title: 11_OC43_3hpi_rep2


title: F8Exon16C321A_B_DMSO_S26

status: Public on Jan 17 2024

type: SRA

city: Santa Cruz

first: Guillermo

middle: A

last: Chacaltana

state: CA

address: 1156 High Street

department: Chemistry

country: USA

institute: University of California, Santa Cruz

library_source: transcriptomic

data_processing:
Paired-end reads were mapped onto reference sequence using rf-map module from RNA-FRAMEWORK V.2.8.2 (modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data)
Mutation counts were then counted using rf-count module on RNA-FRAMEWORK
Resulting mutation count files were normalized using rf-norm module on RNA-FRAMEWORK
Final .txt output files were then supplied to rf-fold module on RNA-FRAMEWORK to drive structural predictions
Supplementary files format and content: Processed .txt data files contain normalization parameters used in rf-norm, reference sequence used as a reference for each read used to obtain mutational counts, and reactivity values computed for each nucleotide position on the reference sequence
Assembly: reference_sequence.txt

molecule: total RNA

organism: Homo sapiens

extract_protocol:
in vitro transcribed RNA was first synthesized and PAGE purified prior to modification with 2A3 and then reverse transcribed. Resulting cDNA was used as input material for library assembly.
RNA is first modified with 2A3 or treated with DMSO control, then fragmented to a median length of 150nt. The fragmented material is used as input for a random hexamer reverse transcription reaction, afterwhich the resulting cDNA is used as starting material for NEBNext Ultra II DNA library prep kit for Illumina.
2'-hydroxyl acylation analyzed by primer extension (SHAPE) Mutational Profiling via High Throughput Sequencing (MaP-seq).

tag: tissue

tag: genotype

tag: treatment

value: SHAPE probed

tag: molecule subtype

value: IVT RNA


title: N2 wild-type, Acetobacter tropicalis, biol rep 1

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

description:
Column_names: op50_r1, op50_r2, op50_r3, ht115_r1, ht115_r2, ht115_r3, acetob_r1, acetob_r2, acetob_r3, komb_1g_r1, komb_1g_r2, komb_1g_r3, komb_5g_r1, komb_5g_r2, komb_5g_r3, komb_mix_r1, komb_mix_r2, komb_mix_r3
raw_gene_read_counts.txt
DESeq2_norm_gene_counts.txt
DESeq2_DEGs_acetob_v_op50.txt

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -p -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Differential expression was calculated relative to the E. coli OP50 sample using the DESeq2 package using a 1% FDR cutoff (Love et al., 2014).
Assembly: WS260
Supplementary files format and content: raw_gene_read_counts.txt: A tab-delimited text file that includes gene level unnormalized read counts for each sample in matrix format
Supplementary files format and content: DESeq2_norm_gene_counts.txt: A tab-delimited text file that includes gene level normalized read counts for each sample in matrix format
Supplementary files format and content: DESeq2_DEGs_sample_v_op50.txt: A tab-delimited text file that includes a list of differentially expressed genes, the log2 FC values, and the p values called by DESeq2 at a 1% FDR threshold for each sample relative to the OP50 sample.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: C. elegans N2 wild-type L1 animals were synchronized by egg prep and grown at 20°C on 10cm NGM Agarose plates (1000 animals/plate) seeded with either E. coli OP50, E. coli HT115, Acetobacter tropicalis, or Kombucha-associated microbes for ~72 hours when they reached day 1 of adulthood.

extract_protocol:
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.
mRNA-Seq libraries were prepared by Novogene Inc.

treatment_protocol: The individual microbes were cultured at 25°C, concentrated by centrifugation, plated on NGM Agarose plates, and incubated at room temperature for 4 days before dropping animals on the lawn.

tag: strain

value: wild-type

value: fed Acetobacter tropicalis

tag: developmental stage

value: Day 1 adults

value: Whole animals

tag: sample type

value: Hermaphrodites


title: Control6_scRNAseq

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

description: processed data files include count matrix, metadata and umap files

library_source: transcriptomic single cell

data_processing:
RNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
RNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
RNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
RNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
RNA-Seq: The output files for 29 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
RNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 50%.
Assembly: RNA-Seq: GRCh38
Supplementary files format and content: scRNA-Seq: EXPORT_scRNAseq_counts.rds: combined count matrix of all 11 samples; EXPORT_snRNAseq_metadata.txt: combined metadata; EXPORT_snRNAseq_umap.txt: UMAP embedding values for identified cell types.
scRNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
scRNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
scRNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
scRNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
scRNA-Seq: The output files for 11 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Assembly: scRNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 15%.
Supplementary files format and content: scRNA-Seq: GRCh38
ATAC-Seq: Cell Ranger ATAC v. 2.0.0 (http://10xgenomics.com) was used to process Chromium single cell ATAC-seq output.
ATAC-Seq: The poor quality cells were removed from the matrix using the following criteria: peak_region_fragments < 3000 & peak_region_fragments > 20000 & pct_reads_in_peaks < 15 & nucleosome_signal > 4 & TSS.enrichment > 2
ATAC-Seq: The output files for 20 samples were aggregated into one matrix using Signac v. 1.3.0.
Assembly: ATAC-Seq: GRCh38
Spatial Transcriptomics: Space Ranger v1.0.0 (http://10xgenomics.com) was used to process Human FFPE Visium output
Spatial Transcriptomics: “spaceranger count” aligned thedata to the human reference genome (GRCh38) by using the human probe dataset (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38) and data mapped to the H & E stained image.
Spatial Transcriptomics: Aligned data was loaded to Seurat object (Seurat . 4.0.1) and normalized by using SCT.
Spatial Transcriptomics: The objects of 7 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Spatial Transcriptomics: The samples were merged together, using “merge” function of Seurat.  Next, the data was subjected to principle component analysis (PCA) for linear dimension reduction and Harmony was used to integrate the datasets.
Assembly: Spatial Transcriptomics: GRCh38
Supplementary files format and content: EXPORT_ST_counts.rds: combined count matrix of all 7 samples; EXPORT_ST_metadata.txt: combined metadata; EXPORT_ST_umap.txt: UMAP embedding values for identified cell types.

source_name: whole kidney tissue

extract_protocol:
RNA-Seq: 10X Genomics Chromium Prep (10X Genomics, PN-1000120). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
RNA-Seq: The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s original protocol.
ATAC-Seq: Chromium Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000110). Transposing and barcoding were performed according to the manufacturer's instructions.
ATAC-Seq: The libraries were constructed using the Chromium Single Cell ATAC Library & Gel Bead Kit and Chromium i7 Multiplex Kit N (10X Genomics, PN-1000084) according to the manufacturer’s original protocol.
Spatial Transcriptomics: 5 µm tissue samples was cut and onto the Visium Spatial gene Expression Slide. After deparaffinization, H & E staining was performed. Keyence 1266 BZ-X810 microscope was used for whole slide imaging.
Spatial Transcriptomics: After scanning, de-crosslinking, probe hybridization, probe release and extension, library preparation was performed by single Index Kit TS Set A (10X Genomics, PN-3000511) according to the manufacturer’s protocol.

tag: disease

value: Control

value: adult kidney

tag: age

tag: gender

value: Female


title: F8Exon16C321A_A_2A3_S27


title: Control5_scRNAseq

value: Male


title: N2 wild-type, E. coli HT115, biol rep 3

description:
Column_names: op50_r1, op50_r2, op50_r3, ht115_r1, ht115_r2, ht115_r3, acetob_r1, acetob_r2, acetob_r3, komb_1g_r1, komb_1g_r2, komb_1g_r3, komb_5g_r1, komb_5g_r2, komb_5g_r3, komb_mix_r1, komb_mix_r2, komb_mix_r3
raw_gene_read_counts.txt
DESeq2_norm_gene_counts.txt
DESeq2_DEGs_ht115_v_op50.txt

value: fed E. coli Ht115


title: Disease13_scRNAseq

value: HKD


title: N2 wild-type, E. coli HT115, biol rep 2


title: F8Exon16C321A_A_DMSO_S25


title: 10_OC43_1.5hpi_rep2

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads were aligned to a contacenated human (ENSEMBL hg38-101) and viral (ATCC_VR_1558) genome: STAR --genomeDir human_OC43_full_index --genomeLoad LoadAndRemove --readFilesIn file_R1.fastq file_R2.fastq
SAM to BAM: samtools view -bS file.sam
BAM sorting: samtools sort file.bam
BAM indexing: samtools index -b file.bam
Coverage map (+strand). Command: bamCoverage -b file.bam --binSize 1 --ignoreForNormalization HCoV_OC43 --exactScaling --filterRNAstrand forward --normalizeUsing CPM
Coverage map (-strand). Command: bamCoverage -b file.bam --binSize 1 --ignoreForNormalization HCoV_OC43 --exactScaling --filterRNAstrand reverse --normalizeUsing CPM
Assembly: ENSEMBL hg38-101 and ATCC_VR_1558
Supplementary files format and content: RNA coverage maps across the human and OC43 genomes

source_name: human cells infected with HCoV-OC43

growth_protocol: MRC5 cells were grown on 6-well plates at 33°C and infected with either HCoV-OC43 at a MOI of 7. As a control, cells were alternatively infected with heat-inactivated OC43.

