title: A375_PRL3_B11

city: Edinburgh

first: Jeanette

middle: Astorga

last: Johansson

state: Scotland

address: Western General Hospital, Crewe Road

department: IGMM

institute: Edinburgh University

data_processing:
Illumina  software used for basecalling.
Sequence quality was checked using FastQC (version 0.11.3)
Reads were aligned to the human genome (GrCh38) using STAR (STAR_2.5.1b) with the default parameters
The quality of the resulting alignment to the transcriptome (Ensembl annotation version GRCh38.91) has been checked using RNASeqQC (v1.1.8.1)
Raw counts of reads covering the transcriptome (Ensembl annotation version GRCh38.91) was obtained using htseq-count (0.6.1) with the “-s reverse” option.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: tab-delimited filed of raw counts at gene level for each sample

growth_protocol: A375 human melanoma cell lines were established by stable transfection with an empty vector or a human PRL3 expression plasmid.   The cells were routinely cultured in DMEM containing 10% FBS and L-glutamine and maintained in 100µg/ml Hygromycin B.

extract_protocol:
90-150 µg total RNA were harvested from 4sU labelled EV and PRL3 cells using Trizol reagent. The purification of 4sU labelled RNA was performed using EZ-link Biotin-HPDP at a concentration of 1 mg /ml. Following chloroform extraction, the biotinylated RNA was magnetically labelled with µMACS Streptavidin MicroBeads and purified using streptavidin µMacs columns. The eluate RNA was rRNA depleted following manufacturer's instructions. Approximately 20 ng of the rRNA depleted 4sU labelled RNA was used for the construction of cDNA sequencing libraries.
cDNA libraries were prepared using NEBNext Ultra Directional RNA library Prep kit for Illumina (NEB) following manufacturer’s instructions. NEBNext® Multiplex Oligos for Illumina® were used to barcode the RNA replicates. Libraries were sequenced on the HiSeq 4000 150PE following the manufacturer's protocols.

treatment_protocol: EV and PRL3 cells were pulsed with 500µM 4-thiouridine (4sU) and incubated for 20 min prior to RNA isolation.

value: human melanoma cell line

tag: genotype/variation

value: stable transfection with human PRL3 expression plasmid


title: RNA-seq_normal_lung53

status: Public on Jul 10 2020

type: SRA

city: Shanghai

first: Linhu

last: Zhai

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong, Shanghai

country: China

institute: Shanghai Institute of Materia Medica

description: paired normal for sample LADC_53

library_source: transcriptomic

data_processing:
RNASeq reads were adapter trimmed and data quality was assessed with the FastQC (version 0.11.7) software
Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using hisat2 software (v2.0.4).
The mapped reads were assembled into transcripts or genes by using StringTie software (v1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf
For quantification purpose, the relative abundance of transcript/gene was measured by a normalized metrics, FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: GTF reports FPKMs, TPMs

molecule: total RNA

organism: Homo sapiens

source_name: Clinical normal lung tissue

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: tissue

value: Lung

tag: disease state

value: normal tissue

tag: age


title: S_6M_14

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 6 months, biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data including background subtraction (GenomeStudioV2011.1 software, gene expression module version 1.9.0), removal of negative values by introducing an offset, quantile normalisation

label: Biotin

organism: Mus musculus

source_name: Lung tissue from mice exposed to cigarette smoke for 6 months, biological replicate 2

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: Exposure to filtered air, cigarette smoke, and LTβR-Ig fusion protein as described in the paper. Briefly, Cigarette smoke (CS) was generated from 3R4F Research Cigarettes (Tobacco Research Institute, University of Kentucky, Lexington, KY), with the filters removed. Mice were whole body exposed to active 100% mainstream CS of 500 mg/m3 total particulate matter (TPM) for 50 min twice per day for 4 and 6 months (m) in a manner mimicking natural human smoking habits as previously described. The TPM level was monitored via gravimetric analysis of quartz fiber filters prior and after sampling air from the exposure chamber and measuring the total air volume. CO concentrations in the exposure chamber were constantly monitored by using a GCO 100 CO Meter (Greisinger Electronic, Regenstauf, Germany) and reached values of 288± 74 ppm. All mice tolerated CS-mediated CO concentrations without any sign of toxicity, with CO-Hb levels of 12.2 ± 2.4%.  In two parallel experiments, mice were treated with an LTβR-Ig fusion protein (80 µg i.p., weekly) (muLTβR-muIgG1, ref #14811-122; and CHO 14.3 Lot #7195-30) or control-Ig (MOPC21, clone #113) for 2m, starting from 2m and 4m of CS exposure. Control mice were kept in a filtered air (FA) environment, but exposed to the same stress as CS-exposed animals. 24 h after the last CS exposure, mice were sacrificed.

tag: strain

value: lung

tag: gender

value: female


title: SL_6M_18

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 6 months plus the LTβR-Ig fusion protein, biological replicate 3

source_name: Lung tissue from mice exposed to cigarette smoke for 6 months plus the LTβR-Ig fusion protein, biological replicate 3


title: SL_15M_26

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 15 months plus the LTβR-Ig fusion protein, biological replicate 2

source_name: Lung tissue from mice exposed to cigarette smoke for 15 months plus the LTβR-Ig fusion protein, biological replicate 2


title: C_6M_10

description: Gene expression data from lung tissue from mice exposed to filtered air for 6 months, biological replicate 1

source_name: Lung tissue from mice exposed to filtered air for 6 months, biological replicate 1


title: C_4M_02

description: Gene expression data from lung tissue from mice exposed to filtered air for 4 months, biological replicate 2

source_name: Lung tissue from mice exposed to filtered air for 4 months, biological replicate 2


title: C_4M_03

description: Gene expression data from lung tissue from mice exposed to filtered air for 4 months, biological replicate 3

source_name: Lung tissue from mice exposed to filtered air for 4 months, biological replicate 3


title: A375_EV_B2

country: United Kingdom

tag: cell line

tag: cell type

value: stable transfection with an empty vector


title: S_6M_13

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 6 months, biological replicate 1

source_name: Lung tissue from mice exposed to cigarette smoke for 6 months, biological replicate 1


title: RNA-seq_normal_lung54

description: paired normal for sample LADC_54


title: S_4M_04

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 4 months, biological replicate 1

source_name: Lung tissue from mice exposed to cigarette smoke for 4 months, biological replicate 1


title: A375_PRL3_B10


title: A375_PRL3_B9


title: S_4M_06

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 4 months, biological replicate 3

source_name: Lung tissue from mice exposed to cigarette smoke for 4 months, biological replicate 3


title: C_4M_01

description: Gene expression data from lung tissue from mice exposed to filtered air for 4 months, biological replicate 1

source_name: Lung tissue from mice exposed to filtered air for 4 months, biological replicate 1


title: S_6M_15

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 6 months, biological replicate 3

source_name: Lung tissue from mice exposed to cigarette smoke for 6 months, biological replicate 3


title: SL_6M_16

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 6 months plus the LTβR-Ig fusion protein, biological replicate 1

source_name: Lung tissue from mice exposed to cigarette smoke for 6 months plus the LTβR-Ig fusion protein, biological replicate 1


title: SL_6M_17

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 6 months plus the LTβR-Ig fusion protein, biological replicate 2

source_name: Lung tissue from mice exposed to cigarette smoke for 6 months plus the LTβR-Ig fusion protein, biological replicate 2


title: SL_4M_08

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 4 months plus the LTβR-Ig fusion protein, biological replicate 2

source_name: Lung tissue from mice exposed to cigarette smoke for 4 months plus the LTβR-Ig fusion protein, biological replicate 2


title: A375_EV_B3


title: S_4M_05

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 4 months, biological replicate 2

source_name: Lung tissue from mice exposed to cigarette smoke for 4 months, biological replicate 2


title: A375_EV_B1


title: Control for Salt 400 mmol T24, biological rep2

city: Ankara

first: Ali

last: ERGÜL

address: Gümüşdere  Yerleşkesi   Keçiören/ ANKARA

department: Biotechnology Institute

country: Turkey

institute: Ankara Üniversitesi  Biotechnology Institute & SİSBİOTEK

description: Gene expression data from 1616C grape leaves- Salt (400 mM NaCl) treatment, 24 hour-Control

hyb_protocol: Following fragmentation, 12μg of aRNA were hybridized for for 16 h at 60 rpm, 45°C on Vitis vinifera Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® 3000 Scanner.

data_processing:
Microarray analysis was performed using BRB-Array Tools Version 4.6.0 (https://brb.nci.nih.gov/BRB-ArrayTools/)
GCRMA was used as the analysis method.

label: biotin

organism: Vitis vinifera

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol:
Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C.
Plantlets with 4–5 leaves were chosen for use in stress treatments.

extract_protocol:
One gram of ground leaf tissue was homogenized in a buffer containing 120 mmol Tris-HCl, pH = 8.5, 1.5% (w/v) lithium dodecyl sulfate, 300 mM LiCl, 10 mM sodium EDTA, 1% w/v sodium deoxycholate, and 1% v/v NP-40.
Following autoclaving, 2 mM aurintricarboxylic acid, 20 mM dithiotheitol (DTT), 10 mM thiourea, and 2% w/v polyvinylpolypyrrolidone were added immediately before use.
Following precipitation with sodium acetate and isopropanol precipitation, samples were extracted once with 25:24:1 phenol:chloroform:isoamyl
and then twice with 24:1 chloroform:isoamyl prior to performing LiCl precipitations to remove DNA contamination.

treatment_protocol: Experiment treatments: the control (C, without any chemical treatment), TM (treated with 5 μg mL-1 tunicamycin (TM)) and salt (treated with 400 mM NaCl).

value: Tissue culture leaves

tag: genotype

value: Rootstock 1616C (V. solonis x V. riparia)

tag: stress

value: Control for salt

tag: time

value: 24 hour


title: RNA-seq_normal_lung52

description: paired normal for sample LADC_52


title: Control for Salt 400 mmol T24, biological rep3

source_name: 1616C grape leaves- Salt (400 mM NaCl) treatment, 24 hour-Control


title: RNA-seq_normal_lung50

description: paired normal for sample LADC_50

source_name: Clinical normal lung tissue


title: RNA-seq_normal_lung49

description: paired normal for sample LADC_49


title: SL_4M_07

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 4 months plus the LTβR-Ig fusion protein, biological replicate 1

source_name: Lung tissue from mice exposed to cigarette smoke for 4 months plus the LTβR-Ig fusion protein, biological replicate 1


title: WNV WT DIII-tetramer specific germinal center B cells

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

country: USA

institute: University of Arizona

data_processing:
Reads were processed and aligned to the mm10 reference genome using the 10X cellranger count pipeline
Filtered counts matrix was loaded into Seurat for subsequen analysis.  Doublets were excluded using 'rscrublet', high quality cells determiend based quality control thresholds of <5% mitochondrial reads, a doublet score <0.20, and >200 unique features.
A small number of non-B cells were identified and filtered for quality control.
Normalization, clustering, dimensionality reduction, and visualization were performed using Seurat and ggplot2
Genome_build: mm10
Supplementary_files_format_and_content: The barcodes.tsv file contains cell barcodes associated with the sample, features.tsv file contains a list of genes found in the sample, and the matrix.mtx file is a sparse matrix of counts for each cell and gene/feature.

