title: HSD17B10_input_2

status: Public on May 31 2020

type: SRA

city: changsha

first: Xiangli

last: Yin

state: Hunan

address: the 2nd Xiangya Hospital

country: China

institute: the 2nd Xiangya Hospital

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of HSD17B10 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

molecule: total RNA

organism: Homo sapiens

source_name: hela cell

extract_protocol:
The HSD17B10-bound RNAs were isolated from the immunoprecipitation of anti-Flag (Sigma, F1804) using TRIzol (Invitrogen).
Complementary DNA (cDNA) libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according the manufacturer’s procedure and high-throughput sequencing of the cDNA libraries was performed on an Illumina Xten platform for 150 bp paired-end sequencing.

tag: cell line

value: HeLa

tag: sample type

value: input


title: HSD17B10_IP_1

value: anti-HSD17B10 RIP


title: HSD17B10_IP_2


title: HSD17B10_input_1


title: ILC2 cells , GFP_16h_1

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

country: USA

institute: OMRF

description: ILC2 cells transduced with MIGR1 vector

data_processing:
Raw fastq files were imported into Strand software (v9.5, Agilent) for trimming, alignment and statistical analysis.  Sequence with a Q score of <30 were discarded, 1 base from the 3’ and 5’, and adaptors sequences were removed.
Reads were aligned to mm10  and duplicate reads were removed. Raw counts  were computed for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id  and raw counts for each gene, in each sample

organism: Mus musculus

source_name: ILC2 cells

extract_protocol:
trizol was used to extract RNA using standard protocol from the vendor.
RNA libraries were prepared for sequencing using standard Illumina protocols
Miseq 50v2

tag: strain

tag: genotype

value: plck-Id1 mice

tag: tissue

value: thymus

tag: cell type

value: ILC2 cells

tag: transduction

value: GFP

tag: time

value: 4-hydroxy-Tamoxifen for 16 hours


title: ILC2 cells , E47_16h_1

description: ILC2 cells transduced with MIGR1 vector expressing E47-ER


title: ILC2 cells , E47_16h_2


title: ILC2 cells , GFP_4h_2

description: ILC2 cells transduced with MIGR1 vector

value: 4-hydroxy-Tamoxifen for 4 hours


title: ILC2 cells , E47_4h_1


title: ILC2 cells , E47_4h_2


title: ILC2 cells , GFP_16h_2

description: ILC2 cells transduced with MIGR1 vector


title: Lgr5.HFcont.2

city: Bronx

first: Wenge

last: Li

state: NY

address: 1300 Morris Park Avenue

department: Medicine

institute: Albert Einstein College of Medicine

description: barcode: CGTACTAG-ATAGAGAG (N702-S502)

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using STAR (v2.4.2a) in per-sample 2-pass mode. The alignment was performed with default parameters, except --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --alignIntronMax 50000
The number of reads aligned to each defined gene was quantified using HTSeq-count (v0.6.1) with unstranded and union overlap resolution modes. Raw counts were normalized by converting the raw expression values to TPM (Transcript Per Million mapped reads) units using edgeR.
Supplementary_files_format_and_content: tab deliminated text file includes count values for each sample
Supplementary_files_format_and_content: tab deliminated text file includes TPM values for each sample
Genome_build: mm9

source_name: Intestinal Stem Cells

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified HF control diet at weaning and until 3 months of age

extract_protocol:
Isolated intestinal crypts were dispersed into single cell suspensions for FACS.  Lgr5 cells were the highest 2-3% subpopulation of Lgr5 fluorescent cells from Lgr5EGFP-creERT2 mice. Lgr5 cells were sorted and collected in bulk for RNA-seq. Total RNA was isolated using the TRI-Regent protocol.
RNA-seq libraries were prepared with a SMART-Seq v4 ultra low input RNA kit (Clontech) according to manufacturer's instructions.  Final library quality was verified with the Bioanalyzer assay (Agilent, Santa Clara, CA).
paired end sequencing libraries were constructed using a NEXTERA XT-library prep kit (Illumina).

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with HF control diet

value: Lgr5 cell

tag: age

value: 3 months old

tag: diet

value: HF control (10% calories from fat, Research Diets, 12450B)

value: intestine

tag: gender

value: female


title: Lgr5.HFcont.3

description: barcode: AGGCAGAA-AGAGGATA (N703-S503)

value: male


title: Lgr5.HFD.3

description: barcode: TAGGCATG-AGAGGATA (N706-S503)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified HFD diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with HFD diet

value: HFD (60% calories from fat, Research Diets, 12492)


title: Lgr5.HFD.2

description: barcode: TCCTGAGC-TCTACTCT (N704-S504)


title: Lgr5.AIN.1.

description: barcode: TCCTGAGC-ATAGAGAG (N704-S502)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on highly purified AIN76A diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with AIN76A diet

value: AIN76A (Research Diets, D10001)


title: Lgr5.HFcont.1

description: barcode: TAAGGCGA-TCTTACGC (N701-S517)


title: Lgr5.HFD.1

description: barcode: GGACTCCT-TCTTACGC (N705-S517)


title: ILC2 cells , GFP_4h_1

description: ILC2 cells transduced with MIGR1 vector


title: Lgr5.AIN.3.

description: barcode: TAGGCATG-TCTTACGC (N706-S517)


title: Lgr5.AIN.2.

