title: 621900 Case

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Brazil

tag: asthma

tag: active asthma

tag: brazil pc1

tag: brazil pc2


title: cKd_1

status: Public on Aug 16 2023

type: SRA

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

country: China

institute: Wenzhou Medical University

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: MSU_V7.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Toxoplasma gondii

source_name: Tachyzoites

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

tag: tissue

value: Tachyzoites

tag: strain

value: TATi-3HA-TgUba1 strains cultured under DMSO (wild strain)

tag: treatment

value: DMSO


title: iBMDM_CHIR_IFNg_3

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

country: USA

institute: Michigan State University

data_processing:
Base calling was performed with Illumina Real Time Analysis (RTA; Version 3.4.4), and the output of RTA was demultiplexed and converted to the FastQ format with Illumina Bcl2fastq (Version 2.20.0).
Read quality was assessed using FastQC (Version 0.11.7)
Read mapping was performed against the GRCm39 mouse reference genome using Bowtie2 (Version 2.4.1)
Aligned read counts were assessed using feature counts from the Subread package (Version 2.0.0)
Differential gene expression analysis was conducted using the DESeq2 package (Version 1.36.0)  in R (Version 4.2.1).
Assembly: Mouse GRCm39
Supplementary files format and content: RawCounts_Compiled.csv - Contains raw read counts produced by Feature Counts for all samples combined into a single data matrix
Supplementary files format and content: Normalized_Counts.csv - Contains normalized read counts produced by DESeq2 for all samples combined into a single data matrix

organism: Mus musculus

source_name: L3 iBMDM

extract_protocol:
A Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) was used to extract RNA according to the manufacturer’s protocol.
Libraries were prepared using an Illumina Stranded mRNA Library Prep kit (Illumina, Cat no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters following the manufacturer’s recommendations, except that half-volume reactions were performed. Generated libraries were quantified and assessed for quality using a combination of Qubit™ dsDNA HS (ThermoFischer Scientific, Cat no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, Cat no. 5067-5584). The libraries were pooled in equimolar amounts, and the pooled library was quantified using an Invitrogen Collibri Quantification qPCR kit (Invitrogen, Cat no. A38524100).

tag: cell line

value: L3 iBMDM

tag: cell type

value: Immortalized BMDM

value: CHIR + IFNg


title: Exp1_TN024_Plate1_K2P1_G05_N715_S503, Child

city: Sydney

first: Fabio

last: Luciani

state: NSW

address: Kensington Campus

country: Australia

institute: UNSW Sydney

description:
CAI7246A1_090
genes.fpkm_table
genes.attr_table
samples.table

library_source: transcriptomic single cell

data_processing:
VDJPuzzle was run to extract TCR and quantify gene expression (FPKM)
Assembly: hg38
Supplementary files format and content: Matrix of FPKM values per sample, per gene
Supplementary files format and content: List of gene names in matrix
Supplementary files format and content: List of sample names in matrix

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Single influenza A2/M158-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMCs

value: CD8+ T cell

tag: epitope

tag: age

value: Child

tag: phenotype

value: Tnaive


title: 654730 Case

city: Baltimore

first: Rasika

middle: M

last: Mathias

state: MD

address: 5501 Bayview Cir

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

data_processing:
Trimming: FastQC0.11.9, BBDuk Version 38.90
Alignment: HISAT2 Version 2.2.21
Read Count Extraction: CoCo Version 2.0.2
Normalization: LIMMA Version 3.50.3, sva Version 3.42.0, edgeR Version 3.36.0
Filtering Genes: DESeq2_1.34.0
Assembly: GrCh38
Supplementary files format and content: full_n536__21831_voom_norm_counts_with_RandomID.csv
Supplementary files format and content: full_n536__raw_counts_with_RandomID.csv

source_name: Nasal Epithelium

extract_protocol: Total RNA with Ribo-Zero kit was used to prepare libraries from nasal epithelial cells depleting the ribosomal RNA

value: Nasal Epithelium

tag: Sex

value: Case

value: Washington DC

value: Asthmatic

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: washington dc_pc1

tag: washington dc_pc2


title: iBMDM_CHIR_IFNg_2


title: Exp1_TN024_Plate1_K2P1_F05_N715_S502, Child

description:
CAI7246A1_089
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: 813099 Case

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Nigeria

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: nigeria pc1

tag: nigeria pc2


title: iBMDM_CHIR_IFNg_1

tag: cell line

tag: cell type

tag: treatment


title: iBMDM_DMSO_IFNg_1

value: DMSO + IFNg


title: 838300 Case

tag: tissue

tag: Sex

value: Barbados

tag: age

tag: rnaseq libraryprep_batch

tag: barbados pc1

tag: barbados pc2


title: 643297 Case

tag: case control_definition

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Exp1_TN024_Plate1_K2P1_B06_N715_S506, Child

description:
CAI7246A1_092
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype


title: Exp1_TN024_Plate1_K2P1_E05_N714_S511, Child

description:
CAI7246A1_088
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: cKd_2

value: Tachyzoites

tag: strain

value: TATi-3HA-TgUba1 strains cultured under DMSO (wild strain)

value: DMSO


title: Exp1_TN024_Plate1_K2P1_D05_N714_S510, Child

description:
CAI7246A1_087
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: CD8+ T cell


title: PC3 shMEK5_rep2

type: RNA

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 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 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PC3 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: RNA was purified following the RNeasy mini kit.

treatment_protocol: PC3 human prostate cancer cells stably expressing a scrambled shRNA (shControl) or MEK5 shRNA were used to isolate RNA

tag: transfection

value: MEK5 shRNA


title: 850284 Case

value: Nasal Epithelium

value: Male

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: washington dc_pc1

tag: washington dc_pc2


title: iBMDM_CHIR_2

tag: cell line

value: L3 iBMDM

tag: cell type

value: Immortalized BMDM

tag: treatment

value: CHIR


title: Exp1_TN024_Plate1_K2P1_C05_N714_S508, Child

description:
CAI7246A1_086
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: age

value: Child

value: Tcm


title: 702283 Case

tag: Sex

value: Female

tag: case control_definition

value: Case

value: Nigeria

value: Asthmatic

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: PC3 shMEK5_rep3

tag: transfection


title: Exp1_TN024_Plate1_K2P1_B05_N714_S507, Child

description:
CAI7246A1_085
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype

value: Tem


title: iBMDM_CHIR_1


title: FLAM_Untreated_3

source_name: FLAM

value: FLAM

value: Alveolar-Like Macrophage

value: Untreated


title: 714648 Case

tag: rnaseq inclusion

tag: site

value: Baltimore

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: baltimore pc1

tag: baltimore pc2


title: 468788 Case

tag: tissue

value: Nasal Epithelium

tag: Sex

tag: case control_definition

tag: age


title: 939029 Case

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Exp1_TN024_Plate1_K2P1_H04_N714_S506, Child

description:
CAI7246A1_084
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope


title: Exp1_TN024_Plate1_K2P1_F04_N714_S505, Child

description:
CAI7246A1_083
genes.fpkm_table
genes.attr_table
samples.table

tag: phenotype


title: FLAM_Untreated_2

tag: cell line

tag: treatment


title: 477803 Case

value: Male

tag: rnaseq inclusion

tag: site

value: Chicago

tag: asthma

tag: active asthma

tag: chicago pc1

tag: chicago pc2


title: FLAM_Untreated_1


title: iBMDM_CHIR_3

value: L3 iBMDM

value: Immortalized BMDM

value: CHIR


title: 892115 Case

tag: tissue

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rin nasalepithelium


title: Exp1_TN024_Plate1_K2P1_D04_N714_S503, Child

description:
CAI7246A1_082
genes.fpkm_table
genes.attr_table
samples.table

tag: age

value: Child

value: Tnaive


title: FLAM_DMSO_IFNg_3

value: DMSO + IFNg


title: Exp1_TN024_Plate1_K2P1_C04_N714_S502, Child

description:
CAI7246A1_081
genes.fpkm_table
genes.attr_table
samples.table


title: DU145 shMEK5_rep2

source_name: DU145 cells

treatment_protocol: DU145 human prostate cancer cells stably expressing a scrambled shRNA (shControl) or MEK5 shRNA were used to isolate RNA

tag: transfection

value: MEK5 shRNA


title: DU145 shMEK5_rep3


title: Exp1_TN024_Plate1_K2P1_B04_N712_S511, Child

description:
CAI7246A1_080
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type


title: PC3 shMEK5_rep1


title: 427020 Case

value: Denver

value: Asthmatic

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: denver pc1

tag: denver pc2


title: FLAM_DMSO_IFNg_2

tag: cell line

value: FLAM

value: Alveolar-Like Macrophage

tag: treatment


title: FLAM_DMSO_3

value: DMSO


title: 226779 Case

value: Nasal Epithelium

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma


title: PC3 shControl_rep1

value: scrambled shRNA


title: 348240 Case

tag: tissue

tag: Sex

value: Male

tag: case control_definition


title: DU145 shMEK5_rep1

tag: transfection


title: Exp1_TN024_Plate1_K2P1_A04_N712_S510, Child

description:
CAI7246A1_079
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Bulk C1R