source_name: Germinal center B cells

growth_protocol: Primary cell

extract_protocol: 10x Genomics Chromium Single cell V(D)J Reagent Kits_ protocol CG000086 Rev M

treatment_protocol: untreated

value: Spleen

value: GCBC


title: RNA-seq_normal_lung51

description: paired normal for sample LADC_51


title: ATAC_FoxA_triple_null_3

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

library_source: genomic

data_processing: Paired-end sequencing reads were aligned to the mouse genome (assembly mm9) using Bowtie2 allowing ends to be soft clipped. Only properly paired alignments were retained for downstream analysis. PCR duplicates were removed using SAMtools (“rmdup”). Reads mapped to mitochondria and ENCODE blacklist regions were removed. All reads aligning to the positive strand were offset by +4 bp, and all reads aligning to the negative strand were offset −5 bp. Quality control metrics were evaluated before alignment using FastQC (version 0.11.8) and after alignment using QualiMap (version 2.2) to ensure comparable quality of sequencing libraries. Bam files were converted to Bedgraph files after normalizing to 1 million reads per library using BEDtools (“genomecov”) and then converted to bigwig format using UCSC toolkit (“bedGraphToBigWig”). For control and FoxA triple null groups, an average bigwig file was also generated from the replicates (“bigWigMerge“).

molecule: genomic DNA

source_name: Liver

extract_protocol: About 50 mg of frozen livers were minced in 1 mL of cold swelling buffer (10 mM Tris-HCl pH 7.5, 2mM MgCl2, 3mM CaCl2). Tissue was homogenized with a Dounce tissue grinder (DWK Life Sciences 357544) using the loose pestle 10 times and was then incubated at 4°C for 20 minutes. Following incubation, the sample was homogenized 20 times with the tight pestle. 3 mL of cold swelling buffer was added to the lysate, and the sample was passed through a 70 μm cell strainer (Corning). The lysate was centrifuged at 600 RCF for 20 minutes at 4°C. The supernatant was discarded, and the pellet was resuspended in 1.8 mL of swelling buffer and 200 μL of glycerol. While vortexing, 2 mL of lysis buffer (1X swelling buffer, 10% glycerol, 1% IGEPAL CA-630) was added drop by drop to the lysate, and the lysate was incubated for 5 minutes at 4°C. Following incubation, 5 mL of lysis buffer was added to the sample, and the sample was centrifuged at 700 RCF for 13 minutes at 4°C. The supernatant was discarded, and the nuclei were resuspended in 2 mL of 1X DPBS (Thermo Fisher 14080055). Nuclei were counted using a hemocytometer, 135,000 nuclei were added to a new 1.5 mL microcentrifuge tube, and nuclei were pelleted by centrifugation at 900 RCF for 10 minutes at 4°C. The supernatant was discarded, and nuclei were resuspended in 75 μL of 2X TD Buffer (Illumina), 49.5 μL of 1X DPBS, 7.5 μL Tn5 Transposase (Illumina), 1.5 μL of 10% Tween-20, 1.5 μL of 1% Digitonin, and 15 μL of DDW. Nuclei were incubated for 30 minutes at 37°C. Following incubation, DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen), and eluted in 10 μL of EB. 25 μL of High-Fidelity 2X PCR Master Mix (New England BioLabs), 2.5 uL of indexing primer, and 10 μL of DDW were added to the 10 μL of purified DNA and the DNA was amplified five cycles using the following PCR program: 72°C for 5 minutes, 98°C for 30 seconds, and then 5 cycles at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Next, 5 μL of the partially amplified library were removed and used to determine the appropriate number of additional cycles by qPCR with the following mix: 3.85 μL of DDW, 0.5 μL of Indexed Primer, 0.15 μL of SYBR Green I Nucleic Acid Gel Stain diluted 1:100 (Thermo Fisher), and 5 μL of High-Fidelity 2X PCR Master Mix. We used the following qPCR program: 98°C for 30 seconds, then 20 cycles at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Additional cycles were determined as one-third of the plateau. The remaining 45 μL of the partially amplified library were further amplified accordingly. Double-sided size selection was performed using Ampure XP beads (Beckman Coulter) by adding 22.5 μL of beads to the library and keeping the supernatant. The supernatant was transferred to another tube and then 58.8 μL of beads were added. The beads were kept and resuspended in 20 μL of DDW, from which the final library was eluted. Libraries were sequenced on the Illumina HiSeq 4000.

value: FoxA triple null


title: RNA-seq_normal_lung46

description: paired normal for sample LADC_46


title: polyclonal isotype-switched memory B cells

source_name: Memory B cells

value: MBC


title: RNA-seq_normal_lung47

description: paired normal for sample LADC_47


title: ATAC_FoxA_triple_null_2


title: RNA-seq_normal_lung45

description: paired normal for sample LADC_45


title: SL_4M_09

description: Gene expression data from lung tissue from mice exposed to cigarette smoke for 4 months plus the LTβR-Ig fusion protein, biological replicate 3

source_name: Lung tissue from mice exposed to cigarette smoke for 4 months plus the LTβR-Ig fusion protein, biological replicate 3


title: ATAC_FoxA_triple_null_1


title: Control for Salt 400 mmol T6, biological rep3

description: Gene expression data from 1616C grape leaves- Salt (400 mM NaCl) treatment, 6 hour-Control

value: 6 hour


title: Control for Salt 400 mmol T24, biological rep1


title: ATAC_control_3

value: control


title: Control for Salt 400 mmol T6, biological rep2

source_name: 1616C grape leaves- Salt (400 mM NaCl) treatment, 6 hour-Control


title: RNA-seq_normal_lung48

description: paired normal for sample LADC_48


title: RNA-seq_normal_lung44

description: paired normal for sample LADC_44


title: ATAC_control_2


title: Salt 400 mmol at T24, biological rep1 stress

description: Gene expression data from 1616C grape leaves- Salt (400 mM NaCl) treatment, 24 hour

value: salt


title: Salt 400 mmol at T24, biological rep3 stress

source_name: 1616C grape leaves- Salt (400 mM NaCl) treatment, 24 hour


title: Salt 400 mmol at T6, biological rep3 stress

description: Gene expression data from 1616C grape leaves- Salt (400 mM NaCl) treatment, 6 hour


title: Salt 400 mmol at T6, biological rep2 stress

source_name: 1616C grape leaves- Salt (400 mM NaCl) treatment, 6 hour


title: Salt 400 mmol at T24, biological rep2 stress


title: Salt 400 mmol at T6, biological rep1 stress


title: Control for Tunicamycin T24, biological rep2

description: Gene expression data from 1616C grape leaves- tunicamycin (TM) treatment, 24 hour-control

value: Control for Tunicamycin


title: Control for Tunicamycin T24, biological rep1

source_name: 1616C grape leaves- tunicamycin (TM) treatment, 24 hour-control


title: Control for Tunicamycin T6, biological rep3

description: Gene expression data from 1616C grape leaves- tunicamycin (TM) treatment, 6 hour-control


title: Control for Tunicamycin T24, biological rep3


title: RNA-seq_normal_lung40

description: paired normal for sample LADC_40

value: Lung


title: RNA-seq_normal_lung42

description: paired normal for sample LADC_42

value: normal tissue


title: Tunicamycin at T24, biological rep2 stress

description: Gene expression data from 1616C grape leaves- tunicamycin (TM) treatment, 24 hour

value: Tunicamycin


title: SMK-MOCP-3

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

description:
muc14450
Drop-seq

data_processing:
For preprocessing of the single cell data of mouse lung tissue cells, the Dropseq computational pipeline was used (version 2.3.0) as previously described (Pubmed ID: 26000488). Briefly, STAR (version 2.5.3a) was used for mapping. Reads were aligned to the mm10 reference genome (GSE63269). For barcode filtering, we excluded barcodes with less than 200 genes detected. A high proportion (> 20%) of transcript counts derived from mitochondria-encoded genes may indicate low cell quality, and we removed these unqualified cells from the downstream analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw count matrix (LTbetaTreatment_raw_counts.mtx) from Drop-seq experiments with 25095 genes and 21413 cells in market matrix format and corresponding column (LTbetaTreatment_genes.txt) and row (LTbetaTreatment_barcodes.txt) labels. Cell-level metadata (LTbetaTreatment_cells_metadata.txt).

source_name: Lung tissue

extract_protocol:
Single cells were diluted in PBS, supplemented with 0.04% bovine serum albumin up to a final concentration of 100 cells/µl. Using a microfluidic PDMS device (Nanoshift), single cells were co-encapsulated in droplets with barcoded beads (Chemgenes Corporation, Wilmington, MA) at a final concentration of 120 beads/uL. Droplets were collected for 15 min/sample. After droplet breakage, beads were harvested, washed, and prepared for on bead mRNA reverse transcription (Maxima RT, Thermo Fisher). Following an exonuclease I (New England Biolabs) treatment for the removal of unused primers, beads were treated with Klenow enzyme to improve single cell transcript quality; thereafter, beads were counted, aliquoted (2000 beads/reaction, equals ~100 cells/reaction), and pre-amplified by 12 PCR cycles (primers, chemistry, and cycle conditions identical to those previously described in Macosko et al., 2015).
PCR products were pooled and purified twice using 0.6x clean-up beads (CleanNA). Prior to tagmentation, cDNA samples were loaded on a DNA High Sensitivity Chip on the 2100 Bioanalyzer (Agilent) to ensure transcript integrity, purity, and amount. For each sample, 1 ng of pre-amplified cDNA from an estimated 1500 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB was used (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC).

treatment_protocol:
Cigarette smoke exposure: Cigarette smoke (CS) was generated from 3R4F Research Cigarettes, with the filters removed. Mice were whole body exposed to active 100% mainstream CS of 500 mg/m3 total particulate matter for 50 min twice per day for 6 months in a manner mimicking natural human smoking habits.
Mice were treated with an LTβR-Ig fusion protein (80 µg i.p., weekly) (muLTβR-muIgG, kindly supplied by Jeffrey Browing, Biogen Idec) or control-Ig (MOPC21, Biogen Idec) for 2m, starting from 4m of CS exposure. Control mice were kept in a filtered air (FA) environment, but exposed to the same stress as CS-exposed animals.

tag: air exposure

value: cigarette smoke

tag: lt-beta-r-lg treatment

value: No

tag: number of cells


title: ATAC_control_1


title: Tunicamycin at T6, biological rep3 stress

description: Gene expression data from 1616C grape leaves- tunicamycin (TM) treatment, 6 hour

value: Tissue culture leaves


title: SMK-MOCP-4

description:
muc14451
Drop-seq


title: Control for Tunicamycin T6, biological rep2

source_name: 1616C grape leaves- tunicamycin (TM) treatment, 6 hour-control

value: Rootstock 1616C (V. solonis x V. riparia)


title: L2_CON_POS_2_TPM

city: Los Angeles

first: Maureen

middle: M

last: Sampson

state: CA

address: 695 Charles Young Drive

department: Molecular Toxicology

institute: UCLA

description: L2 Neuron replicate 2

data_processing:
STAR spliced read aligner was used for alignment.
QC was performed after the alignment to examine the following: level of mismatch rate, mapping rate to the whole genome, repeats, chromosomes, and key transcriptomic regions (exons, introns, UTRs, genes).
 Total counts of read fragments aligned to candidate gene regions within the reference gene annotation were derived using HTS-seq program and used as a basis for the quantification of gene expression. Only uniquely mapped reads were used for subsequent analyses. Following alignment and read quantification, we performed quality control using a variety of indices, including consistency of replicates and average gene coverage.
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: Counts and TPMs

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Neurons

extract_protocol:
ARCTURUS® PicoPure® RNA Isolation Kit (ThermoFisher, KIT0204) or RNeasy Plus Micro Kit (QIAGEN, 74034).
SMART-seq v4 Ultra Low-input RNA sequencing kit with Nextera XT (Takara Bio). Paired-end sequencing was conducted by the UCLA genomic core facility (https://www.semel.ucla.edu/ungc/services).