description: barcode: GGACTCCT-AGAGGATA (N705-S503)


title: Lgr5.chow.3

description: barcode: AGGCAGAA-TCTTACGC (N703-S517)

growth_protocol: Lgr5EGFPcre-ERT2 mice were fed on chow diet at weaning and until 3 months of age

treatment_protocol: Lgr5EGFPcre-ERT2 mouse was fed with chow diet

value: chow (PicoLab 5058, LabDiets)


title: Lgr5.chow.1

description: barcode: TAAGGCGA-TCTACTCT (N701-S504)


title: Lyve-1 negative macrophages from mammary glands of 10-week-old mice, rep2

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

description:
Pooled macrophages isolated from inguinal mammary glands of 4 FVB/N mice by flow cytometry
Lyve1negative_rep2

data_processing:
Fastq files were mapped to the mm10/GRCm38 reference genome using HiSat2 (v. 2.0.2)
Counts were estimated using the Subread featureCounts (v1.5.0) tool using the Mus_musculus.GRCm38.74.gtf annotation
Genes less than 300 nt in length were removed
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts in text file

source_name: macrophage

growth_protocol: Mammary glands from 6-week-old and 10-week-old mice were harvested. After removal of inguinal lymph nodes, #4 mammary glands were dissected, minced, and digested with 1mg/mL Collagenase (Sigma-Aldrich) and 15μg/mL DNase I (Sigma-Aldrich) for 45 minutes with shaking at 37°C. The digested mammary glands were filtered through a 70μm cell strainer and pelleted by centrifugation at 500g for 5 minutes. Red blood cells were lysed with buffer containing 150mM ammonium chloride, 10mM potassium bicarbonate, and 0.1mM sodium EDTA at pH 7.4 and resuspended in FACS buffer (PBS containing 2% FBS and 1mM EDTA). Cells were stained for extracellular markers in FACS buffer at room temperature. Cell sorting was performed with a BD FACSAria II cell sorter. Lyve-1+ and Lyve-1- macrophages were identified and sorted as CD45+CD11b+F4/80+Lyve-1+ and CD45+CD11b+F4/80+Lyve-1-, respectively. Mammary gland #4 from both sides of n=4 mice were pooled for each sample.

extract_protocol:
RNeasy Mini Kit (Qiagen) was used to extract RNA from sorted cells for RNA-sequencing.
Clontech SMARTer Stranded Total RNA-seq Kit-Pico

value: FVB/N

value: week 10


title: Lyve-1 positive macrophages from mammary glands of 10-week-old mice, rep2

description:
Pooled macrophages isolated from inguinal mammary glands of 4 FVB/N mice by flow cytometry
Lyve1positive_rep2


title: Lyve-1 positive macrophages from mammary glands of 10-week-old mice, rep3

description:
Pooled macrophages isolated from inguinal mammary glands of 4 FVB/N mice by flow cytometry
Lyve1positive_rep3


title: Lgr5.chow.2

description: barcode: CGTACTAG-TCTACTCT (N702-S504)


title: Lyve-1 negative macrophages from mammary glands of 10-week-old mice, rep3

description:
Pooled macrophages isolated from inguinal mammary glands of 4 FVB/N mice by flow cytometry
Lyve1negative_rep3


title: Lyve-1 positive macrophages from mammary glands of 6-week-old mice, rep1

description:
Pooled macrophages isolated from inguinal mammary glands of 4 FVB/N mice by flow cytometry
Lyve1positive_rep1

value: week 6


title: Lyve-1 negative macrophages from mammary glands of 6-week-old mice, rep1

description:
Pooled macrophages isolated from inguinal mammary glands of 4 FVB/N mice by flow cytometry
Lyve1negative_rep1


title: Ribo-seq_liver_kd_7days-2

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

institute: Brigham and Women's Hospital

description:
Liver_mapped_reads_count_table.csv
Liver_mapped_reads_count_table.csv

data_processing:
Library strategy: Ribo-seq
analytical pipeline is available here: https://github.com/germaximus/Nesterchuk_2018
Genome_build: GRCm38.p4
Supplementary_files_format_and_content:  "read counts table" - contains mapped read counts per gene per sample; "list of significant GO categories" - contains Gene Onthology categories enriched in either control of eEF2 knockdown phenotype. Abbreviations bp, mp, and cc stand for biological process, molecular function, and cellular component correspondingly; "differential expression" - contains output of differential gene expression analysis with DESeq2 or limma packages in R

molecule: polyA RNA

source_name: liver

extract_protocol:
mRNA extracted with trizol and Direct-Zol kit from Zymo; ribosomal footprints isolated by fractionation of ribosomes using ultracentrifuge and then extracting footprints according to the protocol in the manuscript
mRNA-seq samples were prepared with TruSeq kit, Ribo-seq samples were prepared with custom protocol described in the manuscript; singe end illumina library

value: tissue

value: liver

tag: rna type

value: Ribosomal profiling

value: eef2 kd


title: Ribo-seq_liver_kd_7days-3


title: Ribo-seq_liver_kd_7days-1


title: Ribo-seq_liver_control-2

value: control


title: Ribo-seq_liver_control-1


title: mRNA-seq_liver_kd_12days-1

data_processing:
analytical pipeline is available here: https://github.com/germaximus/Nesterchuk_2018
Genome_build: GRCm38.p4
Supplementary_files_format_and_content:  "read counts table" - contains mapped read counts per gene per sample; "list of significant GO categories" - contains Gene Onthology categories enriched in either control of eEF2 knockdown phenotype. Abbreviations bp, mp, and cc stand for biological process, molecular function, and cellular component correspondingly; "differential expression" - contains output of differential gene expression analysis with DESeq2 or limma packages in R

value: polyA enriched mRNA-seq

value: 12 days


title: mRNA-seq_liver_kd_12days-2


title: mRNA-seq_liver_kd_9days-3

value: 9 days


title: Ribo-seq_liver_control-3


title: mRNA-seq_liver_kd_9days-1


title: mRNA-seq_liver_kd_9days-2


title: mRNA-seq_liver_kd_7days-1

value: 7 days


title: mRNA-seq_liver_control-2


title: mRNA-seq_liver_kd_12days-3


title: mRNA-seq_liver_control-3


title: mRNA-seq_liver_control-1


title: mRNA-seq_liver_kd_7days-3


title: mRNA-seq_liver_kd_7days-2


title: AML12_kd-2

description:
AML12_mapped_reads_count_table.csv
AML12_mapped_reads_count_table.csv

source_name: AML12 cell line

growth_protocol: DMEM medium with 10% FBS serum

treatment_protocol: 10 nM anti-eef2 siRNA

value: cell culture

value: AML12 cell line


title: AML12_kd-1


title: AML12_control-4

treatment_protocol: 10 nM anti-luciferase siRNA


title: AML12_kd-3


title: AML12_control-3


title: AML12_control-2


title: AML12_control-1


title: AML12_kd-4


title: Dp16 pool (miRNA)

