title: cell-K30-shNC2

first: Shuman

last: Li

address: No. 651, Dongfeng Road East

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.  a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: esophageal cancer cell

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture  was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labelingreaction was incubated for 1 h at 16°C. c, Terminated by incubation for 15 min at 65°C.

growth_protocol: All the cells were cultured in Dulbecco’s modified Eagle medium (Gibico, CA) supplemented with 10% fetal bovine serum (HyClone, Logan, UT)

extract_protocol: Total RNA was extracted from ESCC tissues and cell lines using TRIzol reagent (Invitrogen).

treatment_protocol: Lentiviral psi-LVRU6GP containing short hairpin RNAs (shRNA) that target JMJD3 was purchased from GeneCopoeia (Guangzhou, China). Cells transfected with empty vector were used as controls.The transfection was performed by Lipofectamine 2000 according to the manufacturer’s instructions.

value: human esophageal squamous carcinoma

value: shRNA-NC


title: Untreated (MO7) Rep1

status: Public on Sep 02 2020

type: SRA

city: Hershey

first: Melat

middle: T

last: Gebru

state: PA

address: 95A University Manor East

department: Pediatrics

country: USA

institute: Penn State University

description:
Myeloid cells
Parental
mRNA

library_source: transcriptomic

data_processing:
Reads that passed the Illumina CASAVA pipeline were aligned to the human reference genome (hg38) using Tophat (v2.0.9).
FPKM counting and differential expression analysis were performed using the Cuffdiff tool by normalizing to the median of the geometric means of fragment counts across all samples.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.xlsx: Excel files include FPKM values.

molecule: total RNA

organism: Homo sapiens

source_name: MV4-11 cell line

growth_protocol: MV4-11 AML cells were cultured in IMDM supplemented with 10% FBS at 37oC and 5% CO2.

extract_protocol:
RNA was extracted from DTPs and parental MV4-11 cells using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific).
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) per the manufacturer’s instructions and run on Illumina HiSeq 2500.

treatment_protocol: MV4-11 AML cells were treated with 100nM quizartinib for 48h and surviving cells (DTPs) were isolated 48h post-treatment, 13d and 30d culture in drug-free media.

tag: cell line

tag: cell type

value: AML cell line

tag: treatment

value: Untreated


title: P09

type: genomic

city: Jeonju-si

first: Young-Chul

last: Chung

address: 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

department: Psychiatry

country: South Korea

institute: Medical School; Research Institute

description:
genomic DNA from PBMC
patient PBMC sample

hyb_protocol: The whole-genome amplification process requires 250ng of input bisulfite-converted DNA , MA1 and creates a sufficient quantity of DNA (1000X amplification) to be used on a single BeadChip in the infinium methylation assay (Illumina RPM and MSM). After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, then placed in a humidified container for a minimum of 16 h at 48°C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Background correction, BMIQ normalization, M value, box plot, correlation etc.Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: genomic DNA from PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: QIAamp DNA Mini Kit (QIAGEN, Germany)

tag: age

tag: gender

value: Male

tag: sample type

value: PBMC

tag: disease state

value: Schizophreniform disorder(295.40)


title: P20_adjacent non-tumour

city: Singapore

first: Caroline

last: Lee

address: 12 Science Drive 2

country: Singapore

institute: National University of Singapore

data_processing:
The original image data was transferred into sequence data via base calling, which was defined as raw reads and saved as FASTQ file.
The raw reads were filtered by removing adaptor sequences, contamination and low-queality reads.
The clean reads were aligned to a combined genome consisting of the hg19 genome and an HBV-B2 strain using the Tophat aligner (Settings used by Tophat: --min-anchor 8 --splice-mismatches 2 --min-intron-length 50 --max-intron-length 500000 --min-isoform-fraction 0.15 --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --mate-inner-dist 50 --mate-std-dev 20 --no-coverage-search).
Reads per kilo-base per million mapped reads (RPKM) were calculated for each transcript and exon using Partek Genomic Suite 6.6 from output BAM files based on HG19, Refseq version 2015.02.02 annotation.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Liver

extract_protocol:
Liver tissues were homogenized in RLT buffer using the gentleMACS dissociator and total RNA was isloated with RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD012_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male

tag: strain


title: P22_tumor

value: tumor


title: Ton186 CXCR5-CD45RA-CD8+

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

data_processing:
Trimmomatic was used to trim the sequence data by cutting first 25 bases for each reads. Tophat was used for the sequence alignment. HTSeq was used to count the read number of genes from each sample. The reads count by HTSeq were combined to be a matrix. The obtained raw reads count matrix was normalized and variance stabilized using DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: txt file, normalized gene expression matrix

source_name: Ton186 CXCR5-CD45RA-CD8+

extract_protocol: Total RNA from FACS-sorted CD45RA+CD8+, CXCR5-CD45RA-CD8+, and CXCR5+CD45RA-CD8+ T cells from human tonsil samples were extracted using Trizol, followed by purification using NucleoSpin RNA XS kit (CloneTech). The RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). RNA was amplified using the SMARTer® Universal Low Input RNA Kit. The RNA library was prepared following the protocol of TruSeq® Stranded Total RNA Sample Preparation from Illumina. Pair-end reads of 100 nt (2x100 nt) were obtained on Illumina HiSeq 2500.

value: tonsil

value: T cells

tag: cell markers

tag: patient id


title: cell-K30-shNC1

type: RNA

city: Guangzhou

country: China

institute: Sun Yat-sen University Cancer Center


title: P10

value: Female

value: Psychotic disorder NOS


title: P19_tumor


title: P13

value: Schizophrenia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD008_indexed


title: Ton186 CXCR5+CD45RA-CD8+

source_name: Ton186 CXCR5+CD45RA-CD8+


title: Ton186 CD45RA+CD8+

source_name: Ton186 CD45RA+CD8+


title: P06


title: Ton185 CD45RA+CD8+

source_name: Ton185 CD45RA+CD8+


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A9_AD010_indexed


title: MU_06.00_D_3

city: Yokohama

first: Anuphon

last: Laohavisit

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

data_processing:
50 bp single-ends reads were sequenced by Illumina NextSeq 500 and basecalls performed as described in Hasagawa et al., 2018 (doi:10.1038/s41598-018-25963-y)
Quality filtering was performed using the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Low Quality nucleotides (quality score < 30) were removed from the 3’end. Short reads (< 40 bp) and reads which showed at least 95 % nucleotides with low quality score (quality score < 20) were removed.
Filtered reads were mapped onto the Arabidopsis genome (TAIR10) with HISAT v2.1.0  (https://ccb.jhu.edu/software/hisat2/index.shtml) with a following setting: --max-intronlen 5000
Mapped reads were counted using HTseq v0.6.1 (13) (https://htseq.readthedocs.io/) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separate values, HTseq read count values

organism: Arabidopsis thaliana

source_name: 7-day old liquid-grown seedlings

growth_protocol: Arabidopsis seedling (WT-expressing aequorin and card1-2) were grown in liquid media containing half-strength Murashige-Skoog supplemented with 0.25 % sucrose. After 2 days stratification, seedlings were grown at 16 hr: 8 hr, light: dark, 22 C, 50 µE for 7 days