value: L2 Neuron

tag: treatment

value: untreated


title: RNA-seq_normal_lung38

description: paired normal for sample LADC_38


title: RNA-seq_normal_lung41

description: paired normal for sample LADC_41


title: RNA-seq_normal_lung35

description: paired normal for sample LADC_35


title: Tunicamycin at T6, biological rep1 stress

source_name: 1616C grape leaves- tunicamycin (TM) treatment, 6 hour


title: SMK-MOCP-1

description:
muc14448
Drop-seq


title: Fetal_Submandibular_F.446_S6

city: Viken

first: Marie

last: Saitou

state: Viken

address: Ås

country: Norway

institute: NMBU

data_processing:
Quality control of the obtained sequences was performed using FastQC..
The results were further reviewed by MultiQC.
Adaptor sequences, low-quality bases from both sides of the read (<= 3) and reads length smaller than 36 bp were discarded by Trimmomatic.
Filtered reads were mapped to the human transcriptome reference (hg19) from Ensembl and quantified using Kallisto.
Differential expression analysis was performed by DESeq2

extract_protocol:
RNA was isolated from 3 x 30µm sections of human adult and fetal tissue using RNAqueous Micro Kit (Ambion) and total RNA samples were DNase-treated (Ambion). Sample yield and integrity was analyzed using a Bioanalyzer (Illumina).
RNA sequencing was performed by standard operating procedure by GENEWIZ (https://www.genewiz.com/en) using Illumina HiSeq with a 2x150bp configuration.
Life Technologies RNA Isolation Kit AM1931

tag: Stage

value: Fetal

value: Submandibular


title: SMK-MOCP-5

description:
muc14452
Drop-seq


title: Tunicamycin at T24, biological rep1 stress

source_name: 1616C grape leaves- tunicamycin (TM) treatment, 24 hour

value: 24 hour


title: L2_CON_POS_10_TPM

description: L2 Neuron replicate 3


title: RNA-seq_normal_lung33

description: paired normal for sample LADC_33


title: RNA-seq_normal_lung34

description: paired normal for sample LADC_34


title: Tunicamycin at T6, biological rep2 stress


title: SMK-Ltb-4

description:
muc14446
Drop-seq

value: Yes


title: SMK-Ltb-3

description:
muc14445
Drop-seq


title: Control for Salt 400 mmol T6, biological rep1

value: Control for salt

value: 6 hour


title: Fetal_Submandibular_F.257_S5


title: T1_GFP_POS_3_TPM

description: T1 Neuron replicate 3

value: T1 Neuron

value: T1-LexA (from Aljoscha Nern)


title: RNA-seq_normal_lung37

description: paired normal for sample LADC_37

value: Lung


title: RNA-seq_normal_lung30

description: paired normal for sample LADC_30

value: normal tissue


title: T1_GFP_POS_2_TPM

description: T1 Neuron replicate 2


title: T1_GFP_POS_1_TPM

description: T1 Neuron replicate 1


title: SMK-Ltb-5

description:
muc14447
Drop-seq


title: Fetal_Parotid_F.475_S17

value: Parotid


title: RNA-seq_normal_lung29

description: paired normal for sample LADC_29


title: L2_CON_POS_1_TPM

description: L2 Neuron replicate 1


title: SMK-MOCP-2

description:
muc14449
Drop-seq

value: cigarette smoke


title: Tunicamycin at T24, biological rep3 stress

value: Tunicamycin


title: Fetal_Submandibular_F.444_S23


title: Fetal_Sublingual_F.255_S22

value: Sublingual


title: Fetal_Submandibular_F.22_S24


title: Fetal_Sublingual_F.431_S20


title: Fetal_Sublingual_F.445_S21


title: Fetal_Parotid_F.21_S1


title: Fetal_Sublingual_F.202_S19


title: Control for Tunicamycin T6, biological rep1

value: Tissue culture leaves

value: Rootstock 1616C (V. solonis x V. riparia)

value: Control for Tunicamycin


title: Fetal_Sublingual_F.248_S18

value: Fetal


title: Fetal_Sublingual_F.164_S3


title: Fetal_Parotid_F.165_S2


title: RNA-seq_normal_lung27

description: paired normal for sample LADC_27


title: SMK-Ltb-2

description:
muc14444
Drop-seq


title: FA-2

description:
muc14441
Drop-seq

value: filtered air

value: No


title: Adult_Sublingual_A.522_S16

value: Adult


title: Adult_Submandibular_A.509_S14

value: Submandibular


title: RNA-seq_normal_lung25

description: paired normal for sample LADC_25


title: RNA-seq_normal_lung26

description: paired normal for sample LADC_26


title: FA-3

description:
muc14442
Drop-seq


title: SMK-Ltb-1

description:
muc14443
Drop-seq

value: Yes


title: RNA-seq_normal_lung39

description: paired normal for sample LADC_39


title: FA-1

description:
muc14440
Drop-seq


title: Adult_Submandibular_A.504_S25


title: Adult_Sublingual_A.493_S27


title: Adult_Submandibular_A.507_S13


title: Adult_Submandibular_A.505_S26


title: RNA-seq_normal_lung24

description: paired normal for sample LADC_24


title: RNA-seq_normal_lung23

description: paired normal for sample LADC_23


title: RNA-seq_normal_lung28

description: paired normal for sample LADC_28


title: Fetal_Submandibular_F.208_S4


title: Adult_Parotid_A.463_S10


title: ChIP_H3K4me1_tko_1

description:
Input_5716_tko_3_CACTCA.fastq.gz
H3k4me1.KO.mean.bw

data_processing:
Single-end sequencing reads were trimmed with Cutadapt and aligned to mouse genome (assembly mm9) using Bowtie2 version 2.3.4.1. PCR duplicates were removed using picard.jar tool and the command MarkDuplicates with the following flags:”REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. Peak calling was done with macs2 version 2.1.1.20160309. In order to compare differential binding between controls and FoxA triple nulls we used DiffBind version 2.10.0 (29). Peaks were defined as ±250 base pairs from peak center. Normalization was done with DBA_SCORE_RPKM_FOLD and DB.DESeq2 to find statistically significant differences between groups. We took only binding sites with an RPKM average larger than 10 in controls or FoxA triple null and counted as significant only sites with FDR < 0.05. Bam files were converted to Bedgraph files after normalizing to 1 million reads per library using BEDtools (“genomecov”) and then converted to bigwig format using UCSC toolkit (“bedGraphToBigWig”). For control and FoxA triple null groups, an average bigwig file was also generated from the replicates (“bigWigMerge“). Bigwig files were loaded on the WashU browser for visualization. Deeptools (version 2.5.7, “computeMatrix” and “plotHeatmap”) was used to generate enrichment heatmaps surrounding selected regions.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: hepatocytes

extract_protocol: About 130 mg of frozen liver was minced in 2 mL of cold 1X DPBS (Thermo Fisher 14080055). The volume of liver samples were brought up to 10 mL of 1X DPBS and 1% formaldehyde. The samples were incubated at room temperature for 8 minutes with rotation. To quench, reaction was brought to 0.125 M glycine and incubated for 5 minutes at room temperature with rotation. Samples were centrifuged at 2500 RCF for 2 minutes at 4°C and the supernatant was discarded and washed once with 1XDPBS. The pellet was resuspended in 1 mL of cold ChIP cell lysis buffer (10 mM Tris- HCl pH 8.0, 10 mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630, 1X cOmplete protease inhibitor cocktail) and transferred to a 10 mL tissue grinder on ice. The samples were homogenized with a smooth teflon pestle 20 times and incubated at 4°C for 5 minutes. Following incubation, the samples were centrifuged for 5 minutes at 17,000 RCF at 4°C to pellet nuclei. The supernatant was discarded, and nuclei were resuspended in 1 mL of cold ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 5 mM EDTA, 1% SDS, 1X cOmplete protease inhibitor cocktail). The samples were sonicated for two rounds using the Standard Biruptor (diagenode UCD-200) with the following parameters: Intensity = High (H), Multitimer = OFF: 30 sec, ON: 30 sec, Total timer = 7.5 minutes with maintaining 4C tempertures. Biruptor was cooled down for 15 minutes between rounds. Following sonication, the samples were centrifuged at 17,000 RCF for 10 minutes at 4°C and the supernatant containing sheared chromatin was recovered. To determine the amount of material required for precipitation we isolated DNA from sonicated chromatin. DNA was quantified using NanoDrop-1000 (Thermo Fisher) and ran on a BioAnalyzer High Sensitivity Chip. Following quantification, 10 μg of sonicated chromatin was added to 1 mL of ChIp dilution buffer (16. mM Tris-HCl pH 8.0, 167 mM NaCl, 0.01% SDS, 1.1% Triton-X 100, 1X cOmplete protease inhibitor cocktail). 3 μg of the following antibodies, H3K4me1(Abcam ab8895), H3K27ac (Active Motif 39133) and HNF4a (Abcam ab181604) were added to the samples and the samples were incubated at 4°C overnight with rotation. 40 μL of recombinant protein G agarose beads (Thermo Fisher) were washed three times with 1 mL of ChIP dilution buffer by resuspending beads in the buffer. Following the washes, the beads were resuspended in 75 μL of ChIP Dilution Buffer and 5 μL of BSA (New England BioLabs) and incubated at 4°C overnight with rotation for blocking. Then chromatin samples were added to the blocked beads and the samples were incubated at 4°C for 1 hour with rotation. Samples were centrifuged at 100 RCF for 30 seconds and the supernatant was discarded. The beads were then washed sequentially with each of the following buffers by resuspending the beads in 1 mL of buffer, incubating beads at room temperature for 5 minutes with rotation, pelleting beads, and discarding supernatant: TSE I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), TSE II ( 20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), ChIP Buffer III (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% IGEPAL CA-630, 1% Sodium Deoxycholate), TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Following the washes, the beads were resuspended in 100 μL of elution buffer (0.1 M NaHCO3, 1% SDS) and incubated at room temperature for 15 minutes with rotation. 4 μL of 5M NaCl was added to the supernatant and then samples were incubated at 65°C overnight. Next, DNA was isolated from the samples. Enrichment of IP samples was measured through qPCR using the following program: 95°C for 3 minutes, for 40 cycles, 95°C for 5 seconds, 60°C for 20 seconds, with the specific primers. Then, Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.  Libraries were sequenced on the Illumina Hiseq 4000.

