title: expanded HSCs, CD201+CD150+CD48+KSL, rep2

city: Tokyo

first: Hans

middle: Jiro

last: Becker

state: Tokyo

address: Shirokanedai 4-6-1, Minato-ku

department: Institute of Medical Science

institute: The University of Tokyo

data_processing:
CLC Genomics Workbench v 11
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork
Data normalization and comparative analyses were performed with the DESeq2 package in R.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including normalized expression values (DESeq2) for each sample
Supplementary files format and content: comma-separated value file including non-normalized, raw count numbers

source_name: bone marrow

growth_protocol: CD34-CD150+KSL murine hematopoietic stem cells (HSCs) were isolated from the bone marrow of C57BL/6 mice and cultured in expansion medium for one week (F12 medium, 0.1% PVA, 1%PS, 1X ITS, rmTPO 100ng/ml, rmSCF 10ng/ml)

extract_protocol:
Over 5000 cells per population were sorted into 1.5 ml tubes and subsequently lysed in 600 µl Trizol LS reagent (Thermo Fisher Scientific). RNA purification, library preparation and next-generation sequencing was performed by Tsukuba i-Laboratory, LLC.
Libraries were prepared using the SMARTer cDNA synthesis kit (Takara) and the high-output kit v2 (Illumina), followed by sequencing on a NextSeq 500 sequencer (Illumina) at 2x 36 paired end reads.

value: bone marrow

value: primary cells

value: HSC


title: Lung_Printex_Medium_Day30_rep4

status: Public on Jul 19 2023

type: RNA

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description: Gene expression in lung of rat exposed to Printex (15 mg/m3) 30 days post exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 6 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned within 3 hours after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 12.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 30, replicate 4

label_protocol: For each of the 72 samples (6 control, 6 exposed rats to low dose, 6 exposed rats to medium dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry.

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 6.7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to Printex (Low dose: 5 mg/m3, Medium dose: 15 mg/m3, High dose: 50 mg/m3).

tag: strain

value: Sprague Dawley

tag: tissue

value: accessory lobe of lung

tag: gender

value: female

tag: age

value: 13 weeks-old (at the onset of instillation)


title: VBCS-702_AKO3

type: SRA

city: Grand Rapids

first: Ning

last: Wu

state: MI

address: 333 Bostwick Ave NE

country: USA

institute: Van Andel Institute

library_source: transcriptomic

data_processing:
Reads were trimmed with TrimGalore! v0.6.0.
Trimmed reads were aligned with STAR v2.7.8a against mm10 and gene counts were obtained based on GENCODE vM24 annotations.
Assembly: mm10
Supplementary files format and content: Gene counts in tab-delimited format.

organism: Mus musculus

source_name: eWAT macrophage mRNAseq of adipose specific TXNIP KO animals on control diet

extract_protocol:
Total RNA was extracted with a combination of TRIzol and PureLink RNA mini kit (Invitrogen).
For eWAT: Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA Stranded mRNA-Seq Kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA).
For macrophages: Libraries were prepared by the Van Andel Genomics Core from 1-5 ng of total RNA. Total RNA material was converted to dsDNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, v. 091817 (Takara Bio USA, Mountain View, CA, USA ). cDNA was sheared to 200–500 bp using a Covaris E220 Evolution ultrasonicator (Covaris Inc., Woburn, MA USA) and Illumina compatible sequencing libraries were generated using the Kapa HyperPrep kit, v6.17 (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex dual adapters (Bioo Scientific, Austin, TX, USA).

value: eWAT

tag: cell type

value: F4/80+, CD11b+ and CD64+ macrophags

tag: genotype

value: adipose specific TXNIP KO

tag: treatment

value: control diet


title: VAST6958384 ViPS_nTD_V7

city: Oxford

first: Henderson

last: Zhu

address: Oxford Vaccine Group, Old Road, Headington, Old Road, Headington

department: Oxford Vaccine Group, Department of Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
Sequences assigned to be ribosomal RNA, sex chromosome genes, mitochondrial RNA or haemoglobin were excluded from downstream analysis.
Gene features were counted using HTSeq (version 0.9.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries (genes without an abundance greater than 1 count per million in 9 or more samples) were filtered out.
Assembly: Sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38, using STAR (version 2.6.1d).
Supplementary files format and content: R file containig normalized abundance measurements

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Total RNA was extracted from all samples using the Tempus Spin RNA Isolation kit (Life Technologies).
Libraries were prepared using a poly-A selection step to exclude ribosomal RNA species (read length: 75bp paired-end, stranded).

value: whole blood

value: WT

value: ViPS

tag: sequencing pool


title: VAST6958380 ViPS_nTD_V7


title: Lung_Printex_High_Day30_rep3

description: Gene expression in lung of rat exposed to Printex (50 mg/m3) 30 days post exposure

source_name: Rat, Lung, Printex, Exposed to High dose, Day 30, replicate 3


title: expanded HSCs, CD201+CD150+CD48+KSL, rep1

country: Japan

tag: cell line


title: Lung_Printex_Medium_Day30_rep3

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 30, replicate 3


title: Lung_Printex_Medium_Day30_rep2

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 30, replicate 2


title: expanded HSCs, CD201-CD150+CD48+KSL, rep3


title: VAST6958379 ViPS_nTD_D7


title: Lung_Printex_Medium_Day30_rep6

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 30, replicate 6


title: expanded HSCs, CD201-CD150+CD48+KSL, rep2


title: VBCS-702_AKO1


title: VAST6958378 ViPS_nTD_V1


title: expanded HSCs, CD201+CD150+CD48+KSL, rep3


title: Radiation Control

city: Albany

first: Katherine

middle: C

last: MacNamara

state: New York

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Barcode processing, gene counting, and aggregation were done using Cell Ranger software v6.0.1.
Assembly: mm10

source_name: Bone marrow

extract_protocol:
Whole BM was flushed from femus and tibias into HBSS. After RBC lysis, cells suspensions were stained and 7-AAD- CD11b+ Ly6C+ Ly6G- cells were sorted on a BD FACSAria Cell Sorter. Cells from each experimental group (radiation and SAA, n = 3 mice per group) were pooled together.
Library construction was performed according to the manufacter's instructions (single cell 5' v2 protocol, 10x Genomics). Briefly, BM cells were resuspended in the master mix and loaded into the chromium chip with partioninig oil to generate the gel bead-in-emulsion (GEM). Reverse transcription was then performed and cDNA cleaned up with Silane DynaBeads and amplified by PCR. Library construction and sequencing was next performed by the Center for Functional Genomics at SUNY Albany.

value: Bone marrow

value: 300 rads


title: Lung_Printex_Medium_Day30_rep1

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 30, replicate 1


title: Lung_Printex_Low_Day30_rep6

description: Gene expression in lung of rat exposed to Printex (5 mg/m3) 30 days post exposure

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 30, replicate 6


title: VBCS-702_WT6

source_name: eWAT macrophage mRNAseq of WT animals on control diet


title: VAST6958377 ViPS_nTD_D0.12h


title: expanded HSCs, CD201-CD150+CD48+KSL, rep1


title: expanded HSCs, CD201+CD150+CD48-KSL, rep3


title: VAST6958381 ViPS_nTD_V0


title: VBCS-702_AKO2


title: Lung_Printex_Low_Day30_rep4

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 30, replicate 4


title: VBCS-702_WT5


title: Lung_Printex_Low_Day30_rep5

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 30, replicate 5


title: VAST6958376 ViPS_nTD_V0


title: expanded HSCs, CD201+CD150+CD48-KSL, rep2


title: VBCS-702_WT4


title: VAST6958375 ViPS_nTD_D0.12h


title: VBCS-702_WT3


title: Lung_Printex_Low_Day30_rep3

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 30, replicate 3


title: Lung_Printex_Low_Day30_rep2

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 30, replicate 2


title: expanded HSCs, CD201+CD150+CD48-KSL, rep1


title: VBCS-702_WT2


title: P81S12(LT)_Rep2 [ATAC-seq]

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

library_source: genomic

data_processing:
Pre-processing fastq files: Cutadapt (version 2.10) was used to remove adapter contaminations identified by FastQC (version 0.11.9), trim low quality bases from read ends (<20), discard reads shorter than 10 bases and removed reads mapping to ENCODE blacklisted regions.
Alignment: reads were corrected for Tn5 offset (+ve strand: +4bp, -ve strand: -5bp) and were mapped to hg38 using BWA (version 0.7.17).
Peak-calling: peaks were called using MACS2 (version 2.2.7.1) with the following parameters “-f BAM –bdg -g 2913022398 –nomodel –nolambda –shift -100 –extsize 200”
Genome_build: hg38
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: ccRCC cell line

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
Cells at 75% confluency were trypsinised, counted and 50,000 cells were subjected to ATAC-seq protocol directly as previously described (Buenrostro et al., 2013).
Libraries were prepared using the Illumina Nextera DNA library preparation kit (FC-121-1030) and purified using the minElute PCR purification kit (Qiagen 28004). Following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 8-12 cycles and cleaned-up using the Agencourt AMPureXP reagent (A63880) according to manufacturer's recommendations, and pooled in equimolar concentrations prior to sequencing.

treatment_protocol: 0.6μg/ml doxycycline for 1 week - 2 months to induce Cas9 and  shRNA construct expression.

value: ccRCC cell line

tag: genotype/variation


title: P81S12(LT)_Rep3 [ATAC-seq]


title: VBCS-702_WT1


title: P81S12(LT)_Rep1 [ATAC-seq]


title: SUW036083_Naive_baseline

city: Charlestown

first: Debattama

middle: R

last: Sen

state: MA

department: Cancer Center

institute: MGH/Harvard

data_processing:
bcl2fastq (v2.19.1.403) was used to demultiplex raw data from NextSeq 500 machine.
Quality trimming and primer removal in raw fastq files were done with Trimmomatric (v.0.36) using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were aligned to hg19 with Bowtie2 (v.2.2.9) using a maximum insert size of 1,000.
Aligned bams were sorted, duplicates marked (Picard v.2.8.0) , and reads mapping to the blacklist region removed.
Peak-calling using MACS (v.2.1.1) was performed on merged bam files (Samtools v. 1.3) from biological replicates using a q-value threshold of 0.001. Consensus peaks from all biological conditions were merged to create a single peak universe. Cut sites were extracted from each biological replicate and the number of cuts in each peak region was quantified to generate a raw counts matrix.
Normalization and differential expression were performed using DESeq2 (v 1.26.0)
Assembly: hg19
Supplementary files format and content: raw counts
Supplementary files format and content: DESeq2-normalized counts

source_name: blood

extract_protocol:
DNA was purified using a QIAgen MinElute Reaction Cleanup kit
Post-PCR bead cleanup was done using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and library quality was verified using Tapestation analysis.