city: Guangzhou

first: Xiaoling

last: Jiang

state: Guangdong

address: 9 Jinsui Road, Tianhe District

department: Department of Genetics and Endocrinology

institute: Guangzhou Women and Children's Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Tophat2 or BWA(miRNA)
The number of reads per million reads (RPM) were calculated for miRNA and circRNA, Reads Per Kilobase of transcript sequence per million base pairs sequenced (RPKM were calculated for mRNA and lncRNA.
Genome_build: GRCm38
Supplementary_files_format_and_content: Files include RPM values for each sample group

source_name: Hippocampus

extract_protocol:
Hippocampi were fast isolated and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA).Three independent libraries were constructed for miRNA, lncRNA and circRNA sequencing respectively. Specifically, for miRNA sequencing: 5’-adaptor and 3’-adaptor were first added to the total RNA, and a cDNA sub-library with insert of 18-40 nt was isolated by agarose electrophoresis and subject to sequencing; for lncRNA sequencing, ribosomal RNA was removed prior to the library construction by Epicentre Ribo-zero rRNA Removal Kit (Illumina, USA); for circRNA, linear RNA was removed from the ribosomal RNA-depleted RNA by using RNase R before establishing the sequencing libraray.

value: Hippocampus

value: Postnatal day 7

value: Trisomy


title: WT pool (miRNA)

value: WT


title: metastatic CRC peritoneal lesion, 13P

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
bcl2fastq: demultiplexes sequencing data and converts base call (BCL) files into FASTQ files version: v2.20.0.422
Read quality and adapter trimming: cutadapt v1.9.1; parameters: -q 15 -m 50
Read alignment: hisat2 v2.0.4, basen on reference hg19. Parameters: --qc-filter
Gene abundance quantification: htseq v0.9.1, parameters: -m intersection-nonempty -t exon
Genome_build: hg19
Supplementary_files_format_and_content: count table generated in csv, columns denote the patient sample ID, and rows denote the transcript ID

source_name: Colorectal cancer (CRC)

growth_protocol: Organoid cultures were derived from laparoscopic biopsies of peritoneal deposits or surgical resection of primary colorectal cancer as described3 except that all in our study were cultured in low (5%) oxygen conditions. 3. Sato et al., Gastroenterology 2011; 141:1762-72. documented by short tandem repeat DNA profiling to represent the source peritoneal tumor and were ambient shipped overnight between collaborating institutes in Australia and Seattle, USA, with minimal loss of viability.

extract_protocol:
For the RNA extraction, we used the Qiagen RNeasy mini kit (Catalog no 74104). For tissue samples, we follow protocol on page 45 -52 of the handbook. For organoids, we follow protocol on page 27-34 of the handbook. For all RNA extraction, DNase digestion of RNA was performed (page 85-86 of the handbook). RNA was eluted in 30ul of RNAse-free water and analysed using Nanodrop.
Quantity and integrity of total RNA was assessed using the Agilent 4200 TapeStation (Agilent Technologies). Ribosomal RNA was removed from up to 1μg of total RNA using the NEBNext® rRNA Depletion Kit. Illumina compatible Next Generation Sequencing (NGS) libraries were prepared according to standard protocols (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB). Briefly, the RNA was fragmented and first strand cDNA was reverse transcribed from RNA fragments using random primers.  The second strand cDNA was synthesised using a dUTP mix, and hairpin adapters were ligated to the cDNA fragments. The dUTP sites were cleaved, linearising library molecules and retaining only anti-sense strands (directionality). The libraries were amplified using indexed primers. Indexed libraries were pooled and sequenced on an Illumine NextSeq 500 to generate 25-50 million paired-end 75 bp reads per sample

value: peritoneum

tag: metastasis

value: metastatic


title: metastatic CRC peritoneal lesion, 16


title: metastatic CRC peritoneal lesion, 17


title: paired primary CRC resected lesion, 13C

value: colon

value: primary


title: metastatic CRC peritoneal lesion, 12


title: paired primary CRC resected lesion, 6C


title: paired primary CRC resected lesion, 7C


title: metastatic CRC peritoneal lesion, 6P


title: metastatic CRC peritoneal lesion, 8


title: metastatic CRC peritoneal lesion, 7P


title: Patient: 5767710

city: San Diego

first: Zhou

last: Zhu

state: CA

address: 10646 Science Center Drive (CB4)

institute: Pfizer Worldwide Research & Development

description: Targeted RNA profiling by EdgeSeq Oncology BM Panel

data_processing:
The HTG EdgeSeq Parser was used for post-sequencing data processing.
Genome_build: hg19
Supplementary_files_format_and_content: Data are provided as raw counts and normalized.

source_name: Baseline tumor tissue

extract_protocol:
The EdgeSeq system used targeted capture sequencing to quantitate RNA expression levels of gene targets in FFPE tissues.
Targeted RNA-Seq: Library preparation was conducted by following the laboratory process and manufacturer protocols.