extract_protocol:
RNA were extracted using Qiagen RNeasy Plant mini kit with DNaseI-digestion
Libraries were then prepared using KAPA mRNA HyperPrep Kit according to the manufacturer’s instructions

treatment_protocol: Seedlings (7-day old) were treated with 5 µM DMBQ or DMSO (volume equivalent) for 0 hr, 0.5 hr, 1 hr and 6 hr

tag: ecotype

tag: agent

value: 5 microM DMBQ

tag: time point

value: 6 hr

tag: replicate

value: replicate 3

tag: genotype/variation


title: P19_adjacent non-tumour


title: P07

value: Attenuated psychosis syndrome


title: P18_tumor


title: Ton185 CXCR5-CD45RA-CD8+

source_name: Ton185 CXCR5-CD45RA-CD8+

tag: cell type


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD006_indexed


title: P14


title: P17_tumor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD002_indexed


title: P04


title: MU_06.00_D_1

value: replicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD006_indexed


title: Ton185 CXCR5+CD45RA-CD8+

source_name: Ton185 CXCR5+CD45RA-CD8+


title: P17


title: MU_01.00_D_3

value: 1 hr


title: P02

value: PBMC


title: P17_adjacent non-tumour


title: Dmpk;Six5;Mbnl1;Dmwd-KO

city: Shanghai

first: Qing

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

description: DSMD

data_processing:
Basecalls performed using CASAVA version 1.8.2
DNA resequencing reads were aligned to the mm10 genome assembly using bwa version 0.7.12 with the following configurations…
Transfering the raw data into bam file using samtools, marking the PCR duplication with Markduplicates of Picard and analyzing the mapping information through flagstat of samtools
Analyzing the SNV and InDel via HaplotypeCaller of GATK
Supplementary_files_format_and_content: BC171182-1.anno.vcf_exonic.snv

source_name: Androgenetic haploid embryonic stem cells

growth_protocol: 2i/Lif medium

extract_protocol:
The embryonic stem cells were collected and subjected to DNA extraction through Column recovery
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

tag: passages


title: P12

tag: age


title: MU_06.00_D_2

value: replicate 2


title: MU_01.00_D_2


title: Dmpk;Six5;Mbnl1-KO

description: DSM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD012_indexed

value: MOp


title: P03

tag: gender

value: Male


title: P01

tag: sample type


title: P16_tumor

value: tumor


title: P16_adjacent non-tumour

value: adjacent non-tumour


title: MU_01.00_D_1


title: P08

tag: disease state

value: delusional disorder


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD004_indexed

value: male


title: MU_00.50_D_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD006_indexed


title: P15_tumor

tag: tissue


title: P15_adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD002_indexed

tag: brain region


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD010_indexed

tag: Sex


title: P18_adjacent non-tumour


title: P34


title: WT

tag: strain

value: WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD007_indexed


title: MU_00.50_D_1


title: P25

value: Female

value: Schizophreniform disorder(295.40)


title: MU_00.00_D_3

value: 5 microM DMBQ

value: 0 hr


title: P14_adjacent non-tumour 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD001_indexed


title: P14_adjacent non-tumour 1


title: MU_00.00_D_1


title: P13_tumor


title: H5N1_M_24hr_3

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 24hr, bioreplicate 3

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: Influenza A/Vietnam/1203/2004 (H5N1, VN1203) or influenza A/California/04/2009 (H1N1, CA04) viral stocks were used to infect NHBE cells at a multiplicity of infection (MOI) of 1. Infections were allowed to progress for 1 hour. Next, 500,000 PBMC-derived macrophages were place onto each apical transwell surface in a final volume of 500 ul to create co cultures. The co-cultures at a ratio of approximately 2 NHBE cells for every PBMC-derived macrophage were allowed to progress for an additional 11, 15 and 23 hours respectively (12, 16, 24 hours post-infection). An n=5 was used for each condition, which included infection with either H1N1, H5N1, or mock uninfected, of either NHBE-only monocultures or NHBE + PBMC-macrophage co-cultures. In total this infection scheme represented a total of 90 samples for microarray analysis. At the specified time points, 1 ml of TRlzol RNA isolation reagent (Thermo Fischer, 15596-018) that lead to inactivation of samples.

tag: time

tag: virus


title: H5N1_M_24hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 24hr, bioreplicate 4


title: H5N1_M_24hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 24hr, bioreplicate 5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD008_indexed


title: MU_06.00_M_3

tag: ecotype

value: mock (DMSO)

value: 6 hr

value: replicate 3


title: P22

value: PBMC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD012_indexed


title: H5N1_M_24hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 24hr, bioreplicate 1


title: MU_06.00_M_2

tag: agent


title: H5N1_NM_24hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 24hr, bioreplicate 5


title: MU_00.00_D_2

tag: time point


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD006_indexed


title: H5N1_M_24hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 24hr, bioreplicate 2


title: MU_06.00_M_1

tag: replicate

value: replicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A4_AD002_indexed


title: P12_adjacent non-tumour


title: P11_tumor


title: MU_01.00_M_3

value: 1 hr

tag: genotype/variation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD001_indexed

value: MOp


title: cell-K30-JMJD3-sh2

source_name: esophageal cancer cell

value: human esophageal squamous carcinoma

tag: treatment


title: P11_adjacent non-tumour

source_name: Liver


title: H5N1_NM_24hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 24hr, bioreplicate 4


title: P13_adjacent non-tumour


title: H5N1_NM_24hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 24hr, bioreplicate 2


title: H5N1_NM_24hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 24hr, bioreplicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: cell-K30-JMJD3-sh1


title: P05

source_name: genomic DNA from PBMC

value: Male

value: Attenuated psychosis syndrome


title: MU_01.00_M_2

source_name: 7-day old liquid-grown seedlings

value: replicate 2


title: MU_00.50_D_2


title: MU_01.00_M_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD002_indexed

value: male


title: H1N1_M_24hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 24hr, bioreplicate 5


title: H5N1_NM_24hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 24hr, bioreplicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD007_indexed


title: H1N1_M_24hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 24hr, bioreplicate 4


title: MU_00.50_M_3


title: P10_adjacent non-tumour

value: adjacent non-tumour


title: MU_00.50_M_2


title: P9_tumor

value: tumor


title: MU_00.50_M_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD012_indexed


title: P9_adjacent non-tumour


title: MU_00.00_M_3


title: P14_tumor


title: P8_tumor


title: P10_tumor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD008_indexed


title: P8_adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD001_indexed


title: MU_00.00_M_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD010_indexed


title: MU_00.00_M_1


title: P7_tumor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A2_AD001_indexed


title: H1N1_M_24hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 24hr, bioreplicate 2


title: P7_adjacent non-tumour


title: H1N1_M_24hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 24hr, bioreplicate 1


title: P6_tumor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD008_indexed


title: H1N1_NM_24hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 24hr, bioreplicate 4


title: WT_06.00_D_2

value: WT


title: H1N1_NM_24hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 24hr, bioreplicate 5