value: blood

value: sorted CD8+ T cells


title: SUK036043_Naive_baseline


title: SUW036083_HIV_B53_YPLT_baseline


title: P81S11(LT)_Rep3 [ATAC-seq]


title: SUK036043_Naive_1yr


title: P81S11(LT)_Rep2 [ATAC-seq]


title: SUK036043_HIV_B57_KAFS_baseline


title: VBCS-581_AKO7

source_name: eWAT mRNAseq of adipose specific TXNIP KO animals on ketogenic diet

value: ketogenic diet


title: VBCS-581_AKO6


title: SUK036043_HIV_B57_KAFS_1yr


title: VBCS-581_AKO5


title: P81Ctrl(A)_Rep3 [ATAC-seq]


title: P81S11(LT)_Rep1 [ATAC-seq]


title: ST013_Naive_baseline


title: Lung_Printex_Control_Day30_rep6

description: Gene expression in lung of control rat (filtered air) 30 days post exposure

source_name: Rat, Lung, Printex, Control, Day 30, replicate 6

value: Sprague Dawley


title: VBCS-581_AKO8


title: P81Ctrl(A)_Rep2 [ATAC-seq]


title: Lung_Printex_Low_Day30_rep1

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 30, replicate 1

value: accessory lobe of lung


title: Lung_Printex_Control_Day30_rep4

source_name: Rat, Lung, Printex, Control, Day 30, replicate 4

value: female


title: ST013_Naive_1yr


title: Lung_Printex_Control_Day30_rep3

source_name: Rat, Lung, Printex, Control, Day 30, replicate 3

value: 13 weeks-old (at the onset of instillation)


title: Lung_Printex_Control_Day30_rep1

source_name: Rat, Lung, Printex, Control, Day 30, replicate 1


title: Lung_Printex_Control_Day30_rep2

source_name: Rat, Lung, Printex, Control, Day 30, replicate 2


title: Lung_Printex_Control_Day30_rep5

source_name: Rat, Lung, Printex, Control, Day 30, replicate 5


title: ST013_HIV_B07_GPGH_baseline


title: VBCS-581_AKO2

value: eWAT


title: Lung_Printex_High_Day3_rep6

description: Gene expression in lung of rat exposed to Printex (50 mg/m3) 3 days post exposure

source_name: Rat, Lung, Printex, Exposed to High dose, Day 3, replicate 6


title: Lung_Printex_High_Day3_rep5

source_name: Rat, Lung, Printex, Exposed to High dose, Day 3, replicate 5


title: P81Ctrl(A)_Rep1 [ATAC-seq]


title: Ctr.Ctrl(A)_Rep3 [ATAC-seq]

value: shCtrl/sgCtrl


title: ST013_HIV_B07_GPGH_1yr


title: VBCS-581_AKO1

value: adipose specific TXNIP KO


title: ST013_HIV_A03_RLRP_baseline


title: Lung_Printex_High_Day3_rep4

source_name: Rat, Lung, Printex, Exposed to High dose, Day 3, replicate 4


title: Ctr.Ctrl(A)_Rep1 [ATAC-seq]


title: VBCS-581_AKO3


title: VBCS-581_WT8

source_name: eWAT mRNAseq of WT animals on ketogenic diet


title: Lung_Printex_High_Day3_rep3

source_name: Rat, Lung, Printex, Exposed to High dose, Day 3, replicate 3


title: Ctr.Ctrl(A)_Rep2 [ATAC-seq]


title: VBCS-581_AKO4


title: Lung_Printex_High_Day3_rep2

source_name: Rat, Lung, Printex, Exposed to High dose, Day 3, replicate 2


title: VBCS-581_WT6


title: Lung_Printex_High_Day3_rep1

source_name: Rat, Lung, Printex, Exposed to High dose, Day 3, replicate 1


title: ST003_Naive_baseline


title: ST003_Naive_1yr


title: VBCS-581_WT7


title: ST013_HIV_A03_RLRP_1yr


title: VBCS-581_WT5


title: VBCS-581_WT4


title: VAST6958394 Control_TD_D0

source_name: whole blood

value: Control


title: ST003_HIV_B57_KAFS_baseline

source_name: blood


title: P81S12(LT)_Rep3

data_processing:
The processing of the FASTQ files to a read count table was performed on the BlueBee® Genomics Platform. In short, reads were trimmed using Bbduk (v35.92) from the bbmap suite, aligned with STAR aligner (v2.5.2a) to hg38, and counted using HTSeq-count (v0.6.0).
Genome_build: hg38
Supplementary_files_format_and_content: Count file

source_name: ccRCC cell line

extract_protocol:
RNA was extracted from 75% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
Library preparation was performed using the QuantSeq 3 mRNA-Seq Library Prep Kit FWD for Illumina and PCR Add-on Kit for Illumina (Lexogen), with 300ng input RNA. The size of the final libraries was determined using the Agilent 4200 TapeStation System using the high sensitivity D1000 reagents (5067-5592). The concentration of the libraries was determined using the Qubit Flex Fluorometer (Thermo Fisher).

tag: construct


title: P81S12(LT)_Rep1


title: VBCS-581_WT3


title: P81S12(LT)_Rep2


title: P81S12(LT)_Rep4


title: ST003_HIV_B57_KAFS_1yr


title: Lung_Printex_Medium_Day3_rep6

description: Gene expression in lung of rat exposed to Printex (15 mg/m3) 3 days post exposure

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 3, replicate 6


title: Lung_Printex_Medium_Day3_rep3

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 3, replicate 3


title: ST001_Naive_baseline


title: P81S11(LT)_Rep3


title: VBCS-581_WT1


title: VBCS-581_WT2


title: Lung_Printex_Medium_Day3_rep5

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 3, replicate 5


title: Lung_Printex_Medium_Day3_rep4

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 3, replicate 4


title: ST001_Naive_1yr


title: Lung_Printex_Medium_Day3_rep2

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 3, replicate 2


title: P81S11(LT)_Rep2


title: VBCS-520_AKO7

source_name: eWAT mRNAseq of adipose specific TXNIP KO animals on control diet

value: control diet


title: P81S11(LT)_Rep1


title: ST001_HIV_B57_TSTL_baseline


title: P81S12(A)_Rep3


title: Lung_Printex_Medium_Day3_rep1

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 3, replicate 1


title: ST001_HIV_B57_TSTL_1yr


title: SAX032001_Naive_1yr


title: SAX032001_Naive_baseline


title: P81S12(A)_Rep4


title: Lung_Printex_Low_Day3_rep6

description: Gene expression in lung of rat exposed to Printex (5 mg/m3) 3 days post exposure

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 3, replicate 6


title: VBCS-520_AKO5


title: VBCS-520_AKO4


title: P81S11(LT)_Rep4


title: P81S12(A)_Rep2


title: VBCS-520_AKO3


title: Lung_Printex_Low_Day3_rep5

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 3, replicate 5


title: SAX032001_HIV_B07_GPGH_baseline


title: SAX032001_HIV_B07_GPGH_1yr


title: VBCS-520_AKO2


title: VBCS-520_AKO1


title: P81S11(A)_Rep4


title: Lung_Printex_Low_Day3_rep3

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 3, replicate 3


title: Lung_Printex_Low_Day3_rep2

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 3, replicate 2


title: VBCS-520_AKO6


title: SAX032001_HIV_A03_RLRP_baseline


title: Lung_Printex_Low_Day3_rep4

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 3, replicate 4


title: P81S12(A)_Rep1


title: VBCS-520_WT7

source_name: eWAT mRNAseq of WT animals on control diet

value: WT


title: Lung_Printex_Low_Day3_rep1

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 3, replicate 1


title: SAX032001_HIV_A03_RLRP_1yr


title: P81S11(A)_Rep2


title: VBCS-520_WT6


title: P81S11(A)_Rep3


title: SAQ038001_Naive_baseline


title: Lung_Printex_Control_Day3_rep6

description: Gene expression in lung of control rat (filtered air) 3 days post exposure

source_name: Rat, Lung, Printex, Control, Day 3, replicate 6


title: VBCS-520_WT5


title: Lung_Printex_Control_Day3_rep5

source_name: Rat, Lung, Printex, Control, Day 3, replicate 5


title: P81Ctrl(A)_Rep4

source_name: ccRCC cell line


title: SAQ038001_HIV_A03_RLRP_baseline

source_name: blood


title: CW006_Naive_baseline


title: CW006_Naive_1yr


title: P81Ctrl(A)_Rep3


title: VBCS-520_WT4


title: VBCS-520_WT3


title: P81Ctrl(A)_Rep2


title: P81Ctrl(A)_Rep1


title: VBCS-520_WT1


title: Lung_Printex_Control_Day3_rep4

source_name: Rat, Lung, Printex, Control, Day 3, replicate 4


title: CW006_HIV_B07_GPGH_baseline


title: P81S11(A)_Rep1


title: Lung_Printex_Control_Day3_rep2

source_name: Rat, Lung, Printex, Control, Day 3, replicate 2


title: CW006_HIV_B07_GPGH_1yr


title: Lung_Printex_Control_Day3_rep1

source_name: Rat, Lung, Printex, Control, Day 3, replicate 1


title: Ctr.Ctrl(A)_Rep4

description: Cl6 REVIR_R_NTC_Rep4_AACGCC


title: CW001_Naive_baseline


title: Lung_TiO2_High_Day180_rep6

description: Gene expression in lung of rat exposed to TiO2 (15 mg/m3) 180 days post exposure

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 180, replicate 6

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to TiO2 (Low dose: 1.5 mg/m3, Medium dose: 5 mg/m3, High dose: 15 mg/m3).


title: DG_Old_10x_SingleCell

city: Berkeley

first: Danica

last: Chen

address: 335 Morgan Hall

institute: University of California, Berkeley

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma-separated values file

source_name: Dentate gyrus

extract_protocol:
Mice were sacrificed, the brains were promptly isolated, and the dentate gyrus was quickly microdissected under a dissection scope. Cells were dissociated using papain neural-tissue dissociation kit (Miltenyi biotechnology), according to the manufacturer’s protocol. After a final wash in HBSS, the cell pellet was resuspended in catching medium: DMEM/F12 (Thermo Fisher) with B27 supplement (Thermo Fisher, no Vitamin A,1:50), N2 supplement (Thermo Fisher, 1:100), 15 mM HEPES buffer, 0.6% glucose, penicillin–streptomycin–glutamine (Life Technologies, 1:100), and insulin–transferrin–selenium (Life Technologies, 1:1,000). The cell suspension was stained with propidium iodide (PI) (biolegend, 1:1000) for 1 minute. PI negative live cells were FACS-sorted on a BD FACS Aria Fusion, using a 100μm nozzle at 13.1 PSI.
Cells were loaded onto a 10x Genomics Chromium chip per factory recommendations. Reverse transcription and library preparation were performed using the 10x Genomics Single Cell 3’ reagent kits v3 following the 10x Genomics protocol.