value: Liver

tag: antibody

value: tko


title: ChIP_H3K4me1_tko_2

description:
Input_5717_tko_4_5_CAGGCG.fastq.gz
H3k4me1.KO.mean.bw


title: ChIP_H3K27ac_tko_2

description:
Input_5619_tko_2_5_CAAAAG.fastq.gz
H3k27ac.KO.mean.bw


title: Adult_Parotid_A.458_S9


title: Adult_Submandibular_A.454_S11


title: Adult_Submandibular_A.461_S12


title: RNA-seq_normal_lung22

description: paired normal for sample LADC_22

value: Lung


title: ChIP_H3K4me1_control_2

description:
Input_5715_wt_3_5_CACGAT.fastq.gz
H3k4me1.Control.mean.bw

value: wildtype


title: ChIP_H3K27ac_tko_1

description:
Input_5618_tko_1_4_ATGAGC.fastq.gz
H3k27ac.KO.mean.bw


title: Adult_Parotid_A.439_S8

value: Parotid


title: RNA-seq_normal_lung20

description: paired normal for sample LADC_20

value: normal tissue


title: Adult_Parotid_A.437_S7


title: Adult_Sublingual_A.430_S15


title: RNA-seq_normal_lung19

description: paired normal for sample LADC_19


title: RNA-seq_normal_lung18

description: paired normal for sample LADC_18


title: ChIP_H3K4me1_control_1

description:
Input_5714_wt_2_5_CAACTA.fastq.gz
H3k4me1.Control.mean.bw


title: ChIP_H3K27ac_control_2

description:
Bound_Input_5617_wt_1_GGTAGC.fastq.gz
H3k27ac.Control.mean.bw


title: KO-Tcra-Rep1

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
The adapter sequences, contamination, and low-quality reads were filtered using fastp. Then the filtered sequencing reads were analyzed with MIXCR, and V, D, J gene segments alignment and CDR3 extraction were performed. The corresponding germline sequences were mapped to the reference sequences derived from international ImMunoGeneTics (IMGT) information.
Supplementary_files_format_and_content: csv

source_name: Thymocytes

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
Trizol extraction
The 1ug RNA was used for the reverse transcription (RT). The cDNA libraries were performed with oligo(dT)20 primer by 5′Rapid amplification of complementary DNA ends(5’RACE) . During the reverse transcription reaction , A common adaptor (SMART oligonucleotide) was ligated to  the 5’end of each cDNA . The TCR library is then prepared by touchdown PCR amplification using a set of primers: a forward primer to the adaptor and a reverse primer to the constant region of the TCR  . Touchdown PCR was performed under the conditions of 95°C for 3 min, followed by 15 cycles of 98 °C forc15 s, 65 °C(decrease 0.7°C/cycles) for 15 s and 72 °C for 1 min,  20 cycles of 98 °C for 15 s, 60 °C for 15 s and 72 °C for 1 min and one cycle 10 min at 72°C. PCR products, ranged from 300-700bp were gel purified by DNA Gel Purification Kit. Illumina paired end adapters were ligated to TCR libraries, followed by 2rd round PCR with Illumina P5/P7 adaptor primers under 30s at 95°C , 15s at 65 °C, 60s  at 72°C for 10-15 cycles , Plus a final extenaion for 10 min at 72°C. Ampure bead purified PCR product. Finally, the TCR libraries were sequenced on an Illumina HiseqXtenPE150 (2 × 150 nt).

value: thymus

value: 4-12 weeks


title: KO-Tcra-Rep2


title: KO-Tcra-Rep3


title: WT-Tcra-Rep3

value: wild type


title: ChIP_H3K27ac_control_1

description:
Input_5714_wt_2_5_CAACTA.fastq.gz
H3k27ac.Control.mean.bw


title: RNA-seq_LADC91

description: lung adenocarcinoma

data_processing:
RNASeq reads were adapter trimmed and data quality was assessed with the FastQC (version 0.11.7) software
Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using hisat2 software (v2.0.4).
The mapped reads were assembled into transcripts or genes by using StringTie software (v1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf).
For quantification purpose, the relative abundance of transcript/gene was measured by a normalized metrics, FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: GTF

source_name: LUAD

growth_protocol: Clinical LUAD tissue

treatment_protocol: Clinical LUAD tissue


title: WT-Tcra-Rep2


title: Input_5718_tko_5


title: RNA-seq_normal_lung17

description: paired normal for sample LADC_17

source_name: Clinical normal lung tissue


title: WT-Tcra-Rep1


title: KO-Tcrb-Rep3


title: RNA-seq_LADC90

description: lung adenocarcinoma


title: Input_5717_tko_4


title: KO-Tcrb-Rep1


title: KO-Tcrb-Rep2


title: RNA-seq_LADC89

description: lung adenocarcinoma


title: RNA-seq_LADC74

description: lung adenocarcinoma


title: Input_5618_tko_1


title: Input_5619_tko_2


title: WT-Tcrb-Rep2


title: WT-Tcrb-Rep1


title: RNA-seq_LADC73

description: lung adenocarcinoma


title: KO-Tcrg-Rep3


title: KO-Tcrg-Rep2


title: RNA-seq_LADC72

description: lung adenocarcinoma


title: ChIP_HNF4a_tko_3

description:
Input_5717_tko_4_5_CAGGCG.fastq.gz
HNF4a_in_tko.bw


title: RNA-seq_LADC71

description: lung adenocarcinoma


title: RNA-seq_LADC68

description: lung adenocarcinoma


title: WT-Tcrg-Rep2


title: WT-Tcrg-Rep1


title: ChIP_HNF4a_tko_2

description:
Input_5619_tko_2_5_CAAAAG.fastq.gz
HNF4a_in_tko.bw


title: KO-Tcrd-Rep3


title: WT-Tcrg-Rep3


title: KO-Tcrg-Rep1


title: ChIP_HNF4a_tko_1

description:
Input_5618_tko_1_4_ATGAGC.fastq.gz
HNF4a_in_tko.bw


title: RNA-seq_LADC67

description: lung adenocarcinoma


title: KO-Tcrd-Rep1


title: WT-Tcrd-Rep3


title: WT-Tcrb-Rep3


title: Input_5575_wt_4


title: RNA-seq_LADC66

description: lung adenocarcinoma


title: WT-Tcrd-Rep2


title: Input_5715_wt_3


title: WT-Tcrd-Rep1


title: ChIP_HNF4a_tko_4

description:
Input_5718_tko_5_5_CATGGC.fastq.gz
HNF4a_in_tko.bw


title: DNAme_P0_PSG_Nsd1_KO

city: Vancouver

first: Kenjiro

last: Shirane

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
PBAT_WGBS_P0_PSG_Nsd1_KO
WGBS Post-bisulfite adaptor tagging (PBAT)

data_processing:
ChIP-seq: Reads were aligned to the mouse genome (mm10) using bwa (Li and Durbin 2009). PCR duplicates were removed by Picard-tools (http://broadinstitute.github.io/picard) and remaining reads with low mapping quality (MAPQ < 5) were excluded by Samtools (http://www.htslib.org/). Smoothed bigWig files were generated by deeptools (Ramírez et al., 2014) with BINSIZE=100 and SMOOTHLENGTH=1000 options.
WGBS: Reads with adaptor sequences at the 5’-end or low-quality bases at the 3’-end were trimmed by Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and the remaining reads were then aligned to the mouse genome (mm10) using Bismark (Krueger and Andrews 2011) with bowtie2 and pbat options (Langmead and Salzberg 2012). Reads that were not aligned with paired-end mode were then separately mapped to mm10 using single-end mode. bismark_methylation_extractor was used for extracting methylated and unmethylated counts of each CpG.
RNA-seq: Reads were aligned to the mouse genome (mm10) and transcripts using STAR (Dobin et al., 2013) with --sjdbGTFfile and --twopassMode Basic options.
Aligned reads were converted to bigWig format using bedtools (Quinlan et al., 2010) and bedGraphToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: p0 prospermatogonia

extract_protocol:
Testes were isolated and incubated at 37℃ for 5-8 minutes in 0.25% trypsin/0.5 mM EDTA/DNaseⅠ/PBS with serial pipetting to obtain single cell suspensions. After quenching the reaction with fetal bovine serum (FBS), cells were washed once with FACS buffer (2% FBS/1 mM EDTA/PBS), stained with Propidium Iodide (PI) and passed through a 35 μm cell strainer (Falcon). FACS was carried out on a BD Influx. Following removal of doublet/triplet cells, OCT3/4-EGFP+ (PI-) cells were sorted.
Two to four thousand male germ cells spiked with 0.1 ng of lambda phage DNA (Promega) were incubated in cell lysis buffer (0.1% SDS, 1 mg/mL proteinase K, 0.1 mg/mL RNaseA) at 37℃ for 60 min followed by 98℃ for 15 min, as described previously (Shirane et al., 2013) and the lysates were subjected to bisulfite conversion by EZ DNA methylation gold kit (Zymo Research). The TACS-ligation conjugated post-bisulfite adaptor-tagging (PBAT) method (Miura et al., 2012 and 2019) was used for generating PBAT libraries.

tag: strain background

tag: developmental stage

value: postnatal day 0

tag: genotype/variation

value: Nsd1 KO

tag: molecule subtype

value: bisulfite converted genomic DNA


title: Input_5617_wt_1

tag: tissue


title: DNAme_P0_PSG_Nsd1_Control

description:
PBAT_WGBS_P0_PSG_Nsd1_HET
WGBS Post-bisulfite adaptor tagging (PBAT)

value: Nsd1 HET


title: Input_5714_wt_2


title: RNA-seq_LADC63

description: lung adenocarcinoma

tag: age


title: RNA-seq_LADC61

description: lung adenocarcinoma


title: RNA-seq_LADC60

description: lung adenocarcinoma


title: KO-Tcrd-Rep2

tag: strain


title: DNAme_E16.5_PSG_Nsd1_KO1

description:
PBAT_WGBS_E16.5_PSG_Nsd1_KO_1
WGBS Post-bisulfite adaptor tagging (PBAT)

source_name: e16.5 prospermatogonia

value: embryonic day 16.5


title: RNA-seq_LADC57

description: lung adenocarcinoma


title: DNAme_E16.5_PSG_Nsd1_KO2

description:
PBAT_WGBS_E16.5_PSG_Nsd1_KO_2
WGBS Post-bisulfite adaptor tagging (PBAT)


title: ChIP_HNF4a_control_3

description:
HNF4a_peaks_in_control.bed
Input_5715_wt_3_5_CACGAT.fastq.gz
HNF4a_in_control.bw


title: ChIP_HNF4a_control_4

description:
HNF4a_peaks_in_control.bed
Input_5575_wt_4_4_GTAGAG.fastq.gz
HNF4a_in_control.bw


title: RNA-seq_LADC56

description: lung adenocarcinoma


title: DNAme_E16.5_PSG_Nsd1_Control2

description:
PBAT_WGBS_E16.5_PSG_Nsd1_HET_2
WGBS Post-bisulfite adaptor tagging (PBAT)


title: ChIP_HNF4a_control_1

description:
HNF4a_peaks_in_control.bed
Bound_Input_5617_wt_1_GGTAGC.fastq.gz
HNF4a_in_control.bw


title: ChIP_HNF4a_control_2

description:
HNF4a_peaks_in_control.bed
Input_5714_wt_2_5_CAACTA.fastq.gz
HNF4a_in_control.bw


title: RNA_seq_HNF4a_null_4

description:
RPKM_matrix_of_all_samples.txt
HNF4a_vs_control_DE_sumary.txt

data_processing:
RNA-seq reads were mapped to the mouse genome (mm9) using Star version 2.5.2a with the flags: “--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif”. Samtools view version 1.1 was used to remove duplicate with the flag “-bhq 255”. Cufflinks v2.2.1 was used for gene expression quantification. We used the following flags:” -max-mle-iterations 500000 --max-bundle-frags 100000000”. The reads were mapped against Gencode vM1. Then we ran DESeq2 package on R in order to estimate differential expression significance. We kept only genes with higher expression of FPKM >1. Differentially expressed genes were defined as genes with adjusted p-value smaller than 0.01 and fold change greater than 1.5.
Genome_build: mm9
Supplementary_files_format_and_content: All FPKM values for all samples and statstics for comparison between specific groups

source_name: liver

extract_protocol: A maximum of 500,000 hepatocytes were homogenized in TRIzol Reagent (Thermo Fisher) and incubated at room temperature. Then, chloroform purification (Millipore Sigma C2432) was taking place following by ethanol precipitation. Later, RNA was purified using a RNeasy Mini Kit (Quiagen) and eluted with DDW. RNA was quantified using a NanoDrop-1000 (Thermo Fisher) and RNA quality was measured using a BioAnalyzer RNA Nano Chip (Aligent). Libraries were prepared using an Ultra RNA Library Prep Kit for Illumina (New England BioLabs) with 150 ng of input RNA.  Libraries were sequenced on the Illumina Hiseq 4000.