title: WT_06.00_D_1

value: 5 microM DMBQ


title: WT_06.00_D_3


title: WT_01.00_D_3


title: P4_tumor


title: P6_adjacent non-tumour


title: H1N1_NM_24hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 24hr, bioreplicate 3


title: H1N1_NM_24hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 24hr, bioreplicate 2


title: H1N1_NM_24hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 24hr, bioreplicate 1


title: P4_adjacent non-tumour

source_name: Liver


title: Mock_M_24hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 24hr, bioreplicate 5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A11_AD002_indexed


title: WT_01.00_D_2


title: WT_01.00_D_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD010_indexed


title: P3_tumor


title: Mock_M_24hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 24hr, bioreplicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A11_AD001_indexed


title: Mock_M_24hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 24hr, bioreplicate 4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A11_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: P3_adjacent non-tumour


title: Mock_M_24hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 24hr, bioreplicate 2


title: Mock_M_24hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 24hr, bioreplicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD004_indexed


title: WT_00.50_D_2

source_name: 7-day old liquid-grown seedlings


title: P2_adjacent non-tumour


title: P2_tumor


title: WT_00.50_D_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A11_AD010_indexed


title: P1_tumor


title: WT_00.00_D_3

value: 0 hr


title: P12_tumor


title: WT_00.50_D_3


title: WT_00.00_D_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD004_indexed


title: WT_00.00_D_1


title: Mock_NM_24hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 24hr, bioreplicate 3


title: hnRNP U IP Mitosis 2

city: Boston

first: Michael

middle: Demian

last: Blower

state: MA

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Processed data file: UCSCGeneshg38.txt
Processed data file: lncRNAshg19.txt

data_processing:
Basecalls were performed using Illumina Hi-Seq control software.
Reads were aligned to hg19 or hg38 using TopHat.
Reads were counted against UCSC gene models or lncRNA gene models using StringTie.
Genes with a FPKM of 0 in any library were eliminated.
Genome_build: hg19/GRCh37 (lncRNAs), hg38/GRCh38 (UCSC genes)
Supplementary_files_format_and_content: Processed data files were created by merging gene-fpkm counts for all 8 libraries and removing genes with low read counts as described above.

source_name: hTERT-RPE1, mitosis, hnRNP U IP

extract_protocol:
Cells were lysed with lysis buffer containing 25 mM Tris pH 7.4, 150 mM KCl, 5 mM EDTA, 5 mM MgCl2, 1% NP-40, 0.5 mM DTT, and protease inhibitors. Lysates were homogenized by passage through a 22 gauge needle and cleared by centrifugation at 22,000 x G for 30 minutes.
Libraries were prepared from rRNA- RNA using the NEB Next Ultra Directional Kit.

treatment_protocol: Cells were synchronized by incubation with 2mM thymidine for 24 hours, followed by incubation in thymidine-free media for 6 hours, and incubation with S-Trityl-L-cysteine (STLC) overnight.

tag: cell line

tag: cell type

value: hTERT immortalized retinal pigment epithelium cells

tag: ip antibody

value: anti-hnRNP U antibody [3G6] (Abcam, ab10297, lot# GR32083-28)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD010_indexed

tag: age


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD001_indexed


title: H5N1_M_16hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 16hr, bioreplicate 5


title: WT_06.00_M_3

value: mock (DMSO)

value: 6 hr

value: replicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD008_indexed


title: Mock_NM_24hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 24hr, bioreplicate 2


title: RPE Mitosis 2

source_name: hTERT-RPE1, mitosis


title: WT_06.00_M_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD012_indexed


title: Mock_NM_24hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 24hr, bioreplicate 1


title: Mock_NM_24hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 24hr, bioreplicate 4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD010_indexed


title: RPE Interphase 2

source_name: hTERT-RPE1, interphase

treatment_protocol: Cells were synchronized by incubation with 2mM thymidine for 24 hours.


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD001_indexed


title: P1_adjacent non-tumour


title: hnRNP U IP Interphase 2

source_name: hTERT-RPE1, interphase, hnRNP U IP


title: RPE Mitosis 1


title: WT_01.00_M_2

value: 1 hr


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD002_indexed

value: MOp


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD006_indexed


title: H5N1_M_16hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 16hr, bioreplicate 3


title: hnRNP U IP Mitosis 1


title: hnRNP U IP Interphase 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD012_indexed


title: WT_06.00_M_1

value: replicate 1


title: WT_00.50_M_3


title: RPE Interphase 1


title: H5N1_M_16hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 16hr, bioreplicate 4


title: WT_01.00_M_1


title: WT_01.00_M_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A11_AD012_indexed


title: H5N1_NM_16hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 16hr, bioreplicate 5


title: WT_00.50_M_1


title: RNA191204KW_Gbx2_TOM2_S1

city: Portland

first: Patrick

middle: C

last: Kerstein

state: OR

address: 3232 SW Research Drive

department: Vollum Institute

institute: Oregon Heath and Science University

data_processing:
Illumina adapter sequences were removed using Trimmomatic
Reads were aligned to the genome using the program STAR (v2.7.3a)
Read counts were calculated for each each gene during genome alignment using the gene annotation file in the program STAR (v2.7.3a).
A quality control step was used to ensure alignments were of sufficient quality using RNA-SeQC and MultiQC.
Gene-level raw counts were normalized and transformed to log-counts per million with associated sample wise quality weight and observational precision weights using voom method.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized logs-counts per million for every gene and every sample

source_name: FAC-sorted dissociated retina

extract_protocol:
Retinas were removed, dissociated, and FAC-sorted by flourescence markers.  RNA was isolated using Agilent Absolutely RNA Nanoprep Kit.
cDNA libraries were synthesized using the SMART-Seq Ultra Low Input RNA kit (Takara).

value: retina

value: amacrine

tag: genotype

tag: cell fluorescence

value: GFP-negative


title: H5N1_M_16hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 16hr, bioreplicate 1


title: RNA191204KW_Gbx2_GFP3_S4

tag: tissue

value: GFP-positive


title: Mock_NM_24hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 24hr, bioreplicate 5


title: RNA191204KW_Gbx2_GFP2_S3


title: WT_00.00_M_3


title: H5N1_M_16hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 16hr, bioreplicate 2


title: H5N1_NM_16hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 16hr, bioreplicate 3


title: WT_00.00_M_2

source_name: 7-day old liquid-grown seedlings

value: replicate 2


title: H5N1_NM_16hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 16hr, bioreplicate 4


title: H1N1_M_16hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 16hr, bioreplicate 4


title: H5N1_NM_16hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 16hr, bioreplicate 2


title: WT_00.00_M_1


title: RNA191204KW_Gbx2_TOM6_S2


title: JEK16234_CD + PFOA

city: Bloomington

first: Xilin

state: Indiana

address: 2719 E 10th street Rm230

institute: Indiana University

data_processing:
Data included 16 single-read fastq libraries (raw read length 50 nt). Base-calling was done bcl2fastq v2.20.0.422.
Reads were quality filtered using Trimmomatic ver. 0.33 (http://www.usadellab.org/cms/?page=trimmomatic), with the cutoff threshold for average base quality score set at 20 over a window of 3 bases.
Reads shorter than 20 bases post-trimming were excluded.
Cleaned reads were mapped to Mus musculus genome reference (GRCm38) using STAR version STAR_2.5.2b.
Number of reads aligned to the exon regions of each of the annotated genes (gencode M16) were generated using featureCounts tool of subread package version 1.6.0 (https://doi.org/10.1093/bioinformatics/btt656).
Read alignments were considered unstranded. Multiple mapped reads and reads overlapping with multiple features were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of each gene for each sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and total RNA was isolated using Qiagen Rneasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard BGI protocols (non-stranded).