value: Dentate gyrus

value: 16 months old


title: DG_Young_10x_SingleCell

description: 10x Genomics

value: 3 months old


title: CW001_HIV_B07_GPGH_baseline


title: Lung_TiO2_High_Day180_rep5

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 180, replicate 5

value: rat exposed to TiO2 (15 mg/m3) 180 days post exposure


title: Ctr.Ctrl(A)_Rep2

description: Cl6 REVIR_R_NTC_Rep2_AATCCG

value: ccRCC cell line


title: IR, Ins rep3

city: Jinan

first: Zhenyu

last: Yao

state: Shandong Province

address: No.544, Jing 4 Road, Huaiyin District

department: Shandong Provincial Hospital

country: China

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

data_processing:
RNA purity was checked using the NanoPhotometer spectrophotometer (Implen)
Sequencing libraries were generated using NEBNext Ultr RNA Library Prep Kit for Illumina.
Sequencing was performed on an Illumina Hiseq platform.
Reads of each sample were aligned to the mouse genome (NCBI build 38/mm10) using Bowtie v2.2.3.
Assembly: mm10
Supplementary files format and content: Reads of each sample were aligned to the mouse genome (NCBI build 38/mm10) using Bowtie v2.2.3.

source_name: Liver

growth_protocol: The animal experiment was authorized by the Animal Ethics Committee of Shandong First Medical University. Male C57BL/6J mice (19-23 g, 7-week-old) were purchased from Vital River Laboratory Animal Technology and housed under specific pathogen free (SPF) conditions in Shandong Provincial Hospital. The mice were maintained on a 12-h light/dark cycle at 22 ± 0.5°C, 50 –60% humidity, with food and water provided ad libitum.

extract_protocol:
Livers were removed, flash frozen in liquid N2, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To establish the IR model, 8-week-old mice were fed a HFD or chow diet for 6 weeks. For the insulin-treatment, the IR mice were fasted overnight (16h) and stimulated with insulin (0.75 units/kg body weight, i.p.) or its vehicle BSA for 6 h.

value: Liver

value: Insulin


title: VBCS-520_WT2


title: Ctr.Ctrl(A)_Rep1

description: Cl6 REVIR_R_NTC_Rep1_CCTAAG


title: IR, Ins rep2


title: Lung_Printex_Control_Day3_rep3

source_name: Rat, Lung, Printex, Control, Day 3, replicate 3

value: Sprague Dawley


title: Lung_TiO2_High_Day180_rep4

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 180, replicate 4

value: accessory lobe of lung


title: Lung_TiO2_High_Day180_rep3

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 180, replicate 3

value: female


title: IR, Ins rep1


title: Lung_TiO2_High_Day180_rep2

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 180, replicate 2

value: 13 weeks-old (at the onset of instillation)


title: Ctr.Ctrl(A)_Rep3

description: Cl6 REVIR_R_NTC_Rep3_TTTATG


title: Col-0, SynCom-mfec, Rep2

city: Durham

first: Reza

last: Sohrabi

state: NC

address: FFSC Bldg rm 4305, 124 Science Dr,

department: Biology

institute: Duke University

data_processing:
Raw reads were trimmed for adapter sequence and low-quality reads using Trimmomatic version 0.39.
Leading and trailing low-quality bases were trimmed, and reads less than 36 bp in length were removed (LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36).
Trimmed sequence reads were mapped to Arabidopsis thaliana TAIR 10 reference genome using STAR version 2.7.10ac.
Extraction of read counts mapped to genomics features was done using featureCounts in Rsubread package version 2.8.2.
Assembly: Arabidopsis thaliana TAIR 10
Supplementary files format and content: comma-delimited text files include read count values from featureCounts for each Sample

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Methods for plant growth are described in Kremer, Sohrabi et al. Nature Protocol, 2021 and Chen et al, Nature, 2020.

extract_protocol:
Leaf samples collected from three biological replicates per treatment were flash frozen in liquid nitrogen and stored in -80C until processing. A biological replicate is defined as a pool of two leaves collected from individual plants in GnotoPots within the same microbox. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to manufacturer's protocol
Stranded sequencing libraries were prepared using the TruSeq Stranded mRNA library preparation kit according to manufacturer's protocol.

treatment_protocol: Methods for plant growth are described in Chen et al, Nature, 2020.

value: Leaf

tag: ecotype

tag: growth system

value: GnotoPot

value: 26-days old

value: SynCom-mfec


title: Mineral4

city: Ithaca

first: Claudia

last: Fischbach

address: 237 Tower Road

institute: Cornell University

data_processing:
Reads were then trimmed using Trim Galore (version 0.4.4) and aligned to the human reference genome GRCh38 (ENSEMBL) using STAR (version 2.6.0a)
Supplementary files format and content: Counts_matrix_trimmed is a text file that contains the trimmed raw counts matrix for all samples. Counts were acquired using featureCounts.

growth_protocol: Cells were cultured on microfabricated collagen or mineralized collagen for seven days under routine culture conditions.

extract_protocol:
After seven days of culture 'Collagen' or "Mineralized Collagen' cultured MDA-MB-231 cells were harvested with collagenase Type-I. RNA was isolated from each condition using an RNA isolation kit (Qiagen, US) according to the manufacturer’s protocols (n = 4).
Illumina TruSeq RNA stranded kit (Illumina, US) was used for library preparation, and samples were sequenced as 1 × 86 bp single-end reads on the NextSeq500 (Illumina, US), yielding on average 42 M reads per sample.

value: Breast cancer

value: Mineralized Collagen


title: CW001_Naive_1yr

value: blood

value: sorted CD8+ T cells


title: Col-0, SynCom-mfec, Rep3


title: IR, BSA rep3

value: BSA


title: IR, BSA rep2


title: Mineral2

value: WT


title: Mineral3


title: Col-0, SynCom-mfec, Rep1


title: IR, BSA rep1


title: Col-0, SynCom-Col-0, Rep3


title: Mineral1


title: Lung_TiO2_Medium_Day180_rep6

description: Gene expression in lung of rat exposed to TiO2 (5 mg/m3) 180 days post exposure

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 180, replicate 6


title: Lung_TiO2_High_Day180_rep1

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 180, replicate 1

value: rat exposed to TiO2 (15 mg/m3) 180 days post exposure


title: CW001_HIV_B07_GPGH_1yr


title: KO rep3

growth_protocol: The mouse primary hepatocytes were cultured to 80-90% confluence in William's E media (GIBCO) containing 10% fetal bovine serum (FBS, GIBCO). The cells were then incubated overnight at 37°C (95% relative humidity, 5% CO2).

extract_protocol:
RNA samples of liver or primary hepatocytes were extracted using the Trizol reagent (Takara)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No

value: Liver

value: Primary hepatocytes

value: Wdr6 knockout

value: Notreatment


title: Collagen4

value: Collagen


title: Lung_TiO2_Medium_Day180_rep5

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 180, replicate 5

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)

value: rat exposed to TiO2 (5 mg/m3) 180 days post exposure


title: Col-0, SynCom-Col-0, Rep2

value: Leaf

value: GnotoPot

value: 26-days old


title: Lung_TiO2_Medium_Day180_rep4

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 180, replicate 4


title: KO rep2


title: Lung_TiO2_Medium_Day180_rep3

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 180, replicate 3


title: KO rep1


title: Lung_TiO2_Medium_Day180_rep2

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 180, replicate 2


title: Collagen3

value: Breast cancer


title: WT rep3


title: IP_Mock-2

city: shanghai

first: li

last: peng

institute: PSC

data_processing:
Raw paired-end reads (21 to 26 million per sample) were cleaned by Trimimomatic , to trim the adapter sequences, remove low-quality bases and filter short reads (< 36 nt)
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters. Mapped reads with low mapping quality (MAPQ < 30) or multiple positions in the genome were removed by SAMtools(version 1.3) .
Enriched peaks were identified by MACS2 (version 2.2.7.1,  with a cut-off p value 0.01.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional 0.5/1kb up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1). The read coverage of individual genes was visualized with the Gviz package.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph with peak score

source_name: 6-day-old seedlings

growth_protocol: seedlings grown in liquid half-strength MS media supplemented with 1% sucrose

extract_protocol:
Nuclei were extracted from liquid-cultured LHP1:Flag seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with anti-Flag M2 magnetic beads (Sigma).
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: 6-d-old seedlings was treated with 5-µm JA for 3 hr

value: seedlings

value: treated with 5000x-diluted ethanol

tag: material type

tag: experiment

value: IP


title: IP_Mock-3


title: IP_Mock-1


title: IP_JA-2

value: treated with 5-µm JA


title: MCF-7 breast cancer cells condition medium treated rep 3

city: Caserta

first: Gilda

last: Cobellis

address: Viale Abramo Lincoln

country: Italy

institute: University of Campania "Luigi Vanvitelli"

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence by using cutadapt software (version 2.5).
The sample was mapped on reference Human (from GenCode (Release 37 - GRCh38.p13)) genome, using the bioinformatics tool STAR (version 2.7.5c), with the standard parameters for paired reads.
The quantification of transcripts expressed for each sequenced samples was performed using featureCount algorithm (version 2.0). Reads that had a sum read count less than 10 were excluded, in all samples used.
the DESeq2 algorithm was used to detected the differentially expressed genes.
Assembly: HG38-Gencode (Release 37 - GRCh38.p13)
Supplementary files format and content: Matrix table with raw counts for every sample
Supplementary files format and content: tab-delimited text files include normalized values (median of ratio of gene counts) for each Sample.

source_name: not applicable

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted using the RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: not applicable

value: not applicable

tag: disease

value: BREAST CANCER  EPITHELIAL CELLS

value: conditioned medium derived from 3T3L1 mature adipocytes


title: MCF-7 breast cancer cells condition medium treated rep 2


title: WT rep1

value: Liver

value: Primary hepatocytes

value: WT

value: Notreatment


title: MCF-7 breast cancer cells condition medium treated rep 1


title: Col-0, SynCom-Col-0, Rep1


title: IP_JA-1


title: Lung_TiO2_Low_Day180_rep6

description: Gene expression in lung of rat exposed to TiO2 (1.5 mg/m3) 180 days post exposure

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 180, replicate 6

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)


title: Lung_TiO2_Low_Day180_rep4

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 180, replicate 4

value: rat exposed to TiO2 (1.5 mg/m3) 180 days post exposure


title: Lung_TiO2_Low_Day180_rep5

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 180, replicate 5


title: MCF-7 breast cancer cells untreated rep 3

value: untreated


title: Input_Mock-3

value: seedlings

value: input


title: Collagen1

value: Breast cancer

value: Collagen


title: KFNV_ATAC_rep1

city: Hong Kong

first: Mingxi

last: WENG

state: Not Applicable

address: L408A, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

country: Hong Kong

institute: School of Biomedical Sciences, The University of Hong Kong

data_processing:
Reads were trimmed to 35 bp length to remove Tn5 transposase sequence and then mapped to mouse genome assembly mm10 using bowtie2 (--very-sensitive --end-to-end --no-unal --no-mixed -X 2000).
Mapped reads were filtered to removed low quality reads and sorted using samtools (Danecek et al., 2021) (samtools view -q 30 | sort).
Mitochondrial reads were removed afte alignment (grep -v chrM).
PCR duplicates were removed using samtools (rmdup) and only uniquely mapped reads were kept.
The BAM files of replicates of each sample were merged with samtools (merge).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using bedtools (Quinlan et al., 2010) (bamtobed), genomeCoverageBed from bedtools and bedGraphToBigWig. Peak files were generated with MACS2 (Zhang et al., 2008) (with option -g mm -f BAMPE --call-summits).

