimGalore (v. 0.4.5) (https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/), respectively.
The trimmed reads were mapped to the hg38 reference genome using Bowtie2 (v. 2.3.3.1) (23).
Open chromatin regions were identified and quantified using the peak caller MACS2 (v. 2.1.0) (24). MACS2 quantifies the peak signal by calculating a fold enrichment value for the peak summit. against random Poisson distribution with local lambda, which is a dynamic parameter defined for each candidate peak. Local lambda captures the influence of local biases and is robust against occasional low read counts at small local regions.
The regions were annotated using HOMER (v.4.9)
Assembly: hg38
Supplementary files format and content: bigwig and narrow peak
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| Submission date |
Dec 26, 2022 |
| Last update date |
May 15, 2024 |
| Contact name |
Riitta Lahesmaa |
| E-mail(s) |
rilahes@utu.fi
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| Organization name |
University of Turku
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| Department |
Turku Bioscience
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| Lab |
Lahesmaa lab
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| Street address |
Tykistökatu 6A
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| City |
Turku |
| ZIP/Postal code |
20520 |
| Country |
Finland |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE221756 |
Chromatin Accessibility Analysis of LIRIL2R-Deficient and LIRIL2R-Sufficient Induced Regulatory T Cells |
| GSE221759 |
Long Noncoding RNA LIRIL2R Modulates FOXP3 Levels and Suppressive Function of Human CD4+ Regulatory T Cells by Regulating IL2RA |
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| Relations |
| BioSample |
SAMN32409446 |
| SRA |
SRX18851179 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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