extract_protocol:
Cells were harvested using 1mL Tri Reagent, and RNA was extracted according to the manufacturer's protocol.
Following RNA extraction, 3µg of RNA was treated with Turbo DNase. The resulting RNA was ribodepleted using the NEBNext rRNA Depletion Kit. Libraries were prepared using the NEBNext rRNA Depletion Kit for Human/Mouse/Rat .

tag: cell line

value: wild type

tag: infection

tag: timepoint (hr)

tag: translation inhibitor

tag: fraction

value: ribodepleted RNA


title: Control4_scRNAseq


title: F8Exon16C179T_B_2A3_S12


title: N2 wild-type, E. coli HT115, biol rep 1


title: 09_uninfected_rep2

source_name: human cells


title: N2 wild-type, E. coli OP50, biol rep 3

description:
Column_names: op50_r1, op50_r2, op50_r3, ht115_r1, ht115_r2, ht115_r3, acetob_r1, acetob_r2, acetob_r3, komb_1g_r1, komb_1g_r2, komb_1g_r3, komb_5g_r1, komb_5g_r2, komb_5g_r3, komb_mix_r1, komb_mix_r2, komb_mix_r3
raw_gene_read_counts.txt
DESeq2_norm_gene_counts.txt

value: fed E. coli OP50


title: 08_OC43_30hpi_rep1


title: Control3_scRNAseq


title: Disease9_scRNAseq


title: 07_OC43_24hpi_rep1


title: F8Exon16C179T_A_DMSO_S9


title: Disease10_scRNAseq


title: F8Exon16C179T_A_2A3_S11


title: N2 wild-type, E. coli OP50, biol rep 2


title: 06_OC43_18hpi_rep1


title: Control7_scRNAseq


title: N2 wild-type, E. coli OP50, biol rep 1


title: Disease8_scRNAseq

value: DKD


title: N2 pri-1 RNAi rep3

city: Vancouver

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

country: Canada

institute: UBC

description:
Sex: hermaphrodite
WP4_S149

data_processing:
Each RNA library was sequenced across 2 lanes of the flow cell. The two resulting raw read files for each library were concatenated at the begginning of analyses.
Reads were trimmed for adapter sequence / low quality using trimmomatic ver 0.36 (parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Trimed sequence reads were quantified to the C. elegans transcriptome using Salmon Ver 1.4.0 (parameters -l A -p 8 --gcBias --validateMappings)
Transcript-level read counts were imported into R and summed into gene-level read counts using tximport
Genes not expressed at a level greater than 10 reads in at least three of the samples were excluded from further analysis. Differential expression analysis was performed quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR  ver 3.32.1
Assembly: C. elegans Ensembl transcriptome build WBcel235
Supplementary files format and content: Comma seperated value sheet containing CPM for all genes in WBcel235 for all conditions and repeats.

source_name: embryos

growth_protocol: Synchronized L1 N2 worm populations fed EV or pri-1 RNAi were grown for 96 hours at 20oC and allowed to lay eggs. Plates were washed with M9 twice to removed adults and hatched worms before harvesting eggs using a cell scraper. The collected eggs were washed twice with M9 to remove bacteria, and then flash-frozen in an ethanol/dry ice bath.

extract_protocol:
For total RNA extraction, eggs were thawed in Trizol and sonicated. Total RNA was extracted from the mixture using a Trizol and 1-bromo-3-chloropropane extraction, as described (PMID 35285794). RNA integrity and quantity were assessed on an Agilent Technologies 2100 Bioanalyzer System.
Library preparation and sequencing was performed by The Center for Applied Genomics, SickKids (Toronto, ON; http://www.tcag.ca). Briefly, RNA was prepared for sequencing using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760). Sequencing was performed on an Ilumina NovaSeq 6000 equipped with an S4 flow cell generating 150bp paired-end reads.

value: embryos

value: Wild type (strain N2)

value: pri-1 RNAi


title: 05_OC43_12hpi_rep1


title: N2 pri-1 RNAi rep2

description:
Sex: hermaphrodite
WP3_S141


title: Disease6_scRNAseq


title: 03_OC43_6hpi_rep1


title: F8Exon16A333G_Cofold_B_DMSO_S16

value: SHAPE probed

value: IVT RNA


title: 04_OC43_9hpi_rep1


title: Disease5_scRNAseq


title: 02_OC43_3hpi_rep1


title: Disease7_scRNAseq


title: N2 pri-1 RNAi rep1

description:
Sex: hermaphrodite
WP1_S125


title: F8Exon16A333G_Cofold_A_DMSO_S15


title: F8Exon16C179T_B_DMSO_S10


title: Disease4_scRNAseq


title: F8Exon16A333G_Cofold_A_2A3_S13


title: F8Exon16A333G_ASOCOMBO_B_2A3_S16


title: N2 EV RNAi rep3

description:
Sex: hermaphrodite
WE3_S140

value: Empty vector (EV) RNAi


title: 01_uninfected_rep1


title: N2 EV RNAi rep2

description:
Sex: hermaphrodite
WE2_S132


title: Disease3_scRNAseq


title: F8Exon16A333G_ASOCOMBO_B_DMSO_S15


title: F8Exon16A333G_Cofold_B_2A3_S14


title: HSB2341_BA4_NeuN-Ab_pos_SATB2-Ab_plusplus_fansExpID-867

city: New York

first: Christina

last: Pressl

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
The snRNAseq raw data was processed using the count function in Cell Ranger (10X Genomics, version 6.0). Reads were aligned to the human genome (hg38) and including the intron regions, genes were mapped and counted in each nucleus. Counting matrices were generated in Cell Ranger and utilized in downstream analyses. Data was read into R and further processed using Seurat algorithms as well as other Bioconductor packages and custom code.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: raw and filtered feature, barcode, and matrix files

molecule: nuclear RNA

source_name: Cortex BA4

extract_protocol:
Nuclei were loaded and processed on the 10X platform for snRNAseq. 1000121 Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, 16 rxns, 1000215 Dual Index Kit TT Set A 96 rxns, and Chromium Single Cell Controller were used.
snRNA/scRNA-seq

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human cortex, labeled with cell type-specific probes and separated by FACS as described by Pressl et al 2023.

value: Cortex BA4

tag: cell type

value: Nuclei from Mixed Neuronal Populations

tag: sort-gate

value: NeuNpos SATB2plus

tag: donor

tag: Sex

value: F

tag: pmi (hrs)

tag: donor category

value: HD


title: Disease2_scRNAseq

tag: tissue

value: adult kidney

value: Female


title: HCTSU_BA4_NeuN-Ab_pos_SATB2-Ab_plusplus_fansExpID-866

value: HCTSU

value: CTRL


title: F8Exon16A333G_ASOCOMBO_A_2A3_S14

tag: genotype

tag: treatment

tag: molecule subtype


title: C4-2 cells, CDK12KO3

city: Shenzhen

first: Haozhe

last: Zhang

state: Guangdong

address: No.1088 Xueyuan Avenue

department: Department of biochemistry

country: China

institute: Southern University of Science and Technology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ )
Trimmed sequence reads were mapped to GRCH38 using STAR2.7.11a (Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635)
Tab-delimited text file includes raw counts for each Sample tab-delimited text files include Counts values for each Sample
Assembly: GRCH38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: Human prostate tumor

growth_protocol: C4-2 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), and 1 ug of total RNA was used to construct sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol: No treatment.

value: Human prostate tumor

value: Human prostate cancer epithelial-like cells

value: CDK12 knockout


title: F8Exon16A333G_ASOCOMBO_A_DMSO_S13


title: Control1_scRNAseq

tag: disease

value: Control

tag: age


title: Control2_scRNAseq

tag: gender


title: C4-2 cells, CDK12KO2

tag: cell line


title: C4-2 cells, CDK12KO1


title: WT-RBG-R, Right Wilms tumor

city: Nanjing

first: Mingshun

state: Jiangsu

address: 101 Longmian Road

institute: Nanjing Medical University

description: 10x Genomics

data_processing:
Raw reads were processed to generate mRNA profiles using an internal celescope1.3.0 pipeline.
Assembly: GRCH38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
The single cells from each tissue sample were acquired by GEXSCOPE™ Tissue Dissociation kit (Singleron Biotechnologies, Nanjing, China). A microfluidic chip was loaded with the single-cell suspension.
Guided by manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies), the single cell RNA-seq libraries were prepared. Sequencing was performed on an Illumina HiSeq X10 instrument with 150-bp paired-end reads.