source_name: Sox2-GFP MEFs

growth_protocol: Sox2-GFP MEFs were transduced with M2rtTA lentivirus and Dox-inducible lentiviruses of transcription factors in MEF medium (DMEM high glucose supplemented with 10% FBS, 1x NEAA, 1x Glutamax and 1x P/S). 24 hours after transduction, the medium was switched to NSC medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax, 10 ng/mL bFGF, 10 ng/mL EGF) containing 1 μg/mL Dox. The NSC medium switch day was defined as day 0 of reprogramming and cells were further cultured with media change every other day.

extract_protocol: A total of 50,000 cells were collected at day 4 of reprogramming in replicates. Cells were washed once with 50 μL of cold PBS and trypsinized, centrifuged at 300 x g for 5 min and   Nuclei were extracted and QC was performed. After the QC, the nuclei pellets were resuspended in the Tn5 transposase reaction mix consisting of transposase and equimolar adapter1 and adapter 2. The mix of transposition reaction was incubated at 37°C for 30 min. PCR was then performed to enrich the library. The final libraries were purified with the AMPure beads and library quality was assessed. Qubit 2.0 was used for quantification of the final library. The final library was diluted to 1ng/µl based on qubit value. The insert size of the library fragment was assessed with NGS3K. Effective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: Reprogramming intermediate

tag: day of reprogramming

value: Day 4

tag: reprogramming factors

tag: culture medium

value: NSC medium with Dox


title: WT rep2

source_name: Liver

tag: tissue

value: Liver


title: Lung_TiO2_Low_Day180_rep2

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 180, replicate 2

tag: strain

tag: gender

tag: age


title: Lung_TiO2_Medium_Day180_rep1

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 180, replicate 1

tag: treatment

value: rat exposed to TiO2 (5 mg/m3) 180 days post exposure


title: KFNV_ATAC_rep2

tag: cell type


title: Input_Mock-2

value: treated with 5000x-diluted ethanol


title: Collagen2

tag: cell line

tag: genotype

value: WT


title: MCF-7 breast cancer cells untreated rep 2

value: not applicable

value: BREAST CANCER  EPITHELIAL CELLS


title: Input_Mock-1


title: MCF-7 breast cancer cells untreated rep 1


title: No6. 3SC:6

city: Bristol

first: Claire

last: Perks

address: 5 Tyndall Avenue

department: Bristol Medical School

institute: University of Bristol

data_processing:
Read alignment, STAR v2.7.9a.
Read count extraction, featureCounts v2.0.0.
Differential gene expression analysis, DESeq2 v1.24.0.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: All_normalized_counts_DESeq2.csv: Comma-delimited file with normalized read counts.

source_name: adipose

growth_protocol: Tissue samples (0.2–0.5 g) were collected under sterile conditions at the onset of surgery and transferred immediately to the laboratory. The adipose tissue was promptly washed in Hank's balanced salt solution (HBSS), cut into fine pieces and digested with type II collagenase in HBSS, for 60 min at 37°C. The pellet of sedimented preadipocytes (typically < 1000 cells) was resuspended in Dulbecco's modified Eagle's medium/Ham's F-12 (DMEM/Ham's F12) medium (v/v 1:1) supplemented with 20% fetal bovine serum (FBS), 2 mM l-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin. Cells were seeded onto a 75-cm2 gelatin-coated tissue culture flask, maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air and media was changed every 72 h until confluency was attained. All experiments were performed on cells at passages 3–5 to ensure consistency.

extract_protocol:
RNA was harvested using phenol-chloroform method. Min conc 100ng/ul of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA library prep.

value: adipose

tag: diagnosis

value: Normal


title: Input_JA-3

value: treated with 5-µm JA

tag: ecotype


title: Lung_TiO2_Low_Day180_rep1

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 180, replicate 1

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)

value: rat exposed to TiO2 (1.5 mg/m3) 180 days post exposure


title: No5. 3SC:5


title: Lung_TiO2_Control_Day180_rep5

description: Gene expression in lung of control rat (filtered air) 180 days post exposure

source_name: Rat, Lung, TiO2, Control, Day 180, replicate 5


title: Lung_TiO2_Control_Day180_rep4

source_name: Rat, Lung, TiO2, Control, Day 180, replicate 4

value: control rat (filtered air) 180 days post exposure


title: Lung_TiO2_Control_Day180_rep3

source_name: Rat, Lung, TiO2, Control, Day 180, replicate 3


title: Lung_TiO2_Control_Day180_rep6

source_name: Rat, Lung, TiO2, Control, Day 180, replicate 6


title: BKMS2_ATAC_rep1

value: Reprogramming intermediate

value: Day 4


title: BKMS17_ATAC_rep2

value: NSC medium with Dox


title: Input_JA-2

value: seedlings

value: input


title: IP_JA-3

value: IP


title: No4. 3SC:4


title: Input_JA-1


title: BKMS2_ATAC_rep2


title: BKMFNV_ATAC_rep2


title: BKMS17_ATAC_rep1


title: BKMFNV_ATAC_rep1


title: No2. Rohhad p.9

value: ROHHAD Syndrome


title: MOCK_lhp1_3

data_processing:
Paired-end reads were mapped to the genome of Arabidopsis thaliana (TAIR 10) using Tophat
The mapped reads on each gene were counted by htseq-count
The differentially expressed genes (DEGs) were identified using the R package edgeR (FDR < 0.05, log2FoldChange > 1.4)
Genome_build: TAIR 10
Supplementary_files_format_and_content: matrix file with row counts

molecule: polyA RNA

growth_protocol: Seedlings grown in liquid half-strength MS media supplemented with 1% sucrose

extract_protocol:
Total RNAs were extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions
mRNAs were purified using the NEBNext Poly(A) mRNA Magneic Isolation Module kit (New England Biolabs /NEB), and cDNA libraries were constructed using the NEBNext Library Prep kit (NEB) and further sequenced with NovaSeq 6000 (Illumina).

value: treated with 5000x-diluted ethanol

value: seedling


title: No1. Rohhad p.8

value: adipose


title: MOCK_lhp1_2


title: MOCK_lhp1_1


title: LiD24_rep2

data_processing:
Raw reads in fastq format were aligned to the mm10 transcriptome using RSEM (Bo Li et al., 2011) and bowtie 2.0 (Langmead et al., 2012) (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3 (Hutchins et al., 2014).
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq (Risso et al., 2011). GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
The table was used to inspect individual gene expression, generate correlation heatmaps, perform principal components analysis (PCA) and analyze differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names(name). The rest of the columns contain the normalized RNA expression gene counts.

growth_protocol: MEFs were transduced with M2rtTA lentivirus and Dox-inducible lentiviruses of transcription factors in MEF medium (DMEM high glucose supplemented with 10% FBS, 1x NEAA, 1x Glutamax and 1x P/S). 24 hours after transduction, the medium was switched to reprogramming medium. The medium switch day was defined as day 0 of reprogramming and cells were further cultured with media change every other day. or iNSC reprogramming, cells were cultured in NSC medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax, 10 ng/mL bFGF, 10 ng/mL EGF). 1 μg/mL Dox was added for 18 days. For iNSC and iPSC reprogramming in parallel, N2B27 medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax) containing 1 μg/mL Dox was added for 8 days. After day 8, cells were split and cultured in NSC medium or Serum-free LIF/2i medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax, 1x NEAA, 1x sodium pyruvate, 10 ng/mL LIF, 3 μM CHIR99021, 1 μM PD0325901) containing Dox. Dox was withdrawn after day 16.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, #15596018) following the user guide quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. ffective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: Day 24

value: LIF/2i medium


title: Lung_TiO2_Control_Day180_rep2

data_processing: Agilent Feature Extraction Software (v 12.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)

source_name: Rat, Lung, TiO2, Control, Day 180, replicate 2

value: Sprague Dawley

value: accessory lobe of lung


title: LiD24_rep1


title: EV_DNA2 replicate 2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description: EVs were isolated from conditioned medium in which cells were grown

data_processing:
Library strategy: DNA-Seq
Image analysis and base calling was done with Illumina CASAVA-1.8.2.
Sequenced reads were quality-tested using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.8.
For DNA sequencing, samples were mapped to the hg38 human genome using STAR v2.5.3a
Since samples represent technical replicates, the aligned reads were merged with samtools v1.9.
The total number of reads aligning to each chromosome, and the repeat-masked genome length (with repeat sequences removed), were used to calculate the normalized read count for each chromosome.
Genome_build: hg38
Supplementary_files_format_and_content: Excel spreadsheet with normalized read counts per chromosome and associated plots.

source_name: Normal human oral keratinocytes

growth_protocol: Cells were grown in defined keratinocyte serum-free medium on collagen-coated plates and were passaged every 4 days through passage 11 and every 5 days thereafter

extract_protocol:
DNA was extracted from EVs using XCF Exosomal DNA Isolation Kit (System Biosciences #XCF200A-1) according to manufacturer’s protocol.
Library preparation was performed using Nextera XT DNA kit (Illumina #FC-131-1096) according to the manufacturer's instructions and DNA libraries were sequenced on NextSeq500 System (Illumina) using the mid-output kit at paired-end 75bp configuration.

treatment_protocol: Culture at atmospheric O2

value: normal oral keratinocytes

tag: sample type

value: extracellular vesicles (EVs)

tag: passage

value: EVs from late passage normal oral keratinocytes, mostly senescent cells

tag: number and sex

value: 2 female and 1 male donor, combined

value: Donors were 18, 20, and 36 years of age


title: MOCK_WT_3

source_name: 6-day-old seedlings


title: MOCK_WT_2


title: LiD20_rep2

value: Reprogramming intermediate

value: Day 20


title: Col-0, MSU, HO, Rep3

source_name: Rosette

growth_protocol: Methods for plant growth are described in (Kremer, Sohrabi et al. 2021).

extract_protocol:
Samples collected from three biological replicates per treatment were flash frozen in liquid nitrogen and stored in -80C until processing. A biological replicate is defined as a pool of eight rosettes collected from four FlowPots within the same microbox. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to manufacturer's protocol
Stranded sequencing libraries were prepared using the NuGEN Ovation RNA-SEQ System for Model Organisms (Arabidopsis) according to manufacturer's protocol.

treatment_protocol: Methods for inoculation are described in (Kremer, Sohrabi et al. 2021).

value: Rosette

tag: growth system

value: Flowpot

value: 21-days old

value: Holoxenic


title: EV_DNA1 replicate 1


title: MOCK_WT_1

value: treated with 5000x-diluted ethanol

value: seedling


title: Col-0, MSU, HO, Rep2


title: Lung_TiO2_Control_Day180_rep1

source_name: Rat, Lung, TiO2, Control, Day 180, replicate 1

value: female

value: 13 weeks-old (at the onset of instillation)

value: control rat (filtered air) 180 days post exposure


title: LiD20_rep1

tag: day of reprogramming

value: LIF/2i medium


title: LiD16_rep1

value: Day 16

tag: reprogramming factors

value: LIF/2i medium with Dox


title: JA_WT_3

value: treated with 5-µm JA


title: Lung_TiO2_High_Day30_rep5

description: Gene expression in lung of rat exposed to TiO2 (15 mg/m3) 30 days post exposure