treatment_protocol: FFPE (formalin-fixed paraffin-embedded) tissues

tag: subject status

value: breast cancer

tag: subject id

value: Patient 5767710


title: metastatic CRC peritoneal lesion, 4


title: Patient: 13574505


title: metastatic CRC peritoneal lesion, 18


title: Patient: 7814151

value: Patient 7814151


title: metastatic CRC peritoneal lesion, 2


title: metastatic CRC peritoneal lesion, 5


title: metastatic CRC peritoneal lesion, 1


title: Patient: 10624307


title: Patient: 7209803

value: Patient 7209803


title: metastatic CRC peritoneal lesion, 3


title: Patient: 10938880


title: Patient: 14103005


title: Patient: 6032127

value: Patient 6032127


title: Patient: 7546971

value: Patient 7546971


title: Patient: 10889166


title: Patient: 18627396


title: Patient: 11154714


title: Patient: 15682192


title: Patient: 15230090


title: Patient: 15479044


title: metastatic CRC peritoneal lesion, 10


title: Patient: 16025726


title: Patient: 17561718


title: Patient: 8242272

value: Patient 8242272


title: Patient: 7017345

value: Patient 7017345


title: Patient: 7546051

value: Patient 7546051


title: Patient: 4815830

value: Patient 4815830


title: Patient: 13871331


title: Patient: 8993547

value: Patient 8993547


title: Patient: 7049735

value: Patient 7049735


title: Patient: 8165228

value: Patient 8165228


title: Patient: 17785838


title: Patient: 7457891

value: Patient 7457891


title: Patient: 7430345

value: Patient 7430345


title: Patient: 4970694

value: Patient 4970694


title: Patient: 6485896

value: Patient 6485896


title: Patient: 11230924

value: breast cancer


title: Patient: 17232708


title: Patient: 10066884


title: Patient: 9193430

value: Patient 9193430


title: Patient: 13166516


title: Patient: 13191880


title: Patient: 12554084


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title: Patient: 8701902

value: Patient 8701902


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title: Patient: 7874444

value: Patient 7874444


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title: Patient: 6310840

value: Patient 6310840


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value: Patient 7733329


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value: Patient 5377347


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title: Patient: 6871316

value: Patient 6871316


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value: Patient 8576024


title: Patient: 6466540

value: Patient 6466540


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title: Patient: 10525114


title: Patient: 5071071

value: Patient 5071071


title: Patient: 7012534

value: Patient 7012534


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value: Patient 4946494


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title: Patient: 8700754

value: Patient 8700754


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value: Patient 8637449


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value: Patient 7243292


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title: Patient: 16803876


title: Patient: 16146973


title: Patient: 14952444


title: Patient: 8857576

value: Patient 8857576


title: Patient: 17713998

value: breast cancer


title: Patient: 8370526

value: Patient 8370526


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value: Patient 9495337


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value: Patient 6312882


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value: Patient 9277646


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value: Patient 8837531


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value: Patient 6075672


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value: Patient 9708642


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value: Patient 8687552


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value: Patient 7466246


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value: Patient 8316505


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title: Patient: 5758362

value: Patient 5758362


title: Patient: 12514854

value: breast cancer


title: Patient: 19319294


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value: Patient 8052113


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value: Patient 9891108


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value: breast cancer


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value: Patient 7465340


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title: NEXTflex E 1

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

description:
Synthetic miRNA
BioO-13

data_processing:
Primary base calling and quality scoring was performed using RTA v1.18.66.4 (Illumina)
demultiplexing and processing with Bcl2fastq v2.18.0.12 (Illumina)
3' adapter were trimmed using cutadapt v1.15 with parameter -m 10
Remaining reads were mapped to the synthetic miRNA reference or customized miRNA reference based on miRBase v21 using Bowtie v1.1.2 with parameter -a and --norc, no mismatches allowed
Reads were counted a custom python script
Genome_build: synthetic miRNA reference and customized miRNA reference based on miRBase v21

organism: synthetic construct

source_name: Synthetic miRNA

extract_protocol:
Synthetic miRNA samples: no RNA extraction needed, human samples: RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
NEBNext, NEXTflex

tag: library prep kit

value: NEXTflex

tag: mix type/state

value: E

tag: replicate


title: NEXTflex E 2

description:
Synthetic miRNA
BioO-14


title: NEXTflex D 3

description:
Synthetic miRNA
BioO-12

value: D


title: NEXTflex D 2

description:
Synthetic miRNA
BioO-11


title: Patient: 5300287

value: Patient 5300287


title: NEXTflex E 3

description:
Synthetic miRNA
BioO-15


title: Patient: 10660591


title: Patient: 4861964

value: Patient 4861964


title: Patient: 9639886

value: Patient 9639886


title: Patient: 11203617

value: breast cancer


title: Patient: 5598282

value: Patient 5598282


title: NEXTflex D 1

description:
Synthetic miRNA
BioO-10


title: NEXTflex A 3

description:
Synthetic miRNA
BioO-3

value: A


title: NEXTflex C 1

description:
Synthetic miRNA
BioO-7

value: C


title: NEXTflex C 2

description:
Synthetic miRNA
BioO-8


title: NEXTflex B 3

description:
Synthetic miRNA
BioO-6

value: B


title: NEXTflex B 2

description:
Synthetic miRNA
BioO-5


title: NEXTflex C 3

description:
Synthetic miRNA
BioO-9


title: NEXTflex B 1

description:
Synthetic miRNA
BioO-4


title: Patient: 5883640

value: Patient 5883640


title: NEXTflex A 1

description:
Synthetic miRNA
BioO-1


title: NEBNext E 3

description:
Synthetic miRNA
NEB-15

value: NEBNext


title: Patient: 14977982


title: NEXTflex A 2

description:
Synthetic miRNA
BioO-2


title: NEBNext E 1

description:
Synthetic miRNA
NEB-13


title: Patient: 13705820


title: NEBNext D 3

description:
Synthetic miRNA
NEB-12


title: Cech-588-12

city: Boulder

first: Tom

last: Cech

state: CO

address: 3415 Colorado Avenue

department: BioFrontiers Institute

institute: University of Colorado Boulder, Boulder

description:
Crosslinked RNA pulldown by EZH2
fRIPseq_count_genebody.csv
fRIP-Seq

data_processing:
For ChIP-seq, Illumina sequencing adapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC was clipped by cutadapt. BWA was used for alignment with the following options: “-q 5 -l 32 -k 2”.  Samtools was used to keep only the primary alignments whose mapping score was greater than 30. Potential duplicates identified by Picard MarkDuplicates were removed. Coverage files (bigwig) were generated using bedtools and UCSC bedGraphToBigWig after pooling replicates for a given clone. Coverage is scaled as reads per million reads (RPM). Macs2 was used to call peaks with "--keep-dup all --nomodel --extsize X --bdg --broad" where X was found by SPP.
For fRIP-seq, STAR was used for alignment with GENCODE (v27) gene annotation. Samtools was used to keep only the primary alignments. Potential duplicates identified by Picard MarkDuplicates were removed. FeatureCounts were used to count reads in gene bodies (GENCODE v27) in a strand specific way.
For RNA-seq, STAR was used for alignment with GENCODE (v27) gene annotation. The number of reads were counted in a strand specific way for every gene annotated in GENCODE (v27) by featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: For fRIP-seq, comma seperated file has the read counts for every gene in the GENCODE (v27) gene annotation.
Supplementary_files_format_and_content: For RNA-seq, comma seperated file has the transcripts per million reads (TPM) for every gene in the GENCODE (v27) gene annotation.
Supplementary_files_format_and_content: For ChIP-seq, bigwigs and Macs2 peaks were provided for biologically independent clones.

