title: Diff_rep2

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

data_processing:
Promoter Capture Hi-C sequencing data processing: We processed the sequencing reads using the Hi-C User Pipeline (HiCUP) v0.5.9 default settings, except the insert size restrictions for the filtering step were set to 200-600 bp
Promoter Capture Hi-C interaction calling: We detected significant interactions using the Capture Hi-C Analysis of Genome Organization (CHiCAGO) software v1.1.1 using a CHiCAGO score threshold of 5 to define significant interactions. We filtered out inter-chromosomal interactions.
Genome_build: hg19
Supplementary_files_format_and_content: Text file lists the baited (promoter-containing) HindIII fragment and the interacting (other end) HindIII fragment as well as the interaction score from the CHiCAGO software

source_name: Differentiating preadipocytes

growth_protocol: We grew human primary white preadipocytes  (ZenBio, lot L120116E) in preadipocytes growth medium (PromoCell C-27410) supplemented with 1% Gibco Penicillin-Streptomycin (ThermoFisher 15140122). The cells were maintained in a 37-degree incubator with 5% CO2 during the culturing period. For the preadipocyte pCHi-C, cells were grown to <90% confluency in two biological replicates. For the differentiating preadipocyte pCHi-C, PAd were grown to 100% confluency (7-10M cells). We differentiated the preadipocytes for 24 hours (Diff) using preadipocyte differentiation medium (PromoCell C-27436) in two biological replicates.

extract_protocol:
For the promoter Capture Hi-C,, cells were rinsed with serum-free media prior to fixation. We fixed the cells directly in culture plates with 2% formaldehyde (EMD Millipore 344198) in serum-free media (PromoCell). We incubated cells in fixation medium with rocking at room temperature for 10 minutes, and then quenched with 1 M ice-cold glycine for a final concentration of 125 mM. After 5 minutes of rocking incubation at room temperature, we rinsed fixed cells twice with ice-cold PBS. Then we incubated the cells with rocking on ice with ice-cold permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % Igepal CA-630, Complete EDTA-free protease inhibitor cocktail [Roche])36 for 30 minutes. We scraped cells from the culture plate and centrifuged at 2500 x g for 5 minutes at 4ᵒC to pellet nuclei. The supernatant was discarded and nuclei were flash frozen in liquid nitrogen and put at -80ºC.
The Hi-C library was prepared as described in (Rao et al., Cell, 2014) with modifications. We processed nuclei in 5M cell aliquots, closely following Rao et al. protocol I.a.1 except we digested chromatin with 400U of HindIII (New England Biolabs R3104) at 37ºC overnight with shaking (950 rpm). After digestion, we pelleted nuclei with centrifugation at 2500 x g for 5 minutes at 4ºC. We performed end-filling and marked with biotin using biotin-14-dCTP (Invitrogen 19518-018), performed in-nucleus ligation, degraded protein using Proteinase K, and performed ethanol precipitation and purification. We sheared 5 μg of DNA to 250-550 bp using the Covaris M220 instrument. We performed double size-selection to retain fragments from 250-550 bp using Agencourt AMPure XP beads (Beckman Coulter A63881). We immobilized the fragments containing biotin using DYNAL™ MyOne™ Dynabeads™ Streptavidin T1 (Invitrogen 65601) beads. After end-repair and attachment of dATP, we ligated Illumina paired-end adaptors to the bead-bound library following the SureSelectXT user manual for Illumina Paired-End Multiplexed Sequencing (Agilent Technologies). After washing, we resuspended the Hi-C library in 20 μl of 1x Tris buffer and subsequently removed the Streptavidin beads from the DNA by heating at 98ºC for 10 minutes. We then amplified the adaptor-ligated library using 8 PCR cycles and purified using Agencourt AMPure XP beads, following the SureSelectXT user manual. The RNA baits for promoter capture were designed in (Mifsud et al., Nature Genetics, 2015) for capturing HindIII fragments containing gene promoters (Dr. Cameron Osborne kindly shared the exact design). A total of 550 ng of the Hi-C library was hybridized to the biotinylated RNA baits, captured with DYNAL™ MyOne™ Dynabeads™ Streptavidin T1 beads, and amplified in a post-capture PCR to add indexes, using 6 PCR cycles. The library was sequenced on the Illumina HiSeq 4000 platform.
Promoter Capture Hi-C