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 30, replicate 5

value: Sprague Dawley

value: accessory lobe of lung


title: Col-0, MSU, HO, Rep1


title: Lung_TiO2_High_Day30_rep2

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 30, replicate 2

value: rat exposed to TiO2 (15 mg/m3) 30 days post exposure


title: Lung_TiO2_High_Day30_rep3

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 30, replicate 3


title: Lung_TiO2_High_Day30_rep1

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 30, replicate 1


title: JA_WT_2


title: Lung_TiO2_High_Day30_rep6

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 30, replicate 6


title: Lung_TiO2_High_Day30_rep4

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 30, replicate 4


title: Col-0, Malaka, HO, Rep3


title: WT rep4

source_name: Liver

value: Liver

value: Primary hepatocytes

value: WT

value: Notreatment


title: JA_WT_1


title: LiD12_rep1

value: Reprogramming intermediate

value: Day 12

tag: culture medium


title: LiD12_rep2


title: LiD16_rep2


title: Col-0, Malaka, HO, Rep1

tag: tissue

value: Rosette

value: Flowpot

value: 21-days old

value: Holoxenic


title: EFD24_rep2

value: Day 24

value: NSC medium


title: EFD24_rep1


title: Col-0, MSU, AX, Rep3

value: Axenic


title: Lung_TiO2_Medium_Day30_rep6

description: Gene expression in lung of rat exposed to TiO2 (5 mg/m3) 30 days post exposure

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 30, replicate 6

tag: strain

value: female

value: 13 weeks-old (at the onset of instillation)


title: EFD20_rep2

value: Day 20


title: Col-0, MSU, AX, Rep2


title: Lung_TiO2_Medium_Day30_rep4

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 30, replicate 4

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: rat exposed to TiO2 (5 mg/m3) 30 days post exposure


title: Col-0, MSU, AX, Rep1

tag: age


title: Lung_TiO2_Medium_Day30_rep3

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 30, replicate 3

tag: treatment


title: Saliva SP, rep7

city: Milan

first: Irma

last: Saulle

address: G.B. Grassi 74

institute: University of Milan

description: SAMPLE 27

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/mirna/arrayanalysis.php?target
For the normalization it uses RNU6-6p
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
2^-ΔΔCt*100 were calculated for each sample (n30) compared to Sample 1 (HC).

label: SYBR Green

source_name: Group 2

label_protocol: One-hundred nanograms of mature miRNAs, were reverse-transcribed into first-strand cDNA in a 20 μL final volume at 37 °C for 60 min using miScript II RT Kit (Qiagen, Venlo, The Netherlands), in accordance with the manufacturer’s protocol. Expression level of 84 miRNAs with antiviral and/or immunological function was evaluated using a miRNA PCR Array (MIHS-105ZA) (Qiagen). Arrays were performed on CFX ConnectTM Real-Time PCR system (BIO RAD, Hercules, CA, USA). Undetermined raw CT values were set to 35. Expression profile was analysed using the PCR Array Gene Expression Analysis Software (Qiagen). For each miRNA, Ct values were transformed into relative quantities using a normalization factor RNU6-2 for saliva and plasma. Fold regulation of ±2.5 was considered as positive.

extract_protocol: Maxwell® RSC miRNA from plasma or serum kit (Promega) was used to extract miRNA from saliva using the Maxwell® RSC Instrument (Promega)

tag: disease state

value: severe COVID-19

value: saliva


title: Saliva SP, rep9

description: SAMPLE 29


title: Saliva SP, rep10

description: SAMPLE 30


title: Saliva SP, rep8

description: SAMPLE 28


title: Lung_TiO2_Medium_Day30_rep2

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 30, replicate 2


title: Col-0, Malaka, HO, Rep2


title: EFD16_rep2

tag: cell type

value: Reprogramming intermediate

value: Day 16

value: NSC medium with Dox


title: Lung_TiO2_Medium_Day30_rep5

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 30, replicate 5


title: EFD16_rep1


title: Lung_TiO2_Medium_Day30_rep1

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 30, replicate 1


title: Lung_TiO2_Low_Day30_rep6

description: Gene expression in lung of rat exposed to TiO2 (1.5 mg/m3) 30 days post exposure

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 6


title: Col-0, Malaka, AX, Rep2

source_name: Rosette

value: Rosette

value: Flowpot


title: Saliva SP, rep6

description: SAMPLE 26


title: EFD12_rep2

value: Day 12


title: Col-0, Malaka, AX, Rep3

value: 21-days old


title: Lung_TiO2_Low_Day30_rep5

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 5

value: rat exposed to TiO2 (1.5 mg/m3) 30 days post exposure


title: Col-0, Malaka, AX, Rep1

value: Axenic


title: EFD20_rep1

value: NSC medium


title: EFD12_rep1


title: Lung_TiO2_Low_Day30_rep4

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 4

value: female

value: 13 weeks-old (at the onset of instillation)


title: Lung_TiO2_Low_Day30_rep3

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 3

value: Sprague Dawley


title: Saliva SP, rep3

description: SAMPLE 23


title: N2D8_rep2

value: Day 8

value: N2B27 medium with Dox


title: Lung_TiO2_Low_Day30_rep2

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 2

value: accessory lobe of lung


title: N2D8_rep1


title: KPC_A2032

city: Rochester

first: Aram

middle: F.

last: Hezel

address: 601 Elmwood Ave, Box 704

institute: Wilmot Cancer Institute

data_processing:
Raw reads were generated from Illumina HiSeq2500 sequencing and demultiplexed using bcl2fastq version 1.8.4.
Quality filtering and adapter removal were performed using Trimmomatic version 0.36.
Processed/cleaned reads were then mapped to the Mus musculus reference sequence (GRCm38.p5 and gencode version M12 gene annotation) using the STAR version 2.5.2b.
Uniquely aligned reads were counted within the gencode M12 gene annotations using the featureCounts tool from the subread-1.5.0p3 package.
Differential expression analyses and data normalisation were performed using DESeq2-1.14.1 R/Bioconductor package with an adjusted p-value (Benjamini-Hochberg) threshold of 0.05 within the R version 3.3.2 environment ([https://www.r-project.org)/]https://www.R-project.org).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: pancreas

growth_protocol: All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.
mRNA sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit with 200 ng total RNA per manufacturer’s protocol.

treatment_protocol: KPC and KPCAf/f cells were harvested for RNA-seq analyses.

value: pancreas

tag: cell line

value: KPC tumor cell line

value: mouse pancreatic cancer cells

tag: genotype

value: KPC


title: N2D4_rep2

value: Reprogramming intermediate

value: Day 4


title: Saliva SP, rep5

description: SAMPLE 25

value: severe COVID-19

value: saliva


title: KPCA_A2441

value: KPCA tumor cell line

value: KPCAf/f


title: Saliva SP, rep2

description: SAMPLE 22


title: KPCA_A3992


title: N2D4_rep1


title: KPCA_A1925


title: Saliva SP, rep4

description: SAMPLE 24


title: KPC_A2031


title: KFNVD30_rep2

source_name: Sox2-GFP MEFs

value: Day 30

value: NSC medium


title: Saliva MP, rep10

description: SAMPLE 20

source_name: Group 1

value: mild COVID-19


title: KPCA_A1809


title: Saliva MP, rep9

description: SAMPLE 19


title: Saliva MP, rep8

description: SAMPLE 18


title: KPCA_A1693


title: Saliva MP, rep7

description: SAMPLE 17


title: Lung_TiO2_Control_Day30_rep5

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

institute: INRS

source_name: Rat, Lung, TiO2, Control, Day 30, replicate 5

value: Sprague Dawley

value: female

value: 13 weeks-old (at the onset of instillation)

value: control rat (filtered air) 30 days post exposure


title: KFNVD30_rep1


title: Lung_TiO2_Control_Day30_rep2

source_name: Rat, Lung, TiO2, Control, Day 30, replicate 2

value: accessory lobe of lung


title: Lung_TiO2_Control_Day30_rep6

source_name: Rat, Lung, TiO2, Control, Day 30, replicate 6


title: Lung_TiO2_Low_Day30_rep1

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 30, replicate 1

value: rat exposed to TiO2 (1.5 mg/m3) 30 days post exposure


title: KPC_A1625

value: pancreas

value: KPC tumor cell line

value: mouse pancreatic cancer cells


title: Lung_TiO2_Control_Day30_rep3

source_name: Rat, Lung, TiO2, Control, Day 30, replicate 3


title: Saliva MP, rep6

description: SAMPLE 16


title: KPC_A1620

value: KPC


title: KFNVD24_rep2

value: Reprogramming intermediate

value: Day 24


title: KFNVD24_rep1


title: Lung_TiO2_Control_Day30_rep4

source_name: Rat, Lung, TiO2, Control, Day 30, replicate 4


title: KFNVD18_rep2

value: Day 18

value: NSC medium with Dox


title: KFNVD18_rep1


title: Saliva MP, rep4

description: SAMPLE 14

value: saliva


title: Wild-type 4

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

data_processing:
Sequence reads were trimmed for low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GRCm39 using subread.
Read quantification was performed by featureCounts.
Genes with low counts (< 10 in at least 2 samples of any group) were filtered out and normalization was performed by TMM.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: Adult testis

extract_protocol:
Total RNA was extracted from testes using TRIzol reagent and then treated with Dnase for 1 h.
RNA libraries were prepared using the TruSeq RNA kit from Illumina (NEB, USA) according to the manufacturer’s recommendations.

value: Adult testis

value: WT


title: Saliva MP, rep5

description: SAMPLE 15

value: mild COVID-19


title: Lung_TiO2_High_Day3_rep6

description: Gene expression in lung of rat exposed to TiO2 (15 mg/m3) 3 days post exposure