value: Liver

value: 29-30 weeks

value: CD + PFOA


title: JEK16233_CD + PFOA


title: M0 - replicate 3

city: Murfreesboro

first: Rebecca

middle: L

last: Seipelt-Thiemann

state: TN

address: 1301 E Main St Box 60

department: Biology

institute: Middle Tennessee State University

description: Sample 15

data_processing:
quality check using fastQC (version 0.11.5)
STAR alignment (version 2.5.3a) using mouse ENSEMBL genome 38 and genome annotation 39.9
FeatureCount, multi-join, EdgeR to generate feature count table and MDS plot
StringTie and StringTieMerge (version 1.3.3) to generate experiment-specific merged annotation file
cuffDiff (version 2.2.1) to generate differentially expressed genes among sample groups
Genome_build: 38
Supplementary_files_format_and_content: Excel version of FeatureCount table with sample key in first  tab and genes/counts as  second tab; text file of cuffdiff output including genes/comparisons/foldchange

source_name: macrophage-like cell line

growth_protocol: RAW 264.7 cells, a murine macrophage-like cell line, were obtained from the American Type Culture Collection (ATCC, Manassas, VA) and cultured in Dulbecco's Modified Eagle Medium (DMEM; ThermoFisher Scientific, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS; VWR, Radnor, PA), 200 mM L-glutamine, 1% penicillin and streptomycin, and 50 µg/mL gentamicin (all from Sigma Aldrich). Macrophages were maintained at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Macrophages were homogenized in lysis reagent (RLT buffer, Qiagen, Germantown, MD) using a 20-gauge needle and remaining intact Cn were removed by centrifugation at 750 x g for 5 min at 4 °C. RNA was extracted from the lysates using an RNeasy® Mini Kit (Qiagen), according to the manufacturer’s instructions. Genomic DNA was then removed from the total RNA using a Message Clean kit (GenHunter, Nashville, TN) per the manufacturer’s instructions. Clean RNA was resuspended in 10 µL diethyl pyrocarbonate (DEPC)-treated water and RNA integrity and quality was appraised using a Qubit 2 fluorometer (ThermoFisher Scientific).
The cDNA libraries for RNA sequencing were prepared from 1 µg of isolated RNA using the NEBNext UltraTM Directional RNA Library Prep Kit for Illumina, the NEBNext Multiplex Oligos for Illumina Index Primers, and the NEBNext Poly(A) Magnetic Isolation Module (all from New England BioLabs, Ipswich, MA) in accordance with the manufacturer’s instructions.

treatment_protocol: Prior to infection, RAW 264.7 cells were seeded into 6-well plates at a density of 7.5 x 105 cells/well and incubated overnight with 200 U/mL of recombinant murine IFNγ (Biolegend, San Diego, CA) to promote M1-polarization and then infected with opsonized Cn for 2 h at 3:1 MOI or mock infected with PBS. After 2 h, extracellular Cn were removed by washing 2X with PBS and the macrophages were cultured for a further 24 h in fresh growth media containing either IFNγ to maintain the M1 polarization state or 100 ng/mL recombinant interleukin-4 (IL-4; Sigma-Aldrich, St. Louis, MO, and Peprotech, Rocky Hill, NJ) to promote repolarization to the M2 state. Cells were washed and growth medium containing IFNγ or IL-4 was replaced every 6 h to prevent nutrient depletion, remove extracellular Cn, and maintain the appropriate polarizing environment.

tag: infection state

value: not infected

tag: polarization state


title: H5N1_NM_16hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 16hr, bioreplicate 1

tag: time


title: JEK16230_HFD + PFOA

tag: strain

value: HFD + PFOA


title: JEK16229_HFD + PFOA


title: M0 - replicate 1

description: Sample 13


title: M0 - replicate 2

description: Sample 14


title: JEK16228_HFD + PFOA


title: JEK16236_CD + PFOA


title: JEK16235_CD + PFOA


title: doxorubicin treatment replicate 2

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

country: Germany

institute: Universitätsklinikum Halle

data_processing:
Sequences were aligned to the human genome hg19 with alignment program STAR_2.5.2b using Gencode v.25
Mapping to the transcriptome and gene expression analysis was done with Cufflinks v2.2.1 using Gencode v.25
Gene expression was quantified by FPKM (Fragments Per Kilobase per Million)
Genome_build: hg19
Supplementary_files_format_and_content: For each Gene: Ensembl_ID, Gene_symbol, Locus (chr:start-end), FPKM

source_name: human iPS-derived cardiomyocytes

growth_protocol: Beating iPS- derived cardiomyocytes were maintained in RPMI 1640 medium (Thermo Fisher Scientific) supplemented with B27 supplements (Thermo Fisher Scientific). All experiments were performed between day 31 and day 35 after initiation of differentiation. Human iPS-derived CMs were dissociated using prewarmed TrypLE select 10x (Thermo Fisher Scientific) at 37°C. Next, cells were detached, collected and centrifuged using RPMI 1640 with B27 supplement media. The cells were resuspended in RPMI 1640 with B27 supplement media and plated in Matrigel-coated 6 well dishes.

extract_protocol:
RNA was isolated from cultured hiPS cardiomyocytes using the RNeasy mini kit (Qiagen)
The RNA libraries were generated by NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina
The libraries were sequenced on a NovaSeq6000 sequencer with PE50

treatment_protocol: hiPS cardiomyocytes were exposed to doxorubicin 1μM and/ or R-2HG (20mM, (Sigma Aldrich, #H8378) for 24 hours in CDM3 medium

value: cardiac muscle

value: human iPS-derived cardiomyocytes

value: doxorubicin treatment


title: doxorubicin treatment replicate 3


title: doxorubicin treatment replicate 1


title: M2-polarized, pathogen-infected - replicate 3

description: Sample 12

value: infected


title: M2-polarized, pathogen-infected - replicate 2

description: Sample 11


title: JEK16227_HFD + PFOA


title: H1N1_M_16hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 16hr, bioreplicate 2

tag: virus


title: H1N1_M_16hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 16hr, bioreplicate 3


title: H1N1_M_16hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 16hr, bioreplicate 1


