Comment[GEAAccession] E-GEAD-397 MAGE-TAB Version 1.1 Investigation Title Count table of ImmuNexUT Experiment Description RNA-sequencing count table of 28 immune cell subsets from the ImmuNexUT cohort. Immune cell subsets were sorted by flow cytometry. Neutrophils were isolated by MACS. Libraries were prepared using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa), Prepared libraries were sequenced on HiSeq2500 (Illumina) to generate 100bp paired-end reads. Experimental Design case control design translational bias design all pairs Experimental Factor Name disease Experimental Factor Type disease Person Last Name Nagafuchi Person First Name Yasuo Person Affiliation Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo Person Roles submitter Public Release Date 2021-04-30 Publication DOI https://doi.org/10.1016/j.cell.2021.03.056 Protocol Name P-GEAD-648 P-GEAD-649 P-GEAD-650 P-GEAD-651 P-GEAD-652 P-GEAD-653 Protocol Type sample collection protocol nucleic acid extraction protocol nucleic acid labeling protocol nucleic acid hybridization to array protocol array scanning and feature extraction protocol normalization data transformation protocol Protocol Description Various immune cell subsets from 416 ImmunexUT cohort were collected(Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu). Total RNA was extracted using RNeasy Micro Kits (Qiagen) or MagMAX-96 Total RNA Isolation Kits. Libraries for RNA-seq were prepared using SMART-seq v4 Ultra Low Input RNA Kit (Takara). dummy protocol nucleic acid sequencing protocol; Libraries were sequenced on the HiSeq 2500 Illumina platform to obtain 100-bp paired-end reads with HiSeq SBS Kit v4 (Illumina). dummy protocol From sequenced reads, adaptor sequences were trimmed using cutadapt. In addition, 3- ends with low-quality bases (Phred quality score < 20) were trimmed using the fastx-toolkit. Reads containing more than 20% low-quality bases were removed. Subsequently, reads were aligned against the GRCh38 reference sequence using STAR. We excluded samples with uniquely mapped read rates < 90% (with the exception of < 70% for plasmablasts and <85% for the other B cell subsets) or unique read counts < 6 x 10^6. Expression was quantified using HTSeq. For QC of the expression data, in each cell population, we filtered low count genes (< 10 in > 91% of samples), normalized between samples with a trimmed mean of M values implemented in edgeR software, converted to log-transformed count per million, removed batch effects using ComBat software and computed inter-sample Spearman correlations of expression levels between each sample and the remaining samples from the same cell subset. SDRF File E-GEAD-397.sdrf.txt Comment[Number of channel] single-channel Comment[Array Design REF] A-GEAD-11 Comment[AEExperimentType] transcription profiling by array Comment[BioProject] PRJDB10691 Comment[Last Update Date] 2021-05-13