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 3, replicate 6

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

value: Sprague Dawley

value: female


title: Saliva MP, rep3

description: SAMPLE 13


title: Lung_TiO2_Low_Day180_rep3

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 180, replicate 3

value: 13 weeks-old (at the onset of instillation)

value: rat exposed to TiO2 (1.5 mg/m3) 180 days post exposure


title: Lung_TiO2_High_Day3_rep5

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 3, replicate 5

value: accessory lobe of lung

value: rat exposed to TiO2 (15 mg/m3) 3 days post exposure


title: KFNVD12_rep2

value: Day 12


title: Lung_TiO2_High_Day3_rep3

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 3, replicate 3


title: Saliva MP, rep2

description: SAMPLE 12


title: Wild-type 3


title: KFNVD12_rep1


title: Saliva MP, rep1

description: SAMPLE 11


title: Wild-type 2


title: Lung_TiO2_Control_Day30_rep1

source_name: Rat, Lung, TiO2, Control, Day 30, replicate 1

value: control rat (filtered air) 30 days post exposure


title: KFNVD8_rep2

value: Day 8


title: Kpna2 knockout 4


title: Wild-type 1


title: Saliva HC, rep10

description: SAMPLE 10

source_name: Control group

value: control


title: Kpna2 knockout 3


title: KFNVD4_rep2

value: Reprogramming intermediate

value: Day 4


title: Saliva HC, rep9

description: SAMPLE 9


title: No3. Rohhad p.10

source_name: adipose

value: adipose

tag: diagnosis

value: ROHHAD Syndrome


title: Kpna2 knockout 2

value: Adult testis


title: KFNVD4_rep1

value: NSC medium with Dox


title: Lung_TiO2_High_Day3_rep4

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 3, replicate 4


title: Lung_TiO2_High_Day3_rep1

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 3, replicate 1


title: Saliva HC, rep8

description: SAMPLE 8

value: saliva


title: Lung_TiO2_Medium_Day3_rep6

description: Gene expression in lung of rat exposed to TiO2 (5 mg/m3) 3 days post exposure

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 3, replicate 6

value: Sprague Dawley


title: Lung_TiO2_High_Day3_rep2

source_name: Rat, Lung, TiO2, Exposed to High dose, Day 3, replicate 2

value: female


title: Lung_TiO2_Medium_Day3_rep4

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 3, replicate 4

value: 13 weeks-old (at the onset of instillation)

value: rat exposed to TiO2 (5 mg/m3) 3 days post exposure


title: Lung_TiO2_Medium_Day3_rep5

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 3, replicate 5

value: accessory lobe of lung


title: Sox2D30_rep1

source_name: Sox2-GFP MEFs

value: Day 30

value: NSC medium


title: KFNVD8_rep1


title: Kpna2 knockout 1


title: Sox2D24_rep2

value: Day 24


title: Reh_DHS_1

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
Fastq files were aligned to the hg19 genome using bowtie2 using –very-sensitive-local
Peak calling and depth coverage track generation were carried out using macs2 using callpeak -g hs -q 0.001 -B --SPMR --trackline <trackline> --keep-dup all
Assembly: hg19
Supplementary files format and content: bed file containing peak coordinates
Supplementary files format and content: bigWig file containing genome-wide depth coverage

source_name: IRF4WT NHL-derived cell line

growth_protocol: Cells were grown at 37°C with 5% CO2 in DMEM medium with 10% FCS, 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM glutamine at a density of 1-5 105 cells/ml

extract_protocol:
Dnase-Seq was essentially performed as previously described (Kreher et al 2015) with slight modifications. Briefly, cells were washed and resuspended at 108 cells/mL in ice-cold ψ buffer (11 mM KPO4, pH 7.4, 108 mM KCl, 22 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 1 mM dithiothreitol, 1 mM ATP). 1 million Reh, KM-H2 or L428 cells were treated with 12U/mL DnaseI (Worthington) for 3 mins at 22°C. Digestion was stopped with the addition of 200µL lysis buffer (100 mM Tris, pH 8.0, 40 mM +EDTA, 2% SDS, 200 μg/ml proteinase K) overnight at 37°C. Dnase digestion efficiency was checked via low-voltage overnight electrophoresis (10V) on a 0.5% TAE agarose gel. Short-fragment size-selection was performed by cutting out gel bands between 100-200 bp and subsequent purification using the QiaQuick gel extraction kit (Qiagen) according to manufacturer’s instructions
For SOLiD libraries, library preparation was performed using the AB SOLiD 4 System library kit (SOLiD Fragment Library Oligos Kit, SOLiD Barcoding Kit Modules 1-96, SOLiD Fragment Library Construction Kit Reagents , Agencourt AMPure XP, 60 mL Kit, SOLiD Library TaqMan Quantitation Kit, Quanti-iT™ dsDNA HS Assay Kits, 500 Assays, 1x Low TE Buffer, 95% ethanol) according to manufacturer's instructions and sequenced on an AB SOLiD 4 System sequencer. For illumina libraries, library preparation was performed using the KAPA hyperprep kit (Roche) following manufacturer’s guidelines. Library quality was checked via qPCR using TBP, ACTB and gene desert control oligonucleotides (Bevington et al 2016). Libraries were sequenced at 400 million reads per library in single-end mode on separate lanes using an Illumina HiSeq 2000 system according to manufacturer‘s instructions.

value: IRF4WT NHL-derived cell line


title: Sox2D24_rep1


title: Saliva HC, rep6

description: SAMPLE 6

value: control


title: ChIP-seq A549 WCE Dex rep2

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

country: Canada

institute: Centre de recherche du CHU de Québec-Université Laval

data_processing:
Analysis of raw sequencing reads was performed using the ChIP-Seq pipeline developed at the McGill University and Génome Québec Innovation Centre.
High-quality reads were aligned to the human reference genome (hg38) with BWA aligner.
PCR duplicates were removed with picard MarkDuplicates.
Narrow peaks were called using MACS2 callpeak, supplying the sequenced corresponding input DNA as background control.
Assembly: hg38
Supplementary files format and content: List of binding sites in bed format generated with MACS2

source_name: human lung adenocarcinoma

growth_protocol: A549 (ATCC, CCL-185) were grown in F12K medium (Gibco, 21127022). Culture medium were supplemented with 10% fetal bovine serum (Invitrogen, qualified 12483020), 100 μM MEM nonessential amino acids (Cellgro, 25-0250), 2 mM L-glutamine (Gibco, 25030-081), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, 15170-063).

extract_protocol:
Cells were crosslinked for 10 min with 1% formaldehyde and quenched with 125 mM glycine for 5 min. Cells were then washed with PBS, pelleted, flash frozen and stored at -80°C. Lysates were clarified from sonicated nuclei and transcriptional coregulators-DNA complexes were isolated with antibody.
Library were prepared using Illumina TruSeq DNA v1 adaptors. High-throughput sequencing were performed on the Illumina HiSeq 2000 SR50, at the McGill University and Génome Québec Innovation Centre (MUGQIC), Montréal, Canada.

treatment_protocol: Cells were treated with 100 nM dexamethasone (Dex) (Sigma, D1756), a synthetic glucocorticoid, for 1 hour

value: human lung adenocarcinoma

value: Dex

tag: chip antibody


title: Sox2D18_rep2

value: Reprogramming intermediate

value: Day 18


title: Saliva HC, rep5

description: SAMPLE 5


title: Saliva SP, rep1

description: SAMPLE 21

source_name: Group 2

value: severe COVID-19


title: Saliva HC, rep7

description: SAMPLE 7


title: ChIP-seq A549 BRD4 Dex rep2

value: BRD4 (Bethyl Laboratories, A301-985A50)


title: Saliva HC, rep3

description: SAMPLE 3

value: saliva


title: ChIP-seq A549 WCE Dex rep1


title: Sox2D18_rep1

value: NSC medium with Dox


title: Sox2D12_rep2

value: Day 12


title: Saliva HC, rep1

description: SAMPLE 1


title: Saliva HC, rep4

description: SAMPLE 4


title: Saliva HC, rep2

description: SAMPLE 2


title: Lung_TiO2_Medium_Day3_rep3

address: Rue du Morvan

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 3, replicate 3

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

value: Sprague Dawley

value: female

value: 13 weeks-old (at the onset of instillation)


title: Lung_TiO2_Medium_Day3_rep2

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 3, replicate 2

value: accessory lobe of lung

value: rat exposed to TiO2 (5 mg/m3) 3 days post exposure


title: Lung_TiO2_Medium_Day3_rep1

source_name: Rat, Lung, TiO2, Exposed to Medium dose, Day 3, replicate 1


title: ChIP-seq A549 BRD4 Dex rep1


title: Lung_TiO2_Low_Day3_rep5

description: Gene expression in lung of rat exposed to TiO2 (1.5 mg/m3) 3 days post exposure

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 3, replicate 5


title: Lung_TiO2_Low_Day3_rep6

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 3, replicate 6

value: rat exposed to TiO2 (1.5 mg/m3) 3 days post exposure


title: Lung_TiO2_Low_Day3_rep4

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 3, replicate 4


title: Sox2D12_rep1


title: ChIP-seq A549 MED1 Dex rep2

value: MED1 (Bethyl Laboratories, A300-793A)


title: PLASMA SP, rep10

description: SAMPLE 30

extract_protocol: Maxwell® RSC miRNA from plasma or serum kit (Promega) was used to extract miRNA from plasma using the Maxwell® RSC Instrument (Promega)

value: plasma


title: ChIP-seq A549 WCE EtOH rep2

value: human lung adenocarcinoma

value: EtOH


title: Sox2D8_rep2

value: Reprogramming intermediate

value: Day 8


title: Sox2D8_rep1


title: ChIP-seq A549 BRD4 EtOH rep2


title: ChIP-seq A549 MED1 Dex rep1

value: Dex


title: Sox2D4_rep1

value: Day 4


title: ChIP-seq A549 BRD4 EtOH rep1

value: BRD4 (Bethyl Laboratories, A301-985A50)


title: Sox2D4_rep2

value: NSC medium with Dox


title: PLASMA SP, rep7

description: SAMPLE 27

value: severe COVID-19


title: PLASMA SP, rep8

description: SAMPLE 28


title: PLASMA SP, rep9

description: SAMPLE 29


title: Sox17D30_rep1

value: Day 30

value: NSC medium


title: Sox17D24_rep2

value: Day 24


title: ChIP-seq A549 MED1 EtOH rep2


title: Namalwa_RNA_2

data_processing:
Reads were aligned in paired-end mode to the hg19 genome using STAR v2.3.0 using --outSAMattributes Standard --outSAMunmapped None --outReadsUnmapped Fastx --outFilterMismatchNoverLmax 0.02 as parameters
Counts were obtained using featureCounts vXXX with -p -B -C -Q 10 --primary -s 0 as parameters
Normalisation and differential gene expression analysis was performed using DESeq2 vXXX using the standard analysis protocol, performing variance stabilisation transform normalisation
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts

extract_protocol:
Total RNA was isolated using Trizol following manufacturer’s instructions.
Libraries were generated using the Illumina TruSeq protocol according to manufacturer’s guidelines.