title: R-2HG exposure during doxorubicin treatment replicate 2


title: JEK16226_HFD + Vehicle

value: HFD + Vehicle


title: M2-polarized, pathogen-infected - replicate 1

description: Sample 10


title: R-2HG exposure during doxorubicin treatment replicate 1


title: R-2HG exposure during doxorubicin treatment replicate 3


title: R-2HG exposure replicate 3

value: R-2HG exposure


title: M2-polarized, mock-infected - replicate 2

description: Sample 8

value: mock-infected


title: H1N1_NM_16hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 16hr, bioreplicate 5


title: JEK16224_HFD + Vehicle


title: R-2HG exposure replicate 1


title: JEK16225_HFD + Vehicle


title: M1-polarized, pathogen-infected - replicate 3

description: Sample 6


title: M2-polarized, mock-infected - replicate 3

description: Sample 9


title: M2-polarized, mock-infected - replicate 1

description: Sample 7


title: JEK16222_HFD + Vehicle


title: JEK16220_CD + Vehicle

value: CD + Vehicle


title: M1-polarized, pathogen-infected - replicate 2

description: Sample 5


title: Mock_M_16hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 16hr, bioreplicate 4


title: Mock_M_16hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 16hr, bioreplicate 5


title: Control replicate 2

value: Control


title: Mock_M_16hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 16hr, bioreplicate 3


title: H1N1_NM_16hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 16hr, bioreplicate 2


title: JEK16219_CD + Vehicle


title: Control replicate 3


title: H1N1_NM_16hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 16hr, bioreplicate 3


title: H1N1_NM_16hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 16hr, bioreplicate 4


title: Control replicate 1


title: JEK16218_CD + Vehicle


title: M1-polarized, mock-infected - replicate 3

description: Sample 3


title: Mock_M_16hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 16hr, bioreplicate 1


title: H1N1_NM_16hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 16hr, bioreplicate 1


title: R-2HG exposure replicate 2


title: JEK16221_CD + Vehicle


title: M1-polarized, mock-infected - replicate 2

description: Sample 2


title: Patient Sample, C042_d28

first: James

middle: John

last: Kaminski

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Boston Children's Hospital

data_processing:
Trim reads with trimmomatic. Settings :-phred33 ILLUMINACLIP:Nextera-SE.fa:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:80
Align to human index using kallisto v0.46.1 (Human index built using Ensembl v99 annotation and GRCh38.p13 reference genome.)
Load matrix of counts into DESeq2 with tximport
Filter matrix to genes with biotype protein_coding or lncRNA.
Retrieve normalized counts from DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Bulk_RNASeq_Normalized_Counts.tsv contains normalized RNA-Seq abundances from DESeq2

extract_protocol:
We sorted CD8+ T cells from blood samples obtained from hematopoietic cell transplant patients in the placebo-control arm of the ABA2 clinical trial (NCT# NCT01743131)
RNA was isolated from CD4 and CD8 sorted T cells for each patient using the RNeasy Micro kit  (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent  Bioanalyzer and two nanograms of total RNA was used as input for cDNA synthesis using the  Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s  instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using  the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary  electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and  sequenced on an Illumina HiSeq3000 at 100SR, yielding approximately 20 million reads per  sample.

tag: patient id

value: 28 days since the patient's hematopoietic cell transplant

value: blood

value: CD8+ T cells


title: Patient Sample, C042_d21

value: 21 days since the patient's hematopoietic cell transplant


title: N5_03_nCOV_OIRRA_Lib46_20200423 (1)

city: Liestal

first: Ronny

last: Nienhold

address: Mühlemattstrasse 11

department: Institute of Pathology

country: Switzerland

institute: Cantonal Hospital Baselland

description:
batch effect control
N5_03_nCOV_OIRRA_Lib46_20200423_IonXpress_046 (1)
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

data_processing:
De-multiplexing and gene expression level quantification were performed with the standard setting of the ImmuneResponseRNA plugin, provided as part of the OIRRA.
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values

source_name: Lung

extract_protocol:
RecoverAll Total Nucleic Acid Isolation Kit (Cat No. AM1975, Thermo Fisher Scientific, Waltham, MA, USA)
Oncomine Immune Response Research Assay (OIRRA, Cat No. A32881, Thermo Fisher Scientific, Waltham, MA, USA)
targeted RNA-seq

tag: material

value: FFPE

tag: Sex

value: M

tag: diagnosis

value: Control (other cause of death)

tag: topography

value: Lung, left superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: M1-polarized, mock-infected - replicate 1

description: Sample 1

tag: cell line

tag: infection state

tag: polarization state


title: M1-polarized, pathogen-infected - replicate 1

description: Sample 4


title: N4_04_nCOV_OIRRA_Lib45_20200423(1)

description:
batch effect control
N4_04_nCOV_OIRRA_Lib45_20200423_IonXpress_045 (1)
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, right superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)


title: Patient Sample, C041_d28

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Mock_NM_16hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 16hr, bioreplicate 4

tag: virus


title: Mock_NM_16hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 16hr, bioreplicate 2


title: C9_02_nCOV_OIRRA_Lib43_20200423

description:
C9_02_nCOV_OIRRA_Lib43_20200423_IonXpress_043
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: Lung, left superior lobe

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: WT_00.50_M_2

source_name: 7-day old liquid-grown seedlings

tag: ecotype

tag: agent

value: mock (DMSO)

tag: time point

tag: replicate

value: replicate 2

tag: genotype/variation

value: WT


title: Sample_49_GCB_H1_DKO_H3K27Ac_rep3_ChIPseq

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
ATAC-seq paired-end sequencing reads were trimmed to remove adapter sequences using NGmerge with option “-a”, and trimmed reads were aligned to mm10 reference genome using bowtie2 with options “-X2000 –local”. Alignments were filtered using samtools v1.8 to retain only uniquely mapping read pairs and to discard mitochondrial mapping reads. Read duplicates were detected and removed using the MarkDuplicates program in Picard Tools 2.18.11.
ATAC-seq peaks were called using MACS2
Cut and Run reads from two replicated aligned to mm10 using Bowtie2 and merged, filtering out non-unique and blacklist regions (PMID:31249361)
ChIP-seq reads were aligned to mm10 using BWA with default parameters
ChIP-seq peaks were called using narrow MACS2 for H3K4me3 and H3K27Ac and SICER2 for H3K9me2 and H3K9me3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited

extract_protocol:
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer
Cut and Run libraries for H3K4me3 (EpiCypher 13-0041), H3K9me2 (Millipore 05-1249), and H3K9me3 (Abcam 176916) were prepared using EpiCypher CUTANA v1.5.1 protocol
ChIP-seq libraries for H3K27ac (pAb 39133 Active Motif) were prepared using TrueMicroChip kit according to the manufacturer

treatment_protocol: Included as additional column of SAMPLES section

tag: genotype

value: Constitutive H1c-/-;H1e-/-

tag: cell type

value: GC B cell

tag: anitbody

value: H3K27Ac (ActiveMotif, cat.# 39133, lot 1518010)


title: Sample_48_GCB_H1_DKO_H3K27Ac_rep2_ChIPseq


title: Mock_NM_16hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 16hr, bioreplicate 5

tag: time

tag: virus


title: Mock_NM_16hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 16hr, bioreplicate 3