source_name: iPSC

growth_protocol: Undifferentiated iPSCs were cultured in Essential 8 Flex medium on Vitronection-coated plates. Cardiomyocyte differentiation was induced using GSK3 inhibitor CHIR99021 and Wnt inhibitor IWP2 (GiWi protocol, Lian et al. Nature Protocol 2013)

extract_protocol:
Total RNA or RNA samples in fRIP-seq were extracted with Trizol following manufactuer's protocol. DNA samples in ChIP-seq was extracted using phenol-chloroform.
KAPA RNA Hyperprep kit with riboerase (RNA-seq and fRIP-seq), KAPA HyperPlus Kit (ChIP-seq)

value: iPSC

tag: clone

value: MT-B

tag: genotype/variation

value: mutant EZH2

tag: differentiation

value: Undifferentiated


title: NEBNext D 2

description:
Synthetic miRNA
NEB-11


title: NEBNext D 1

description:
Synthetic miRNA
NEB-10


title: HC11_LPS

type: RNA

city: Bethesda

first: Kristin

middle: V

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK

data_processing:
Normalization of Nanostring nCounter data was performed as described previously (Urrutia A et al.), using nSolver (v. 2.5) for quality and negative and positive control analysis. Differences in RNA input were normalized using six housekeeping genes (EEF1G, RPL19, PPIA, TBP, G6PD, POLR2A), selected with the geNorm method. We estimated a lower limit of detection (LoD) of 4 counts using genes with consistent, low, non-zero expression across multiple samples, and retained 520 genes with expression above this LoD in greater than or equal to 1/3 of samples from any stimulation in either subject group. Multi-dimensional scaling (MDS) of gene counts revealed batch differences associated with the sample quantification method; ComBat in the sva R package was used to remove this batch effect prior to downstream analyses. Data were log2 transformed, and differential gene expression was determined using limma-voom, accounting for non-independence of samples from the same subject using limma’s duplicateCorrelation. Comparisons of the stimulation effect between groups used the interaction term between disease status and stimulus to capture the difference between groups in the change from the unstimulated sample. Multiple comparisons were adjusted using the Benjamini-Hochberg false discovery rate (FDR).
value definition: nonlog2 geNorm normalized values

source_name: whole blood

extract_protocol: After blood draw and incubation, supernatant and cells were separated for downstream assays of secreted proteins and mRNA, respectively.  Gene expression was quantified from stimulated whole blood samples using the Nanostring nCounter Human Immunology kit v2, which profiles 579 immunology-related genes and 15 reference genes. Total mRNA was extracted from TruCulture cell pellets stabilized in Trizol LS (Sigma) using a modified protocol of the NucleoSpin 96 RNA tissue kit protocol (Macherey-Nagel) as previously described (Urrutia A et al. Standardized whole-blood transcriptional profiling enables the deconvolution of complex induced immune responses. Cell Rep. 2016). 100 ng of total RNA were analyzed per sample.

treatment_protocol: Peripheral blood was drawn directly into TruCulture tubes (Myriad RBM, Austin, Texas, USA) for stimulation following manufacturer’s instructions and as previously described. Tubes were pre-loaded with cell culture media and one of the following immune stimuli: SEB (0.4 ug/ml), IL-1B (25 ng/ml or 1760 IU/ml), LPS (1 ng/ml), IFN-B (1000 IU/ml), polyIC (20 ug/ml), or a no-stimulus null control, with stimulus concentrations previously determined  (Duffy D et al. Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli. Immunity 2014).

tag: patientid

tag: disease

value: Healthy control

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

value: tecan

tag: ageatdraw

tag: Sex

value: male

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue

value: whole blood


title: HC11_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: Patient: 14817370

tag: subject status

value: breast cancer

tag: subject id


title: Cech-588-10

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: Overnight culture of Salmonella Typhimurium exposed to chlorine for 30 min

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: The labeled mixtures were further purified using a QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from the treatment and control were used to hybridize on S. Typhimurium LT2 genome microarrays (version 2), obtained from JCVI (formerly, TIGR, Rockville, MD) and provided by the Pathogen Functional Genome Resource Center (PFGRC). These arrays were amplicon arrays with 6780 ORF each, with 2 replicate spots per ORF. The labeled cDNA was applied to the above arrays. Hybridization was carried out overnight at 42°C in a water bath using Corning hybridization chamber. The pre- and post-hybridization was carried out using the the PFGRC SOP #M008.

scan_protocol: The slides were washed and scanned using a GenePix 4100A scanner (Axon Instruments Inc., Union City, CA) at 532 nm (Cy3 channel) and 635 nm (Cy5 channel), and the images were stored for further analysis.

data_processing:
The slides were prehybridized following PFGRC's SOP # M007.
The signal intensity of each gene was globally normalized using LOWESS within the R statistics package. The normalized data was analyzed using commercial SAS 9.1.3 program (SAS Institute Inc. Cary, NC).

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Untreated Salmonella Typhimurium

label_protocol: Total RNA (5 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNA was labeled with Cy-5 mono-Reactive Dye (GE Health Care).

extract_protocol: Total RNA was isolated from the cultures using an RNeasy mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocol. RNAprotect bacteria reagent (QIAGEN, Inc., Valencia, CA) was added to the cultures to stabilize RNA before isolation. The RNase-free DNase set (QIAGEN, Inc., Valencia, CA) was used for on-column DNase digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using ND-1000 spectrophotometer (NanoDrop® Technologies, Wilmington, DE) and bioanalyser 2100 (Agilent Technologies, Santa Clara, CA) respectively.