tag: cell type

value: Bulk C1R cell line

tag: epitope

tag: age

tag: phenotype


title: PC3 shControl_rep2


title: FLAM_DMSO_2


title: PC3 shControl_rep3


title: 705879 Case

value: Female

value: Case

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Exp1_TN024_Plate1_K2P1_F03_N712_S508, Child

description:
CAI7246A1_078
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Child

value: Tscm


title: FLAM_DMSO_1

tag: cell line

tag: treatment


title: Exp1_TN024_Plate1_K2P1_E03_N712_S507, Child

description:
CAI7246A1_077
genes.fpkm_table
genes.attr_table
samples.table

value: Tnaive


title: 588925 Case

tag: rnaseq inclusion

tag: site

value: Nigeria

tag: asthma

value: Asthmatic

tag: nigeria pc1

tag: nigeria pc2


title: DU145 shControl_rep2

tag: transfection


title: 400191 Case

tag: tissue

tag: Sex

tag: case control_definition

tag: active asthma

value: Active Asthma


title: FLAM_CHIR_IFNg_2

value: FLAM

tag: cell type

value: Alveolar-Like Macrophage

value: CHIR + IFNg


title: FLAM_CHIR_IFNg_3


title: Exp1_TN024_Plate1_K2P1_D03_N712_S506, Child

description:
CAI7246A1_076
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: age

tag: phenotype

value: Tcm


title: Exp1_TN024_Plate1_K2P1_C03_N712_S505, Child

description:
CAI7246A1_075
genes.fpkm_table
genes.attr_table
samples.table


title: DU145 shControl_rep3

value: scrambled shRNA


title: 429965 Case

value: Nasal Epithelium

value: Male

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: 707015 Case

tag: rnaseq inclusion

tag: site

tag: asthma


title: Exp1_TN024_Plate1_K2P1_B03_N712_S503, Child

description:
CAI7246A1_074
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: FLAM_CHIR_IFNg_1

tag: cell line

tag: treatment


title: Exp1_TN024_Plate1_K2P1_A03_N712_S502, Child

description:
CAI7246A1_073
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: Bulk C1R

value: Bulk C1R cell line


title: Diffuse large B-cell lymphoma specimens, S625416

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.
Significant analysis of microarray (SAM) was performed to identify differentially expressed mRNAs between progressive and progression-free tissues, with fold-change > 1.2 and associated p < 0.001 indicating significant differences.

label: Biotin

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip™ 3' IVT Pico Kit (Cat#902790, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted and purified using RecoverAllTM  Total Nucleic Acid Isolation (Cat#AM1975, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse-free

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: 394201 Case

tag: Sex

tag: case control_definition

value: Case

value: Nigeria

tag: active asthma

tag: nigeria pc1

tag: nigeria pc2


title: FLAM_CHIR_3

tag: cell type

value: CHIR


title: Exp1_TN024_Plate1_K2P1_H02_N711_S511, Child

description:
CAI7246A1_072
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: epitope

tag: age

value: Child

tag: phenotype

value: Tnaive


title: Exp1_TN024_Plate1_K2P1_G02_N711_S510, Child

description:
CAI7246A1_071
genes.fpkm_table
genes.attr_table
samples.table


title: FLAM_CHIR_2

value: FLAM

value: Alveolar-Like Macrophage


title: 546831 Case

value: Nasal Epithelium

value: Female

tag: rnaseq inclusion

tag: site

value: Brazil

value: Asthmatic

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: FLAM_CHIR_1

tag: cell line

tag: treatment


title: DU145 shControl_rep1

tag: transfection

value: scrambled shRNA


title: 7day72h LPS AM Rep3 Batch3 [ABM28]

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

data_processing:
Applied cutadapt for sequencing trimming.
Reads were aligned to the reference genome using BWA.
Quantification of genomic features using FeatureCounts.
Genomic features were normalized to CPM using edgeR.
Gene annotation database is mm10 Ensembl.
Assembly: mm10
Supplementary files format and content: txt

source_name: Lung macrophage

extract_protocol:
The flow sorted alveolar macrophages were collected and then isolated RNA by using Qaigen RNeasy® Mini Kit Cat # 74104
Illumina NovaSeq oligo-dT library prep plus 30M PE100 clusters in sequencing.

value: Lung macrophage

tag: genotype

value: LPS Inhalation 7ml (1mg/ml) + LPS Inhalation 7ml (1mg/ml)

tag: time


title: Diffuse large B-cell lymphoma specimens, S737401

tag: tissue

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse-free

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Exp1_TN024_Plate1_K2P1_F02_N711_S508, Child

description:
CAI7246A1_070
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

tag: phenotype


title: 752610 Case

tag: Sex

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: 871674 Case

tag: tissue

value: Male

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: 72h LPS AM Rep3 Batch3 [ABM27]

tag: cell type

tag: genotype

tag: treatment

value: LPS Inhalation 7ml (1mg/ml)

tag: time

value: 72 hour


title: 123884 Case

value: Nasal Epithelium

tag: Sex

tag: case control_definition

value: Washington DC

tag: age

tag: washington dc_pc1

tag: washington dc_pc2


title: Diffuse large B-cell lymphoma specimens, S563247

tag: disease

tag: disease status

tag: age-adjusted international index [aaipi] score


title: 7day LPS AM Rep3 Batch3 [ABM26]

value: Day 7


title: Exp1_TN024_Plate1_K2P1_D02_N711_S506, Child

description:
CAI7246A1_068
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

value: Child

tag: phenotype

value: Tnaive


title: 672934 Case

tag: tissue

tag: rnaseq inclusion

tag: site

value: Baltimore

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: Control Alveolar Macrophage Rep3 Batch3 [ABM25]

tag: cell type

value: Lung macrophage

tag: genotype

tag: treatment

value: No

tag: time

value: Day 0


title: Diffuse large B-cell lymphoma specimens, S545312

tag: age

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse-free

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Exp1_TN024_Plate1_K2P1_C02_N711_S505, Child

description:
CAI7246A1_067
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

value: CD8+ T cell

tag: epitope

tag: phenotype

value: Tcm


title: Diffuse large B-cell lymphoma specimens, S541849


title: Diffuse large B-cell lymphoma specimens, S608655

value: relapse


title: 739383 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch


title: Diffuse large B-cell lymphoma specimens, S560699


title: Exp1_TN024_Plate1_K2P1_B02_N711_S503, Child

description:
CAI7246A1_066
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: Child

value: Tscm


title: Exp1_TN024_Plate1_K2P1_H01_N711_S502, Child

description:
CAI7246A1_065
genes.fpkm_table
genes.attr_table
samples.table


title: 72h LPS AM Rep2 Batch2 [ABM15]

tag: genotype

tag: treatment

value: LPS Inhalation 7ml (1mg/ml)

tag: time

value: 72 hour


title: 916037 Case

value: Male

value: Baltimore

tag: age

value: Asthmatic

value: Active Asthma

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: 512700 Case

tag: tissue

tag: Sex

tag: case control_definition

value: Chicago

tag: chicago pc1

tag: chicago pc2


title: Exp1_TN024_Plate1_K2P1_G01_N710_S511, Child

description:
CAI7246A1_064
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype

value: Tnaive


title: Diffuse large B-cell lymphoma specimens, S536345

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse-free

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: 7day72h LPS AM Rep2 Batch2 [ABM16]

tag: cell type

value: Lung macrophage

tag: genotype

tag: treatment

value: LPS Inhalation 7ml (1mg/ml) + LPS Inhalation 7ml (1mg/ml)

tag: time


title: 123162 Case

value: Nasal Epithelium

value: Female

value: Case

tag: rnaseq inclusion

tag: site

tag: age

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Exp1_TN024_Plate1_K2P1_E02_N711_S507, Child

description:
CAI7246A1_069
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

value: CD8+ T cell

tag: epitope

value: Child

tag: phenotype


title: Diffuse large B-cell lymphoma specimens, S539384

tag: disease

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score


title: 7day LPS AM Rep2 Batch2 [ABM14]

tag: cell type

tag: genotype

tag: treatment

value: LPS Inhalation 7ml (1mg/ml)

tag: time

value: Day 7


title: Control Alveolar Macrophage Rep2 Batch2 [ABM13]

value: No

value: Day 0


title: Diffuse large B-cell lymphoma specimens, S535115

tag: age

value: lymph node biopsy or puncture


title: Diffuse large B-cell lymphoma specimens, S527812

value: Diffuse large B-cell lymphoma (DLBCL)


title: Exp1_TN024_Plate1_K2P1_F01_N710_S510, Child

description:
CAI7246A1_063
genes.fpkm_table
genes.attr_table
samples.table

value: Tnaive


title: Diffuse large B-cell lymphoma specimens, S527675

value: relapse-free

value: 2 or 3


title: 7day72h LPS AM Rep1 Batch1 [ABM4]

value: Lung macrophage

value: LPS Inhalation 7ml (1mg/ml) + LPS Inhalation 7ml (1mg/ml)


title: Exp1_TN024_Plate1_K2P1_E01_N710_S508, Child

description:
CAI7246A1_062
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: 548963 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Denver