value: liver


title: RNA-seq_LADC55

description: lung adenocarcinoma


title: DNAme_P0_PSG_Setd2_KO

description:
PBAT_WGBS_P0_PSG_Setd2_KO
WGBS Post-bisulfite adaptor tagging (PBAT)

value: Setd2 KO


title: DNAme_E16.5_PSG_Nsd1_Control1

description:
PBAT_WGBS_E16.5_PSG_Nsd1_HET_1
WGBS Post-bisulfite adaptor tagging (PBAT)


title: RNA-seq_LADC54

description: lung adenocarcinoma


title: DNAme_P0_PSG_Setd2_Control

description:
PBAT_WGBS_P0_PSG_Setd2_HET
WGBS Post-bisulfite adaptor tagging (PBAT)

value: Setd2 HET


title: RNA_seq_HNF4a_null_3


title: RNA_seq_HNF4a_null_2


title: RNA-seq_LADC58

description: lung adenocarcinoma


title: RNA-seq_LADC53

description: lung adenocarcinoma


title: DNAme_E16.5_PSG_Setd2_KO

description:
PBAT_WGBS_E16.5_PSG_Setd2_KO
WGBS Post-bisulfite adaptor tagging (PBAT)


title: RNA_seq_HNF4a_null_1


title: DNAme_E16.5_PSG_Setd2_Control

description:
PBAT_WGBS_E16.5_PSG_Setd2_HET
WGBS Post-bisulfite adaptor tagging (PBAT)


title: RNA_seq_HNF4a_control_2


title: RNA_seq_HNF4a_control_1


title: RNA_seq_FoxA3_null_4

description:
RPKM_matrix_of_all_samples.txt
FoxA_triple_null_compared_with_FoxA3_null.txt

value: hepatocytes


title: RNA-seq_LADC50

description: lung adenocarcinoma


title: RNA-seq_LADC48

description: lung adenocarcinoma


title: RNA-seq_LADC49

description: lung adenocarcinoma


title: RNA_seq_FoxA3_null_3


title: RNA-seq_LADC52

description: lung adenocarcinoma


title: RNA-seq_LADC51

description: lung adenocarcinoma


title: RNA-seq_LADC47

description: lung adenocarcinoma


title: RNA_seq_FoxA3_null_2


title: non-carcinoma tissue,biological rep4 (miRNA)

city: haerbin

first: Ming

last: Liu

address: No. 246 xuefu road, nangang district

institute: The Second Affiliated Hospital, Harbin Medical University

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing: Use the free miRNA QC Tool software (Affymetrix) for data summarization, normalization, and quality control.

source_name: larynx adjacent non-carcinoma epithelial tissue

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

growth_protocol: The samples were acquired from patients diagnosed with laryngeal squamous cell carcinoma who underwent partial or total laryngectomy at the Department of Otorhinolaryngology, the Second Affiliated Hospital of Harbin Medical University.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The tissues were stored in liquid nitrogen within 10 minutes after surgical resection.

tag: disease state

value: laryngeal carcinoma

tag: tnm


title: RNA-seq_LADC46

description: lung adenocarcinoma

value: Lung


title: RNA_seq_FoxA3_null_1

tag: genotype


title: RNA-seq_LADC45

description: lung adenocarcinoma


title: non-carcinoma tissue,biological rep5 (miRNA)

value: larynx adjacent non-carcinoma epithelial tissue


title: non-carcinoma tissue,biological rep2 (miRNA)


title: non-carcinoma tissue,biological rep3 (miRNA)


title: RNA-seq_LADC44

description: lung adenocarcinoma


title: RNA_seq_FoxA1/A2_Cre_alfp_3

description:
RPKM_matrix_of_all_samples.txt
Comparison_FoxA_triple_null_vs_FoxA12crealfp_summary.txt


title: RNA_seq_FoxA1/A2_Cre_alfp_2


title: RNA-seq_LADC43

description: lung adenocarcinoma


title: laryngeal carcinoma tissue,biological rep4 (miRNA)

source_name: larynx cancer tissue

value: larynx cancer tissue


title: laryngeal carcinoma tissue,biological rep5 (miRNA)


title: laryngeal carcinoma tissue,biological rep3 (miRNA)


title: laryngeal carcinoma tissue,biological rep2 (miRNA)


title: RNA-seq_LADC42

description: lung adenocarcinoma


title: non-carcinoma tissue,biological rep1 (miRNA)


title: RNA_seq_FoxA1/A2_Cre_alfp_1


title: RNA_seq_FoxA1/A2_lox_3

description:
RPKM_matrix_of_all_samples.txt
Comparison_FoxA_triple_null_vs_control_no_deletion.txt


title: laryngeal carcinoma tissue,biological rep1 (miRNA)


title: RNA_seq_FoxA1/A2_lox_2


title: Spatial transcriptomics Cecal ligation puncture 1

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
The cDNA libraries were prepared and then sequenced on an Illumina NovaSeq 6000.
Using Seurat 3.1.4, we identified anchors between the integrated single cell object and the spatial transcriptomics datasets and used those to transfer the cluster data from the single cell to the spatial transcriptomics.
For each spatial transcriptomics spot, this transfer assigns a score to each single cell cluster. We selected the cluster with the highest score in each spot to represent its single cell associated cluster.
Using a Loupe Browser, expression data was visualized overlying the hematoxylin-eosin image.
Genome_build: mm10
Supplementary_files_format_and_content: csv, count matrix

source_name: Kidney

growth_protocol: wild type 129sv mouse grown to approximately 10 weeks old

extract_protocol:
The 129sv mouse was sacrificed 6 hours after cecal ligation puncture and tissue was placed in an OCT mold and stored at -80 C. A septic mouse kidney was immediately frozen in Optimal Cutting Temperature media (O.C.T.). A 10 ?m frozen tissue section was cut and affixed to a Visium Spatial Gene Expression library preparation slide (Catalogue # 1000200, 10X Genomics, Pleasanton, California, USA). The specimen was fixed in methanol and stained with hematoxylin-eosin reagents. Images of hematoxylin-eosin-labeled tissues were collected as mosaics of 10x fields using a Keyence BZ-X810 fluorescence microscope equipped with a Nikon 10X CFI Plan Fluor objective. The tissue was then permeabilized for 12 minutes and RNA was isolated.
Visium protocol (10x genomics)
Visium Library preparation (10x genomics)
The cDNA libraries were prepared and then sequenced on an Illumina NovaSeq 6000.

value: 10 weeks

value: cecal ligation puncture

value: Kidney


title: RNA-seq_LADC40

description: lung adenocarcinoma


title: 231 NAB

type: genomic

city: Lebanon

first: Meghan

middle: E.

last: Muse

state: NH

address: One Medical Center Drive, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Normalized using functional normalization (Fortin et. al. Genome Biology 2014)

label: Cy5 and Cy3

source_name: subject 231 contralateral-normal tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the manufacturer’s protocol for the BiOstic DNA FFPE Tissue Kit (MoBio)

tag: subject

tag: slide

tag: array

value: 52 years

tag: Sex

value: F

tag: parity

value: contralateral-normal


title: footprint GR Sample 8

city: San Francisco

last: Li

department: Biochemistry and Biophysics

institute: UCSF

description:
footprint GR
ribosome protected mRNA
protocol-2

data_processing:
Illumina Casava1.7 software used for basecalling.
The resulting sequences were aligned using the following method: the linker sequences at the 3’ends were removed prior to alignment.
The SOAP2.20 was used to align the sequence reads (allowing no more than 2 total mismatches)
Reads after linker removal were aligned against a library of S.cerevisiae rRNA and tRNA sequences. Reads with any alignment against rRNA and tRNA were eliminated from further analysis.
the none-rRNA and none-tRNA reads were aligned against the S.cerevisiae genomic sequences.
reads with no alignment against S.cerevisiae genomics sequences were re-aligned against the library of S.cerevisiae processed protein-coding transcripts.
Genome_build: Recent genome build(03/14/2012) from the Saccharomces Genome Database (SGD)

organism: Saccharomyces cerevisiae

source_name: GR

extract_protocol:
The RNA were extracted as described in Ingolia et al, 2011.
Deep-sequencing libraries were constructed as described in Ingolia et al, 2011.
RNA-seq and Ribosome Profiling

treatment_protocol: Cells were separated from the media by spin-down at 3000 g for 5 minutes and re-suspended in SD and GR media respectively. All samples were incubated for another hour before harvesting.

tag: medium

value: GR


title: RNA-seq_LADC39

description: lung adenocarcinoma


title: 290 NAB

source_name: subject 290 contralateral-normal tissue

value: 50 years


title: 290 Tumor

source_name: subject 290 tumor tissue

value: tumor


title: RNA-seq_LADC38

description: lung adenocarcinoma


title: RNA_seq_FoxA1/A2_Cre_alfp_4


title: 257 AB

source_name: subject 257 ipsilateral-normal tissue

value: 46 years

value: ipsilateral-normal


title: 308 Tumor

source_name: subject 308 tumor tissue

value: 32 years


title: footprint SD Sample 7

description:
footprint SD
ribosome protected mRNA
protocol-2

source_name: SD

value: SD


title: 308 NAB

source_name: subject 308 contralateral-normal tissue


title: 290 AB

source_name: subject 290 ipsilateral-normal tissue


title: 257 Tumor

source_name: subject 257 tumor tissue


title: 231 AB

source_name: subject 231 ipsilateral-normal tissue


title: 229 Tumor

source_name: subject 229 tumor tissue

value: 42 years


title: mRNA GR Sample 6

description:
mRNA GR
polyA+ mRNA
protocol-2


title: RNA-seq_LADC37

description: lung adenocarcinoma

source_name: LUAD

value: Lung


title: 251 NAB

source_name: subject 251 contralateral-normal tissue

value: 49 years


title: RNA_seq_FoxA_triple_null_4

description:
RPKM_matrix_of_all_samples.txt
Comparison_FoxA_triple_null_vs_control_no_deletion.txt
Comparison_FoxA_triple_null_vs_FoxA12crealfp_summary.txt
Copmparison_Hepatobalst_to_adult_FoxA_triple_null_DE_summary.txt

source_name: hepatocytes

value: hepatocytes


title: RNA_seq_FoxA_triple_null_3


title: 251 AB

source_name: subject 251 ipsilateral-normal tissue


title: 251 Tumor

source_name: subject 251 tumor tissue


title: 257 NAB

source_name: subject 257 contralateral-normal tissue


title: footprint GR Sample 4-2

description:
footprint GR
ribosome protected mRNA
protocol-1

source_name: GR


title: RNA-seq_LADC34

description: lung adenocarcinoma


title: 229 NAB

source_name: subject 229 contralateral-normal tissue


title: RNA_seq_FoxA1/A2_lox_1


title: 229 AB

source_name: subject 229 ipsilateral-normal tissue


title: RNA_seq_FoxA_triple_null_1


title: footprint GR Sample 4-1


title: RNA-seq_LADC35

description: lung adenocarcinoma


title: RNA-seq_LADC33

description: lung adenocarcinoma


title: RNA-seq_LADC41

description: lung adenocarcinoma


title: footprint SD Sample 3-2

description:
footprint SD
ribosome protected mRNA
protocol-1


title: RNA-seq_LADC30

description: lung adenocarcinoma


title: mRNA SD Sample 5

description:
mRNA SD
polyA+ mRNA
protocol-2


title: Heart at 7 days after AR, biological rep2

city: Chongqing

first: Chunyu

last: Zeng

state: Chongqing

address: 10 Changjiangzhilu Road

institute: Third Military Medical University

description: Gene expression data from ventricle prepared by removing scar of AR heart 7 days after surgery