tag: protocol

value: Untreated

source_name: Overnight grown culture of Salmonella Typhimurium exposed to 30 minute of Chlorine


title: Fresh culture of Salmonella Typhimurium exposed to chlorine for 30 minutes

source_name: Fresh culture of Salmonella Typhimurium exposed to 30 minute of Chlorine


title: HC11_IL1

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC11_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: tissue


title: Cech-588-9

tag: cell type

tag: clone

value: MT-A

tag: genotype/variation

tag: differentiation


title: HC11_Null

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: Overnight culture of Salmonella Typhimurium exposed to chlorine for 0 min

tag: protocol

source_name: Overnight grown culture of Salmonella Typhimurium exposed to 0 minute of Chlorine


title: Cech-588-8

tag: cell type


title: T1D03_SEB

tag: patientid

tag: disease

value: type 1 diabetes

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Fresh culture of Salmonella Typhimurium exposed to chlorine for 0 min

source_name: Fresh culture of Salmonella Typhimurium exposed to 0 minute of Chlorine


title: NEBNext C 1

description:
Synthetic miRNA
NEB-7

tag: library prep kit

value: NEBNext

tag: mix type/state

value: C

tag: replicate


title: NEBNext E 2

description:
Synthetic miRNA
NEB-14

value: E


title: HC11_IFNb

value: IFNb

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: Cech-588-11

tag: cell type

value: iPSC

tag: clone

value: MT-B

tag: genotype/variation

value: mutant EZH2

tag: differentiation

value: Undifferentiated


title: T1D03_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

value: male

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC06_IFNb

value: Healthy control

value: female

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

value: whole blood


title: T1D03_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: Cech-588-7

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: HC06_IL1

value: tecan

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D03_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: NEBNext C 3

description:
Synthetic miRNA
NEB-9

tag: library prep kit

tag: mix type/state

tag: replicate


title: HC06_Null

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: T1D03_IFNb

tag: patientid

tag: disease

value: type 1 diabetes

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: tissue


title: NEBNext C 2

description:
Synthetic miRNA
NEB-8

tag: library prep kit

tag: mix type/state

tag: replicate


title: HC06_LPS

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: HC06_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: il-1 beta

tag: tnf-alpha


title: HC06_PolyIC

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: absolute monocytes

tag: tissue


title: NEBNext A 2

description:
Synthetic miRNA
NEB-2

tag: library prep kit

value: NEBNext

tag: mix type/state

value: A

tag: replicate


title: NEBNext A 3

description:
Synthetic miRNA
NEB-3


title: HC01_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: T1D03_IL1

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: il-1 beta

tag: tnf-alpha


title: HC01_IFNb

tag: patientid

tag: disease

tag: stimulusid

value: IFNb

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: absolute monocytes

tag: tissue


title: HC01_Null

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: NEBNext A 1

description:
Synthetic miRNA
NEB-1

tag: library prep kit

tag: mix type/state

tag: replicate


title: Cech-588-2

tag: cell type

value: iPSC

tag: clone

value: WT-A

tag: genotype/variation

value: wild type

tag: differentiation


title: NEBNext B 3

description:
Synthetic miRNA
NEB-6

value: B


title: HC01_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: absolute monocytes

tag: il-1 beta

tag: tnf-alpha


title: Cech-588-6

tag: cell type

tag: clone

value: WT-B

tag: genotype/variation

value: Undifferentiated


title: HC01_PolyIC

tag: patientid

tag: disease

value: Healthy control

tag: Sex

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: tissue


title: HC01_SEB

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: absolute monocytes

value: whole blood


title: Cech-588-1

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: NEBNext B 2

description:
Synthetic miRNA
NEB-5

tag: library prep kit

tag: mix type/state

tag: replicate


title: T1D17_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

value: tecan

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-588-5

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: T1D17_Null

tag: patientid

tag: disease

tag: stimulusid

tag: quantmachine

tag: ageatdraw

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: absolute monocytes


title: NEBNext B 1

description:
Synthetic miRNA
NEB-4

tag: library prep kit

tag: mix type/state

tag: replicate


title: T1D17_IL1

tag: extractionbatch

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-588-4

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: T1D17_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: quantmachine

tag: ageatdraw

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: absolute monocytes


title: Cech-468-11

description:
Crosslinked RNA input
fRIPseq_count_genebody.csv
fRIP-Seq

value: MT-B

value: mutant EZH2


title: Cech-588-3


title: Cech-468-10


title: T1D17_SEB

value: type 1 diabetes

value: SEB

tag: extractionbatch

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D14_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: quantmachine

tag: ageatdraw

value: male

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: T1D14_IFNb

value: IFNb

tag: extractionbatch

value: qubit

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: absolute monocytes


title: T1D17_PolyIC

tag: percent monocytes

tag: percent neutrophils

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-468-9

tag: cell type

value: iPSC

tag: clone

value: MT-A

tag: genotype/variation

tag: differentiation


title: Cech-468-8


title: T1D14_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: T1D14_Null

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D14_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: T1D15_LPS

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-468-7

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: Cech-468-6

value: WT-B

value: wild type


title: Cech-468-5

value: Undifferentiated


title: T1D15_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-468-4


title: T1D15_PolyIC

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: T1D15_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D15_IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC16_LPS

value: Healthy control

value: female

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: HC16_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

value: tecan

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

value: whole blood


title: HC16_IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-468-3

tag: cell type

tag: clone

value: WT-A

tag: genotype/variation

tag: differentiation


title: HC16_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-468-2


title: HC13_IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC16_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: HC13_Null

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: HC16_IL1

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-468-1

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: Cech-659-24

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: MT-B

value: mutant EZH2

value: Day12 cardiomyocytes


title: HC13_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

value: male

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: HC13_LPS

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D14_IL1

tag: patientid

tag: disease

value: type 1 diabetes

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: T1D13_PolyIC

value: PolyIC

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-659-22

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

value: iPSC

tag: clone

tag: genotype/variation

tag: differentiation


title: HC13_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D13_IL1

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-659-21

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: HC13_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D15_IL1