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: denver pc1

tag: denver pc2


title: 971303 Case

tag: tissue

value: Male

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Diffuse large B-cell lymphoma specimens, S524309

tag: disease

tag: disease status

tag: age-adjusted international index [aaipi] score


title: Diffuse large B-cell lymphoma specimens, S518319

tag: age


title: 72h LPS AM Rep1 Batch1 [ABM3]

tag: cell type

tag: genotype

tag: treatment

value: LPS Inhalation 7ml (1mg/ml)

tag: time

value: 72 hour


title: Exp1_TN024_Plate1_K2P1_D01_N710_S507, Child

description:
CAI7246A1_061
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: CD8+ T cell

tag: epitope

value: Child

tag: phenotype


title: Diffuse large B-cell lymphoma specimens, S525012

value: lymph node biopsy or puncture

value: Diffuse large B-cell lymphoma (DLBCL)

value: relapse


title: 7day LPS AM Rep1 Batch1 [ABM2]

value: Lung macrophage

value: Day 7


title: 232787 Case

value: Nasal Epithelium

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: denver pc1

tag: denver pc2


title: Control Alveolar Macrophage Rep1 Batch1 [ABM1]

value: No

value: Day 0


title: 350325 Case

tag: tissue

value: Case

value: Denver

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Exp1_CB143_Plate1_C2P1_G10_N710_S503, Newborn

description:
CAI7246A1_058
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: age

value: Newborn

value: Tnaive


title: 225875 Case

value: Male

value: Asthmatic

value: Active Asthma


title: Exp1_TN024_Plate1_K2P1_C01_N710_S506, Child

description:
CAI7246A1_060
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: CD8+ T cell

tag: epitope

tag: phenotype


title: 907477 Case

tag: Sex

value: Female

tag: case control_definition

value: Nigeria

tag: nigeria pc1

tag: nigeria pc2


title: Exp1_CB143_Plate1_C2P1_H10_N710_S505, Newborn

description:
CAI7246A1_059
genes.fpkm_table
genes.attr_table
samples.table


title: TrainedBasalRep2

description: countsFromATAC.csv

library_source: genomic

data_processing:
Adapters were trimmed by TrimGalore.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2.
Unique reads with a quality score equal or more than 30 were kept. Tn5 offset was asjusted.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Irreproducibility Discovery Rate framework was applied to get peaks that were consistent among biological replicates.
Count tables were generated using Rsubread R package.
Assembly: mm10
Supplementary files format and content: narrowPeak, csv

molecule: genomic DNA

extract_protocol:
The flow sorted alveolar macrophages were collected. 200,000 cells were then further used for ATACseq using Active Motif Kit Cat #  53150 by following the manufraturer protocol
Library were contructed with 10 cycles of PCR using the Active motif Kit Cat # 53150, index promer according to the manufracturer protocol

tag: group


title: TrainedBasalRep1

description: countsFromATAC.csv


title: Diffuse large B-cell lymphoma specimens, S512593

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Exp1_CB143_Plate1_C2P1_F10_N710_S502, Newborn

description:
CAI7246A1_057
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue


title: Diffuse large B-cell lymphoma specimens, S505853

value: relapse-free


title: 282040 Case

value: Nasal Epithelium

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch


title: Diffuse large B-cell lymphoma specimens, S493901

tag: age


title: Diffuse large B-cell lymphoma specimens, S490899


title: Diffuse large B-cell lymphoma specimens, S508104


title: 841196 Case

value: Case

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Diffuse large B-cell lymphoma specimens, S486671


title: 128302 Case

tag: Sex

tag: case control_definition

tag: nigeria pc1


title: NaiveBasalRep2

description: countsFromATAC.csv

tag: group

value: naive

tag: cell type

value: Lung macrophage


title: Exp1_CB143_Plate1_C2P1_D10_N707_S510, Newborn

description:
CAI7246A1_055
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

value: Newborn

tag: phenotype

value: Tnaive


title: NaiveBasalRep1

description: countsFromATAC.csv


title: 881110 Case

tag: tissue

value: Male

tag: rnaseq inclusion

value: Asthmatic

tag: nigeria pc2


title: Exp1_CB143_Plate1_C2P1_A10_N707_S506, Newborn

description:
CAI7246A1_052
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 3 CCC-54

city: Kobe

first: Genshiro

middle: A.

last: Sunagawa

state: Hyogo

address: 2-2-3, Minatojimaminamimachi, Chuo-ku, Kobe

country: Japan

institute: RIKEN Center for Biosystems Dynamics Research

data_processing:
The reads were mapped to the mouse genome (GRCm38) using hisat2 version 2.1.1
Expression counts of the transcripts were estimated using featureCounts version 2.0.0
Assembly: GRCm38
Supplementary files format and content: csv-delimited text files (CCC-??.counts.csv) include raw counts for each sample
Supplementary files format and content: csv-delimited text file all_counts.csv includes raw counts for all samples
Supplementary files format and content: csv-delimited text file sample_info.csv includes the minimal infomation of the samples

extract_protocol:
RNeasy Mini Kit (Cat# 74104, Qiagen)
TruSeq Stranded mRNA Kit (Illumina)

value: Embryonic stem cell

tag: strain

value: MYS

tag: cell line

tag: treatment

value: Cultured at 37 C


title: Exp1_CB143_Plate1_C2P1_B10_N707_S507, Newborn

description:
CAI7246A1_053
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: age


title: Exp1_CB143_Plate1_C2P1_E10_N707_S511, Newborn

description:
CAI7246A1_056
genes.fpkm_table
genes.attr_table
samples.table


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 2 CCC-53


title: 977917 Case

value: Female

tag: site

value: Barbados

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: barbados pc1

tag: barbados pc2


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 1 CCC-52

tag: cell type


title: Diffuse large B-cell lymphoma specimens, S479858

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 2 CCC-50

value: Cultured at 31 C


title: Diffuse large B-cell lymphoma specimens, S473118

tag: tissue

value: relapse-free


title: 352857 Case

value: Nasal Epithelium

tag: Sex

tag: case control_definition

value: Case

tag: rnaseq inclusion

value: Nigeria

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: Exp1_CB143_Plate1_C2P1_F09_N707_S505, Newborn

description:
CAI7246A1_051
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: epitope

tag: age

value: Newborn

tag: phenotype

value: Tnaive


title: Exp1_CB143_Plate1_C2P1_E09_N707_S503, Newborn

description:
CAI7246A1_050
genes.fpkm_table
genes.attr_table
samples.table


title: 366906 Case

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: barbados pc1


title: Exp1_CB143_Plate1_C2P1_C10_N707_S508, Newborn

description:
CAI7246A1_054
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

value: CD8+ T cell


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 1 CCC-49

value: Embryonic stem cell

tag: strain

value: MYS

tag: cell line

tag: treatment


title: 136466 Case

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

value: Barbados

value: Active Asthma

tag: full pc1

tag: full pc2

tag: barbados pc2


title: Diffuse large B-cell lymphoma specimens, S478265

tag: age

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score


title: Diffuse large B-cell lymphoma specimens, S459046

value: 2 or 3


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 3 CCC-48

value: Cultured at 37 C


title: Diffuse large B-cell lymphoma specimens, S461469


title: Diffuse large B-cell lymphoma specimens, S451735


title: Diffuse large B-cell lymphoma specimens, S456376

value: relapse-free


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 3 CCC-51

value: Cultured at 31 C


title: Exp1_CB143_Plate1_C2P1_A09_N706_S511, Newborn

description:
CAI7246A1_048
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: epitope

tag: phenotype


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 2 CCC-47


title: 204240 Case

tag: tissue

value: Nasal Epithelium

value: Case

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: barbados pc1


title: 925278 Case

tag: Sex

value: Male

tag: case control_definition

tag: rnaseq inclusion

value: Nigeria

value: Asthmatic

tag: full pc1

tag: nigeria pc1

tag: nigeria pc2


title: Exp1_CB143_Plate1_C2P1_G08_N706_S510, Newborn

description:
CAI7246A1_047
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: CD8+ T cell

tag: age

value: Newborn

value: Tnaive


title: Exp1_CB143_Plate1_C2P1_E08_N706_S508, Newborn

description:
CAI7246A1_046
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 3 CCC-45