value: IRF4WT NHL-derived cell line


title: PLASMA SP, rep5

description: SAMPLE 25


title: PLASMA SP, rep4

description: SAMPLE 24


title: PLASMA SP, rep6

description: SAMPLE 26


title: Sox17D24_rep1


title: Lung_TiO2_Low_Day3_rep1

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 3, replicate 1

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)


title: Lung_TiO2_Low_Day3_rep2

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 3, replicate 2

value: rat exposed to TiO2 (1.5 mg/m3) 3 days post exposure


title: Lung_TiO2_Control_Day3_rep6

source_name: Rat, Lung, TiO2, Control, Day 3, replicate 6

value: control rat (filtered air) 3 days post exposure


title: Lung_TiO2_Control_Day3_rep4

source_name: Rat, Lung, TiO2, Control, Day 3, replicate 4


title: Lung_TiO2_Control_Day3_rep5

source_name: Rat, Lung, TiO2, Control, Day 3, replicate 5


title: Lung_TiO2_Control_Day3_rep3

source_name: Rat, Lung, TiO2, Control, Day 3, replicate 3


title: Namalwa_RNA_1


title: PLASMA SP, rep3

description: SAMPLE 23

value: plasma


title: Lung_TiO2_Low_Day3_rep3

source_name: Rat, Lung, TiO2, Exposed to Low dose, Day 3, replicate 3


title: Lung_TiO2_Control_Day3_rep2

source_name: Rat, Lung, TiO2, Control, Day 3, replicate 2


title: Uho1_RNA_2

source_name: IRF4C99R HL-derived cell line

value: IRF4C99R HL-derived cell line


title: Sox17D18_rep1

source_name: Sox2-GFP MEFs

value: Reprogramming intermediate

value: Day 18


title: Uho1_RNA_1


title: Sox17D18_rep2


title: Sox17D12_rep2

value: Day 12


title: KPC_A1081

source_name: pancreas

value: pancreas

value: KPC tumor cell line

value: mouse pancreatic cancer cells

value: KPC


title: SUDHL4_RNA_1

source_name: IRF4WT NHL-derived cell line


title: SUDHL4_RNA_2


title: Sox17D12_rep1

value: NSC medium with Dox


title: PLASMA SP, rep1

description: SAMPLE 21

source_name: Group 2

value: severe COVID-19


title: PLASMA SP, rep2

description: SAMPLE 22


title: PLASMA MP, rep9

description: SAMPLE 19

source_name: Group 1

value: mild COVID-19


title: PLASMA MP, rep10

description: SAMPLE 20


title: PLASMA MP, rep8

description: SAMPLE 18


title: Sox17D8_rep2

value: Day 8


title: Lung_TiO2_Control_Day3_rep1

source_name: Rat, Lung, TiO2, Control, Day 3, replicate 1

value: Sprague Dawley

value: accessory lobe of lung

value: female


title: BJAB_RNA_2

value: IRF4WT NHL-derived cell line


title: BJAB_RNA_1


title: Reh_RNA_2


title: Lung_DQ12_High_Day180_rep5

description: Gene expression in lung of rat exposed to DQ12 (10 mg/rat) 180 days post exposure

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 180, replicate 5

label_protocol: For each of the 36 samples (6 control and 6 exposed rats per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry.

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 6.6, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed to DQ-12 (10 mg/rat) by endotracheal instillation.

value: 13 weeks-old (at the onset of instillation)


title: Reh_RNA_1


title: Lung_DQ12_High_Day180_rep3

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 180, replicate 3


title: Lung_DQ12_High_Day180_rep6

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 180, replicate 6


title: Lung_DQ12_High_Day180_rep4

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 180, replicate 4


title: PLASMA MP, rep5

description: SAMPLE 15

value: plasma


title: PLASMA MP, rep6

description: SAMPLE 16


title: Sox17D4_rep2

value: Reprogramming intermediate

value: Day 4


title: Sox17D4_rep1


title: FNVD30_rep2

value: Day 30

value: NSC medium


title: FNVD30_rep1


title: L540Cy_RNA_1

source_name: IRF4WT HL-derived cell line

value: IRF4WT HL-derived cell line


title: Lung_DQ12_High_Day180_rep2

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 180, replicate 2


title: Sox17D8_rep1


title: FNVD24_rep2

value: Day 24


title: PLASMA MP, rep7

description: SAMPLE 17


title: PLASMA MP, rep3

description: SAMPLE 13


title: L540_RNA_2


title: FNVD24_rep1


title: PLASMA MP, rep2

description: SAMPLE 12


title: PLASMA MP, rep1

description: SAMPLE 11


title: Lung_DQ12_High_Day180_rep1

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 180, replicate 1


title: PLASMA MP, rep4

description: SAMPLE 14


title: L540Cy_RNA_2


title: L540_RNA_1


title: Lung_DQ12_Control_Day180_rep2

description: Gene expression in lung of control rat (vehicule instillation) 180 days post exposure

source_name: Rat, Lung, DQ12, Control, Day 180, replicate 2


title: Lung_DQ12_Control_Day180_rep5

source_name: Rat, Lung, DQ12, Control, Day 180, replicate 5


title: Lung_DQ12_Control_Day180_rep4

source_name: Rat, Lung, DQ12, Control, Day 180, replicate 4


title: Lung_DQ12_Control_Day180_rep6

source_name: Rat, Lung, DQ12, Control, Day 180, replicate 6


title: FNVD18_rep2

source_name: Sox2-GFP MEFs

value: Day 18


title: HDLM2_RNA_2


title: FNVD18_rep1

value: NSC medium with Dox


title: PLASMA HC, rep10

description: SAMPLE 10

source_name: Control group

value: control


title: PLASMA HC, rep9

description: SAMPLE 9


title: HDLM2_RNA_1


title: L591_RNA_1


title: Lung_DQ12_Control_Day180_rep3

source_name: Rat, Lung, DQ12, Control, Day 180, replicate 3


title: KMH2_RNA_2


title: FNVD12_rep1

value: Day 12


title: Lung_DQ12_High_Day30_rep6

description: Gene expression in lung of rat exposed to DQ12 (10 mg/rat) 30 days post exposure

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 30, replicate 6


title: KMH2_RNA_1


title: Lung_DQ12_Control_Day180_rep1

source_name: Rat, Lung, DQ12, Control, Day 180, replicate 1


title: PLASMA HC, rep8

description: SAMPLE 8


title: FNVD8_rep1

value: Day 8


title: L1236_RNA_2


title: PLASMA HC, rep7

description: SAMPLE 7


title: L591_RNA_2


title: PLASMA HC, rep5

description: SAMPLE 5


title: PLASMA HC, rep6

description: SAMPLE 6


title: FNVD12_rep2


title: FNVD4_rep1


title: FNVD4_rep2


title: L1236_RNA_1


title: FNVD8_rep2


title: PLASMA HC, rep3

description: SAMPLE 3


title: Lung_DQ12_High_Day30_rep4

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 30, replicate 4

value: Sprague Dawley


title: Lung_DQ12_High_Day30_rep1

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 30, replicate 1

value: accessory lobe of lung


title: Lung_DQ12_High_Day30_rep5

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 30, replicate 5

value: female


title: PLASMA HC, rep2

description: SAMPLE 2


title: F4miNSC_rep2

source_name: Sox2-GFP iNSCs

value: Passage 15


title: L428_RNA_2

source_name: IRF4C99R HL-derived cell line

value: IRF4C99R HL-derived cell line


title: Lung_DQ12_Control_Day30_rep6

description: Gene expression in lung of control rat (vehicule instillation) 30 days post exposure

source_name: Rat, Lung, DQ12, Control, Day 30, replicate 6

value: 13 weeks-old (at the onset of instillation)


title: L428_RNA_1


title: Lung_DQ12_Control_Day30_rep5

source_name: Rat, Lung, DQ12, Control, Day 30, replicate 5


title: F4miNSC_rep1

value: Reprogramming intermediate


title: Lung_DQ12_High_Day30_rep2

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 30, replicate 2


title: F2miNSC_rep2


title: PLASMA HC, rep4

description: SAMPLE 4

value: plasma


title: PLASMA HC, rep1

description: SAMPLE 1


title: T3_2

city: xinxiang

first: chune

last: zhou

address: jian she east road 46

institute: henan normal university

data_processing:
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: Embryos

extract_protocol:
Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit  (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Embryos

value: WT

tag: developmental stage


title: JunB_L428_2

data_processing:
Fastq files were aligned to the hg19 genome using bowtie2 using –very-sensitive-local
Peak calling and depth coverage track generation were carried out using macs2 using callpeak -g hs -q 0.001 -B --SPMR --trackline <trackline> --keep-dup auto
Assembly: hg19
Supplementary files format and content: bed file containing peak coordinates
Supplementary files format and content: bigWig file containing genome-wide depth coverage

extract_protocol:
ChIP was globally performed as previously described (Cauchy et al 2015) using double-crosslinking. Cells were resuspended at 3.3x106 cells/ml in PBS and first crosslinked with 8.3l/ml DSG (Sigma) for 45 mins at room temperature, subsequently washed 4x and crosslinked with 1% formaldehyde for 10 mins at room temperature, with both crosslinking methods entailing sustained tube rotation. Crosslinking was quenched in 0.2M glycine and cells were washed 2x.  Cells were lysed in Buffer A (10 mM Hepes, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X100), then in Buffer B (10 mM Hepes, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01 % Triton X100), at 1x107 cells/ml and 4°C with rotation for 10 mins for both stages. Nuclei were resuspended at 2x107 cells/ml in 4°C IP Buffer I (25 mM Tris, 150 mM NaCl, 2 mM EDTA, 1% Triton X100, 0.25% SDS) and sonicated in 6x 300 µl per reaction using a Picoruptor sonicator (Diagenode) at 240W with 30 cycles of 30s on, 30s off at 4°C. Cell debris was pelleted via 10 min 16,000g centrifugation and diluted in IP Buffer II (8.33 mM Tris, 50 mM NaCl, 6.33 mM EDTA, 0.33 % Triton X100 0.0833 % SDS, 5 % glycerol final concentration). 5% of chromatin was saved as input control. Immunoprecipitation was carried out overnight using Maximum Recovery tubes (Axigen) with rotation at 4°C in 50 µL PBS+0.02% Tween 20 with 15 µL protein G dynabeads that were washed blocked with 0.5% BSA and conjugated with either sc-6059-X (IRF4) or sc-46-X (JunB) antibodies for 4 hours at 4°C with rotation. Beads were subsequently washed on ice by magnetic separation using 1x PBS+0.02% Tween 20, 2x Wash Buffer 1 (20 mM Tris, 150 mM NaCl, 2 mM EDTA, 1 % Triton X100, 0.1 % SDS), 1x Wash Buffer 2 (20 mM Tris, 500 mM NaCl, 2 mM EDTA, 1 % Triton X100, 0.1 % SDS), 1x with LiCl Buffer (10 mM Tris, 250 mM LiCl, 1 mM EDTA, 0.5 % NP40, 0.5 % Na-deoxycholate), 2x with TE/NaCl Buffer (10mM Tris, 50 mM NaCl, 1 mM EDTA). Beads were eluted using 2x 50 µl Elution Buffer (100 mM NaHCO3, 1% SDS) with shaking for 15 min at RT and eluates were pooled. Chromatin was reverse-crosslinked overnight at 65 °C in Elution Buffer + 200 mM NaCl, followed by 100 µg/ml Rnase A and 0.25 mg/ml proteinase K digestion for 1h at 37 °C and 55 °C, respectively. DNA was purified using via phenol-chloroform extraction. ChIP efficiency was checked using IL3 -40, CSF1R FIRE, and gene desert control oligonucleotides (Bevington et al., 2016).
Library preparation was performed using the KAPA hyperprep kit (Roche) following manufacturer’s guidelines. Libraries were sequenced in single-end mode at 50 million reads per library using an Illumina HiSeq 2000 system according to manufacturer‘s instructions.