title: Patient Sample, C040_d21

tag: patient id

tag: tissue


title: C9_03_nCOV_OIRRA_Lib44_20200423

description:
C9_03_nCOV_OIRRA_Lib44_20200423_IonXpress_044
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, left inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Sample_47_GCB_H1_DKO_H3K27Ac_rep1_ChIPseq

tag: genotype

tag: cell type

tag: anitbody


title: Patient Sample, C041_d21

tag: patient id

tag: time

tag: tissue


title: C8_03_nCOV_OIRRA_Lib41_20200423

description:
C8_03_nCOV_OIRRA_Lib41_20200423_IonXpress_041
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, right superior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

value: unclear

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Patient Sample, C039_d28

tag: patient id

tag: time

value: 28 days since the patient's hematopoietic cell transplant

tag: tissue

value: blood

tag: cell type

value: CD8+ T cells


title: C9_01_nCOV_OIRRA_Lib42_20200423

description:
C9_01_nCOV_OIRRA_Lib42_20200423_IonXpress_042
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

value: FFPE

tag: age

tag: Sex

value: M

tag: diagnosis

tag: topography

value: Lung, right inferior lobe

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Patient Sample, C038_d21

tag: patient id

tag: time

value: 21 days since the patient's hematopoietic cell transplant

tag: tissue


title: Mock_NM_16hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 16hr, bioreplicate 1

tag: virus


title: Sample_45_GCB_WT_H3K27Ac_rep2_ChIPseq

tag: genotype

value: WT littermate control

tag: cell type

tag: anitbody


title: Patient Sample, C037_d28


title: H5N1_M_12hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 12hr, bioreplicate 5


title: C8_01_nCOV_OIRRA_Lib39_20200423

description:
C8_01_nCOV_OIRRA_Lib39_20200423_IonXpress_039
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, left middle lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_44_GCB_WT_H3K27Ac_rep1_ChIPseq

tag: genotype

tag: cell type

tag: anitbody


title: H5N1_M_12hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 12hr, bioreplicate 4

tag: time

tag: virus


title: Patient Sample, C037_d21

tag: patient id

tag: tissue


title: Sample_46_GCB_WT_H3K27Ac_rep3_ChIPseq


title: H5N1_M_12hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 12hr, bioreplicate 3


title: H5N1_M_12hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 12hr, bioreplicate 1


title: Sample_37_GCB_H1_DKO_repl4_ATACseq


title: Patient Sample, C036_d28


title: H5N1_M_12hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H5N1-inoculated, 12hr, bioreplicate 2


title: C21_04_nCOV_OIRRA_Lib37_20200423

description:
C21_04_nCOV_OIRRA_Lib37_20200423_IonXpress_037
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, right superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Sample_35_GCB_H1_DKO_repl2_ATACseq

tag: genotype

tag: cell type


title: Sample_36_GCB_H1_DKO_repl3_ATACseq


title: C21_03_nCOV_OIRRA_Lib36_20200423

description:
C21_03_nCOV_OIRRA_Lib36_20200423_IonXpress_036
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Lung, left superior + inferior lobe

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: H5N1_NM_12hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 12hr, bioreplicate 5

tag: time

tag: virus


title: Patient Sample, C035_d28

tag: patient id

tag: tissue


title: Sample_34_GCB_H1_DKO_repl1_ATACseq

tag: genotype

value: Constitutive H1c-/-;H1e-/-

tag: cell type


title: C8_02_nCOV_OIRRA_Lib40_20200423

description:
C8_02_nCOV_OIRRA_Lib40_20200423_IonXpress_040
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Patient Sample, C036_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: H5N1_NM_12hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 12hr, bioreplicate 4

tag: virus


title: H5N1_NM_12hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 12hr, bioreplicate 3


title: N5_03_nCOV_OIRRA_Lib46_20200423

description:
batch effect control
N5_03_nCOV_OIRRA_Lib46_20200423_IonXpress_046
processed data file:
user_S5-0093-278-OIRRA_20200423_580.bcmatrix.csv
user_S5-0093-278-OIRRA_20200423_580.mean_hk_scaled_log2_count.csv
user_S5-0093-278-OIRRA_20200423_580.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Control (other cause of death)

tag: topography

tag: time post mortem (h)

tag: bmi

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Patient Sample, C035_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: N4_04_nCOV_OIRRA_Lib45_20200423

description:
batch effect control
N4_04_nCOV_OIRRA_Lib45_20200423_IonXpress_045
processed data file:
user_S5-0093-278-OIRRA_20200423_580.bcmatrix.csv
user_S5-0093-278-OIRRA_20200423_580.mean_hk_scaled_log2_count.csv
user_S5-0093-278-OIRRA_20200423_580.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Sample_33_GCB_WT_repl4_ATACseq

tag: genotype

value: GC B cell


title: Patient Sample, C034_d28

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Sample_32_GCB_WT_repl3_ATACseq


title: C15_14_nCOV_OIRRA_Lib24_20200423

description:
C15_14_nCOV_OIRRA_Lib24_20200423_IonXpress_024
processed data file:
user_S5-0093-278-OIRRA_20200423_580.bcmatrix.csv
user_S5-0093-278-OIRRA_20200423_580.mean_hk_scaled_log2_count.csv
user_S5-0093-278-OIRRA_20200423_580.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, left superior lobe

tag: time post mortem (h)

tag: bmi

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: H5N1_NM_12hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 12hr, bioreplicate 2

tag: time

tag: virus


title: C21_21_nCOV_OIRRA_Lib38_20200423

description:
C21_21_nCOV_OIRRA_Lib38_20200423_IonXpress_038
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv

tag: material

tag: age

value: Lung, right superior lobe

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Patient Sample, C033_d21

tag: patient id

tag: tissue

tag: cell type


title: Sample_31_GCB_WT_repl2_ATACseq

tag: genotype


title: N5_03_nCOV_OIRRA_Lib27_20200409 (1)

description:
batch effect control
N5_03_nCOV_OIRRA_Lib27_20200409_IonXpress_027 (1)
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: H5N1_NM_12hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H5N1-inoculated, 12hr, bioreplicate 1

tag: time

tag: virus


title: H1N1_M_12hr_5

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 12hr, bioreplicate 5


title: Patient Sample, C032_d28

tag: patient id

tag: tissue

tag: cell type


title: Sample_30_GCB_WT_repl1_ATACseq

tag: genotype


title: C7_03_nCOV_OIRRA_Lib23_20200409

description:
C7_03_nCOV_OIRRA_Lib23_20200409_IonXpress_023
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

source_name: Lung

tag: material

tag: age

tag: Sex

value: F

tag: diagnosis

tag: topography

value: Lung, left inferior lobe

tag: time post mortem (h)

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

value: 1 to 2

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: N4_04_nCOV_OIRRA_Lib26_20200409(1)

description:
batch effect control
N4_04_nCOV_OIRRA_Lib26_20200409_IonXpress_026 (1)
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: bmi