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: T1D13_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D13_IFNb

value: IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-20

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation

value: Day8 cardiomyocytes


title: T1D13_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-659-19

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: MT-A


title: Cech-659-23

description:
rRNA-depleted RNA
rnaseq_tpm.csv


title: HC04_SEB

value: Healthy control

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-18

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

value: WT-B

tag: genotype/variation

value: wild type

tag: differentiation


title: HC04_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

value: tecan

value: female

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

value: whole blood


title: HC04_PolyIC

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-17

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

value: WT-A

tag: genotype/variation

tag: differentiation


title: Cech-659-16

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: MT-B

value: mutant EZH2

value: Day12 cardiomyocytes


title: HC04_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: T1D13_LPS

value: type 1 diabetes

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC04_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: HC14_SEB

value: SEB

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: HC04_IL1

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-15

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

value: iPSC

tag: clone

tag: genotype/variation

tag: differentiation


title: HC14_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: HC14_IL1

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC14_IFNb

tag: patientid

tag: disease

tag: stimulusid

value: IFNb

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: Cech-659-14

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: HC14_Null

value: Healthy control

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D07_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC14_LPS

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-659-12

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation

value: Day8 cardiomyocytes


title: T1D07_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D07_SEB

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-13

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

value: wild type

tag: differentiation


title: T1D07_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D07_Null

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-10

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

value: WT-B

tag: genotype/variation

tag: differentiation


title: T1D07_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

value: tecan

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: Cech-659-11

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: MT-A


title: T1D04_Null

value: female

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue

value: whole blood


title: T1D04_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: Cech-659-9

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

value: WT-A

tag: genotype/variation

tag: differentiation


title: Cech-468-12

value: MT-B

value: mutant EZH2

value: Undifferentiated


title: T1D04_IFNb

value: type 1 diabetes

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: Cech-659-8

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: iPSC

value: Day12 cardiomyocytes


title: T1D04_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D02_Null

value: male

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: T1D04_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D02_IFNb

value: IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D02_IL1

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: Cech-659-5

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

value: wild type

tag: differentiation


title: Cech-659-6

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: WT-B


title: T1D02_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D02_LPS

value: LPS

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-659-4

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation

value: Day8 cardiomyocytes


title: T1D02_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: HC05_PolyIC

value: Healthy control

value: tecan

value: female

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue

value: whole blood


title: T1D04_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: Cech-659-3

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

value: MT-A

tag: genotype/variation

value: mutant EZH2

tag: differentiation


title: Cech-659-2

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: iPSC


title: HC05_IFNb

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: YL7

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: Undifferentiated


title: Cech-659-7

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: Day12 cardiomyocytes


title: YL6

description:
rRNA-depleted RNA
rnaseq_tpm.csv


title: HC05_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC05_Null

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: HC05_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: YL8

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

value: MT-B

tag: genotype/variation

tag: differentiation


title: T1D01_SEB

value: type 1 diabetes

value: SEB

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: YL5

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: WT-A

value: wild type


title: Cech-659-1

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: Day8 cardiomyocytes


title: T1D01_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf


title: T1D01_IFNb

value: IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: Dp16 pool (lncRNA)

description:
mRNA_exp.txt
lncRNA_exp.txt

tag: strain

tag: tissue

value: Hippocampus

tag: age

value: Postnatal day 7

tag: genotype

value: Trisomy


title: YL3

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: YL2

description:
rRNA-depleted RNA
rnaseq_tpm.csv

value: WT-B


title: T1D01_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

value: female

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

value: whole blood


title: T1D01_LPS

value: LPS

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: tissue


title: WT pool (lncRNA)

description:
mRNA_exp.txt
lncRNA_exp.txt

tag: strain

tag: age

tag: genotype

value: WT


title: Dp16 pool (circRNA)


title: HC05_LPS

tag: patientid

tag: disease

value: Healthy control

tag: stimulusid

tag: extractionbatch

value: tecan

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)


title: WT pool (circRNA)


title: YL1

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

value: iPSC

tag: clone

tag: genotype/variation

tag: differentiation

value: Undifferentiated


title: T1D01_PolyIC

value: type 1 diabetes

value: PolyIC

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-454-28

description:
DNA input
Cech-454-28_S28.markDup.scaled.sorted.bw

library_source: genomic

molecule: genomic DNA

tag: cell type

value: MT-B

value: mutant EZH2


title: T1D12_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

value: male

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)


title: T1D12_Null

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: T1D12_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D12_SEB

value: SEB

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)


title: Cech-454-27

description:
DNA input
Cech-454-27_S27.markDup.scaled.sorted.bw

tag: cell type

tag: clone

value: MT-A

tag: genotype/variation

tag: differentiation


title: Cech-454-25

description:
DNA input
Cech-454-25_S25.markDup.scaled.sorted.bw

value: WT-A

value: wild type


title: Cech-454-26

description:
DNA input
Cech-454-26_S26.markDup.scaled.sorted.bw

value: WT-B


title: Cech-491-12

description:
DNA pulldown by H3K27me3
MTb_H3K27me3.pooled.RPM.sorted.bw
MTb_H3K27me3_peaks.broadPeak


title: T1D12_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf

value: whole blood


title: Cech-491-11


title: T1D12_IFNb

value: IFNb

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: YL4

description:
rRNA-depleted RNA
rnaseq_tpm.csv

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: T1D06_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: Cech-491-10


title: Cech-491-8

description:
DNA pulldown by H3K27me3
MTa_H3K27me3.pooled.RPM.sorted.bw
MTa_H3K27me3_peaks.broadPeak


title: Cech-491-9


title: T1D06_SEB

tag: quantmachine

value: tecan

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-491-7

tag: cell type

value: iPSC

tag: clone

tag: genotype/variation

tag: differentiation


title: T1D06_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: T1D06_Null

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-491-6

description:
DNA pulldown by H3K27me3
WTb_H3K27me3.pooled.RPM.sorted.bw
WTb_H3K27me3_peaks.broadPeak