value: Embryonic stem cell

tag: strain

tag: cell line

tag: treatment


title: Diffuse large B-cell lymphoma specimens, S449765

tag: tissue

value: lymph node biopsy or puncture

tag: disease

tag: disease status

tag: age-adjusted international index [aaipi] score


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 1 CCC-46


title: 323051 Case

tag: Sex

tag: site

value: Barbados

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: 889663 Case

tag: case control_definition

tag: rnaseq inclusion

tag: age

tag: full pc1


title: Exp1_CB143_Plate1_C2P1_C08_N706_S507, Newborn

description:
CAI7246A1_045
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

tag: epitope

tag: phenotype


title: 481550 Case

tag: Sex

tag: site

value: Washington DC

tag: washington dc_pc1

tag: washington dc_pc2


title: Exp1_CB143_Plate1_C2P1_B09_N707_S502, Newborn

description:
CAI7246A1_049
genes.fpkm_table
genes.attr_table
samples.table


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 2 CCC-44

tag: strain

tag: cell line

tag: treatment


title: Exp1_CB143_Plate1_C2P1_B08_N706_S506, Newborn

description:
CAI7246A1_044
genes.fpkm_table
genes.attr_table
samples.table


title: Diffuse large B-cell lymphoma specimens, S447093

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Diffuse large B-cell lymphoma specimens, S436258


title: Diffuse large B-cell lymphoma specimens, S432332


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 1 CCC-43

value: Cultured at 31 C


title: Exp1_CB143_Plate1_C2P1_A08_N706_S505, Newborn

description:
CAI7246A1_043
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Bulk Naive CD8+ T cells


title: 750185 Case

value: Nasal Epithelium

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

value: Baltimore

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: Diffuse large B-cell lymphoma specimens, S430136

tag: age

tag: tissue

value: relapse-free


title: Diffuse large B-cell lymphoma specimens, S430458


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 3 CCC-42

tag: cell type

tag: strain

tag: cell line

value: Cultured at 37 C


title: 315866 Case

tag: Sex

value: Male

tag: site

value: Asthmatic

tag: full pc1


title: Exp1_CB143_Plate1_C2P1_H07_N706_S503, Newborn

description:
CAI7246A1_042
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: epitope

value: Newborn

tag: phenotype

value: Tnaive


title: Exp1_CB143_Plate1_C2P1_F07_N706_S502, Newborn

description:
CAI7246A1_041
genes.fpkm_table
genes.attr_table
samples.table


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 2 CCC-41

value: Embryonic stem cell

tag: treatment


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 1 CCC-40


title: Exp1_CB143_Plate1_C2P1_C07_N705_S510, Newborn

description:
CAI7246A1_039
genes.fpkm_table
genes.attr_table
samples.table


title: 748488 Case

tag: case control_definition

tag: rnaseq inclusion

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium


title: 372742 Case

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: Exp1_CB143_Plate1_C2P1_B07_N705_S508, Newborn

description:
CAI7246A1_038
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

tag: age


title: 935378 Case

tag: Sex

tag: site

value: Chicago

tag: full pc1

tag: chicago pc1

tag: chicago pc2


title: 919873 Case

tag: case control_definition

tag: rnaseq inclusion


title: Exp1_CB143_Plate1_C2P1_D07_N705_S511, Newborn

description:
CAI7246A1_040
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 3 CCC-39

tag: strain

tag: cell line

tag: treatment

value: Cultured at 31 C


title: 234097 Case

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 2 CCC-38

tag: cell type


title: Diffuse large B-cell lymphoma specimens, S429106

tag: age

tag: tissue

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Exp1_CB143_Plate1_C2P1_A07_N705_S507, Newborn

description:
CAI7246A1_037
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Bulk Naive CD8+ T cells

tag: epitope


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 1 CCC-37


title: 977825 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: full pc1

tag: chicago pc1

tag: chicago pc2


title: Diffuse large B-cell lymphoma specimens, S423396

value: relapse-free


title: Diffuse large B-cell lymphoma specimens, S422967


title: 186360 Case

value: Denver

tag: asthma

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: denver pc1

tag: denver pc2


title: Diffuse large B-cell lymphoma specimens, S422551

tag: age

tag: tissue

tag: disease


title: Diffuse large B-cell lymphoma specimens, S427999

tag: disease status

tag: age-adjusted international index [aaipi] score


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 3 CCC-36

tag: cell type

tag: strain

value: MYS

tag: cell line

tag: treatment

value: Cultured at 37 C


title: Diffuse large B-cell lymphoma specimens, S428705


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 2 CCC-35

value: Embryonic stem cell


title: Exp1_CB143_Plate1_C2P1_G06_N705_S505, Newborn

description:
CAI7246A1_035
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: epitope

value: Newborn

tag: phenotype

value: Tnaive


title: 706417 Case

tag: Sex

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

value: Active Asthma

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: 167158 Case

tag: tissue

tag: age

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: denver pc1

tag: denver pc2


title: Exp1_CB143_Plate1_C2P1_D06_N704_S511, Newborn

description:
CAI7246A1_032
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 3 CCC-33

tag: strain

tag: cell line

tag: treatment

value: Cultured at 31 C


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 2 CCC-32


title: 577298 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site


title: 962129 Case

value: Nigeria

tag: asthma

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 1 CCC-34


title: Exp1_CB143_Plate1_C2P1_E06_N705_S502, Newborn

description:
CAI7246A1_033
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

tag: age

tag: phenotype


title: Exp1_CB143_Plate1_C2P1_H06_N705_S506, Newborn

description:
CAI7246A1_036
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 1 CCC-31

tag: strain

tag: cell line


title: Diffuse large B-cell lymphoma specimens, S400725

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Diffuse large B-cell lymphoma specimens, S411946

value: relapse


title: Diffuse large B-cell lymphoma specimens, S401508


title: Diffuse large B-cell lymphoma specimens, S401354


title: Exp1_CB143_Plate1_C2P1_C06_N704_S510, Newborn

description:
CAI7246A1_031
genes.fpkm_table
genes.attr_table
samples.table


title: Diffuse large B-cell lymphoma specimens, S400482


title: Diffuse large B-cell lymphoma specimens, S400299


title: Exp1_CB143_Plate1_C2P1_B06_N704_S508, Newborn

description:
CAI7246A1_030
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_CB143_Plate1_C2P1_A06_N704_S507, Newborn

description:
CAI7246A1_029
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 3 CCC-30

tag: treatment


title: Exp1_CB143_Plate1_C2P1_F06_N705_S503, Newborn

description:
CAI7246A1_034
genes.fpkm_table
genes.attr_table
samples.table


title: 676465 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Barbados

tag: asthma

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: barbados pc1

tag: barbados pc2


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 2 CCC-29

tag: cell type

value: Embryonic stem cell

value: Cultured at 37 C


title: 389606 Case

tag: tissue

tag: age

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: Exp1_CB143_Plate1_C2P1_F05_N704_S505, Newborn

description:
CAI7246A1_027
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: epitope

value: Newborn

tag: phenotype

value: Tnaive


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 3 CCC-27

tag: strain

tag: cell line

tag: treatment

value: Cultured at 31 C


title: 265055 Case

tag: Sex

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Nigeria

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium


title: Exp1_CB143_Plate1_C2P1_H05_N704_S506, Newborn

description:
CAI7246A1_028
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

tag: cell type

tag: age


title: 192370 Case

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: 146827 Case


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 1 CCC-28

tag: strain

tag: cell line

tag: treatment


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 2 CCC-26


title: Exp1_CB143_Plate1_C2P1_E05_N704_S503, Newborn

description:
CAI7246A1_026
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype


title: 913750 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Washington DC

tag: asthma

tag: washington dc_pc1

tag: washington dc_pc2


title: Diffuse large B-cell lymphoma specimens, S397616

tag: age

tag: tissue

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Diffuse large B-cell lymphoma specimens, S395786


title: Diffuse large B-cell lymphoma specimens, S397318


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 1 CCC-25

tag: cell type

tag: strain


title: Diffuse large B-cell lymphoma specimens, S393842

value: relapse-free


title: Diffuse large B-cell lymphoma specimens, S395253


title: Diffuse large B-cell lymphoma specimens, S392619


title: 680724 Case

value: Nasal Epithelium

value: Female

value: Case

value: Asthmatic

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 2 CCC-23

value: Embryonic stem cell

tag: cell line

tag: treatment

value: Cultured at 37 C


title: 312945 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: rin nasalepithelium


title: Exp1_CB143_Plate1_C2P1_A05_N703_S510, Newborn

description:
CAI7246A1_023
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: Bulk C1R

value: Bulk C1R cell line

tag: epitope

tag: age

value: Newborn

tag: phenotype


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 3 CCC-24

tag: cell type

tag: strain


title: Exp1_CB143_Plate1_C2P1_B05_N703_S511, Newborn

description:
CAI7246A1_024
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Tnaive


