Chip-seq/ATAC-seq/CUT&RUN Demo Data

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U, Rabadan R, Ghosh S. An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function. Immunity. 2017 Sep 19;47(3):450-465.e5. doi: 10.1016/j.immuni.2017.08.010. Epub 2017 Sep 7. PMID: 28889947; PMCID: PMC5679261. Library preparation and sequencing were performed by Admera Health. Library was constructed on immunoprecipitated DNA according to manufacturer’s recommendations (KAPA Hyper Prep Kit).

Leao FB, Vaughn LS, Bhatt D, Liao W, Maloney D, Carvalho BC, Oliveira L, Ghosh S, Silva AM. 2020. Toll-like Receptor (TLR)-induced Rasgef1b expression in macrophages is regulated by NF-κB through its proximal promoter. Int J Biochem Cell Biol, 127: 105840.

Library preparation and sequencing were performed by Columbia University’s JP Sulzberger Genome Center and Admera Health.

Liu J, Zhu S, Hu W, Zhao X, Shan Q, Peng W, and Xue, H. 2023. CTCF mediates CD8+ effector differentiation through dynamic redistribution and genomic reorganization. J Exp Med, 220(4): e20221288.

The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq2000 in paired read mode with the read length of 150 nucleotides at the Admera Health.

Macas J, Robledillo, LA, Kreplak J, Novak P, Koblizkova A, Vrbova I, Burstin J, and Neumann P. 2023. Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes. PLoS Genet, 19(2): e1010633.

DNA fragments were purified from the immunoprecipitated samples, and the corresponding control samples (Input; digested chromatin not subjected to immunoprecipitation) were sequenced on the Illumina platform (Admera Health, NJ, USA) in paired-end, 150 bp mode

Cvitanic MT, Vojvoda Zeljko T, Pasantes JJ, Garcia-Souto D, Grzan T, Despot-Slade E, Plohl M, and Satovic E. 2020. Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas. Genes, 11(6): 695.

Next-generation sequencing (NGS) library preparation and sequencing of one genomic DNA sample, one Input, and one ChIP sample (the first biological replicate using anti-Cg-CenH3) were performed by Admera Health facility (USA) on the Illumina HiSeqX platform, using multiplexing of the samples in a single lane.

Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U, Rabadan R, and Ghosh S. 2017. An NF-kB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function. Immunity, 47(3): 450-465.

The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq X Five/Ten sequencing systems in paired-end 150bp reads at the Admera Health.

Shan Q, Hu SS, Zhu S, Chen X, Badovinac VP, Peng W, Zang C, and Xue H. 2022. Tcf1 preprograms the mobilization of glycolysis in central memory CD8+ T cells during recall responses. Nat Immunol, 23(3): 386-398.

The libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides at the Admera Health.