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation

value: Undifferentiated


title: T1D06_PolyIC

tag: patientid

tag: disease

value: type 1 diabetes

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: T1D06_LPS

value: LPS

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-491-4

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: Cech-491-3

description:
DNA pulldown by H3K27me3
WTa_H3K27me3.pooled.RPM.sorted.bw
WTa_H3K27me3_peaks.broadPeak


title: Cech-491-2


title: HC15_IFNb

tag: patientid

tag: disease

value: Healthy control

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: HC15_LPS

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-491-1

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: HC15_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: HC15_IL1

tag: quantmachine

value: qubit

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-558-22

description:
DNA pulldown by EZH2
MTb_EZH2.pooled.RPM.sorted.bw
MTb_EZH2_peaks.broadPeak

tag: cell type

tag: clone

value: MT-B

tag: genotype/variation

value: mutant EZH2

tag: differentiation


title: Cech-558-23


title: Cech-558-24


title: HC15_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

value: male

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: Cech-491-5


title: HC17_LPS

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-558-20

description:
DNA pulldown by EZH2
MTa_EZH2.pooled.RPM.sorted.bw
MTa_EZH2_peaks.broadPeak

tag: cell type

tag: clone

value: MT-A

tag: genotype/variation

tag: differentiation


title: Cech-558-21


title: HC17_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: gm-csf


title: DLD/OHP1

city: Nishinomiya

first: Tomoki

last: Yamano

state: Hyogo

address: 1-1 Mukogawa-cho

department: Department of Surgery

country: Japan

institute: Hyogo College of Medicine

description: Gene expression without drug treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Scanned data was imported and normalized by GeneSpring GX (normalize to 75 percentile).

source_name: DLD/OHP1 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Colon cancer cell lines were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol: RNA was extracted using TRIzol and TRIzol RNA Purification kit (Invitrogen) following the manufacture's instructions.

treatment_protocol: Colon cancer cells were seeded at a density of one million cells in P10 plate and cultured for 24h hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: DLD/OHP1 (clone derived from DLD1)

tag: oxaliplatin resistance

value: resistant


title: HC17_PolyIC

value: PolyIC

tag: quantmachine

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: DLD/OHP5

description: Gene expression without drug treatment

source_name: DLD/OHP5 cells

value: DLD/OHP5 (clone derived from DLD1)


title: Cech-558-19

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: HCT/OHP5

description: Gene expression without drug treatment

source_name: HCT/OHP5 cells

tag: cell line

value: HCT/OHP5 (clone derived from HCT116)

tag: oxaliplatin resistance


title: HCT/OHP3

description: Gene expression without drug treatment

source_name: HCT/OHP3 cells

value: HCT/OHP3 (clone derived from HCT116)


title: DLD1

description: Gene expression without drug treatment

source_name: DLD1 cells

value: DLD1 colon cancer cell line

value: sensitive


title: DLD/OHP4

description: Gene expression without drug treatment

source_name: DLD/OHP4 cells

value: DLD/OHP4 (clone derived from DLD1)


title: HCT/OHP1

description: Gene expression without drug treatment

source_name: HCT/OHP1 cells

value: HCT/OHP1 (clone derived from HCT116)


title: Cech-558-18

description:
DNA pulldown by EZH2
WTb_EZH2.pooled.RPM.sorted.bw
WTb_EZH2_peaks.broadPeak

value: iPSC

value: WT-B

value: wild type

value: Undifferentiated


title: HCT116

description: Gene expression without drug treatment

source_name: HCT116 cells

value: HCT116 colon cancer cell line


title: HC17_IFNb

tag: patientid

tag: disease

value: Healthy control

tag: stimulusid

value: IFNb

tag: extractionbatch

tag: quantmachine

value: tecan

tag: ageatdraw

tag: Sex

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: gm-csf

value: whole blood


title: HC15_PolyIC

value: PolyIC

value: male

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-558-17

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: HC10_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: HC10_PolyIC

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC17_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: HC17_SEB

value: SEB

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils


title: HC10_IFNb

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Cech-558-16

tag: cell type

tag: clone

tag: genotype/variation

tag: differentiation


title: Cech-558-14

description:
DNA pulldown by EZH2
WTa_EZH2.pooled.RPM.sorted.bw
WTa_EZH2_peaks.broadPeak

value: WT-A


title: Cech-558-15


title: Cech-558-13


title: HC10_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes


title: HC10_SEB

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC08_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)


title: BMP_stim_1

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: matrix.txt

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38.27) using STAR 2.6.1d with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 08.03.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

source_name: PASMCs

growth_protocol: Anaeestetise and heparinise the animal interperitoneally and place one incision into the right heart ventricle and insert the catheter into the pulmonary artery and another incision into the left ventricle for drainage. Perfuse the lung with 3 ml PBS and instill the lung with 3 ml Iron-Agarose (0.5% Iron III Oxide and 0.5% Agarose in Medium 199). And then instill agarose (1% Agarose in Medium 199) into the trachea until the lung is completely filled. Wait shortly, then pull out the catheter and close the ligature and remove the lung out of the thorax and incubate the lung in the cold PBS for 10 minutes. Under a sterile hood, remove heart, aorta, oesophagus and any connective tissue from the lung and add 1-2ml of PBS to the lung lobes and mince the lobes into small pieces with scalpels. Pipette the minced lung slurry into sterile 50 ml conical tube. Add 10-30ml PBS and place tube into the magnetic holder (Invitrogen, MPC-1 Magnet,12001D), wait shortly, then aspirate and discard the liquid. Repeat 3 times. After washing, resuspend the lung pellet into 3 ml Collagenase type 2 (80U/ml in Medium 199 + 1% Pen/Strep) and place on a petri dish and incubate it for 1hour at 37°C. After incubation homogenize the tissue-Collagenase solution by aspirating and releasing it several times through a 15G needle and then an 18G needle. Wash via magnetic holder 3 times with PromoCell medium containing supplements and pour the pellets into a culture dish. Four days later, pour the supernatant into a new conical tube and wash the pellet via magnetic holder 3 times with PBS and culture the iron-containing pellet with PromoCell medium containing supplements. Once there are cells grown around the particles, the iron can be washed off and either seeded again or thrown away. Once the particles are taken off, media should be changed every 2 days.

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set; Qiagen) to avoid contamination by genomic DNA according to manufacturer's instructions.
Whole transcriptome libraries were constructed with SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian.

treatment_protocol: The cells were stimulated in Promocell medium without supplements with BMP9 (R&D 5566-BP-010) and BMP10 (R&D 6038-BP) at 1 ng/mL and 5 ng/mL respectively for 6 hours.

tag: strain

tag: cell type

value: smooth muscle cells

tag: treatment