title: 321646 Case

value: Washington DC

tag: active asthma

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: washington dc_pc1

tag: washington dc_pc2


title: Exp1_CB143_Plate1_C2P1_G04_N703_S507, Newborn

description:
CAI7246A1_021
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: Exp1_CB143_Plate1_C2P1_H04_N703_S508, Newborn

description:
CAI7246A1_022
genes.fpkm_table
genes.attr_table
samples.table


title: 358504 Case

tag: Sex

value: Baltimore

tag: full pc1

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 3 CCC-21

tag: cell line

tag: treatment

value: Cultured at 31 C


title: Exp1_CB143_Plate1_C2P1_C05_N704_S502, Newborn

description:
CAI7246A1_025
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: epitope


title: Exp1_CB143_Plate1_C2P1_C04_N703_S506, Newborn

description:
CAI7246A1_020
genes.fpkm_table
genes.attr_table
samples.table

tag: age

tag: phenotype


title: 388758 Case

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: rin nasalepithelium


title: Diffuse large B-cell lymphoma specimens, S390633

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Diffuse large B-cell lymphoma specimens, S386667

value: relapse-free


title: Diffuse large B-cell lymphoma specimens, S386132


title: Diffuse large B-cell lymphoma specimens, S379763


title: Diffuse large B-cell lymphoma specimens, S376907


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 1 CCC-19

tag: cell type

value: Embryonic stem cell

tag: strain


title: Exp1_CB143_Plate1_C2P1_A04_N703_S505, Newborn

description:
CAI7246A1_019
genes.fpkm_table
genes.attr_table
samples.table


title: 538092 Case

value: Nasal Epithelium

tag: Sex

value: Male

value: Case

value: Chicago

value: Asthmatic

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: Exp1_CB143_Plate1_C2P1_H03_N703_S503, Newborn

description:
CAI7246A1_018
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: CD8+ T cell

tag: epitope

tag: age

value: Newborn

tag: phenotype

value: Tnaive


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 1 CCC-22

tag: cell line

tag: treatment

value: Cultured at 37 C


title: Exp1_CB143_Plate1_C2P1_G03_N703_S502, Newborn

description:
CAI7246A1_017
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 2 CCC-20

value: Cultured at 31 C


title: Diffuse large B-cell lymphoma specimens, S362306

value: lymph node biopsy or puncture

tag: disease

tag: disease status

tag: age-adjusted international index [aaipi] score


title: 335973 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Denver

tag: asthma

value: Active Asthma

tag: rin nasalepithelium

tag: denver pc1

tag: denver pc2


title: 306300 Case

tag: tissue

value: Female

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: 161192 Case

tag: age


title: 185178 Case

tag: chicago pc1

tag: chicago pc2


title: Diffuse large B-cell lymphoma specimens, S382661

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse-free

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 2 CCC-17

tag: cell type

value: Embryonic stem cell

tag: strain

value: MYS

tag: cell line

tag: treatment


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 3 CCC-15


title: 222032 Case

value: Nasal Epithelium

tag: Sex

value: Male

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

tag: rin nasalepithelium

tag: denver pc1

tag: denver pc2


title: Exp1_CB143_Plate1_C2P1_D03_N702_S510, Newborn

description:
CAI7246A1_015
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: CD8+ T cell

tag: epitope

tag: age

value: Newborn

tag: phenotype


title: Huh7 cells, si-BRF2

city: Jinan

first: guangxiao

last: meng

address: 107 West Wen Hua Road, Jinan, 250012, China.

institute: Qilu Hospital of Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing low-quality sequences and adapter contamination.
The reference genome was indexed using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count.
Assembly: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using RNA Fast200 kit (fastagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for sequencing using standard illumina protocols.

value: Liver

value: Human HCC cells

tag: genotype


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 3 CCC-18

tag: cell type

value: Cultured at 37 C


title: HD-SB

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

description: RNA-seq

data_processing:
Quality control of the raw reads by Illumina HiSeq™2500 sequencing was assessed by Fast-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The remaining clean reads were mapped to the reference human genome (GRCh38) using HISAT2 software (version 2.1.0, https://daehwankimlab.github.io/hisat2/). To predict circRNAs, circRNAs were identified and quantified from mapped splice junction reads using ACFS2 (https://github.com/arthuryxt/acfs).
Differentially expressed circRNAs between HD-SB group and control were analyzed using the DE-Seq algorithm, with significant differences defined as absolute |log2 fold-change| > 1 and p value < 0.05.
The differentially expressed circRNAs and their functional enrichment were further analyzed by Gene Ontology (GO) and KEGG database in DAVID software (6.8). hsa_circ_0039933-miRNAs-wnt11 networks were predicted by miRanda 3.3 and drawn by cytoscape 3.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

growth_protocol: Human colorectal cancer cell lines (HT-29, HCT-116, and SW620) were purchased from Cellcook (Guangzhou, China). HT-29 cells were cultured in L-15 high-glucose medium (CM2001, CellCook, China) with 10% fetal bovine serum (FBS, CellCook), 1% penicillin and streptomycin (P/S, 15140-122, Gibco), while HCT-116 and SW620 cells were cultured in RPMI-1640 medium (11875, Gibco) with 10% FBS, 1% P/S, then cultured in 37°C, 5% CO2 incubator. SW620 cells were treated with HD-SB at 1 mg/mL, then collected after 24 h for subsequent experiments.

extract_protocol:
Total RNA was extracted by use of TRIzol reagent (TR118-500, MRC, USA)
RiboMinus™ Eukaryote System v2 kit was used to remove rRNA from total RNA, and RNase R was used to digest linear RNA to enrich circRNAs. RNA was fragmented for circRNAs library construction using the TrueLib mRNA Library Prep Kit for Illumina. The RNA was reverse transcribed to synthesize a two-stranded product, repaired at its end with a plus dA tail, and ligated to Adapter. The enriched product was amplified by pcr reaction. After that, the fragments were screened and purified to obtain the desired libraries.

value: colorectal cancer cell lines

value: Hedyotis diffusa-Sculellaria barbata (HD-SB)


title: Exp1_CB143_Plate1_C2P1_F03_N702_S511, Newborn

description:
CAI7246A1_016
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Tnaive


title: Diffuse large B-cell lymphoma specimens, S358475

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse

tag: age-adjusted international index [aaipi] score


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 37°C, biological replicate 1 CCC-16

value: Embryonic stem cell

tag: strain

tag: cell line

tag: treatment


title: Huh7 cells, si-NC

value: control


title: Exp1_CB143_Plate1_C2P1_C03_N702_S508, Newborn

description:
CAI7246A1_014
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: 453307 Case

value: Nasal Epithelium

tag: Sex

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Denver

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 2 CCC-14

value: MYS

value: Cultured at 31 C


title: RNA-seq of mus musclus: MYS/Mz, ES cell cultured at 31°C, biological replicate 1 CCC-13


title: Exp1_CB143_Plate1_C2P1_B03_N702_S507, Newborn

description:
CAI7246A1_013
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: CD8+ T cell

tag: epitope

tag: age

value: Newborn

tag: phenotype


title: HFG 49

first: Sumantra

last: Chatterjee

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Grossman School of Medicine

data_processing:
The BCL (base calls) binary were converted into FASTQ utilizing illumina package bcl2fastq
Reads were mapped using STAR 2.6.0a software and number reads per gene was counted (option: --quantMode GeneCounts)
DESeq2 (version: 1.24.0)  was used to stabilize the variance across the means of samples using the variance stabilizing transformation (VST) to derive normalized read counts. DESeq2 was always used for differential analyis
Genome_build: hg19
Supplementary_files_format_and_content: .csv format file with normalized read count. The column header is the sample id

source_name: RR GUTS FROM CS14

extract_protocol:
RNA was extracted from frozen gut samples received from HDBR using the Qiagen RNeasy mini kit
Library was constructed using standard Ilumina tagemntation based method

value: fetal gut

tag: genotype

value: Homozygous for Resistant haplotype (RR)

tag: developmental stage


title: 198289 Case

value: Case

tag: asthma

tag: rin nasalepithelium

tag: denver pc1

tag: denver pc2


title: HFG 48

source_name: RS GUTS FROM CS14

value: Heterzygous for Resistant/Susceptible haplotype (RS)