treatment_protocol: please see SAMPLES column: characteristics: treatment

value: Human primary white preadipocytes

value: PromoCell C-27436 preadipocyte differentiation medium (24h)


title: Diff_rep1

status: Public on Apr 04 2023

type: SRA

state: New Jersey

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: Astrocytes, Untreated, 1week, 3

city: New Delhi

first: Kartikeya

last: Singh

address: Outer Ring road

country: India

data_processing:
We used the FastQC tool to perform quality check on fastq files containing raw sequenced reads and bad quality reads were removed using Trim Galore.
The trimmed fastq reads were aligned to the genome using Bowtie2.
We used Samtools to convert the SAM output files from Bowtie2 into sorted BAM files and to remove reads aligned to mitochondrial chromosomes.
We used MACS2 to call chromatin accessibility peaks and the peaks that were found in the blacklisted regions of the genome (ENCODE) were removed before further analyses.
Assembly: mm10
Supplementary files format and content: ATAC-seq peak counts dataframe

organism: Mus musculus

source_name: Astrocyte

growth_protocol: We isolated primary NSCs from the ventricular zone of single wild type mouse brains (C57BL/6J, Harlan, The Netherlands) at embryonic day 14 (E14) as described before. Primary cultures of neurospheres (NSPs) were kept under proliferating conditions in neurobasal medium (DMEM F12; Lonza) supplemented with 1% B27 without vitamin A (Life Technologies), penicillin (100 U/ml; Lonza), streptomycin (100 g/ml; Lonza), and 20 ng/ml EGF (Epidermal Growth Factor; Life Technologies). We differentiated NSPs into astrocytes on 6-well or 12-well plates coated with poly-L-ornithine and by exchanging the proliferation medium with DMEM containing 10% FBS (Fetal Bovine Serum; Gibco), penicillin (100 U/ml; Lonza), and streptomycin (100 g/ml; Lonza). We differentiated cells into astrocytes at different time points (24, 48, 72 hours and 1 week) at 37°C in 5% CO2 and we kept them under normal conditions or treated with TNF (50 ng/ml; R&D Systems).

extract_protocol:
800 μl of resuspension buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) were added to the cells. Following cell counting, we centrifuged 50,000 cells at 500 g for 10 min in a pre-chilled (4°C) fixed-angle centrifuge. The cell pellet was re-suspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl transposase, 17 μl PBS, 0.5 μl 10% Tween-20 and 5 μl water). Transposition reactions were incubated at 37°C for 40 min in a thermomixer with shaking at 1’000 rpm. Reactions were cleaned up with MinElute Raction purification kit (Qiagen) following manufacturer’s recommendations.
Library fragments were amplified using 1× NEBnext PCR master mix and 0.6 μM of custom PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Full libraries were amplified for five cycles, after which an aliquot of the PCR reaction was used together with 9 μl of the PCR cocktail with Sybr Green at a final concentration of 0.05×. We ran this reaction for 30 cycles to determine the additional number of cycles needed for the remaining reaction. Libraries were purified using AMPure XP magnetic beads (Beckman Coulter), quantified using qubit fluorimeter and diluted to make 4nM final concentration.

treatment_protocol: Cells grown as either free floating spheres (NSPs) or as astrocytes (for 24h and 72h non-treated or treated with TNF and for 1 week without TNF treatment) in poly-L-ornithine coated plates were washed once with ice-cold PBS and were spun at 500 g for 5min in a pre-chilled (4°C) fixed-angle centrifuge. We then re-suspended the cells in 200 μl of lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) and incubated them for 20 min on ice.

value: Astrocyte

value: Untreated

tag: time


title: Astrocytes, Untreated, 1week, 2


title: PAd_rep2

source_name: Preadipocytes

value: untreated


title: CRF506 canagliflozin-treated

type: RNA

city: Swansea

first: Benjamin

middle: James

last: Jenkins

address: Singleton Park

country: United Kingdom

institute: Swansea University

description: CRF506 C

hyb_protocol: RNA samples stored at -80°C were thawed on ice prior to hybridisation reactions. Reporter probes were diluted in 70 μl of hybridisation buffer and gently mixed to create a master mix. To set up the hybridisation reactions, 5 μl of each sample was added to 8 μl of master mix. Hybridisation reactions were then completed by adding 2 μl of Capture ProbeSet and incubation at 65°C for 20 h. Probe set-target RNA hybridisation solution is then further diluted to a final volume of 35 μl. 33 μl of the diluted hybridisation solution is loaded onto a SPRINT microfluidic cartridge, with an air bubble also inserted to the stop point.