value: tumor tissue

value: kidney

value: 6 months old


title: WT-RBG-N, Normal Kidney tissue

description: 10x Genomics

value: kidney tissue


title: F8Exon16A333G_B_2A3_S32

value: SHAPE probed

value: IVT RNA


title: C4-2 cells, VEC3

value: WT


title: Disease1_scRNAseq

value: DKD


title: F8Exon16A333G_A_2A3_S31


title: FLASH HSPA8 rep2

city: Cambridge

first: Andrés

middle: Manuel

last: Herrero-Ruiz

address: Gleeson Building, Tennis Court Road

department: MRC Toxicology Unit

institute: MRC-University of Cambridge

data_processing:
Demultiplexing (flexbar, version 3.3) and UMI trimming and header labelling (UMITools, Version 0.5.1)
Adapter trimming, quality control and demultiplexing barcodes (only R2) (trim_galore (Version 0.4.4) --stringency 3 -q 30 --paired --retain_unpaired -r1 15 -r2 15 --fastqc --three_prime_clip_R2 13 --length 14 --clip_R1 6 )
Paired-end reads were merged using bbmerge from bbmap (Version 37.54)
Genome alignment, allowing up to 1000 mapping locations (STAR (Version 2.6.0b) --outFilterMultimapNmax 150  --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --alignEndsType EndToEnd --alignIntronMax 100000)
Duplicated reads into individual crosslinking events with UMITools (Version 0.5.1)
Peak calling (yodel.py (1.0) --mph 5) and alternative contigs removal (GNU Awk 4.0.2)
Bigwigs were generated using bamCoverage from deeptools2
Assembly: GRCH38
Supplementary files format and content: BED File (yodel output) and bigwig (normalisation: None)

source_name: HEK293 T-Rex

growth_protocol: HEK293 Flp-In T-Rex cells were cultured in DMEM high glucose medium supplemented with 10% FBS (Sigma-Aldrich F0804), 2mM L-glutamine (Sigma-Aldrich, G7513) and 1% penicillin-streptomycin (Sigma-Aldrich, P4333). Cells were kept at 37 °C in 5% CO2 incubator. All cell lines were routinely checked for mycoplasma contamination by PCR.

extract_protocol:
FLASH-seq protocol was applied as described in Aktaş et al., 2017. Briefly, cells were crosslinked with 0.2mJ/cm2 UV-C irradiation, lysed with 1xNLB and homogenized by waterbath-sonication. Target protein of interest were affinity purified in tandem with nickel-charged paramagnetic beads and streptavidin-coupled paramagnetic beads against the tagged protein of interest. After a brief RNAseI-digestion, RNA 3'-ends were healed with T4 PNK. Custom-made, barcoded adapters were ligated using T4 RNA Ligase 1, for 1 hr at 25˚C. Custom FLASH adapters contained two barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNBBNTTTTTTNN (N: random tag nucleotide, T: tag nucleotide, B: RY-space tag nucleotide). Random tags were used to merge PCR-duplicates, regular tags were used to specify the pulldown condition, and semi-random RY-space tags were used to distinguish the biological replicates (RR: replicate A, YY: replicate B, R: purine, Y: pyrimidine). Excess adapters were washed away and RNA was isolated with Proteinase K treatment and column purification. Isolated RNA was reverse-transcribed and RNaseH-treated. cDNA was column-purified and circularized with CircLigase for 16hrs. Circularized cDNA was directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode.
Libraries were prepared according to NEBNext Ultra II DNA Library preparation kit (NEB#E7645S)

treatment_protocol: Expression of 3xFLAG-HBH tagged proteins was induced with 1 μg/ml tetracycline (Sigma-Aldrich, T7660)

value: HEK293 Flp-In T-Rex cells


title: 614658

city: Tianjin

first: Hao

last: Wang

address: Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin 300070, China

institute: Tianjin Medical University

data_processing:
The FASTQ files were analyzed with the Cell Ranger Software Suite (version 3.1; 10x Genomics) against the GRCh38 human reference genome.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung adenocarcinoma cells

extract_protocol:
Resected tumor was transported in MACS Tissue Storage Solution (Miltenyi Biotec) on ice immediately after surgical procurement.
Single cell RNA sequencing libraries were prepared using Chromium Single Cell 3’v2 Reagent Kit (10x Genomics).

value: human primary lung adenocarcinoma


title: F8Exon16A333G_A_DMSO_S29


title: C4-2 cells, VEC1


title: C4-2 cells, VEC2


title: 591146


title: WT-RBG-L, Left Wilms tumor

description: 10x Genomics


title: N2 EV RNAi rep1

description:
Sex: hermaphrodite
WE1_S124

value: embryos

value: Wild type (strain N2)

value: Empty vector (EV) RNAi


title: ChIP HSPA1A rep1

library_source: genomic

data_processing:
ChIPseq experiment was analysed with snakePipes version 2.4.3
Adapter trimming, quality control ( cutadapt (version 2.8 with Python 3.7.10))
Genome alignment (Bowtie2, Version 2.3.5.1, default parameters) and index (samtools, version 1.10)
Remove duplicated read (sambamba, version  0.7.1)
Bigwigs were generated using bamCoverage from deeptools (version 3.3.2)
Genome_build: GRCH38
Supplementary_files_format_and_content: Bigwig (RPGC (reads per genomic content) normalisation)

molecule: genomic DNA

extract_protocol:
Cells were fixed using 2mM Di(N-succinimidyl) glutarate (DSG; Sigma-Aldrich, 80424-50MG-F) for 40 minutes and 1% methanol-free formaldehyde (Thermo Scientific, 28906) for 10 minutes in 1xPBS at room temperature, followed by 5 min blocking in 0.125 M glycine. Cells were washed twice with ice-cold PBS. The cell pellet was resuspended in Farnham buffer (5 mM PIPES, pH 8; 85 mM KCl; 0.5% Igepal). Cell suspensions were sonicated for 3 minutes in 1 ml Covaris tubes (Covaris, 520130) using Covaris S220 with the following settings: peak power = 75; duty factor = 2; cycles/ burst = 200. Isolated nuclei were washed with Farnham buffer and suspended in shearing buffer (10 mM Tris-HCl, pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared by sonication in 1-ml Covaris tubes using the following settings: peak power = 140; duty factor = 5; cycles/burst = 200, time = 25–30 min. Debris was removed by centrifugation at 16000 x g. A DNA fragment–size distribution of 200–600 bp was considered as ideal chromatin for ChIP. Chromatin was diluted 1:1 with IP buffer (10 mM Tris-HCl, pH 8; 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxicholate, 0.1% N-lauroylsarcosine) to achieve a final 0.05% SDS concentration. Good quality chromatin (200 μg) was used for immunoprecipitation. Protein G magnetic beads (Life Technologies, 10002D and 10004D, respectively) were incubated (rotated) with 5–10 μ g of FLAG antibody (Sigma-Aldrich, F1804-200UG) for 6 h at 4 °C. This bead–antibody complex was then incubated overnight at 4 °C with sheared chromatin. An aliquot of chromatin was saved as input DNA. Beads were washed and DNA–protein complexes were eluted from the beads by heating at 65 °C in elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS). Crosslinking was reversed for 6 h at 70 °C and samples were treated with 200 μg/ml RNase A (Thermo Scientific, EN0531) and 200 μg/ml proteinaseK (Sigma-Aldrich, P2308). ChIP DNA was purified with phenol–chloroform extraction and ethanol precipitation and used either for library preparation for next-generation sequencing. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina (NEB E7645S). Some 2–5 ng of immunoprecipitated DNA was used for library preparation. Library size distribution was monitored by capillary electrophoresis (Agilent 2100 Bioanalyzer, High Sensitivity DNA Chips (Agilent, 5067–4626)). Libraries were sequenced paired-end on NextSeq500 or NovaSeq6000 instruments (Illumina).
Libraries were prepared according to NEBNext Ultra II DNA Library preparation kit (NEB #E7645S).Libraries were sequenced paired-end on HiSeq 2500, HiSeq 3000 or NextSeq 500 instruments (Illumina)

tag: chip target


title: Cerebellum, LPS female

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4
Supplementary files format and content: Mmul_8.0.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: cerebellum

extract_protocol:
Flash frozen cerebellar hemispheres from 2 rhesus macaque fetuses per group were homogenized and lysed with Triton X-100in RNase-free water for nuclei isolation. Isolated nuclei were purified, centrifuged, and resuspended in PBS with RNase inhibitor, and diluted to 700 nuclei/µl for standardized 10x capture and library preparation protocol using 10x Genomics Chromium Next GEM 3’ Single Cell Reagent kits v3.1 (10x Genomics, Pleasanton, CA).
Library was performed according to the manufacter’s instructions. The libraries were sequenced with a Illumina NovaSeq 6000 (Illumina, San Diego, CA). Raw sequencing files were processed with CellRanger 5.0 (10x Genomics) and mapped to the rhesus macaque genome (Mmul_8.0.1) with the option include introns and generated count matrices.
snRNA-seq

value: cerebellum

tag: developmental stage

value: fetus, 131 days

value: female

value: intra-amniotic LPS 1mg


title: F8Exon16_B_2A3_S20


title: Cerebellum, LPS male

description: 10x Genomics

value: fetus, 133 days

value: male


title: FLASH HSPA8 rep1


title: FLASH HSPA1A rep2

description: The second replicate of FLASH-seq experiment was only used to identify common peaks. Both BED files are uploaded. However, only replicate 1 signal (bigwig) is shown along the paper.

