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| Status |
Public on Jun 20, 2023 |
| Title |
HiC_PLN-CD4_HPAP-025_T1D_Rep1T |
| Sample type |
SRA |
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| Source name |
CD4+ T cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreatic Lymph Node
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| Treatment protocol |
Spleen of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning), red blood cells were depleted using ACK lysis buffer (Gibco, Invitrogen). Naive CD4+ T cells were selected using negative selection beads (StemCell, Cat# 19765). For in vitro polarization, flat bottom 96-well plates were coated with 2 mg/mL of anti-CD3 (Clone: 145-2C11, BioLegend, Cat#100302) in PBS overnight at 4°C or 4 hrs at 37°C. For Th1 polarization, naive CD4+ T cells were cultured in RPMI 1640 medium (Invitrogen), supplemented with 10% fetal bovine serum (Fisher Scientific), 1mM sodium pyruvate (Gibco), 1% non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 1% HEPES (Gibco), 1% penicillin-streptomycin and 0.1% 2-Mercaptoethanol (Gibco). For Th1 polarization, 0.2x106 naive CD4+ T cells were cultured in presence of 10 ng/mL of recombinant IL-12 (BioLegend, Cat#577002), 1 ng/mL of recombinant IL-2 (BioLegend, Cat#575402) and 1 mg/mL of soluble anti-CD28 (Clone: 37.51, BD Biosciences, Cat# 553294) for 6 days at 37°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C libraries were generated on 1×106 cells using with Arima-HiC+ kit (Arima Genomics) following manufacturer's recommendations.
Library was prepared using Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations. Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.8.1) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Valid pairs (VI), self-circle (SC) and dangling-end (DE) interactions in cis were used as input for significant interaction calling in ‘.bedpe’ format. Mango (version 1.2.0) step 4 identified putative significant interaction anchors by MACS peak calling (Zhang et al., 2008) with MACS_qvalue = 0.05 and MACS_shiftsize = 75. Mango step 5 identified significant interactions with default parameters except maxinteractingdist = 2000000 and MHT = found. In NOD mice, the BEDPE was shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910).
Assembly: GRCm38
Supplementary files format and content: hic file obtained from Juicer tools.
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| Submission date |
Aug 13, 2022 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Golnaz Vahedi |
| E-mail(s) |
vahedi@pennmedicine.upenn.edu
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| Phone |
215-898-8439
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| Organization name |
University of Pennsylvania
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| Department |
Department of Genetics
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| Lab |
Vahedi Lab
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| Street address |
421 Curie Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE211176 |
The hyperconnected 3D clique at the Ets1 locus is required for T cell function (Hi-C) |
| GSE211178 |
The hyperconnected 3D clique at the Ets1 locus is required for T cell function |
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| Relations |
| BioSample |
SAMN30303526 |
| SRA |
SRX17054090 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6454840_Arima-HiC_HPAP-025_T1D_PLN_CD4_1M_ultraDeep_200885694_S4_001_genome.bwt2pairs.validPairs.hic |
2.6 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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