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 3 CCC-12

tag: cell type

tag: strain

tag: cell line

tag: treatment

value: Cultured at 37 C


title: Exp1_CB143_Plate1_C2P1_A03_N702_S506, Newborn

description:
CAI7246A1_012
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Bulk C1R

value: Bulk C1R cell line


title: Diffuse large B-cell lymphoma specimens, S352712

value: lymph node biopsy or puncture

tag: disease

value: Diffuse large B-cell lymphoma (DLBCL)

tag: disease status

value: relapse-free

tag: age-adjusted international index [aaipi] score

value: 2 or 3


title: Exp1_CB143_Plate1_C2P1_H02_N702_S505, Newborn

description:
CAI7246A1_011
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: Tnaive


title: HFG 47


title: 640562 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Nigeria

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: 566830 Case

value: Male

tag: age

tag: asthma

tag: rin nasalepithelium


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 2 CCC-11

tag: cell type

value: Embryonic stem cell

tag: strain

tag: cell line

tag: treatment


title: RNA-seq of mus musclus: STM2, ES cell cultured at 37°C, biological replicate 1 CCC-10


title: Exp1_CB143_Plate1_C2P1_G02_N702_S503, Newborn

description:
CAI7246A1_010
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: CD8+ T cell

tag: epitope

value: Newborn

tag: phenotype


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 3 CCC-09

value: Cultured at 31 C


title: HFG10

source_name: SS GUTS FROM CS22

value: fetal gut

tag: genotype

value: Homozygous for Susceptible haplotype (SS)

tag: developmental stage


title: Exp1_CB143_Plate1_C2P1_D02_N701_S511, Newborn

description:
CAI7246A1_008
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: HFG22


title: 200792 Case

tag: Sex

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 2 CCC-08


title: 766213 Case

tag: age

tag: asthma

tag: rin nasalepithelium

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: 633908 Case

tag: tissue

value: Barbados

tag: barbados pc1

tag: barbados pc2


title: RNA-seq of mus musclus: STM2, ES cell cultured at 31°C, biological replicate 1 CCC-07

tag: cell type

tag: strain

tag: cell line

tag: treatment


title: Exp1_CB143_Plate1_C2P1_E02_N702_S502, Newborn

description:
CAI7246A1_009
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype

value: Temra


title: 801514 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: HFG42

source_name: RS GUTS FROM CS22

tag: genotype

value: Heterozygous for Resistant/Susceptible haplotype (RS)

tag: developmental stage


title: Exp1_CB143_Plate1_C2P1_C02_N701_S510, Newborn

description:
CAI7246A1_007
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: age

value: Tnaive


title: 547200 Case

value: Nasal Epithelium

tag: asthma

tag: rin nasalepithelium

tag: full pc1

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: Exp1_CB143_Plate1_C2P1_B02_N701_S508, Newborn

description:
CAI7246A1_006
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: phenotype


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 3 CCC-06

tag: strain

tag: cell line

tag: treatment

value: Cultured at 37 C


title: HFG41


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 2 CCC-05


title: 178250 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Asthmatic

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: Exp1_CB143_Plate1_C2P1_H01_N701_S507, Newborn

description:
CAI7246A1_005
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: age


title: HFG35

tag: genotype

tag: developmental stage


title: HFG43


title: Exp1_CB143_Plate1_C2P1_G01_N701_S506, Newborn

description:
CAI7246A1_004
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 37°C, biological replicate 1 CCC-04


title: Exp1_CB143_Plate1_C2P1_F01_N701_S505, Newborn

description:
CAI7246A1_003
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope


title: HFG33


title: 163723 Case

value: Female

value: Washington DC

tag: asthma

value: Active Asthma

tag: rin nasalepithelium

tag: full pc1

tag: full pc2

tag: washington dc_pc1

tag: washington dc_pc2


title: HFG31


title: 951563 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 2 CCC-02

value: Embryonic stem cell

tag: strain

tag: cell line

tag: treatment


title: HFG23

tag: tissue


title: Exp1_CB143_Plate1_C2P1_B01_N701_S502, Newborn

description:
CAI7246A1_001
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: age

value: Newborn

tag: phenotype


title: Exp1_CB143_Plate1_C2P1_E01_N701_S503, Newborn

description:
CAI7246A1_002
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type


title: HFG17

value: fetal gut

tag: genotype

tag: developmental stage


title: HFG36


title: DMSO_24h_0620_3 [AB243]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Single read R2 contain sample barcode and UMI

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl mm10 -count 3utr -condenseGenes -strand +
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: choroid plexus

growth_protocol: Cell cultures were produced as previously described12. Briefly, CP tissue was excised following perfusion and kept on ice in 0.25% trypsin (Sigma), then digested at 37 ºC under agitation and manually dissociated into a single-cell suspension.

extract_protocol:
Messenger RNA was purified from cultured cells using Dynabeads mRNA purification kit (Invitrogen). Libraries were prepared using a modified MARS-seq protocol for bulk sequencing. Briefly, mRNA was reverse-transcribed into cDNA and amplified. cDNA was then fragmented into 300-500 kb fragments, and sample barcode and Illumina adapter sequences were added to each molecule using polymerase chain reaction (PCR).
Library constracted using a modified MARS-seq technique (Keren-Shaul et al, Nature Protocols 2019). Briefly mRNA was barcoded, converted  into cDNA and amplified by PCR.

treatment_protocol: 24-OH (10 µM diluted in DMSO (Sigma)); or DMSO-only control were added to the cells for 12h/24h as indicated

tag: condition

value: CP culture (24h after DMSO)

value: DMSO

value: choroid plexus

tag: timepoint

tag: experiment


title: PAF1 ChIPseq in MM1.S cells

city: London

first: Nick

last: Crump

address: Du Cane Road

department: Dept of Immunology and Inflammation

country: United Kingdom

institute: Imperial College London

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Multiple myeloma cell line (MM1.S)

growth_protocol: Cells were continuously grown in RPMI with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (PAF1). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).

value: Multiple myeloma cell line (MM1.S)

value: Plasma cell line derived from multiple myeloma with t(14;16) translocation

tag: chip antibody

value: Bethyl A300-172A


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 1 CCC-01

value: Cultured at 31 C


title: HFG44

source_name: RR GUTS FROM CS22

value: Homozygous for Resistant haplotype (RR)


title: DMSO_24h_0620_2 [AB242]


title: DMSO_24h_0620_1 [AB241]


title: HFG39


title: TB6458, DMSO Control, replicate 2

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

description: Microwell-based scRNA-seq, 8-base index read, 26-base read 1, 58-base read 2

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 57 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
Genome build:  GRCh38
supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: acute slice culture of glioma resection

growth_protocol: Patient specimens were collected immediately after surgical removal  and kept in ice-cold artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3 for transportation. collected tumor specimens were placed in a drop of ice-cold ACSF and sliced using a tissue chopper (McIlwain) at a thickness of 500 µm under sterile conditions. The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Intact and well-shaped slices (approximately 5-10 mm diameter) were then placed on top of a porous membrane insert (0.4 µm, Millipore). Then the membrane inserts were placed into 6-well plates containing 1.5 mL maintenance medium consisting of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 µl of culture medium was added directly on top of each slice to prevent the slice surface from drying. The slices were first rested for 6 hrs with the maintenance medium in a humidified incubator at 37℃ and 5% CO2 before drug treatment.

extract_protocol:
Tissue slices were collected for dissociation using the Adult Brain Dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions.
mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

treatment_protocol: We performed an 18-hour drug perturbation with 50 nM RSL3 or drug vehicle (DMSO) on spatially adjacent slices. Slices were cultured  in a humidified incubator at 37℃ and 5% CO2. For three patient tumor resections (TB6181, TB6328 and TB6458), we also co-treated slice cultures with 50 nM RSL3 and 10 µM Ferrostatin-1.

value: acute slice culture of glioma resection

tag: disease diagnosis

value: Glioblastoma, WHO Grade IV

value: M

tag: location

value: Right frontal

value: drug vehicle (DMSO), 18-hour


title: 659979 Case

value: Nasal Epithelium

tag: Sex

value: Male

tag: case control_definition

value: Case

tag: site

value: Washington DC

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: washington dc_pc1

tag: washington dc_pc2


title: HFG37

tag: tissue

value: fetal gut

tag: genotype

tag: developmental stage


title: 24OH_24h_0620_3 [AB240]

tag: condition

value: CP culture (24h after 24-OH)

tag: treatment

value: choroid plexus

tag: timepoint

tag: experiment


title: RNA-seq of mus musclus: C57BL/6J, ES cell cultured at 31°C, biological replicate 3 CCC-03

tag: cell type

value: Embryonic stem cell

tag: strain

tag: cell line


title: 250170 Case

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Baltimore

tag: age

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: baltimore pc1

tag: baltimore pc2


title: TB6458, RSL3 + Ferrostatin

tag: tissue

value: acute slice culture of glioma resection

tag: disease diagnosis

tag: location

value: 50 nM RSL3 and 10 µM Ferrostatin-1, 18-hour


title: 340148 Case

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: washington dc_pc1

tag: washington dc_pc2


title: 500940 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion


title: HFG25

tag: genotype

value: Homozygous for Resistant haplotype (RR)

tag: developmental stage


title: 24OH_24h_0620_2 [AB239]

tag: condition

tag: treatment

tag: timepoint

tag: experiment


title: TB6458, RSL3

tag: tissue

tag: disease diagnosis

value: Glioblastoma, WHO Grade IV

tag: age

value: M

value: Right frontal

value: 50 nM RSL3, 18-hour


title: 796482 Case

value: Nasal Epithelium

value: Case

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: HFG24


title: 958312 Case

tag: Sex

tag: case control_definition

value: Asthmatic

tag: full pc1

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: 24OH_12h_1020_3 [AB453]