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: IRAK4 KO + rescue 2

city: St. Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
oligo-dT

treatment_protocol: KO of IRAK4 was achieved by infection of KP2 cells with plentiCRISPR vectors encoding sgRNAs against IRAK4

tag: cell line

tag: genotype

value: IRAK4 KO + rescue

tag: cell type

value: Pancreatic cancer line from KPC mouse

tag: passages

value: <10 from being generated

tag: strain


title: C7_02_nCOV_OIRRA_Lib22_20200409

description:
C7_02_nCOV_OIRRA_Lib22_20200409_IonXpress_022
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

value: FFPE

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: IRAK4 KO + rescue 1

tag: cell line

tag: genotype

tag: cell type

tag: passages

tag: strain


title: IRAK4 KO 2

value: IRAK4 KO


title: Patient Sample, C032_d21

tag: patient id

tag: time

value: 21 days since the patient's hematopoietic cell transplant

tag: tissue

value: blood

value: CD8+ T cells


title: IRAK4 KO 1


title: Patient Sample, C031_d21


title: C6_03_nCOV_OIRRA_Lib20_20200409

description:
C6_03_nCOV_OIRRA_Lib20_20200409_IonXpress_020
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: M

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: C7_01_nCOV_OIRRA_Lib21_20200409

description:
C7_01_nCOV_OIRRA_Lib21_20200409_IonXpress_021
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Patient Sample, C030_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Patient Sample, C031_d28

value: 28 days since the patient's hematopoietic cell transplant


title: H1N1_M_12hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 12hr, bioreplicate 2

tag: virus


title: Patient Sample, C029_d28


title: Wild-type 2

tag: cell line

tag: genotype

value: Wild-type

tag: passages

tag: strain


title: C6_02_nCOV_OIRRA_Lib19_20200409

description:
C6_02_nCOV_OIRRA_Lib19_20200409_IonXpress_019
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: H1N1_M_12hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 12hr, bioreplicate 1

tag: time

tag: virus


title: Patient Sample, C029_d21

tag: patient id

tag: tissue

tag: cell type


title: H1N1_M_12hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 12hr, bioreplicate 4


title: Wild-type 1

tag: cell line

tag: genotype

tag: passages

tag: strain


title: H1N1_NM_12hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 12hr, bioreplicate 5


title: C6_01_nCOV_OIRRA_Lib18_20200409

description:
C6_01_nCOV_OIRRA_Lib18_20200409_IonXpress_018
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Sample_25_GCB_H1 DKO_Input_repl3_ChIPseq

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
TPM were obtained using Rsubread using RefSeq
ChIP-seq reads were aligned to mm10 using BWA with default parameters
Peaks were called using SICER
Genome_build: mm10
Supplementary_files_format_and_content: TPM, SICER peaks

source_name: GC B cell

extract_protocol:
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer
ChIP-seq libraries for H3K27me3 (C36B11 - Cell Signaling #9733) and H3K36me2 (C75H12 - CellSignaling #2901) were prepared using TrueMicroChip kit according to the manufacturer

tag: genotype

value: Constitutive H1c-/-;H1e-/-


title: H1N1_NM_12hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 12hr, bioreplicate 4

tag: time

tag: virus


title: Patient Sample, C028_d28

tag: patient id

tag: tissue

tag: cell type


title: H1N1_NM_12hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 12hr, bioreplicate 3


title: H1N1_NM_12hr_2

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 12hr, bioreplicate 2


title: C5_03_nCOV_OIRRA_Lib17_20200409

description:
C5_03_nCOV_OIRRA_Lib17_20200409_IonXpress_017
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Patient Sample, C028_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: H1N1_M_12hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, H1N1-inoculated, 12hr, bioreplicate 3

tag: virus


title: Sample_24_GCB_H1 DKO_Input_repl2_ChIPseq

tag: genotype


title: C5_02_nCOV_OIRRA_Lib16_20200409

description:
C5_02_nCOV_OIRRA_Lib16_20200409_IonXpress_016
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, left superior lobe

tag: time post mortem (h)

tag: bmi

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: Sample_23_GCB_H1 DKO_Input_repl1_ChIPseq

tag: genotype


title: Sample_22_GCB_WT_Input_repl3_ChIPseq

value: WT littermate control


title: Patient Sample, C027_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Sample_21_GCB_WT_Input_repl2_ChIPseq


title: N5_03_nCOV_OIRRA_Lib27_20200409

description:
batch effect control
N5_03_nCOV_OIRRA_Lib27_20200409_IonXpress_027
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Control (other cause of death)

tag: topography

value: Lung, left superior + inferior lobe

tag: time post mortem (h)

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: N4_04_nCOV_OIRRA_Lib26_20200409

description:
batch effect control
N4_04_nCOV_OIRRA_Lib26_20200409_IonXpress_026
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

value: Lung, right superior + inferior lobe

tag: bmi

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes


title: C5_01_nCOV_OIRRA_Lib15_20200409

description:
C5_01_nCOV_OIRRA_Lib15_20200409_IonXpress_015
processed data file:
user_S5-0093-273-OIRRA_2_20200409_575.bcmatrix.csv
user_S5-0093-273-OIRRA_2_20200409_575.mean_hk_scaled_log2_count.csv
user_S5-0093-273-OIRRA_2_20200409_575.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, right superior lobe

tag: time post mortem (h)

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)


title: Patient Sample, C026_d28

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Patient Sample, C027_d28


title: H1N1_NM_12hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, H1N1-inoculated, 12hr, bioreplicate 1

tag: virus


title: Patient Sample, C026_d21


title: C20_09_nCOV_OIRRA_Lib11_20200409

description:
C20_09_nCOV_OIRRA_Lib11_20200409_IonXpress_011
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

value: Lung, left inferior lobe

tag: bmi

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

value: 1 to 2

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_20_GCB_WT_Input_repl1_ChIPseq

tag: genotype


title: Patient Sample, C025_d28

tag: patient id

tag: time

tag: tissue

tag: cell type


title: C19_04_nCOV_OIRRA_Lib9_20200409

description:
C19_04_nCOV_OIRRA_Lib9_20200409_IonXpress_009
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

tag: material

value: FFPE

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)


title: Sample_18_GCB_H1 DKO_H3K36me2_repl2_ChIPseq

tag: genotype

tag: antibody

value: H3K36me2 (Cell Signaling, cat.# 2901, lot 4)


title: Patient Sample, C025_d21

tag: patient id

tag: time

value: 21 days since the patient's hematopoietic cell transplant

tag: tissue

tag: cell type


title: Mock_M_12hr_4

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 12hr, bioreplicate 4

tag: virus


title: Mock_M_12hr_2

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 12hr, bioreplicate 2


title: Mock_M_12hr_3

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 12hr, bioreplicate 3


title: C17_04_nCOV_OIRRA_Lib6_20200409

description:
C17_04_nCOV_OIRRA_Lib6_20200409_IonXpress_006
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Mock_M_12hr_1