scan_protocol: Detection and scanning were performed by the nCounter® SPRINT Profiler analysis system (Nanostring).

data_processing: Raw data appraisal, quality control and normalisation were all performed using the nSolver™ analysis software. Quality control included an imaging QC of > 75% FOV registration, binding density QC within a range of 0.1 - 2.25, positive control linearity QC with R2 ≥ 0.95, and a positive control limit of detection QC set as 0.5 fM positive control above 2 standard deviations above the negative controls. Normalisation was performed using negative controls, positive controls and housekeeping genes selected by the nSolver™ normalisation module and normalised data was used as input for further analysis.

label: Nanostring capture and reporter codeset

molecule: total RNA

source_name: human peripheral blood

label_protocol: Sample RNA is hybridised with target-specific capture and reporter probes in order to create a library of unique target-probe complexes. Each target is labelled with a specific molecular barcode, which can then be detected and counted using an automated fluorescence microscope

extract_protocol: RNA isolation was performed using an RNeasy® Mini Kit as per the manufacturers’ guidelines (all Qiagen – unless otherwise stated). Cells were lysed in a 1:1 solution of RLT buffer and 70% high-grade ethanol (Fisher Bioreagents) and mixed well with a needled syringe. Lysed cells were then transferred to an RNeasy® Mini spin column placed in a 2 ml collection tube and centrifuged at 8000 x g for 15 s. The spin column was then washed once with RW1 buffer, followed by two wash steps using RPE buffer, with subsequent centrifugation at 8000 x g for 15 – 120 s following the addition of each reagent. The resulting flow-through was discarded each time. Following washing, the spin column was placed in a new collection tube and 30 μl of RNase-free water was added directly to the spin column membrane in order to elute the RNA following centrifugation at 8000 x g for 1 min. The collected eluate was re-placed on the spin column membrane and centrifuged again to further increase the final concentration of the collected RNA. Purity was assessed using a NanoDrop™ spectrophotometer by measuring the ratio of absorbance at 260 nm versus 280 nm or 230 nm. Measured A260/A280 and A260/A230 ratios were typically ~2.0. Any RNA samples with A260/230 ratio below 2.0 were precipitated using 0.3 M sodium acetate solution (ThermoFisher) and isopropanol. RNA was diluted to 300 μl in RNase-free water before addition of sodium acetate. An equal volume of isopropanol was then added to the RNA solution, which was incubated overnight at -20°C. RNA was recovered by centrifugation at 14000 x g for 10 min at 4°C and the resulting pellet was washed twice in 70% ethanol. The final pellet was dried at RT before dissolving in RNase-free water. Subsequent measured A260/A230 ratios were typically improved to ≥ 2.0. Once purity was established, RNA was stored at -80°C until required for downstream analysis. Freeze-thaw cycles were avoided in order to prevent RNA degradation.

treatment_protocol: Isolated T cells were cultured in human plasma-like medium (HPLM; Gibco), unless stated otherwise, and seeded at a density of 1x10^6 cells per ml. Cell culture plates were coated overnight with 2 μg/ml anti-CD3 antibody (Biolegend) prior to T cell activation. T cells were co-stimulated with 20 μg/ml anti-CD28 (Biolegend). Cells were treated with 10 μM canagliflozin (Cambridge Bioscience), 10 μM dapagliflozin (Combi-Blocks) or dimethyl sulphoxide (DMSO) vehicle control (Merck). Plates were incubated at 37˚C in 5% CO2 for the desired amount of time. Following 3 h incubation, culture medium was supplemented with 10% dialysed FBS to prevent impaired T cell activation.

tag: tissue

value: peripheral blood

value: naïve T cells

value: canagliflozin


title: CRF405 vehicle control

description: CRF405 V

value: vehicle


title: CRF360 vehicle control

description: CRF360 V


title: CRF423 vehicle control

description: CRF423 V


title: CRF423 canagliflozin-treated

description: CRF423 C


title: CRF360 canagliflozin-treated

description: CRF360 C


title: Astrocytes, Untreated, 1week, 1


title: sg_trcSL1c10_rep2

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: transcriptomic

data_processing:
(1) FastQC package was used to check the quality of sequence reads.
(2) Bowtie package was used to align reads to reference.
(3) Samtools package was used to write sequence file.
(4) Cufflink package was used to obtain transcriptomic data.
Assembly: E. coli BL21(DE3) (Genbank CP001509.3) was used as the reference genome.
Supplementary files format and content: gtf, Fragments per kilobase per millions mapped reads (FPKM) values for each gene

organism: Escherichia coli

growth_protocol: The cells were cultured in LB media with Chloramphenicol and spectinomycin antibiotics. Cells were cultured at OD ~1.5 after aTc induction.