data_processing:
Library strategy: FLASH-seq
Demultiplexing (flexbar, version 3.3) and UMI trimming and header labelling (UMITools, Version 0.5.1)
Adapter trimming, quality control and demultiplexing barcodes (only R2) (trim_galore (Version 0.4.4) --stringency 3 -q 30 --paired --retain_unpaired -r1 15 -r2 15 --fastqc --three_prime_clip_R2 13 --length 14 --clip_R1 6 )
Paired-end reads were merged using bbmerge from bbmap (Version 37.54)
Genome alignment, allowing up to 1000 mapping locations (STAR (Version 2.6.0b) --outFilterMultimapNmax 150  --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --alignEndsType EndToEnd --alignIntronMax 100000)
Duplicated reads into individual crosslinking events with UMITools (Version 0.5.1)
Peak calling (yodel.py (1.0) --mph 5) and alternative contigs removal (GNU Awk 4.0.2)
Bigwigs were generated using bamCoverage from deeptools2
Genome_build: GRCH38
Supplementary_files_format_and_content: BED File (yodel output) and bigwig (normalisation: None)

extract_protocol:
FLASH-seq protocol was applied as described in Aktaş et al., 2017. Briefly, cells were crosslinked with 0.2mJ/cm2 UV-C irradiation, lysed with 1xNLB and homogenized by waterbath-sonication. Target protein of interest were affinity purified in tandem with nickel-charged paramagnetic beads and streptavidin-coupled paramagnetic beads against the tagged protein of interest. After a brief RNAseI-digestion, RNA 3'-ends were healed with T4 PNK. Custom-made, barcoded adapters were ligated using T4 RNA Ligase 1, for 1 hr at 25˚C. Custom FLASH adapters contained two barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNBBNTTTTTTNN (N: random tag nucleotide, T: tag nucleotide, B: RY-space tag nucleotide). Random tags were used to merge PCR-duplicates, regular tags were used to specify the pulldown condition, and semi-random RY-space tags were used to distinguish the biological replicates (RR: replicate A, YY: replicate B, R: purine, Y: pyrimidine). Excess adapters were washed away and RNA was isolated with Proteinase K treatment and column purification. Isolated RNA was reverse-transcribed and RNaseH-treated. cDNA was column-purified and circularized with CircLigase for 16hrs. Circularized cDNA was directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode.
Libraries were prepared according to NEBNext Ultra II DNA Library preparation kit (NEB #E7645S)


title: F8Exon16_B_DMSO_S18


title: RNA seq rep2

data_processing:
Adapter trimming, quality control (trim_galore (Version 0.6.4) --stringency 3 -q 30 --paired)
Ribosome read removal (Bowtie2, Version 2.4.2)
Genome alignment (STAR, Version 2.6.0b, default parameters)
Genome_build: GRCH38
Supplementary_files_format_and_content: HEK293_RNAseq_chaperome_expression_RPKM.xlsx (excel). Chaperone genes RPKM in HEK293

extract_protocol:
RNA was harvested from HEK293T cells using Trizol reagent. TruSeq stranded Total RNA (Gold), Illumina was used for the construction of sequencing libraries.
Libraries were prepared according to Illumina protocols


title: FLASH GFP rep2


title: F8Exon16_A_2A3_S19


title: F8Exon16A333G_B_DMSO_S30


title: Cerebellum, Control male

description: 10x Genomics

value: fetus, 130 days

value: no intervention


title: RNA seq rep1


title: FLASH GFP rep1


title: Cerebellum, Control female

description: 10x Genomics


title: FLASH HSPA1A rep1


title: F8Exon16_A_DMSO_S17

value: SHAPE probed


title: ChIP input rep1

value: none (input)


title: NONO Cut&Run shNONO_Eto

status: Public on Jan 16 2024

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For Cut&Run-seq, reads were mapped to hg19 and E.coli withBowtie2,  and then normalized based on E.coli reads or on read depth.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: Cut&Run

source_name: Bone Marrow

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
Cut&Run DNA
Cut&Run DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

treatment_protocol: Treatment as indicated

value: Bone Marrow

value: osteosarcoma cell line

value: Dox inducible shNONO

value: Dox, 1µg/ml, 24 h; Eto, 20µM, 2h

tag: antibody

value: NONO


title: NONO Cut&Run shCtrl_Eto

tag: cell type

value: Dox inducible shCtrl


title: NONO Cut&Run shNONO_NoEto

value: Dox, 1µg/ml, 24 h


title: NONO Cut&Run shCtrl_NoEto


title: V5-RnaseH1-WT_Cut&Run siCtrl_Eto

value: siCTR transfection, 48h; V5-RnaseH1-WT transfection, 24h

value: Eto, 20µM, 2h


title: H2BK120ac Cut&Run shNONO_Eto


title: V5-RnaseH1-D210N_Cut&Run siCtrl_Eto

value: siCTR transfection, 48h; V5-RnaseH1-D210N transfection, 24h


title: NONO Cut&Run H3K4me3 control

value: Pooled cells from all conditions

value: control


title: V5-RnaseH1-D210N_Cut&Run H3K4me3 control


title: V5-RnaseH1-D210N_Cut&Run siNONO_Eto

value: siNONO transfection, 48h; V5-RnaseH1-D210N transfection, 24h


title: V5-RnaseH1-WT_Cut&Run siNONO_Eto

value: siNONO transfection, 48h; V5-RnaseH1-WT transfection, 24h


title: V5-RnaseH1-D210N_Cut&Run siCtrl


title: H2BK120ac Cut&Run shNONO_NoEto


title: H2BK120ac Cut&Run shCtrl_Eto


title: H2BK120ac Cut&Run shNONO_Eto with mCherryNONO rescue

value: siNONO transfection, 24h ; mCherry NONO transfection, 24h


title: H2BK120ac Cut&Run shCtrl_NoEto


title: H2BK120ac Cut&Run H3K4me3 control


title: H2BK120ac Cut&Run shNONO_NoEto with mCherryNONO rescue


title: H2BK120ac Cut&Run shCtrl_Eto with mCherryNONO rescue

value: siCTR transfection, 24h ; mCherry NONO transfection, 24h


title: H2BK120ac Cut&Run shCtrl_NoEto with mCherryNONO rescue


title: H2BK120ac Cut&Run H3K4me3 control with mCherryNONO rescue


title: mNETseq_Input_Eto

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For mNET-seq, reads were mapped to hg19 and mm10 withBowtie2, and then normalized based on mouse reads
Assembly: hg19
Supplementary files format and content: bedgraph

extract_protocol:
nascent RNA from pSer2-RNAPII-IP followed by Mnase digestion (mNET-seq)
nascent RNA was used for library preparation with NEBNext Multiplex Small RNA Library Prep Set for Illumina Set 1, Set 2, Index Primers 1–48 and Multiplex Compatible Set1 (E7300). The libraries were amplified with 16 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the HS Small Fragment (50-1,500 bp; Agilent Technologies) and NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform
mNET-seq

tag: fraction

value: nascent RNA


title: IgG_control_all

description:
IgG_control_all_v1.bedgraph (IgG_control_all)
IgG_control_all_v2.bedgraph (NONO Cut&Run IgG control)
We started with one set of fastq-files (IgG_control_all_F.fastq & IgG_control_all_R.fastq), and produced different bedgraph-files from these (IgG_control_all_v1.bedgraph & IgG_control_all_v2.bedgraph), by random down-sampling. These 2 bedgraph-files simply differ in the number of reads they contain.

value: Bone Marrow

value: IgG


title: BLISS siNONO rep3

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0. Reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1. barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
reads were aligned with Bowtie2 v2.3.4.1 to hg19 and filtered with bedtools intersect v2.26.0. Reads were counted for specific regions using the R package exomeCopy v1.18.0
Assembly: hg19
Supplementary files format and content: bedgraph

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol. Sequencing was done on Illumina NextSeq2000.