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Ventricular sample prepared by removing scar of AR heart 7 days after surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After completing surgeries for all pups in a litter, mix the pups with the mother's bedding and excrement before returning them to the mother's nest for nursing.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: To induce apex resection model, surgery was performed on neonatal mice according to previous published procedures. Briefly, pups were placed on an ice bed to achieve hypothermia anesthesia, and thoracotomy was carried out along the fourth intercostal area. Then apex was exteriorized by gentle pressure on the abdomen, and approximately 15% resection of the left ventricle was carefully applied without endocardium damage. For sham-operated control neonates, the surgical procedure of resection was excluded.

value: Ventricle


title: Heart at 7 days after AR, biological rep3


title: KII040419

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

data_processing:
Initial data processing was performed using the Cell Ranger version 2.0 pipeline (10X Genomics)
Loupe Browser files for mouse datasets were generated using aggregate function in Cell Ranger pipeline with normalization on mapped reads and can be viewed using Single Cell Browser (10x Genomics)
Post-processing, including filtering by number of genes expressed per cell, was performed using the Seurat package V2.3.4 and R 3.5.3.
Following clustering and visualization with t-Distributed Stochastic Neighbor Embedding (t-SNE).
Identification of cell clusters was performed on the final aligned object guided by marker genes.
Genome_build: mm10
Supplementary_files_format_and_content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

source_name: lung

extract_protocol:
Lungs were perfused with PBS to remove the blood and minced with scissors, followed by incubation with pre-warmed collagenase solution (2 mg/ml in PBS with Ca2+/Mg2+ ) for 1 hour at 370C with mild agitation. The resulting single cell suspension was filtered through a 40 µm nylon cell strainer, and erythrocytes were lysed using a lysing buffer. Cells were resuspended in cold 0.1% BSA/PBS. Following live/dead staining with viability dye, cells were incubated with a Fc-blocking reagent for 5 minutes at 4oC and an anti-CD45.2 mAb-PE-Cy7 antibody for 1 hour at 4oC. Cells were then sorted using a 100 μm nozzle and 40 psi pressure
Single-cell 3’ RNA-seq libraries were prepared using Chromium Single Cell V3 Reagent Kit and Controller (10X Genomics)

value: lung

tag: disease

value: acute lung injury


title: 308 AB

source_name: subject 308 ipsilateral-normal tissue


title: 156 AB

source_name: subject 156 ipsilateral-normal tissue

value: 61.3 years


title: RNA-seq_LADC29

description: lung adenocarcinoma

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: Heart at 7 days after AR, biological rep1


title: WTI040419

value: wild type


title: 156 NAB

source_name: subject 156 contralateral-normal tissue

value: F

value: contralateral-normal


title: non-carcinoma tissue,biological rep5 (circRNA)

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(G2565CA)

data_processing:
Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by quantile normalization.
normalized_data.txt reports log2 quantile-normalized signal

source_name: larynx adjacent non-carcinoma epithelial tissue

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: Total RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.

value: laryngeal carcinoma


title: mRNA GR Sample 2

description:
mRNA GR
polyA+ mRNA
protocol-1

value: GR


title: footprint SD Sample 3-1

source_name: SD


title: Heart LncRNA-DRR-KO rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 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 standard Illumina protocols

treatment_protocol: To induce MI model, 8-weeks-old mice were subjected to permanent ligation of the left anterior descending (LAD) coronary artery. Briefly, under anesthesia by 2% isoflurane inhalation, LAD ligation was sutured with 7-0 silk at 2-3mm distal to the left atrial appendage. Sham-operated animals were subjected to the same procedures but without tied suture under LAD.

value: myocardial infarction

value: 10 weeks old

value: lncRNA-DRR-/-


title: RNA-seq_LADC28

description: lung adenocarcinoma

source_name: LUAD


title: 156 Tumor

source_name: subject 156 tumor tissue

value: tumor


title: non-carcinoma tissue,biological rep4 (circRNA)

value: larynx adjacent non-carcinoma epithelial tissue


title: 141 Tumor

source_name: subject 141 tumor tissue

value: 66.8 years


title: Heart at 7 days after sham, biological rep2

description: Gene expression data from ventricle prepared by removing apex of sham heart 7 days after surgery

source_name: Ventricular sample prepared by removing apex of sham heart 7 days after surgery


title: Heart LncRNA-DRR-KO rep2


title: RNA-seq_LADC27

description: lung adenocarcinoma

value: Lung


title: non-carcinoma tissue,biological rep3 (circRNA)


title: RNA-seq_LADC26

description: lung adenocarcinoma


title: non-carcinoma tissue,biological rep2 (circRNA)


title: mRNA SD Sample 1

description:
mRNA SD
polyA+ mRNA
protocol-1

value: SD


title: 141 NAB

source_name: subject 141 contralateral-normal tissue


title: Heart at 7 days after sham, biological rep1

value: Ventricle


title: Heart at 7 days after sham, biological rep3


title: non-carcinoma tissue,biological rep1 (circRNA)


title: RNA-seq_LADC25

description: lung adenocarcinoma


title: Heart LncRNA-DRR-KO rep1


title: carcinoma tissue,biological rep5 (circRNA)

source_name: larynx cancer tissue

value: larynx cancer tissue


title: RNA_seq_FoxA_triple_null_2

source_name: hepatocytes

value: hepatocytes


title: Heart WT rep2


title: RNA-seq_LADC24

description: lung adenocarcinoma


title: carcinoma tissue,biological rep4 (circRNA)


title: Heart WT rep1


title: RNA-seq_LADC23

description: lung adenocarcinoma


title: Heart WT rep3


title: RNA-seq_LADC22

description: lung adenocarcinoma


title: RNA-seq from dmazEF+pF strain

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
nEMOTE reads were processed with the R package EMOTE v0.2 (https://github.com/pradosj/EMOTE). The package check the reads and parse them to extract the mapping sequence as well as the UMI sequence; it then aligns the reads on the genome (with Rbowtie package) and quantify the number of read with unique UMI starting at each genomic position.
The genomic positions with less than 4 UMI in ΔmazEF pRAB11-mazF-1_+PNK or ΔmazEF pRAB11-mazF-2_+PNK were not further considered
A beta-binomial model is used to estimate the probability that +PNK condition is significantly enriched compared to the corresponding -PNK condition. The p-values obtained for the 2 replicates are combined with Fisher's method, and the FDR computed to correct for multiple testing.
To determine confident 5’-OH ends generated by MazF, each genomic position had to match the following criteria:  an FDR < 0.1 for ΔmazEF pRAB11-mazF condition, and an FDR > 0.1 in ΔmazEF condition
Genomic position falling into a rRNA feature are processed separately
Remaining mazF cleavages are further annotated with genomic informations (DNA sequence arround the position, nearest gene)
RNA-seq reads are aligned on the reference genome with "bwa mem" command and "samtools" to generate files in BAM format. The BAM files are further processed to quantify the number of read in genes with the method "summarizeOverlaps(mode='IntersectionStrict',inter.feature=FALSE)" from R package GenomicAlignments. Quantification arround the cleavage sites are obtained with the method "coverage()" of the R package "GenomicAlignments"
Genome_build: NC_007795.1

organism: Staphylococcus aureus

source_name: bacterial cell

growth_protocol: S. aureus HG003 and S. aureus HG003 ΔmazEF were electroporated with anhydrotetracycline (ATc) inducible pRAB11 and pRAB11-mazF constructed vector. Strains carrying the pRAB11 vector were always grown in presence of chloramphenicol (15 µg/mL). Overnight cultures were diluted 1/1000 in 10 mL of Mueller-Hinton broth (cation adjusted, Difco) and incubated at 37ºC with shaking. At OD600 0.3, ATc was added to a final concentration of 0.2 µM. At each time point (0, 15, 30, 60 minutes postinduction) the samples were subject to 10-fold serial dilutions in 96-well plates using saline solution (0.9% NaCl), 10 µL aliquots were spotted in Mueller-Hinton (Difco) agar plates and incubated at 37ºC overnight. Colonies were then counted.

extract_protocol:
Overnight cultures were diluted 1/50 in 20 mL of Mueller-Hinton broth and incubated at 37ºC without shaking until OD600 0.3. ATc was added to a final concentration of 0.2 µM and incubated at 37ºC during 10 min. 8 mL of bacterial culture were immediately transferred to 40 mL of ice-cold ethanol:acetone (1:1), and centrifugated at 5000 rpm and 4ºC during 10 min. The supernatant was discarded, and pellet was washed with 1X TE. The pelleted cells were treated with lysostaphin (200 µg/mL) and RNasin Plus (Promega) in a final volume of 100 µL then placed in a heat block at 37ºC during 10 min. RNA extractions were done on the same day using the ReliaPrep (Promega) following the manufacturer’s instructions. Total RNA was frozen and kept at -80ºC.
TruSeq mRNA stranded kit + bacterial Ribo-Zero RNA removal kit

value: dmazEF


title: 137 Tumor

source_name: subject 137 tumor tissue

value: 47.8 years


title: carcinoma tissue,biological rep3 (circRNA)


title: RNA-seq_LADC20

city: Shanghai

last: Zhai

institute: Shanghai Institute of Materia Medica

description: lung adenocarcinoma


title: RNA-seq from dmazEF strain


title: 5-FU resistant gastric cancer organoid biological rep 3

city: hiroshima

first: Shoichi

last: Ukai

address: minami-ku kasumi 1-2-3

country: Japan

institute: Hiroshima University

description:
GCO3/5-FUR_181115_(Clariom_D_Human).CEL
5-FU resistant gastric cancer

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on Clariom D Array, Human. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) ver.4.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: 5-FU resistant gastric cancer organoid

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.3 ug total RNA.

growth_protocol: The organoids are cultured in frequently used medium. The medium was changed every 2‐3 days. The organoids were split at a ratio of 1:3 every 7‐8 days.

treatment_protocol: The organoids are collected using PBS and immediately frozen.

value: 5-FU resistant gastric cancer organoid

value: female


title: 5-FU resistant gastric cancer organoid biological rep 2

description:
GCO2/5-FUR_181115_(Clariom_D_Human).CEL
5-FU resistant gastric cancer

value: male


title: carcinoma tissue,biological rep2 (circRNA)

value: laryngeal carcinoma


title: carcinoma tissue,biological rep1 (circRNA)


title: 137 NAB

source_name: subject 137 contralateral-normal tissue

value: F

value: contralateral-normal


title: RNA-seq_LADC18

first: Linhu

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong, Shanghai

description: lung adenocarcinoma


title: RNA-seq_LADC19

description: lung adenocarcinoma


title: Antibody Oligo Capture Library of 6 Calcitonin-Treated and Control ACFs

city: Oxford

first: Svetlana

last: Reilly

state: Oxfordshire

address: JOhn Radcliffe Hospita, Headley Way

department: Cardiovascular Medicine, Radcliffe Dept of Medicine

institute: University of Oxford

description:
Hashtag HTO
feature_barcode_sheet.csv
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz

data_processing:
Hashtag RNA:  Read 1 contains cell barcode, followed by UMI. Read 2 contains cellular cDNA
Hashtag HTO:  Read 1 contains cell barcode, followed by UMI. Read 2 contains antibody oligo tag. Oligo sequences for each antibody tag are contained in Cellranger-ready format "feature_barcode_sheet.csv".
Raw data were processed using cellranger pipeline, version 3.1.0
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger raw UMI counts matrices (RNA and matching HTO) and sample annotation for hashing antibodies:
feature_barcode_sheet.csv (Hashing antibody information, in Cellranger pipeline format.)
barcodes.tsv.gz (Cellranger raw matrix cell barcodes)
matrix.mtx.gz (Cellranger raw matrix UMI counts)
features.tsv.gz (Cellranger raw matrix features)

source_name: cardiac right atria

growth_protocol: Cells were cultured in FBM-3 media (#CC-3131, Lonza, USA) containing 10% FBS and a supplement pack (#CC-4525, Lonza, USA)

extract_protocol:
10x droplet capture
The sample exome library was processed to a sequence ready library using the V3 3’ Prime Gene Expression kit as per manufacturer’s protocol. The hashing library was processed as per the hashing method Version: 2019-02-13 New York Genome Center Technology Innovation Lab (www.CITE-SEQ.com).
3' capture, paired end 10x feature barcoding

treatment_protocol: Cells were initially cultured in FBM-3 media (#CC-3131, Lonza, USA) containing 10% FBS and a supplement pack (#CC-4525, Lonza, USA); then starved for ~16 hours  and treated with CT in serum-free media for 24 hours.