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 12hr, bioreplicate 1

tag: time

tag: virus


title: C17_03_nCOV_OIRRA_Lib5_20200409

description:
C17_03_nCOV_OIRRA_Lib5_20200409_IonXpress_005
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)


title: Sample_17_GCB_H1 DKO_H3K36me2_repl1_ChIPseq

tag: genotype

tag: antibody


title: C16_04_nCOV_OIRRA_Lib4_20200409

description:
C16_04_nCOV_OIRRA_Lib4_20200409_IonXpress_004
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

value: F

tag: topography

tag: time post mortem (h)

tag: bmi

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_16_GCB_WT_H3K36me2_repl3_ChIPseq


title: Mock_NM_12hr_5

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 12hr, bioreplicate 5

tag: time

tag: virus


title: Patient Sample, C024_d21

tag: patient id

tag: tissue

value: blood

tag: cell type

value: CD8+ T cells


title: Patient Sample, C023_d28

value: 28 days since the patient's hematopoietic cell transplant


title: Mock_NM_12hr_4

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 12hr, bioreplicate 4


title: Mock_NM_12hr_1

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 12hr, bioreplicate 1


title: N6_03_nCOV_OIRRA_Lib1_20200409

description:
N6_03_nCOV_OIRRA_Lib1_20200409_IonXpress_001
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

source_name: Lung

tag: material

tag: age

tag: Sex

value: M

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)


title: Patient Sample, C022_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Sample_12_GCB_H1 DKO_H3K27me3_repl2_ChIPseq

tag: genotype

value: Constitutive H1c-/-;H1e-/-

tag: antibody

value: H3K27me3 (Cell Signaling, cat.# 9733, lot 12)


title: Sample_14_GCB_WT_H3K36me2_repl1_ChIPseq

value: WT littermate control


title: C16_03_nCOV_OIRRA_Lib3_20200409

description:
C16_03_nCOV_OIRRA_Lib3_20200409_IonXpress_003
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_19_GCB_H1 DKO_H3K36me2_repl3_ChIPseq

tag: genotype

tag: antibody


title: Patient Sample, C024_d28

tag: patient id

tag: time

tag: tissue

tag: cell type


title: C4_3_nCOV_OIRRA_Lib48_20200402

description:
C4_3_nCOV_OIRRA_Lib48_20200402_IonXpress_048
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, right inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)


title: Patient Sample, C023_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Sample_13_GCB_H1 DKO_H3K27me3_repl3_ChIPseq

tag: genotype

tag: antibody


title: Patient Sample, C020_d28


title: Patient Sample, C021_d21


title: N6_04_nCOV_OIRRA_Lib2_20200409

description:
N6_04_nCOV_OIRRA_Lib2_20200409_IonXpress_002
processed data file:
user_S5-0093-272-OIRRA_20200409_574.bcmatrix.csv
user_S5-0093-272-OIRRA_20200409_574.mean_hk_scaled_log2_count.csv
user_S5-0093-272-OIRRA_20200409_574.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Control (other cause of death)

tag: topography

tag: time post mortem (h)

tag: bmi

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_15_GCB_WT_H3K36me2_repl2_ChIPseq

tag: genotype

tag: antibody


title: Sample_11_GCB_H1 DKO_H3K27me3_repl1_ChIPseq


title: C4_2_nCOV_OIRRA_Lib47_20200402

description:
C4_2_nCOV_OIRRA_Lib47_20200402_IonXpress_047
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: Lung, left superior lobe

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)


title: Patient Sample, C020_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: C3_1_nCOV_OIRRA_Lib45_20200402

description:
C3_1_nCOV_OIRRA_Lib45_20200402_IonXpress_045
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

tag: material

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

value: unclear (symptoms a few days before hospitalisation)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_10_GCB_WT_H3K27me3_repl3_ChIPseq

tag: genotype

tag: antibody


title: Patient Sample, C019_d28

tag: patient id

tag: time

tag: tissue

tag: cell type


title: Mock_NM_12hr_3

source_name: Primary normal human bronchial epithelial cells, without macrophage cells, mock-inoculated, 12hr, bioreplicate 3

tag: virus


title: ExVivoBlood_Max. Neutron_rep4

first: Sanjay

last: Mukherjee

address: 630 W 168th street

institute: Columbia University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60○C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.  Data were filtered to exclude features not positive and significant in 25% of the samples, or those without at least a 1.5-fold change in expression values across the samples.
Please note that the reduced data set (of 12,905 data rows) resulted from the filtering for bad features. Out of 34184 features 12905 passed through the filtering criteria (Feature Non-uniform outliers or Features not Positive and significant were excluded).

source_name: ExVivoBlood_Max. Neutron

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: After irradiation, blood samples were diluted 1:1 with RPMI 1640 medium (Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Logan, UT), as previously described (Grace et al., Int J Radiat Biol 2002; 78:1011-21; PMID 12456288), and were incubated for 24 h  at 37○ C in a humidified incubator with 5% CO2

extract_protocol: The RNA was prepared using the QiaAmp blood RNA mini kit (Qiagen) following the manufacturer recommendations. This protocol differentially lyses red and white blood cells in whole blood to preferentially deplete   globin mRNA. Remaining globin mRNA was further reduced using GLOBINclear (Ambion Inc., Austin, TX) specifically to remove both a- and b-globin. The RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood from healthy volunteers was drawn into 0.105 mol/l sodium citrate Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ). The blood was divided into 3-ml aliquots and exposed to neutrons followed by X-ray to a cumulative dose of 3Gy containing different percentges of Neutrons. Pure X-ray of 3Gy exposure was considered as 0% neutron. One aliquote of blood tubes from each donor was Sham-irradiated which served as control.

tag: donor id

value: Donor 4

value: Peripheral blood

tag: treatment


title: ExVivoBlood_Max. Neutron_rep5

value: Donor 5


title: ExVivoBlood_Max. Neutron_rep3

value: Donor 3


title: ExVivoBlood_25% Neutron_rep5

source_name: ExVivoBlood_25% Neutron

value: 25%Neutron-X-ray mixed field-irradiated


title: ExVivoBlood_Max. Neutron_rep2

value: Donor 2


title: ExVivoBlood_25% Neutron_rep4


title: Sample_9_GCB_WT_H3K27me3_repl2_ChIPseq

source_name: GC B cell


title: ExVivoBlood_Max. Neutron_rep1

value: Donor 1


title: C1_2_nCOV_OIRRA_Lib41_20200402

description:
C1_2_nCOV_OIRRA_Lib41_20200402_IonXpress_041
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

tag: material

value: FFPE

tag: age

tag: Sex

value: F

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

value: Negativ (high Ct value)

tag: hypertension

tag: cvrf


title: Sample_8_GCB_WT_H3K27me3_repl1_ChIPseq

tag: genotype

tag: antibody


title: Sample_7_GCB_H1_DKO_repl3_RNAseq

value: Constitutive H1c-/-;H1e-/-


title: Patient Sample, C019_d21

tag: patient id

tag: time

value: 21 days since the patient's hematopoietic cell transplant

tag: tissue

value: blood

tag: cell type

value: CD8+ T cells


title: Patient Sample, C018_d21


title: Sample_6_GCB_H1_DKO_repl2_RNAseq


title: Patient Sample, C017_d21


title: Patient Sample, C017_d28

value: 28 days since the patient's hematopoietic cell transplant