value: osteosarcoma cell line

value: siNONO transfection, 48h


title: mNETseq_IP_Eto


title: mNETseq_IP_Ctrl


title: BLISS siNTC Etoposide rep3

value: siNTC transfection, 48h

value: Eto, 20µM, 2h with 5h chase


title: V5-RnaseH1-D210N_Cut&Run siNONO


title: BLISS siNTC Etoposide rep2


title: BLISS siNONO Etoposide rep2


title: BLISS siNONO Etoposide rep1


title: BLISS siNONO rep1


title: BLISS siNTC Etoposide rep1


title: BLISS siNTC rep1


title: APEX2-seq  shNONO_Eto rep2

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For APEX2-seq, reads were mapped to hg19 and t2t withBowtie, and then normalized based on read depth
Assembly: t2t
Supplementary files format and content: tabular
Library strategy: APEX2-seq

extract_protocol:
total RNA
RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 10-16 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: Dox inducible shNONO

value: Dox, 1µg/ml, 48h; Eto, 20µM, 2h


title: APEX2-seq  shCtrl_Eto rep1

value: Dox inducible shCtrl


title: APEX2-seq  shNONO_Eto rep1


title: BLISS siNTC rep2


title: APEX2-seq  shNONO_NoEto rep1

value: Dox, 1µg/ml, 48h


title: APEX2-seq  shCtrl_Eto rep3


title: APEX2-seq  shNONO_NoEto rep2


title: mNETseq_Input_Ctrl


title: APEX2-seq  shNONO_NoEto rep3


title: APEX2-seq  shCtrl_Eto rep2


title: BLISS siNONO Etoposide rep3


title: APEX2-seq  shCtrl_NoEto rep2


title: APEX2-seq  shCtrl_UL rep1


title: APEX2-seq  shCtrl_UL rep2


title: APEX2-seq  shCtrl_NoEto rep1


title: 4sU_shNONO_Eto rep3

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For 4sU-seq, reads were mapped to hg19 and mm10 withSTAR , and then normalized based on mouse reads.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: 4sU-seq

extract_protocol:
total RNA
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 10-16 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: Dox, 1µg/ml, 24h; Eto, 20µM, 2h


title: BLISS siNTC rep3

value: control


title: 4sU_shCtrl_Eto rep3


title: 4sU_shCtrl_NoEto rep3

value: Dox, 1µg/ml, 24h


title: 4sU_shNONO_Eto rep2


title: 4sU_shNONO_NoEto rep2


title: BLISS siNONO rep2


title: APEX2-seq  shCtrl_NoEto rep3


title: 4sU_shCtrl_Eto rep2


title: 4sU_shCtrl_NoEto rep1


title: 4sU_shNONO_NoEto rep1


title: EDTA_WholeBlood__P50

city: Heidelberg

first: Bruno

last: Steinkraus

state: Baden-Württemberg

address: Im Neuenheimer Feld 583

institute: HUMMINGBIRD DIAGNOSTICS GMBH

data_processing:
Raw sequence reads were adapter trimmed and depleted of PCR duplicates based on the UMIs.
Only sequences that had at least one read in at least three samples per blood component type and that were longer than 17 nucleotides were kept.
For 25 cellular fractions (4.6% of derivatives, 25/539) the purification process did not meet the prespecified quality standard (purity > 70% as determined by flow cytometry). These samples were excluded from further analyses. See 'quality filter for processed data'
As additional quality control, the normalized data of the blood component samples was converted to a two-dimensional T-distributed Stochastic Neighbor Embedding (t-SNE) space. When plotting the two embedding vectors against each other, four samples did not cluster with the samples of the same blood component type (0.8% of derivatives, 4/514) and were excluded from further analysis. See 'quality filter for processed data'
The pre-processed sRNA sequences were annotated using the annotation pipelines unitas  and SPORTS. In case of multi-assignments, the annotation was prioritized in the following manner: miRNA > tRNA > rRNA > YRNA > snoRNA > lncRNA > snRNA > piRNA.
Assembly: hg38
Supplementary files format and content: csv files including log2-transformed RPM values per small RNA name for all blood component samples (1 file) and for all whole blood samples (1 file)

source_name: peripheral blood

extract_protocol:
The fractional blood derivatives as well as the whole blood samples were directly lysed in Qiazol. For RNA isolation the miRNeasy Serum/Plasma mini kit was combined with minElute columns.
Dual indexed sRNA libraries with unique molecular identifiers (UMIs) adaptors were generated using the QIAseq miRNA Library Kit.

value: peripheral blood


title: 4sU_shNONO_NoEto rep3


title: EDTA_WholeBlood__P49


title: EDTA_WholeBlood__P48


title: EDTA_WholeBlood__P47


title: EDTA_WholeBlood__P43


title: EDTA_WholeBlood__P51


title: EDTA_WholeBlood__P46


title: EDTA_WholeBlood__P52


title: EDTA_WholeBlood__P45


title: EDTA_WholeBlood__P44


title: EDTA_WholeBlood__P38


title: EDTA_WholeBlood__P39


title: EDTA_WholeBlood__P42


title: EDTA_WholeBlood__P36


title: EDTA_WholeBlood__P41


title: EDTA_WholeBlood__P37


title: 4sU_shNONO_Eto rep1


title: EDTA_WholeBlood__P35


title: EDTA_WholeBlood__P33


title: EDTA_WholeBlood__P31


title: 4sU_shCtrl_Eto rep1


title: EDTA_WholeBlood__P32


title: EDTA_WholeBlood__P34


title: EDTA_WholeBlood__P30


title: EDTA_WholeBlood__P29


title: EDTA_WholeBlood__P26


title: EDTA_WholeBlood__P28


title: EDTA_WholeBlood__P40


title: EDTA_WholeBlood__P27


title: EDTA_WholeBlood__P25


title: EDTA_WholeBlood__P23


title: EDTA_WholeBlood__P24


title: EDTA_WholeBlood__P20


title: EDTA_WholeBlood__P18


title: EDTA_WholeBlood__P19


title: EDTA_WholeBlood__P17


title: EDTA_WholeBlood__P21


title: EDTA_WholeBlood__P13


title: EDTA_WholeBlood__P15


title: dKO GBS 0212

type: RNA

city: ROCHESTER

first: Kathryn

last: Knoop

state: MN

address: 2511 Boulder Ridge Dr NW

department: Internal Medicine, Gastroenterology Division

institute: Mayo Clinic

description: 2ul of 200.6 ng/ul

hyb_protocol: RNA hybridization was performed according to Nanostring manufacturer’s instructions. Samples were incubated for 24 hours at 65°C

scan_protocol: Samples were run on the nCounter Prep Station 5s before being placed on the nCounter Digital Analyzer.

data_processing: The ROSALIND platform was used for data analysis.

label: Codeset Probe

organism: Mus musculus

source_name: Brain

label_protocol: Nanostring nCounter Mouse Immunology Max Kit was used following mRNA isolation from the brain.

extract_protocol: Brains were homogenized in 1 mL of sterile PBS using a dounce homogenizer. 100 uL of brain homogenate was used for mRNA isolation with the Quiagen RNeasy Mini Kit according to manufacturer’s instructions.

treatment_protocol: Neonatal mice were infected on postnatal day 7 (P7) intraperitoneal with either 2X10^4 CFUs E. coli and 1x10^6 CFUs GBS

value: Brain

value: neonatal

tag: infection

value: GBS

value: TCRd KO


title: Thrombocytes__P50

source_name: peripheral blood cells

value: peripheral blood cells

value: Thrombocytes

tag: quality filter_for_processed_data

value: does NOT pass cellsorting purity filter


title: Thrombocytes__P47


title: dKO GBS 0210

description: 2ul of 184.8 ng/ul


title: Thrombocytes__P48


title: dKO Ecoli 0112

description: 2ul of 216.5 ng/ul

value: E. coli


title: Thrombocytes__P46


title: Thrombocytes__P49


title: dKO Ecoli 0111

description: 2ul of 215.0 ng/ul


title: dKO Ecoli 0110

description: 2ul of 196.9 ng/ul


title: Thrombocytes__P45


title: EDTA_WholeBlood__P22


title: dKO Uninf 0209

description: 2ul of 200.6 ng/ul

value: Uninfected


title: dKO Uninf 0208

description: 2ul of 180.6 ng/ul


title: EDTA_WholeBlood__P16


title: Thrombocytes__P42


title: Thrombocytes__P43


title: EDTA_WholeBlood__P14


title: WT GBS 02052

description: 2ul of 194.9 ng/ul

value: WT


title: WT GBS 0205

description: 2ul of 165.7 ng/ul


title: Thrombocytes__P39


title: Thrombocytes__P41


title: Thrombocytes__P37


title: WT GBS 0204

description: 2ul of 167 ng/ul


title: dKO GBS 0211

description: 2ul of 180.6 ng/ul


title: Thrombocytes__P38


title: WT Ecoli 0106

description: 2ul of 262.5 ng/ul


title: WT Ecoli 0105

description: 2ul of 257.5 ng/ul


title: Thrombocytes__P34


title: Thrombocytes__P33


title: Thrombocytes__P35


title: WT Uninf 0102

description: 2ul of 292.5 ng/ul


title: WT Uninf 0103

description: 2ul of 216.5 ng/ul


title: dKO Uninf 0207

description: 2ul of 184.8 ng/ul


title: WT Ecoli 0104

description: 2ul of 153.2 ng/ul


title: WT Uninf 0101

description: 2ul of 258.3 ng/ul


title: Thrombocytes__P31


title: 35_LXR-aKO_LPS_3h_(p65)_rep2

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

data_processing:
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Assembly: mm10
Supplementary files format and content: Processed files include bed files

source_name: Bone marrow

growth_protocol: For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRβ-/- mice were isolated and cultured for 7 days in RPMI supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin). To analyze LXRα-dependent response, cells were cultured in RPMI supplemented with 10% FBS, 1% antibiotics (penicillin and streptomycin) and 100 nM of Lipopolysachaaride (LPS) during 3 or 24 hours. Genome-wide locations of LXRα, p65 (NF-κB) and H3K27ac acetylation mark were analized in response to treatment with LPS.