tag: cell type

value: primary atrial fibroblasts

tag: cell culture

value: Yes

tag: passages

tag: treatment

value: mixed sample (non-demultiplexed) of Calcitonin-Treated and Control treatments

tag: antibodies

value: BioLegend TotalSeq-A


title: Gene Expression Library of 6 Calcitonin-Treated and Control ACFs

description:
Hashtag RNA
feature_barcode_sheet.csv
barcodes.tsv.gz
matrix.mtx.gz
features.tsv.gz


title: E18brain (951 cells) [Nanopore]

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Cells from a combined cortex, hippocampus and sub ventricular zone of an E18 mouse.
PolyA RNA

data_processing:
10x Genomics cellranger v2.0 possorted_genome bam files. The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Processing of Nanopore reads is described at https://github.com/ucagenomix/Sicelore
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx: Cellranger v2.0 filtered gene barcodes matrices.
Supplementary_files_format_and_content: *.isoforms.matrix.txt: Gene/cell barcode matrices of UMIs count as the isoform level.

source_name: E18 brain

extract_protocol:
Samples were processed on the 10x Genomics Chromium system following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry).
Single cell RNA-Seq libraries were made following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry). Libraries were sequenced as follows: 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 57bp Read 2 (transcript), and 8bp i7 library barcode. For Nanopore sequencing cDNA was re-amplified, sequencing libraries were prepared with the Oxford Nanopore LSK-109 library preparation kit.

tag: tissue

value: Cortex, hippocampus and sub ventricular zone

tag: developmental stage


title: RNA-seq_LADC17

description: lung adenocarcinoma

value: Lung

tag: age


title: OmniATAC MM099 untreated

city: Leuven

first: k

last: spanier

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
The 10x samples were processed (alignment, barcode assignment and UMI counting) with the CellRanger count pipeline; pools with samples from different cell lines were demultiplexed using demuxlet (Kang et al. 2018); cells expressing less than 1000 genes and cells with more than 20% mitochondrial reads were removed
The Drop-seq samples were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011) and processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools pipeline (v1.12) developed by James Nemesh from the McCarroll lab (Macosko et al. 2015), using Picard tools (v1.140; Broad Institute) and the STAR aligner (v2.5.1b; Dobin 2013); cells expressing less than 1000 genes, more than 50000 and/or more than 10% mitochondrial reads were removed.
bulk RNA-Seq reads were cleaned with fastq-mcf from the ea-utils package (v1.04.807; Aronesty 2011), mapped using STAR (v2.5.1b; Dobin 2013) and counted with HTSeq (v0.6.1p1; Anders 2014); normalized count matrices were made with DESeq2 (v1.18.1; Love et al. 2014)
Omni-ATAC-Seq raw reads were mapped using Bowtie (v2.2.6; Langmead and Salzberg 2012); Duplicate reads were removed with Picard (v1.134; Broad Institute 2019) and low quality reads were removed with SAMtools (Q30) (v1.8; Li et al. 2009). bigWig files were created with deepTools (Ramírez et al. 2016).
Genome_build: hg19

source_name: melanoma cell line

extract_protocol: Not Provided

treatment_protocol: The MM lines were cultured in Ham's F10 nutrient mix (ThermoFisher Scientific) supplemented with 10% fetal bovine serum (Invitrogen) and 100 µg ml-1 penicillin/streptomycin (ThermoFisher Scientific). The A375 cell line was maintained in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Invitrogen) and penicillin-streptomycin (ThermoFisher Scientific). Cell cultures were kept at 37°C, with 5% CO2 and were regularly tested for mycoplasma contamination, and were found negative. Knockdown of SOX10 was performed using a SMARTpool of four siRNAs (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00, Dharmacon) at a final concentration of 20nM in Opti-MEM medium (Thermo Fisher Scientific) after which cells were sampled at the indicated time points. To control for transfection artefacts, we used a pool of non-targeting siRNAs (SMARTpool: ON-TARGETplus Non-targeting Pool, number D001810-10-05, Dharmacon). Inhibition of CDK7-dependent transcription was achieved by treatment with THZ2 (HY-12280, MedChemExpress). For each treated melanoma culture, IC50 concentrations were calculated for 48 hours of treatment. As a control, DMSO treatment was used. For bulk RNA-seq, RNA was extracted from attached cells using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions. For scRNA-seq and Omni-ATAC-seq, cells were detached by trypsinization, counted and processed according to downstream protocols.

value: melanoma cell line

tag: cell line

value: no treatment

tag: sequencing method

value: Omni-ATAC-Seq


title: E18brain (190 cells) [Nanopore]

tag: strain


title: 141 AB

source_name: subject 141 ipsilateral-normal tissue

tag: subject

tag: slide

value: 66.8 years

value: ipsilateral-normal


title: 5-FU resistant gastric cancer organoid biological rep 1

description:
GCO1/5-FUR_181115_(Clariom_D_Human).CEL
5-FU resistant gastric cancer

value: 5-FU resistant gastric cancer organoid

tag: Sex


title: Parental gastric cancer organoid biological rep 1

description:
GCO1_181115_(Clariom_D_Human).CEL
Gastric cancer

source_name: parental gastric cancer organoid

value: Gastric cancer organoid

value: female


title: Parental gastric cancer organoid biological rep 3

description:
GCO3_181115_(Clariom_D_Human).CEL
Gastric cancer


title: Sodium_hypochlorite_Rifampicin_3

status: Public on Jul 09 2020

city: Davis

first: Ilias

last: Tagkopoulos

state: California

address: 1 Shields Ave, Davis, CA 95616

institute: University of California, Davis

description: The name of each file starts with the name of a biocide and followed by an antibiotic.

data_processing:
Trimmomatic was used to remove the adapters and low quality reads.
Bowtie2 was used to align the reads to the reference genome, U0000963.
FeatureCount was used to count the reads mapped to each gene.
EdgeR and DeSeq2 were used to detect differential expressed genes.
Supplementary_files_format_and_content: A processed data file has 7 columns with a one-line header.

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: Escherichia coli MG1655 was grown in minimal media (M9) with 0.4% w/v glucose  at 37°C in a plate reader (BioTeK HT).

extract_protocol:
Total RNA was extracted from the bacterial samples using the RNeasy mini kit (Qiagen), and any possible DNA contamination was removed by performing on-column DNAse digestion (Qiagen).
mRNA was enriched by removing ribosomal RNA using the capture oligonucleotide mix (MICROBExpress, Ambion). RNA-Seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina platforms (Kapa Biosystems), and instructions suggested by the manufacturer were followed. Double size selection of libraries was performed using Agencourt AMPure XP magnetic beads (Beckman Coulter), where cDNA fragments ranging from 200-500 bp were enriched.
The DNA concentration of the final pooled library was determined with Bioanalyzer DNA high sensitivity assay (Agilent, DNA Technologies Core, UC Davis). Sequencing was performed with HiSeq4000 SR50 (DNA Technologies Core, UC Davis).

treatment_protocol: Escherichia coli MG1655 was grown in minimal media (M9) with 0.4% w/v glucose for 12 h (mid to late exponential growth, OD~0.8) at 37°C. Next, 30 µL were added to 3 mL M9 0.4% glucose tubes containing one of ten biocides or no biocide. The concentrations used were sub-inhibitory. After 7 to 12h growth, when cells reached mid to late exponential phase (OD600 0.6-1.0), the appropriate volume of one out of four antibiotics was added, and the tubes were incubated for an additional hour. Tubes without any antimicrobial (antibiotic or biocide) served as controls. To stop growth, cold 5% (v/v) phenol:ethanol was added to each tube (1.5 mL per 3 mL sample). The cells were pelleted by centrifugation at 4000 rpm at 4°C for 10 min and stored at -80°C until further use. All experiments were performed in triplicate