tag: antibody

value: JunB


title: JunB_L428_1


title: T3_1


title: T2_2


title: F2miNSC_rep1

value: NSC medium


title: T2_1


title: pmNSC_rep2

source_name: Sox2-GFP NSCs

value: Primary neural stem cells


title: pmNSC_rep1


title: JunB_KM-H2_1

source_name: IRF4WT HL-derived cell line

value: IRF4WT HL-derived cell line


title: JunB_KM-H2_2


title: Lung_DQ12_Control_Day30_rep4

source_name: Rat, Lung, DQ12, Control, Day 30, replicate 4


title: T1_2


title: Lung_DQ12_High_Day30_rep3

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 30, replicate 3


title: S2GMEF_rep2

source_name: Sox2-GFP MEFs

value: Mouse embryonic fibroblasts

value: Passage 1

value: MEF medium


title: IRF4_L428_2


title: T1_1


title: Lung_DQ12_Control_Day30_rep3

source_name: Rat, Lung, DQ12, Control, Day 30, replicate 3

value: Sprague Dawley


title: S2GMEF_rep1


title: IRF4_KM-H2_2


title: IRF4_L428_1


title: Sle1.Yaa [w241SP1]

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
s4 Novaseq paired end sequencing
Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base
Removal of 5 small contaminating clusters of T cells, B cells and platelets
Raw sequencing reads were aligned, counted, and demultiplexed by cellranger v5.0.0 with default parameters using mouse genome mm10 as reference. The raw gene-cell counts were then used as input for Seurat 3.1.5 [1] for quality control, normalization, unsupervised clustering and visualization. Genes expressed in less than 3 cells and cells expressed less than 200 genes were filtered out as poor quality. Cells with >= 20% RNA content from mitochondrial genes were considered dead and filtered out. Doublets were predicted using scrublet v0.2.3 [2] with doublet_score > 0.1 and removed from further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file of gene expression profile, with gene as rows and cell as columns

source_name: Spleen

growth_protocol: None (primary cells)

extract_protocol:
EBIs were isolated using BSA gradients and dissociated using EDTA and gentle mechanical dissociation
10X Genomics V3.1

value: Erythroblastic island cells

tag: Sex

value: male

tag: genotype/variation

value: control

tag: group

value: Non-Anemic


title: IRF4_KM-H2_1


title: Lung_DQ12_Control_Day30_rep1

source_name: Rat, Lung, DQ12, Control, Day 30, replicate 1

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)


title: Sle1.Yaa [w241BM2]

source_name: Bone marrow


title: Lung_DQ12_Control_Day30_rep2

source_name: Rat, Lung, DQ12, Control, Day 30, replicate 2


title: Sle1.Yaa.huTLR8tg [t239OSP3]

value: TLR8 transgene

value: Anemic


title: L428_DHS_2

value: IRF4C99R HL-derived cell line


title: Sle1.Yaa [BMC274RU]


title: Sle1.Yaa.huTLR8tg [S265LURU]


title: Sle1.Yaa [BMC267]


title: Lung_DQ12_High_Day1_rep3

description: Gene expression in lung of rat exposed to DQ12 (10 mg/rat) 1 days post exposure

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 1, replicate 3


title: Lung_DQ12_High_Day1_rep1

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 1, replicate 1


title: Lung_DQ12_High_Day1_rep6

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 1, replicate 6


title: Lung_DQ12_High_Day1_rep5

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 1, replicate 5


title: KM-H2_DHS_1


title: Sle1.Yaa.huTLR8tg [BMC265RU]


title: Lung_DQ12_High_Day1_rep4

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 1, replicate 4


title: hASCs, induced to adipocyte treated with oleacein_rep3

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description: Gene expression data from hASCs induced to adipocyte for first 7days, and then treated with 20 uM oleacein for 14 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (VALUE). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space)
algorithm: signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: The Human adipose-derived stem cells (hASCs) was purchased from ATCC® (SCRC-4000TM, Manassas, VA, USA). These cells were isolated from the adipose tissue of a White female. Cells culture was performed using a modified process based on previous describe. Briefly, cells were cultured in DMEM/F12 (11320033, Thermo Fisher Scientific) based medium. This medium was consist of 10%(v/v) fetal bovine serum (FBS), 1%(v/v) penicillin/streptomycin, 1% GlutaMax (35050061, Thermo Fisher Scientific) and 1‰ (v/v) 2-mercaptoethanal (21985023, Thermo Fisher Scientific), under the condition at 37°C in 5% CO2 environment. Cells were seeded at a density of 5,000 viable cells per cm2 and passaged after reaching 80% confluence as recommended by the provider.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: White adipocyte differentiation of hASCs was performed using DMEM/F12 based medium as previously described recording to regularly used protocol with slight modifications to ensure adipocyte induced successfully. Adipogenic differentiation operated on the second postconfluence day, followed by an induction (7-day) and maintenance period (14 days). oleacein was adding 20 μM together with maintenance period. The induction cocktail contains 100nM insulin (093-06351, Wako), 1μM dexamethasone (10008980, Cayman Chemical), 0.5mM IBMX (10008978, Cayman Chemical) and 1μM rosiglitazone. For maintenance medium, 100nM insulin and 1μM dexamethasone were prepared with DMEM/F12 based medium. To generate white adipocytes, hASCs were seeded at a density of 5 × 104 cells per cm2 and grown to confluency. Both induction and maintenance medium was subsequently changed every 4 days for total 21 days. oleacein were added from the first day of maintenance process.

value: human adipose-derived stem cells


title: Lung_DQ12_Control_Day1_rep6

description: Gene expression in lung of control rat (vehicule instillation) 1 days post exposure

source_name: Rat, Lung, DQ12, Control, Day 1, replicate 6


title: Lung_DQ12_Control_Day1_rep5

source_name: Rat, Lung, DQ12, Control, Day 1, replicate 5


title: Lung_DQ12_High_Day1_rep2

source_name: Rat, Lung, DQ12, Exposed to high dose, Day 1, replicate 2


title: hASCs, induced to adipocyte treated with oleacein_rep1

source_name: hASCs induced to adipocyte for first 7days, and then treated with 20 uM oleacein for 14 days


title: hASCs, induced to adipocyte_rep3

description: Gene expression data from hASCs induced to adipocyte for first 7days, and then maintenance for 14 days


title: hASCs, induced to adipocyte_rep2

source_name: hASCs induced to adipocyte for first 7days, and then maintenance for 14 days


title: L428_DHS_1

source_name: IRF4C99R HL-derived cell line


title: Reh_DHS_3

source_name: IRF4WT NHL-derived cell line

value: IRF4WT NHL-derived cell line


title: Sle1.Yaa.huTLR8tg [BMC265LU]


title: hASCs, induced to adipocyte treated with oleacein_rep2

value: hASCs induced to adipocyte for first 7days, and then treated with 20 uM oleacein for 14 days


title: KM-H2_DHS_2

source_name: IRF4WT HL-derived cell line

value: IRF4WT HL-derived cell line


title: Reh_DHS_2


title: hASCs, induced to adipocyte_rep1

value: hASCs induced to adipocyte for first 7days, and then maintenance for 14 days


title: 2 weeks post transection 3

status: Public on Jul 18 2023

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
Sequences were aligned to the zebrafish genome (danRer10) using Bowtie2 (v 2.2.5)
The mapped reads were filtered by samtools (v 1.3.1, with parameter -q 30) and duplicates were removed by picard (v 1.91)
Peak calls were determined using MACS2 (v 2.1.0, with parameter -f BAM -g 1.5e9 -q 0.05 --nomodel --shift 37 --extsize 73), and csaw(v 1.20.0, cutoff P value <0.05).
DiffBind(v 2.14.0) was used to call differential accessible sites.
Supplementary_files_format_and_content: bigwig files were generated by deeptools::bamCoverage (v 2.1.0) and normalized to 1x sequencing depth by ignore chrX for extaned reads

source_name: spinal cord

extract_protocol:
Sham injured and injured (2 mm rostral and caudal to the lesion site) spinal cords were dissected into a single cell suspension using 0.25% trypsin-EDTA; dissociated cells were processed for FACS sorting using an Astrios sorter, to collect live and single cells. 50.000 cells were processed for ATAC-seq.
Library preparation as described in Buenrostro et al., 2015
Libraries were sequenced on the Illumina HiSeq 4000 platform, with over 40 million 150 bp paired-end reads obtained for each library.


title: 2 weeks post transection 2


title: Lung_DQ12_Control_Day1_rep3

source_name: Rat, Lung, DQ12, Control, Day 1, replicate 3


title: 2 weeks post transection 1


title: hASCs, preadipocyte_rep3

description: Gene expression data from hASCs cultured in preadipocyte medium

source_name: hASCs cultured in preadipocyte medium

value: hASCs cultured in preadipocyte medium


title: sham 2

value: sham


title: spinal cord, 1 week post transection 3 (RNA-seq)

data_processing:
Reads were trimed by trim_galore and them aligned to the zebrafish genome (danRer10) using Tophat2 (v 2.2.1)
Mapped reads were filtered by samtools (v 1.3.1)and counted by htseq-count (v 0.6.0)
Differential analyses were performed by Bioconductor package DESeq2 (v 1.26.0)
Supplementary_files_format_and_content: text file contain raw counts for genes exported by htseq-counts (v 0.6.0)

source_name: spinal cord, 1 week post transection

extract_protocol:
Sham injured and injured (2 mm rostral and caudal to the lesion site) spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit (Zymo Research).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Hiseq4000 (50bp, SR, 1 lane)

value: injured

value: spinal cord


title: hASCs, preadipocyte_rep2


title: hASCs, preadipocyte_rep1


title: sham 1


title: spinal cord, 1 week post transection 2 (RNA-seq)


title: spinal cord, 1 week post transection 1 (RNA-seq)


title: spinal cord, sham 3 (RNA-seq)

source_name: spinal cord, sham

value: uninjured


title: Lung_DQ12_Control_Day1_rep1

source_name: Rat, Lung, DQ12, Control, Day 1, replicate 1

value: Sprague Dawley


title: spinal cord, sham 2 (RNA-seq)


title: spinal cord, sham 1 (RNA-seq)


title: Lung_DQ12_Control_Day1_rep4

source_name: Rat, Lung, DQ12, Control, Day 1, replicate 4

value: accessory lobe of lung


title: spinal cord, 1 week post transection 2 (ATAC-seq)

data_processing:
Sequences were aligned to the zebrafish genome (danRer10) using Bowtie2 (v 2.2.5)
The mapped reads were filtered by samtools (v 1.3.1, with parameter -q 30) and duplicates were removed by picard (v 1.91)
Peak calls were determined using MACS2 (v 2.1.0, with parameter -f BAM -g 1.5e9 -q 0.05 --nomodel --shift 37 --extsize 73), and csaw(v 1.20.0, cutoff P value <0.05).
DiffBind(v 2.14.0) was used to call differential accessible sites.
Supplementary_files_format_and_content: bigwig files were generated using deeptools (v 3.1.3) Scores represent count per million reads