extract_protocol:
Cells were fixed with DSG (2 mM) for 30 minutes and 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorruptor plus (Diagenode) and LXR-DNA, p65-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
to create the sequencing library, DNA was end-repaired and ligated to stem-loop adaptors (DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions). Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

value: Bone marrow

value: bone marrow-derived macrophage

tag: chip antibody

value: NF-κB p65 (Cell Signaling, #6956 & #8242)

value: LXR-aKO

value: Lipopolysaccharide 100 nM 3 hours


title: Bisulfite RNA-seq of non-modified in-vitro transcripts (IVTs) m1, m2, m3, m4

city: Canberra

first: AKANKSHA

last: SRIVASTAVA

state: Australian Capital Territory

address: 131 Garran Rd

department: The Shine-Dalgarno Centre for RNA Innovation

country: Australia

institute: Australian National University

description: Bisulfite RNA sequencing

data_processing:
For the analysis of the Illumina reads from the bisulfitetreated data we used meRanTK (Rieder, D., Amort, T., Kugler, E., Lusser, A. & Trajanoski, Z. meRanTK: methylated RNA analysis ToolKit. Bioinformatics 32, 782–5 (2016).) , adjusting the parameters to make it more permissive to m5C detection: the edit distance was changed from the default 2 to 200, the number of Cs per Illumina read was changed from the default 3 to 200, the minimum methylation ratio of a single C needed for methylation was changed from the default 0.2 to 0, and the minimum coverage at a given reference site above which methylation call is performed was changed from the default 20 to 0.
Assembly: synthetic constructs
Supplementary files format and content: txt format outout from meRanTK
Library strategy: Bisulfite RNA-seq

organism: synthetic construct

extract_protocol: We performed RNA bisulfite treatment (bsRNA-seq) following the protocol from Johnson et al (Johnson, Z., Xu, X., Pacholec, C. & Xie, H. Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis. NAR genomics Bioinforma. 4, lqac045 (2022))There were nodeviations done for the protocol except the fact that a GE50 spin column was used for the removal of the excess of bisulfite reagent (sodium bisulfide and hydroquinone) instead of a GE25. This protocol was applied to RNA fully modified with m5C or non-modified obtained from in-vitro transcripts (IVTs) m1, m2, m3, m4  built from four non-overlapping fragments from the mouse canonical pre-rRNA (~13kb long)


title: Thrombocytes__P30


title: Thrombocytes__P29


title: 33_LXR-WT_LPS_3h_(p65)_rep2

value: LXR-WT


title: 34_LXR-aKO_LPS_3h_(p65)_rep1


title: Bisulfite RNA-seq of modified m5C in-vitro transcripts (IVTs) m1, m2, m3, m4

description: Bisulfite RNA sequencing


title: Thrombocytes__P26


title: 30_LXR-aKO_LPS_24h_(p65)_rep1

value: Lipopolysaccharide 100 nM 24 hours


title: 32_LXR-WT_LPS_3h_(p65)_rep1


title: Thrombocytes__P27


title: Thrombocytes__P25


title: 29_LXR-aKO_CTRL_(p65)_rep2

value: Vehicle


title: Thrombocytes__P24


title: 28_LXR-aKO_CTRL_(p65)_rep1


title: 31_LXR-aKO_LPS_24h_(p65)_rep2


title: Thrombocytes__P23


title: Thrombocytes__P32


title: Thrombocytes__P21


title: Thrombocytes__P22


title: 26_LXR-WT_LPS_24h_(p65)_rep1


title: 25_LXR-WT_CTRL_(p65)_rep2


title: Thrombocytes__P20


title: 24_LXR-WT_CTRL_(p65)_rep1


title: Thrombocytes__P19


title: Thrombocytes__P18


title: Thrombocytes__P13


title: Thrombocytes__P17


title: Thrombocytes__P16


title: BMDM, H3K27ac, unstimulated, r2

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
Raw reads were mapped to mm9 reference genome using bowtie 2 (bowtie2 -t --very-sensitive).
Reads mapped to chrM and unassembled "random" contigs were removed (sed '/chrM/d;/random/d;/chrUn/d'). The reads with more than one alignment were also removed (grep -v XS:i).
Genomic sites enriched with aligned reads were identified and called peaks by using HOMER (findPeaks -style factor). The called peaks from each sample were merged to generate a combined probe list using HOMER.
All the sorted bam files were imported into seqMonk for quantification. Raw reads among each combined probe site were converted to reads per kilobases of the probe and per million reads of total read counts (RPKM).
Assembly: mm9
Supplementary files format and content: tab-deliminaed text files include raw read counts

growth_protocol: Bone marrow precursors were grown in BMDM media (20% FBS, 10% CMG condition medium [containing M-CSF], 1x Pen-Strep [GIBCO, #15140-122], 1x L-Glutamine [GIBCO, #25030-081], 0.5 mM sodium pyruvate [GIBCO, #11360-070] in Dubecco’s Modified Eagle Medium) for 6 days to obtain mature BMDMs prior to stimulation.

extract_protocol:
BMDMs were fixed in 1% formaldehyde for 10 min and quenched with 500mM Tris pH8.0 for 15 min. After cell lysis, chromatin was sheared with Covaris M220 sonicator. Sonicate lysate were incubated with Rel-A (Santa Cruz #sc-372), IRF-3 (Santa Cruz # sc-9082 X) and Brg1 (Cell Signaling # 9284S) overnight at 4oC. The DNA/protein-antibody complexes were captured by Dynabeads protein A/G. DNA fragments were extracted and prified by phenol-chloroform and ethanol precipitation.
Libraries were prepared with Kapa Hyper Prep Kit Illumina Platform (#KK8504) according to the manufacturer's instructions.

treatment_protocol: BMDMs from C57/B16 mice were stimulated with lipid-A for 0, 15, 30, 60 or 120 minutes.

tag: strain

value: primary culture

value: bone marrow-derived macrophages

value: wildtype

value: Unstimulated


title: BMDM, H3K27ac, input control, r2

tag: tissue


title: BMDM, H3K27ac, stimulated 120', r2

tag: genotype

value: lipid A stimulation


title: BMDM, H3K27ac, stimulated 120', r1

tag: treatment


title: BMDM, H3K27ac, input control, r1


title: Plasma_Norgen__P52

source_name: peripheral blood plasma

value: peripheral blood plasma

value: Plasma


title: Plasma_Norgen__P50


title: Plasma_Norgen__P46


title: BMDM, P300, input control, r2


title: BMDM, H3K27ac, unstimulated, r1


title: BMDM, P300, stimulated 120', r2


title: BMDM, P300, stimulated 120', r1


title: Thrombocytes__P28

value: peripheral blood cells

value: Thrombocytes


title: 27_LXR-WT_LPS_24h_(p65)_rep2

value: Bone marrow


title: Plasma_Norgen__P44


title: BMDM, P300, unstimulated, r2


title: BMDM, P300, unstimulated, r1


title: Plasma_Norgen__P42


title: Plasma_Norgen__P38


title: Plasma_Norgen__P41


title: BMDM, chrRNA, stimulated 120', r2

description: chromatin associated RNA

data_processing:
Raw reads were mapped to mm9 reference genome using hisat 2 (parameter: hisat2 --known-splicesite-infile --rna-strandness R -k 1).
Reads mapped to chrM and unassembled "random" contigs were removed (sed '/chrM/d;/random/d;/chrUn/d').
Read counts were extracted and normalized using SeqMonk software.
Assembly: mm9
Supplementary files format and content: tab-deliminaed text files include raw read counts

growth_protocol: Bone marrow precursors were grown in BMDM media (20% FBS, 10% CMG condition medium [containing M-CSF], 1x Pen-Strep [GIBCO, #15140-122], 1x L-Glutamine [GIBCO, #25030-081], 0.5 mM sodium pyruvate [GIBCO, #11360-070] in Dubecco’s Modified Eagle Medium) for 6 days to obtain mature BMDMs prior to stimulation. J2 immortalized bone marrow-derived macrophages were grown in BMDM media to stimulation.

extract_protocol:
Total RNA was extracted from BMDMs or macrophage cells using TRIzol reagent (ThermoFisher #15596018) followed by Qiagen RNAeasy plus mini kit (QIAGEN #74136) according to the manufacturer's instructions.
Libraries were prepared with Illumina TruSeq RNA Library Preparation Kit 2.0 (Illumina #RS-122-2001) according to the manufacturer's instructions.

treatment_protocol: BMDMs from C57/B16 mice and J2 immortalized macrophage cells were stimulated with lipid-A for 0, 15, 30, 60 or 120 minutes.