title: Parental gastric cancer organoid biological rep 2

description:
GCO2_181115_(Clariom_D_Human).CEL
Gastric cancer

value: male


title: Normal gastric organoid biological rep 4

source_name: normal gastric organoid

value: Normal gastric organoid


title: Sodium_hypochlorite_Rifampicin_2


title: Sodium_hypochlorite_Rifampicin_1


title: Normal gastric organoid biological rep 2


title: Sodium_hypochlorite_Norfloxacin_1


title: Sodium_hypochlorite_Norfloxacin_3


title: Sodium_hypochlorite_Norfloxacin_2


title: Sodium_hypochlorite_Kanamycin_2


title: Sodium_hypochlorite_Ampicillin_3


title: Rifampicin_2


title: Sodium_hypochlorite_Kanamycin_3


title: Sodium_hypochlorite_Ampicillin_2


title: Sodium_hypochlorite_Ampicillin_1


title: Povidone_iodine_Rifampicin_3


title: Povidone_iodine_Norfloxacin_3


title: Povidone_iodine_Rifampicin_2


title: Sodium_hypochlorite_Kanamycin_1


title: Rifampicin_3


title: Povidone_iodine_Rifampicin_1


title: Rifampicin_1


title: Povidone_iodine_Norfloxacin_1


title: Povidone_iodine_Kanamycin_3


title: Povidone_iodine_Norfloxacin_2


title: Normal gastric organoid biological rep 1


title: Normal gastric organoid biological rep 3


title: Povidone_iodine_Kanamycin_2


title: Povidone_iodine_Ampicillin_1


title: Povidone_iodine_Ampicillin_3


title: Povidone_iodine_Ampicillin_2


title: Povidone_iodine_Kanamycin_1


title: Phenol_Rifampicin_2


title: Phenol_Rifampicin_3


title: Phenol_Rifampicin_1


title: Phenol_Norfloxacin_3


title: Phenol_Norfloxacin_2


title: Phenol_Norfloxacin_1


title: Phenol_Ampicillin_2


title: Phenol_Ampicillin_1


title: Phenol_Kanamycin_2


title: Phenol_Kanamycin_3


title: Phenol_Ampicillin_3


title: Percetic_acid_Rifampicin_3


title: Percetic_acid_Rifampicin_2


title: Percetic_acid_Rifampicin_1


title: Percetic_acid_Norfloxacin_1


title: Percetic_acid_Norfloxacin_3


title: Percetic_acid_Norfloxacin_2


title: Percetic_acid_Kanamycin_2


title: Percetic_acid_Ampicillin_2


title: Percetic_acid_Ampicillin_1


title: Percetic_acid_Ampicillin_3


title: Percetic_acid_Kanamycin_1


title: Norfloxacin_3


title: Norfloxacin_2


title: Phenol_Kanamycin_1


title: Kanamycin_3


title: Isopropanol_Rifampicin_2


title: Kanamycin_1


title: Isopropanol_Rifampicin_3


title: Isopropanol_Rifampicin_1


title: Percetic_acid_Kanamycin_3


title: Isopropanol_Norfloxacin_3


title: Isopropanol_Norfloxacin_1


title: Isopropanol_Norfloxacin_2


title: Isopropanol_Ampicillin_1


title: Isopropanol_Ampicillin_2


title: Isopropanol_Ampicillin_3


title: H2O2_Rifampicin_2


title: H2O2_Rifampicin_3


title: Isopropanol_Kanamycin_1


title: Isopropanol_Kanamycin_3


title: H2O2_Norfloxacin_1


title: Isopropanol_Kanamycin_2


title: H2O2_Norfloxacin_2


title: H2O2_Norfloxacin_3


title: H2O2_Rifampicin_1


title: Norfloxacin_1


title: H2O2_Kanamycin_2


title: H2O2_Kanamycin_1


title: H2O2_Ampicillin_1


title: H2O2_Ampicillin_2


title: H2O2_Ampicillin_3


title: Kanamycin_2


title: H2O2_Kanamycin_3


title: Glutaraldehyde_Rifampicin_3


title: Glutaraldehyde_Rifampicin_1


title: Glutaraldehyde_Norfloxacin_3


title: Glutaraldehyde_Norfloxacin_1


title: Glutaraldehyde_Norfloxacin_2


title: Glutaraldehyde_Kanamycin_3


title: Glutaraldehyde_Kanamycin_2


title: Glutaraldehyde_Rifampicin_2


title: Ethanol_Rifampicin_2


title: Ethanol_Rifampicin_1


title: Ethanol_Rifampicin_3


title: Ethanol_Norfloxacin_3


title: Glutaraldehyde_Ampicillin_2


title: Ethanol_Ampicillin_3


title: Ethanol_Kanamycin_1


title: Glutaraldehyde_Ampicillin_3


title: Ethanol_Norfloxacin_1


title: Glutaraldehyde_Kanamycin_1


title: Ethanol_Kanamycin_3


title: Ethanol_Kanamycin_2


title: Ethanol_Ampicillin_2


title: Ethanol_Ampicillin_1


title: Control_2


title: Chlorexidine_Rifampicin_2


title: Control_1


title: Chlorexidine_Rifampicin_1


title: Chlorexidine_Rifampicin_3


title: Chlorexidine_Norfloxacin_3


title: Chlorexidine_Norfloxacin_2


title: Chlorexidine_Norfloxacin_1


title: Chlorexidine_Kanamycin_3


title: Glutaraldehyde_Ampicillin_1


title: Ethanol_Norfloxacin_2


title: Chlorexidine_Kanamycin_1


title: Chlorexidine_Kanamycin_2


title: Chlorexidine_Ampicillin_2


title: Bezalkonium_chloride_Norfloxacin_2


title: Bezalkonium_chloride_Rifampicin_3


title: Chlorexidine_Ampicillin_1


title: Control_3


title: Bezalkonium_chloride_Norfloxacin_1


title: Bezalkonium_chloride_Norfloxacin_3


title: Bezalkonium_chloride_Ampicillin_3


title: Bezalkonium_chloride_Kanamycin_2


title: Bezalkonium_chloride_Kanamycin_3


title: Bezalkonium_chloride_Kanamycin_1


title: Bezalkonium_chloride_Ampicillin_1


title: Ampicillin_3


title: Ampicillin_1


title: Ampicillin_2


title: Thymus_Rep1_RNA

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

institute: APHP

data_processing:
The ABI SOLiD system was used to produce sequence files in colour space formats.
For quality filtering, sequencing reads were trimmed for low quality (less than 20) using in house Perl script.
The quality control statistics for the reads before and after trimming were obtained using FastQC.
The trimmed reads were aligned to the human genome version Hg19 using Tophat2 with the -C option for the colour space.
The reads aligned to unique chromosomal positions were retained.
The total numbers of reads that overlap with the transcripts or genes (exonic region only) were obtained using the Cuffdiff function from Cufflinks
Normalization and differential expression were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Log2 transformed counts of genes and their informations according to differential analysis.

source_name: thymus

growth_protocol: Human thymic subpopulations were sorted using FACS ARIA III

extract_protocol:
RNA from sorted thymic subpopulations was harvested using Trizol reagent.
Paired-end stranded RNA-seq was performed with ribodepleted Total RNA using ABI SOLiD platform version 4

value: thymus


title: Thymus_Rep2_RNA


title: Chlorexidine_Ampicillin_3


title: Thymus_Rep3_RNA


title: SP8_RNA

source_name: Single positive CD8+ thymic subpopulation


title: LC_RNA

source_name: Late cortical thymic subpopulation


title: EC_RNA

source_name: Early cortical thymic subpopulation


title: ISP_RNA

source_name: ISP thymic subpopulation


title: CD34+_RNA

source_name: CD34+ thymic subpopulation


title: SP4_RNA

source_name: Single positive CD4+ thymic subpopulation


title: Bezalkonium_chloride_Rifampicin_1


title: Bezalkonium_chloride_Rifampicin_2


title: Bezalkonium_chloride_Ampicillin_2


title: s506f

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstr. 74

institute: Institut für Klinische Chemie und Laboratoriumsmedizin

data_processing:
Illumina Casava1.7 software used for basecalling
kallisto" was used to quantify TPM of genes using the following command line parameters "quant --single -l 75 -s 5 -i transcriptome.idx  -b 100
Genome_build: mm10
Supplementary_files_format_and_content: Per Sample Zipped Folders containing text, h5 and json files for the read quantification from kallisto

source_name: Adrenal Glands

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Female

value: Adrenal Glands

value: 8-16 weeks

tag: genotype


title: s559m

value: Male


title: MWCNT_D07_0.5mg/kg MWCNT

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Rat lung, Day07, 0.5mg/kg MWCNT, replicate 4

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Rat Genome Microarray (G4131F; Agilent Technologies) at 65 °C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent, G2505C) at 5 μm resolution.

data_processing: The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.

organism: Rattus norvegicus

source_name: 7 day post-instillation in 0.5mg/kg MWCNT-exposed rat lung

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Seven-week-old male Sprague-Dawley (Crl:CD[SD]) rats were purchased from Charles River Laboratories Japan (Yokohama, Japan). Rats were housed in metal cages with in a room with 35%– 70% humidity and a controlled temperature of 20°C–26°C and fed a chow diet ad libitum. All procedures and animal handling were approved by the Institutional Animal Care and Use Committee of the National Institute of Advanced Industrial Science (Tsukuba, Japan) and Technology and the BioSafety Research Center Inc. (Iwata, Japan)..

extract_protocol: Blood-perfused rat right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 0.5, 1.0 and 2.0 mg/mL of CNF (CNF1, CNF2, and CNF3) and MWCNT suspensions were prepared with distilled water with preservatives as each vehicle control. Each rat received a single intratracheal instillation dose (1 mg/kg) of the CNFs, MWCNT, and vehicles. Rats were dissected at 1, 3, 7, 30, and 90 days post-instillation. Lungs were perfused with physiological saline, excised, and used for whole genome microarray analysis.

value: Sprague-Dawley (Crl:CD[SD])

value: 0.5mg/kg MWCNT

tag: time

value: lung


title: MWCNT_D30_Control for MWCNT

description: Rat lung, Day30, Control for MWCNT, replicate 4

source_name: 30 day post-instillation in rat lung as cotrol for MWCNT

value: Control for MWCNT


title: MWCNT_D90_1.0mg/kg MWCNT

description: Rat lung, Day90, 1.0mg/kg MWCNT, replicate 4

source_name: 90 day post-instillation in 1.0mg/kg MWCNT-exposed rat lung

value: 1.0mg/kg MWCNT


title: MWCNT_D07_2.0mg/kg MWCNT

description: Rat lung, Day07, 2.0mg/kg MWCNT, replicate 4

source_name: 7 day post-instillation in 2.0mg/kg MWCNT-exposed rat lung

value: 2.0mg/kg MWCNT


title: CNF3_D90_0.5mg/kg CNF3

description: Rat lung, Day90, 0.5mg/kg CNF3, replicate 4

source_name: 90 day post-instillation in 0.5mg/kg CNF3-exposed rat lung

value: 0.5mg/kg CNF3


title: MWCNT_D01_2.0mg/kg MWCNT

description: Rat lung, Day01, 2.0mg/kg MWCNT, replicate 4

source_name: 1 day post-instillation in 2.0mg/kg MWCNT-exposed rat lung


title: CNF3_D90_Control for CNF3

description: Rat lung, Day90, Control for CNF3, replicate 4

source_name: 90 day post-instillation in rat lung as cotrol for CNF3

value: Control for CNF3


title: MWCNT_D03_1.0mg/kg MWCNT

description: Rat lung, Day03, 1.0mg/kg MWCNT, replicate 3

source_name: 3 day post-instillation in 1.0mg/kg MWCNT-exposed rat lung


title: MWCNT_D07_Control for MWCNT

description: Rat lung, Day07, Control for MWCNT, replicate 4

source_name: 7 day post-instillation in rat lung as cotrol for MWCNT


title: MWCNT_D30_1.0mg/kg MWCNT

description: Rat lung, Day30, 1.0mg/kg MWCNT, replicate 4

source_name: 30 day post-instillation in 1.0mg/kg MWCNT-exposed rat lung


title: MWCNT_D90_2.0mg/kg MWCNT

description: Rat lung, Day90, 2.0mg/kg MWCNT, replicate 4

source_name: 90 day post-instillation in 2.0mg/kg MWCNT-exposed rat lung


title: MWCNT_D90_Control for MWCNT

description: Rat lung, Day90, Control for MWCNT, replicate 4

source_name: 90 day post-instillation in rat lung as cotrol for MWCNT


title: MWCNT_D30_2.0mg/kg MWCNT

description: Rat lung, Day30, 2.0mg/kg MWCNT, replicate 4

source_name: 30 day post-instillation in 2.0mg/kg MWCNT-exposed rat lung


title: CNF3_D30_1.0mg/kg CNF3

description: Rat lung, Day30, 1.0mg/kg CNF3, replicate 4

source_name: 30 day post-instillation in 1.0mg/kg CNF3-exposed rat lung

value: 1.0mg/kg CNF3


title: MWCNT_D03_0.5mg/kg MWCNT

description: Rat lung, Day03, 0.5mg/kg MWCNT, replicate 4

source_name: 3 day post-instillation in 0.5mg/kg MWCNT-exposed rat lung


title: MWCNT_D01_Control for MWCNT

description: Rat lung, Day01, Control for MWCNT, replicate 4

source_name: 1 day post-instillation in rat lung as cotrol for MWCNT


title: MWCNT_D90_0.5mg/kg MWCNT

description: Rat lung, Day90, 0.5mg/kg MWCNT, replicate 4

source_name: 90 day post-instillation in 0.5mg/kg MWCNT-exposed rat lung


title: MWCNT_D30_0.5mg/kg MWCNT

description: Rat lung, Day30, 0.5mg/kg MWCNT, replicate 4

source_name: 30 day post-instillation in 0.5mg/kg MWCNT-exposed rat lung


title: CNF3_D90_2.0mg/kg CNF3

description: Rat lung, Day90, 2.0mg/kg CNF3, replicate 4

source_name: 90 day post-instillation in 2.0mg/kg CNF3-exposed rat lung

value: 2.0mg/kg CNF3


title: CNF3_D30_0.5mg/kg CNF3

description: Rat lung, Day30, 0.5mg/kg CNF3, replicate 4

source_name: 30 day post-instillation in 0.5mg/kg CNF3-exposed rat lung

value: male


title: MWCNT_D01_1.0mg/kg MWCNT

description: Rat lung, Day01, 1.0mg/kg MWCNT, replicate 4

source_name: 1 day post-instillation in 1.0mg/kg MWCNT-exposed rat lung