tag: condition

value: CP culture (12h after 24-OH)

tag: treatment

tag: timepoint


title: 24OH_24h_0620_1 [AB238]

tag: tissue

tag: experiment


title: TB6328,  RSL3 + Ferrostatin, replicate 2

tag: disease diagnosis

tag: age

value: F

tag: location

value: Left frontal


title: ChIP seq Input for PAF1 in MM1.S cells

tag: cell line

value: Multiple myeloma cell line (MM1.S)

tag: cell type

value: Plasma cell line derived from multiple myeloma with t(14;16) translocation

tag: chip antibody


title: HFG21

value: fetal gut

tag: genotype

tag: developmental stage


title: 162630 Case

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Baltimore

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: 910004 Case

tag: tissue

value: Male

tag: age

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: HFG20

tag: genotype

value: Homozygous for Resistant haplotype (RR)


title: 259704 Case


title: HFG14

tag: developmental stage


title: 24OH_12h_1020_2 [AB452]

tag: condition

tag: treatment

value: choroid plexus

tag: timepoint

tag: experiment


title: 24OH_12h_1020_1 [AB451]


title: 341050 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma


title: TB6328, RSL3, replicate 2

value: acute slice culture of glioma resection

tag: disease diagnosis

value: Glioblastoma, WHO Grade IV

tag: location


title: TB6328,  RSL3 + Ferrostatin, replicate 1

tag: tissue

tag: age

value: 50 nM RSL3 and 10 µM Ferrostatin-1, 18-hour


title: DMSO_12h_1020_3 [AB450]

value: CP culture (12h after DMSO)

value: DMSO


title: TB6328, RSL3, replicate 1

value: 50 nM RSL3, 18-hour


title: 406700 Case

value: Nasal Epithelium

value: Case

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: baltimore pc1


title: DMSO_12h_1020_2 [AB449]

tag: condition

tag: treatment

tag: timepoint

tag: experiment


title: EBB059.Neg.Ep

city: Seattle

first: Ryan

middle: C

last: Murphy

state: WA

address: 850 Republican St.

department: Division of Pulmonary, Critical Care, and Sleep Medicine

institute: University of Washington

data_processing:
Sequencing was performed using an Illumina HiSeq 4000 instrument. Base calls were generated in real-time on the HiSeq instrument, and RTA-generated BCL files were converted to FASTQ files. Sequence read and base quality were checked using the FASTX-toolkit and FastQC, and adaptor and low-quality bases were trimmed. Sequences were aligned to GRCh37 using STAR (v2.5.3a). Transcript abundances were quantified using Kallisto (v0.43.1). Genes with a raw count of at least 10 went into further analysis leaving 26,323 unique genes. Count dataunderwent variance stabilization andwere converted into log2-counts per millionvia the Bioconductor packageDESeq2.
Differential gene expression between EIB(-) and EIB(+) individuals was determined using DESeq2 package in R. OmicSoft human gene model
Assembly: hg19
Supplementary files format and content: Abundance counts

source_name: epithelial brushing

extract_protocol:
Research bronchoscopy was conducted and 4 epithelial brushings were obtained from second- to fifth-generation airways of the left lower lobe and lingula using a 3-mm nylon cytology brush. Epithelial brushings were available from 20 individuals with asthma (9 EIB(-)  and 11 EIB(+)).
The 4 brushings from individual participants were pooled and placed in TRIzol reagent, then RNA was isolated using the Direct-zolTM RNA MiniPrep kit (Zymo Research, Irvine, CA)
RNA-seq was performed at University of Washington’s Northwest Genomics Center (http://nwgc.gs.washington.edu/).Library generation was performed using TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) using 1 ug total RNA.

value: epithelial brushing

tag: group

value: Asthma without EIB


title: TB6328, DMSO Control, replicate 2

tag: Sex

value: F

value: Left frontal

value: drug vehicle (DMSO), 18-hour


title: TB6458, DMSO Control, replicate 1

tag: disease diagnosis

value: M

value: Right frontal


title: 127000 Case

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Baltimore

tag: asthma

value: Active Asthma

tag: baltimore pc2


title: EBB052.Neg.Ep

tag: tissue


title: DMSO_12h_1020_1 [AB448]

value: choroid plexus


title: TB6328, DMSO Control, replicate 1

value: acute slice culture of glioma resection

value: Glioblastoma, WHO Grade IV

tag: age

tag: location


title: 577594 Case

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: EBB050.Neg.Ep

tag: treatment

tag: group


title: 992487 Case

tag: Sex

tag: baltimore pc1


title: EBB042.Neg.Ep


title: TB6181, RSL3 + Ferrostatin

tag: disease diagnosis

value: Anaplastic Astrocytoma, WHO Grade III

value: Fronal and temporal

value: 50 nM RSL3 and 10 µM Ferrostatin-1, 18-hour


title: 187945 Case

value: Nasal Epithelium

value: Male

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Asthmatic


title: DMSO_24h_0920_2 [AB423]

tag: condition

value: CP culture (24h after DMSO)

value: DMSO

tag: tissue

tag: timepoint

tag: experiment


title: TB6181, RSL3

tag: age

value: F

tag: location

value: 50 nM RSL3, 18-hour


title: DMSO_24h_0920_1 [AB422]


title: 24OH_24h_0920_3 [AB421]

value: CP culture (24h after 24-OH)


title: TB6181, DMSO Control, replicate 1

value: drug vehicle (DMSO), 18-hour


title: TB6181, DMSO Control, replicate 2


title: EBB020.Neg.Ep

value: epithelial brushing

value: Asthma without EIB


title: HFG7

value: fetal gut

tag: genotype

value: Homozygous for Resistant haplotype (RR)

tag: developmental stage


title: DMSO_24h_0920_3 [AB424]

value: choroid plexus


title: 24OH_24h_0920_2 [AB420]


title: EBB040.Neg.Ep


title: 912562 Case

value: Baltimore

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: baltimore pc2


title: 226750 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Chicago

tag: chicago pc1

tag: chicago pc2


title: 481302 Case

tag: tissue

value: Male

value: Case

tag: age

value: Asthmatic


title: EBB015.Neg.Ep

tag: treatment

tag: group


title: SS4-VDJ

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

data_processing:
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v3.0, 10X Genomics). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering. Filtered gene-barcodes matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded.
TCR reads sequenced by V(D)J assay were aligned to GRCh38 reference transcriptome using Cell Ranger VDJ. T cells were assigned with productive CDR3 regions for TCR alpha and TCR beta chains.
Each clonotype was assigned with a unique identifier based on amino acid sequences of the CDR3 regions and V(D)J genes of the two chains, which was then used to match clonotypes across samples
Assembly: GRCH38
Supplementary files format and content: csv files include assembled TCR heavy chain and light chain sequences and VDJ annotation for each T cell
Supplementary files format and content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq
Library strategy: VDJ-seq

source_name: Peripheral blood of Sezary syndrome

extract_protocol:
Peripheral blood was collected in green tip herapin tubes or via apheresis (ECP). PBMCs were sorted to CD4+CD26- T cells via STEM CELL kits.
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 5’ v 1.1 and V(D)J Reagent Kits.  50,000 or 5,000 sequencing reads per cell for scRNA-seq or VDJ libraries, respectively, were generated on the Illumina NextSeq 500 instrument.

tag: cancer type

value: Sezary syndrome

tag: cell type

value: CD4+ CD26- T cells


title: 24OH_24h_0920_1 [AB419]

tag: condition

value: CP culture (24h after 24-OH)

tag: timepoint

tag: experiment


title: 475110 Case

value: Denver

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: denver pc1

tag: denver pc2


title: SS3-VDJ


title: 24OH_24h_0221_3 [AB530]

tag: tissue


title: SS2-VDJ


title: EBB024.Neg.Ep

tag: treatment

value: epithelial brushing


title: 760312 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: age


title: 819271 Case

tag: chicago pc1

tag: chicago pc2


title: SS1-VDJ

tag: cancer type

tag: cell type


title: 24OH_24h_0221_2 [AB529]

tag: condition

tag: timepoint

tag: experiment


title: EBB097.Pos.Ep

tag: group

value: Asthma and EIB


title: 554529 Case

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: denver pc1


title: EBB062.Pos.Ep

tag: treatment

tag: tissue


title: MF3-VDJ

source_name: Peripheral blood of Mycosis Fungoides

value: Mycosis fungoides


title: 254466 Case

source_name: Nasal Epithelium

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: age

tag: denver pc2


title: EBB053.Pos.Ep

tag: group


title: EBB047.Pos.Ep


title: 359995 Case

tag: asthma


title: MF2-VDJ

tag: cancer type

tag: cell type


title: DMSO_24h_0221_3 [AB527]