value: 120 min


title: Plasma_Norgen__P37


title: BMDM, chrRNA, stimulated 60', r2

description: chromatin associated RNA

value: 60 min


title: BMDM, chrRNA, stimulated 120', r1

description: chromatin associated RNA


title: Plasma_Norgen__P51


title: Plasma_Norgen__P36


title: BMDM, chrRNA, stimulated 60', r1

description: chromatin associated RNA


title: Plasma_Norgen__P35


title: Plasma_Norgen__P33


title: BMDM, chrRNA, stimulated 30', r1

description: chromatin associated RNA

value: 30 min


title: BMDM, chrRNA, stimulated 15', r1

description: chromatin associated RNA

value: 15 min


title: BMDM, P300, input control, r1


title: BMDM, chrRNA, stimulated 30', r2

description: chromatin associated RNA


title: BMDM, chrRNA, unstimulated, r2

description: chromatin associated RNA

value: unstimulated


title: Plasma_Norgen__P32


title: Plasma_Norgen__P23


title: BMDM, chrRNA, unstimulated, r1

description: chromatin associated RNA


title: Plasma_Norgen__P28


title: Plasma_Norgen__P43


title: Plasma_Norgen__P26


title: Plasma_Norgen__P31


title: BMDM, chrRNA, stimulated 15', r2

description: chromatin associated RNA


title: BMDM, RelA, input control, r2

value: RelA

value: input control


title: Plasma_Norgen__P22


title: BMDM, RelA, input control, r1

value: primary culture


title: BMDM, RelA, stimulated 120', r2

value: bone marrow-derived macrophages

value: stimulated 120'


title: Plasma_Norgen__P21


title: Plasma_Norgen__P20


title: Plasma_Norgen__P19


title: BMDM, RelA, stimulated 60', r1

value: stimulated 60'


title: BMDM, RelA, stimulated 60', r2


title: Plasma_Norgen__P17


title: Plasma_Norgen__P30


title: Plasma_Norgen__P16


title: BMDM, RelA, stimulated 15', r2

value: stimulated 15'


title: BMDM, RelA, stimulated 30', r2

value: stimulated 30'


title: Plasma_Norgen__P14

value: peripheral blood plasma

value: Plasma


title: BMDM, RelA, stimulated 30', r1


title: Plasma_Norgen__P15


title: Plasma_Norgen__P13


title: BMDM, RelA, stimulated 15', r1


title: Neutrophils__P51

value: peripheral blood cells

value: Neutrophils

value: does NOT pass t-SNE filter


title: Neutrophils__P48


title: BMDM, Irf3, input control, r2

value: Bone marrow


title: Neutrophils__P49


title: BMDM, Irf3, stimulated 60', r2


title: BMDM, RelA, unstimulated, r2


title: BMDM, RelA, unstimulated, r1


title: BMDM, Irf3, stimulated 120', r2


title: BMDM, Irf3, input control, r1


title: Neutrophils__P50


title: BMDM, RelA, stimulated 120', r1


title: BMDM, Irf3, stimulated 120', r1


title: Neutrophils__P47


title: Neutrophils__P46


title: Neutrophils__P42


title: Neutrophils__P45


title: BMDM, Irf3, stimulated 30', r1


title: BMDM, Irf3, stimulated 15', r1


title: Neutrophils__P41


title: Neutrophils__P44


title: BMDM, Irf3, unstimulated, r2


title: BMDM, Irf3, stimulated 30', r2


title: BMDM, Irf3, unstimulated, r1


title: Neutrophils__P43


title: BMDM, Brg1, input control


title: BMDM, Irf3, stimulated 60', r1


title: Neutrophils__P38


title: BMDM, Irf3, stimulated 15', r2


title: Neutrophils__P52


title: iCAF_1

city: Copenhagen

first: Mikkel

last: Morsing

state: Nørrebro

address: Blegdamsvej 3b

department: Department of Cellular and Molecular Medicine and Danish Stem Cell Center

country: Denmark

institute: University of Copenhagen

data_processing:
Used SOAPnuke software to filter reads
Data processing included removing adaptors, removing reads in which unknown bases(N) are more than 1% and low-quality reads from raw reads.
After reads filtering, we map clean reads to reference genome using HISAT
Assembly: hg19

source_name: Female breast ER+ carcinoma

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fischer) and a spin column method according to the manufacturer’s instructions (Zymo Research)
DNAse treated total RNA samples were sent to BGI, Hong Kong for RNA-seq. There, total RNA was enriched for mRNAs using oligo dT magnetic beads. The mRNAs were fragmented and reverse transcribed to double-strand cDNA by random-hexamer primers. The synthesized cDNA was subjected to end-repair and was then 3’Adenylated. Adaptors were ligated to the ends of these 3’ Adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on the DNBseq platform resulting in on average ~30 million reads per sample.

value: Female breast ER+ carcinoma

value: hTERT immortalized

value: Fibroblast


title: iCAF_2


title: BMDM, Brg1, unstimulated

value: unstimulated


title: BMDM, Brg1, stimulated 2h

value: stimulated 2h


title: Neutrophils__P37


title: Neutrophils__P36


title: Neutrophils__P39


title: myCAF_1


title: Neutrophils__P33


title: Neutrophils__P32


title: Neutrophils__P40


title: Neutrophils__P34


title: Neutrophils__P31


title: Neutrophils__P30


title: Neutrophils__P29


title: myCAF_2


title: Neutrophils__P28


title: Neutrophils__P25


title: Neutrophils__P26


title: Neutrophils__P27


title: Case 69

type: genomic

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Hyderabad

address: Jawahar nagar

department: Biological Sciences

country: India

institute: Birla Institute of Technology and Science

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R06C01

hyb_protocol: DNA is incubated overnight at 37 degrees

scan_protocol: Scanning is done with in 72 hrs after the process is completed.BeadChip positions in the scanner is noted down.

data_processing:
Data is loaded with the standard cluster file first and then re clustering is done. Control summery, B allele frequency and log R ratio is observed to evaluate the data quality
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

source_name: Blood

label_protocol: DNA quality is checked by Picogreen a dye very specific for binding DNA, Quality check is done by UV spectrophotometer at 260/280 ratio.After the quantification  the samples are normalized to 50ng/ul (12ul). A gel check is also performed to check the normalization on 0.8% Agarose Gel.

extract_protocol: Extraction of genomic DNA from blood was performed using proteinase K and repeated phenol-chloroform extraction. The DNA samples were purified with ZR 96 well DNA   clean up kit supplied by zymo research. The elution is done twice with 40+30 ul respectively

value: Female


title: Case 63

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R03C01

value: Male


title: Case 67

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R05C01


title: Case 68

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R05C02


title: Case 66

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R04C02


title: Case 65

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R04C01


title: Case 64

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R03C02


title: Neutrophils__P24


title: Case 70

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R06C02


title: Case 60

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R01C02


title: Neutrophils__P35


title: Case 61

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R02C01


title: Neutrophils__P23


title: Case 62

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R02C02


title: Control 77

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R12C01


title: Neutrophils__P22


title: Control 76

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R11C02


title: Neutrophils__P19


title: Case 59

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R01C01


title: Control 78

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R12C02


title: Neutrophils__P21


title: Neutrophils__P20


title: Neutrophils__P18


title: Control 74

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R10C02


title: Neutrophils__P14


title: Neutrophils__P17


title: Control 75

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R11C01


title: Neutrophils__P16


title: Control 71

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R08C01


title: Neutrophils__P15


title: Neutrophils__P13


title: Control 69

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R07C01


title: NK_cells__P50

value: Natural killer cells


title: NK_cells__P49


title: Case 57

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R08C02


title: NK_cells__P52


title: NK_cells__P51


title: Control 72

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R09C01


title: Control 73

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R10C01


title: NK_cells__P48


title: NK_cells__P47


title: Control 67

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R06C01


title: NK_cells__P45


title: Control 64

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R04C02


title: NK_cells__P43


title: Control 65

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R05C01


title: Case 58

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R09C02


title: NK_cells__P46

value: does NOT pass cellsorting purity filter


title: Control 70

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R07C02


title: Control 66

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R05C02


title: Control 63

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R04C01


title: NK_cells__P44


title: Control 61

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R03C01


title: NK_cells__P42


title: Control 60

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R02C02


title: Control 59

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R02C01


title: NK_cells__P38


title: NK_cells__P37


title: Control 62

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R03C02


title: NK_cells__P41


title: Control 55

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R12C01


title: Control 68

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R06C02


title: NK_cells__P40


title: NK_cells__P31


title: NK_cells__P33


title: Control 57

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R01C01


title: Control 53

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R11C01


title: Control 52

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R10C02


title: NK_cells__P39


title: Control 58

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570043_R01C02


title: NK_cells__P36


title: Control 51

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R10C01


title: Case 56

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R09C02


title: NK_cells__P35


title: Control 49

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R08C01


title: Control 56

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R12C02


title: NK_cells__P34


title: Control 48

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R07C02


title: Control 54

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R11C02


title: NK_cells__P32


title: NK_cells__P21


title: Control 50

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R09C01


title: Control 45

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R04C02


title: Case 53

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R05C01


title: NK_cells__P19


title: NK_cells__P29


title: Control 47

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R07C01


title: Case 52

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R04C01


title: NK_cells__P26


title: Case 55

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R08C02


title: Case 54

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R06C01


title: NK_cells__P28


title: NK_cells__P18


title: Control 46

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R05C02


title: NK_cells__P23


title: NK_cells__P24


title: NK_cells__P22


title: Case 50

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R02C01


title: NK_cells__P25


title: NK_cells__P20


title: NK_cells__P30


title: NK_cells__P17


title: NK_cells__P27


title: Control 44

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R03C02


title: NK_cells__P14


title: Control 43

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R02C02


title: Case 51

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R03C01


title: Case 49

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R01C01


title: Monocytes__P50

value: Monocytes


title: Case 47

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R11C02


title: Case 48

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R12C02


title: Monocytes__P47


title: Control 39

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R10C01


title: Case 46

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R10C02


title: NK_cells__P13


title: NK_cells__P16


title: NK_cells__P15


title: Control 41

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R12C01


title: Control 38

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R09C01


title: Monocytes__P48


title: Monocytes__P52


title: Case 45

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R09C02


title: Control 40

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R11C01


title: Monocytes__P51


title: Control 42

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570042_R01C02


title: Monocytes__P49


title: Case 44

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R08C02


title: Control 37

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R08C01


title: Monocytes__P44


title: Case 43

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R07C02


title: Monocytes__P42


title: Case 42

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R07C01


title: Monocytes__P41


title: Monocytes__P40


title: Case 40

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R06C01


title: Monocytes__P46


title: Case 41

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R06C02


title: Monocytes__P45


title: Case 39

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R05C02


title: Case 36

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R04C01


title: Case 38

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R05C01


title: Case 37

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R04C02


title: Control 36

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R03C02


title: Monocytes__P38


title: Monocytes__P36


title: Monocytes__P35


title: Monocytes__P33


title: Case 35

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R03C01


title: Control 35

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R02C02


title: Monocytes__P31


title: Monocytes__P34


title: Case 34

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R02C01


title: Control 34

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R01C02


title: Monocytes__P43


title: Monocytes__P30


title: Case 32

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R12C02


title: Monocytes__P29


title: Case 31

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R12C01


title: Monocytes__P39


title: Case 30

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R11C02


title: Case 33

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700026_R01C01


title: Case 29

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R11C01


title: Monocytes__P26


title: Monocytes__P37


title: Monocytes__P25


title: Monocytes__P24


title: Monocytes__P23


title: Case 24

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R08C02


title: Monocytes__P32


title: Case 27

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R10C01


title: Monocytes__P21


title: Case 25

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R09C01


title: Case 23

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R08C01


title: Case 26

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R09C02


title: Monocytes__P22


title: Monocytes__P20


title: Case 22

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R07C02


title: Monocytes__P19


title: Monocytes__P18


title: Case 21

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R07C01


title: Monocytes__P28


title: Case 20

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R06C02


title: Monocytes__P16


title: Monocytes__P17


title: Monocytes__P27


title: Case 19

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R06C01


title: Monocytes__P15


title: Case 18

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R05C02


title: Case 28

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R10C02


title: Monocytes__P13


title: Case 17

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R05C01


title: Case 16

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R04C02


title: Case 15

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R04C01


title: Case 14

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R03C02


title: Erythrocytes__P52

value: Erythrocytes


title: Erythrocytes__P51


title: Case 13

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R03C01


title: Case 12

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R02C02


title: Case 11

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R02C01


title: Erythrocytes__P48


title: Case 10

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R01C02


title: Erythrocytes__P50


title: Erythrocytes__P47


title: Case 9

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700025_R01C01


title: Erythrocytes__P46


title: Erythrocytes__P45


title: Control 33

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R12C01


title: Case 8

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R12C02


title: Case 7

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R11C02


title: Erythrocytes__P44


title: Erythrocytes__P42


title: Erythrocytes__P49


title: Erythrocytes__P43


title: Erythrocytes__P41


title: Monocytes__P14


title: Case 6

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R10C02


title: Control 31

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R10C01


title: Erythrocytes__P40


title: Erythrocytes__P39


title: Erythrocytes__P38


title: Control 32

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R11C01


title: Control 30

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R09C01


title: Case 4

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R08C02


title: Erythrocytes__P37


title: Control 29

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R08C01


title: Erythrocytes__P35


title: Case 3

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R07C02


title: Erythrocytes__P36


title: Erythrocytes__P33


title: Erythrocytes__P34


title: Control 28

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R07C01


title: Erythrocytes__P32


title: Control 27

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R06C01


title: Control 26

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R05C01


title: Control 24

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R04C01


title: Control 25

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R04C02


title: Erythrocytes__P30


title: Case 1

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R05C02


title: Case 5

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R09C02


title: Erythrocytes__P29


title: Control 22

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R03C01


title: Erythrocytes__P27


title: Erythrocytes__P28


title: Control 23

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R03C02


title: Erythrocytes__P26


title: Control 21

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R02C02


title: Erythrocytes__P25


title: Control 20

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R02C01


title: Erythrocytes__P24


title: Erythrocytes__P23


title: Control 19

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R01C02


title: Control 16

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R12C01


title: Control 18

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R01C01


title: Erythrocytes__P20


title: Erythrocytes__P31


title: Erythrocytes__P21


title: Erythrocytes__P18


title: Control 10

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R09C01


title: Erythrocytes__P17


title: Erythrocytes__P15


title: Control 12

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R10C01


title: Control 11

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R09C02


title: Erythrocytes__P13


title: Control 9

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R08C02


title: Erythrocytes__P19


title: Eosinophils__P50

value: Eosinophils


title: Control 6

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R07C01


title: Case 2

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700024_R06C02


title: Control 15

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R11C02


title: Eosinophils__P51


title: Erythrocytes__P22


title: Erythrocytes__P14


title: Control 13

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R10C02


title: Control 14

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R11C01


title: Eosinophils__P48


title: Control 5

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R06C02


title: Control 7

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R07C02


title: Eosinophils__P46


title: Eosinophils__P49


title: Eosinophils__P47


title: Control 17

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R12C02


title: Control 4

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R06C01


title: Control 3

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R05C02


title: Control 1

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R04C02


title: Control 8

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R08C01


title: Control 181

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R04C01


title: Eosinophils__P44


title: Eosinophils__P42


title: Eosinophils__P43


title: Eosinophils__P38


title: Eosinophils__P41


title: Eosinophils__P34


title: Eosinophils__P40


title: Eosinophils__P33


title: Control 180

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R12C02


title: Case 192

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R12C01


title: Control 176

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R08C02


title: Eosinophils__P35


title: Case 191

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R11C01


title: Control 179

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R11C02


title: Control 177

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R09C02


title: Eosinophils__P32


title: Eosinophils__P37


title: Control 178

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R10C02


title: Eosinophils__P39


title: Control 175

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R07C02


title: Case 189

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R09C01


title: Case 190

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R10C01


title: Control 2

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203419700012_R05C01


title: Eosinophils__P45


title: Case 188

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R08C01


title: Case 187

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R07C01


title: Control 174

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R06C02


title: Eosinophils__P29


title: Case 186

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R06C01


title: Eosinophils__P31


title: Eosinophils__P36


title: Eosinophils__P30


title: Control 173

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R05C02


title: Eosinophils__P27


title: Eosinophils__P26


title: Eosinophils__P25


title: Eosinophils__P24


title: Case 183

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R03C01


title: Case 184

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R04C01


title: Control 172

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R04C02


title: Eosinophils__P28


title: Eosinophils__P22


title: Case 185

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R05C01


title: Case 182

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R02C01


title: Eosinophils__P20


title: Eosinophils__P21


title: Control 169

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R01C02


title: Control 170

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R02C02


title: Eosinophils__P18


title: Case 181

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R01C01


title: Eosinophils__P23


title: Control 168

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R12C02


title: Eosinophils__P19


title: Case 180

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R12C01


title: Eosinophils__P17


title: Control 167

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R11C02


title: Erythrocytes__P16


title: Eosinophils__P16


title: Case 179

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R11C01


title: Eosinophils__P13


title: CD8__P52

value: CD8+ T cells


title: Control 171

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110065_R03C02


title: CD8__P51

value: peripheral blood cells


title: CD8__P50


title: CD8__P46


title: CD8__P48


title: CD8__P47


title: Control 165

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R08C02


title: Case 176

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R09C01


title: Case 173

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R06C01


title: Control 164

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R07C02


title: CD8__P49


title: Case 172

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R05C02


title: Control 163

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R06C02


title: Case 177

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R09C02


title: CD8__P45


title: CD8__P43


title: Case 174

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R07C01


title: CD8__P41


title: CD8__P44


title: Control 162

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R05C01


title: CD8__P42


title: CD8__P40


title: CD8__P39


title: Control 161

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R04C02


title: Case 171

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R04C01


title: CD8__P38


title: Control 166

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R10C02


title: Case 178

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R10C01


title: CD8__P37


title: Case 175

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R08C01


title: Control 160

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R03C02


title: CD8__P36


title: Case 170

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R03C01


title: Case 169

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R02C01


title: Control 159

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R02C02


title: CD8__P34


title: CD8__P32


title: CD8__P35


title: CD8__P33


title: Control 158

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R10C02


title: Case 164

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R11C01


title: CD8__P31


title: Case 163

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R10C01