tag: condition

value: CP culture (24h after DMSO)

value: DMSO

tag: timepoint

tag: experiment


title: MF1-VDJ


title: 265510 Case

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: EBB035.Pos.Ep

tag: treatment

tag: tissue


title: EBB010.Neg.Ep

value: Asthma without EIB


title: SS4-GEX

data_processing:
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v3.0, 10X Genomics). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering. Filtered gene-barcodes matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded.
TCR reads sequenced by V(D)J assay were aligned to GRCh38 reference transcriptome using Cell Ranger VDJ. T cells were assigned with productive CDR3 regions for TCR alpha and TCR beta chains.
Each clonotype was assigned with a unique identifier based on amino acid sequences of the CDR3 regions and V(D)J genes of the two chains, which was then used to match clonotypes across samples
Assembly: GRCH38
Supplementary files format and content: csv files include assembled TCR heavy chain and light chain sequences and VDJ annotation for each T cell
Supplementary files format and content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq


title: 668110 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: age

value: Active Asthma

tag: denver pc1


title: DMSO_24h_0221_1 [AB525]

tag: condition

value: choroid plexus


title: EBB032.Pos.Ep

tag: group


title: 974464 Case

value: Nasal Epithelium

tag: asthma

tag: denver pc2


title: SS3-GEX

tag: cancer type

tag: cell type


title: EBB026.Pos.Ep


title: 24OH_24h_0221_1 [AB528]

tag: timepoint

tag: experiment


title: MIA6026

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.6.2
FASTQs aligned to the mm10 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the Ensembl v91 mouse gene annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed files is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

source_name: mouse lung tissue

extract_protocol:
Total RNA was extracted using a Direct-zol™ RNA MicroPrep kit
Total RNA was prepped for sequencing with the Nugen Universal mRNA Prep Kit according to manufacturer's protocols

treatment_protocol: Challenged mice were exposed to MAB microparticles diluted in 50μL at a concentration equal to 1,000,000 bacteria intratracheally. Treatment group also recived 5μg subdermal MIA 602 daily for 3 weeks.

value: lung

value: M. abscessus particles followed by MIA602

tag: strain

value: male


title: MIA6025

tag: treatment


title: 324673 Case

tag: tissue

value: Male

value: Case

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: SS2-GEX

value: Sezary syndrome

value: CD4+ CD26- T cells


title: MIA6024

tag: Sex


title: EBB023.Pos.Ep

value: epithelial brushing

tag: group


title: EBB025.Pos.Ep

value: Asthma and EIB


title: SNU1750 WT clone #5, Input

city: Singapore

first: Shamaine

last: Ho

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
For Nano ChIP-seq, sequenced reads were first trimmed to remove the first and last ten bases. No trimming was required for TF ChIP-seq. Sequenced reads were mapped to the human genome assembly (hg19) using Burrows-Wheeler Aligner (BWA-MEM, version 0.7.10). Only reads with MAPQ value of at least 10 were retained, and PCR duplicates were removed using SAMtools (version 0.1.19). Significant ChIP enrichment peaks relative to input were identified using MACS2 callpeak function. Wiggle track visualizations were generated using MEDIPS (version 1.20.1).
For RNA-seq, sequenced reads were aligned to hg19 using STAR mapper and gene expression abundance was estimated with RSEM as fragments per kilobase per million (FPKM) using default parameters (pipeline available at https://github.com/gis-rpd/pipelines/tree/master/rnaseq/star-rsem).
Assembly: hg19 for ChIP-seq and RNA-seq
Supplementary files format and content: wig/bigwig files for ChIP-seq, RSEM gene count files for RNA-seq

source_name: Gastric Cancer Line

extract_protocol:
For ChIP-seq, sheared chromatin were subjected to immunoprecipitation with 2 μg antibody against H3K27ac (ab4729, Abcam), H3K4me1 (ab8895, Abcam) or 5 μg antibody against TEAD1 (610923, BD Biosciences). For RNA-seq, total RNA was extracted following manufacturer’s protocols (Qiagen)
For Nano histone ChIP-seq, ChIP and input DNA were subjected to whole-genome amplification using the WGA4 kit (Sigma-Aldrich) and a universal primer linked to BpmI restriction site (Qiagen). 30ng of BpmI-digested DNA was used for ChIP-seq library preparation according to manufacturer’s protocols (New England Biolabs). For TF ChIP-seq, 30ng of ChIP and input DNA was used for library preparation. For RNA-seq, libraries were prepared accordingly using Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit (Illumina), with an input of 1 μg total RNA.

tag: cell line

tag: chip antibody

value: Input

tag: genotype

value: TEAD1 WT


title: SS1-GEX

tag: cancer type

tag: cell type


title: DMSO_24h_0221_2 [AB526]

tag: condition

value: CP culture (24h after DMSO)

value: DMSO

tag: timepoint

tag: experiment


title: 680602 Case

data_processing:
Trimming: FastQC0.11.9, BBDuk Version 38.90
Alignment: HISAT2 Version 2.2.21
Read Count Extraction: CoCo Version 2.0.2
Normalization: LIMMA Version 3.50.3, sva Version 3.42.0, edgeR Version 3.36.0
Filtering Genes: DESeq2_1.34.0
Assembly: GrCh38
Supplementary files format and content: full_n536__21831_voom_norm_counts_with_RandomID.csv
Supplementary files format and content: full_n536__raw_counts_with_RandomID.csv

tag: tissue

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Denver

tag: age

tag: asthma

value: Active Asthma

tag: denver pc1

tag: denver pc2


title: 282160 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: EBB003.Pos.Ep

tag: treatment

tag: group


title: SNU1750 WT clone #4, Input

tag: cell line

tag: chip antibody

tag: genotype


title: MF2-GEX

tag: cancer type

value: Mycosis fungoides

tag: cell type


title: 100837 Case

tag: tissue

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: age

tag: asthma


title: EBB002.Pos.Ep


title: SNU1750 WT clone #3, Input


title: MF1-GEX


title: 634324 Case

tag: Sex

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: denver pc1

tag: denver pc2


title: SS4-ATAC

library_source: genomic single cell

data_processing:
Raw sequencing reads generated from 10X ATAC assay were processed by cellranger-atac workflow in Cell Ranger (v6.1, 10X Genomics) with default settings to generate mapping and chromatin accessibility. The mapping and chromatin accessibility data were imported to R package Signac v1.3.0 (31) for downstream analysis.
Low-quality cells with < 3,000 or > 20,000 fragments in peaks, < 15% fraction of fragments in peaks, > 4 ratio of mononucleosomal to nucleosome-free fragments, or < 2 transcriptional start site (TSS) enrichment score were filtered out. A latent semantic indexing (LSI) dimension reduction was performed on the filtered cells.
Assembly: GRCH38
Supplementary files format and content: csv files include peaks( local enrichment of transposase cut-sites) identified from ATAC data

source_name: Peripheral Blood of CTCL

extract_protocol:
Peripheral Blood was collected from CTCL patients via green top herapin tubes or apheresis (ECP) and isolated for malignant CD4+CD26- Tcells via STEM CELL kits
The scATAC-Seq libraries were prepared following the protocol provided by the 10X genomics. Target nuclei number for encapsulation was 6,000 to 10,000 cells for single cell ATAC sequencing.  Libraries were prepared with Chromium Single Cell ATAC Reagent kit (v1.1 Chemistry) (10X Genomics, Inc., Pleasanton, CA) and run on NextSeq 500 150 cycles (50bp x 50bp). Read depth was approximately 25,000 reads per sample.

value: CD4+CD26- T cells


title: 407037 Case

extract_protocol: Total RNA with Ribo-Zero kit was used to prepare libraries from nasal epithelial cells depleting the ribosomal RNA

value: Male

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: donor8_IL13_2d

city: Iowa City

first: Alejandro

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p13 using kallito software version 0.45.0
Assembly: GRCh38.p13
Supplementary files format and content: HDF5 format file containing counts and abundance for each gene (row) and sample (column)

source_name: lung

growth_protocol: DMEM/F12 media with Ultroser G was replaced every two days.

extract_protocol:
RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit # 74804.
mRNA libraries were prepared using Illumina TruSeq Stranded Total RNA Gold

treatment_protocol: Air-liquid interface cultures of primary airway epithelia from 1 de-identified human donor with no known disease were exposed to apical and basolateral IL13 or vehicle at a concentration of 20ng/mL for up to 21 days.

tag: treatment

tag: time point

value: lung


title: donor8_IL13_3w

tag: tissue


title: SNU1750 WT clone #1, Input

tag: cell line

tag: chip antibody

tag: genotype


title: SS3-ATAC

tag: cancer type

tag: cell type


title: MF3-GEX


title: donor8_DMSO


title: SNU1750 Homo clone #5, Input

value: TEAD1 KO