extract_protocol:
total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) with on-column DNase treatment using RNase-Free DNase Set (Qiagen).
rRNA was depleted with Ribo-Zero plus rRNA Depletion Kit (Illumina) and cDNA library was constructed using KAPA Stranded RNA-Seq Kits (Kapa Biosystems).

treatment_protocol: The cells were treated with RNAprotect Bacteria Reagent (Qiagen).

tag: strain

tag: plasmid 1

tag: plasmid 2


title: Zebrafish_7000 uM PFBS 3

first: Eun Ki

last: Min

address: 232, Gongneung-ro, Nowon-gu

department: Environmental engineering

institute: Seoul National University of Science and Technology

data_processing:
Filtered reads, quality (>20) and length (>50), were aligned to the Ensembl reference genome on Danio_rerio (GCA_000002035.4).
Assembly: GCA_000002035.4
Supplementary files format and content: RPKM, TPM values

organism: Danio rerio

source_name: Whole body

extract_protocol:
The RNA extraction was conducted with RNAzol® reagent (Molecular Research Center Inc., Cincinnati, OH, USA), and appropriate amounts (>200 ng) of RNA were obtained.
A KAPA Library Quantification Kit was used to quantify the sequencing library

value: AB (wild type)

value: Whole body

tag: develpomental stage

value: 120 hpf


title: CRF318 vehicle control

description: CRF318 V


title: CRF119 canagliflozin-treated

description: CRF119 C


title: sg_trcSL1c10_rep1


title: CutnTag: Embryonic day 10.5 wildtype mouse r4 motor neurons with NR2F1 antibody rep1

city: Boston

first: Elizabeth

middle: C

last: Engle

address: 3 Blackfan Circle

institute: Boston Childrens Hospital

data_processing:
10x Cell Ranger ATAC mkfastq pipeline for fastq file generation
10x Cell RangerATAC count  pipeline for data filtering and alignment
Assembly: mm10
Library strategy: CUT&Tag

source_name: hindbrain

extract_protocol:
Single cell suspensions of microdissected embryonic hindbrain tissue was performed using the Papain Dissociation System (Worthington). Isl1mn-GFPon cells were isolated using FACS, with the gates opened to GFP-negative cells at the conclusion of the sort to a total cell number of approximately 10,000-12,000
“Single Cell CUT and Tag on 10X genomics platform” protocol from www.protocol.io and 10x Genomics Chromium Next GEM Single Cell ATAC Kit

treatment_protocol: Timed Isl1mn-GFP embryonic litters were collected, hindbrains were accessed dorsally through the 4th ventricle and Isl1mn-GFP-expression was used to identify and remove the region of the rhombomere 4 germinal zone, lateral tissues containing migrating inner ear efferents, and any caudally-migrating facial motor neurons.

value: hindbrain

value: microdissected rhombomere 4 and adjacent tissue

tag: genotype

value: wildtype


title: sg_trcSL1c5_rep2


title: Control_2

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: Mouse embryonic fibroblasts_Control

growth_protocol: Cells were cultured in 10%FBS DMES usign standard prrocedure

extract_protocol:
Total RNA was extracted by Qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Control

value: Mouse embryonic fibroblasts


title: Zebrafish_7000 uM PFBS 1


title: sg_trcSL1c5_rep1


title: CutnTag: Embryonic day 10.5 mutant mouse r4 motor neurons with NR2F1 antibody rep1

value: mutant


title: Zebrafish_7000 uM PFBS 2


title: CRF405 canagliflozin-treated

description: CRF405 C


title: sg_trcSL1c2_rep1


title: CutnTag: Embryonic day 10.5 wildtype mouse r4 motor neurons with NR2F1 antibody rep2


title: sg_trcSL1c2_rep2


title: PAd_rep1

value: Human primary white preadipocytes


title: Zebrafish_3500 uM PFBS 3


title: sg_PC_rep2


title: sg_WT_rep1


title: Zebrafish_3500 uM PFBS 2


title: CRF318 canagliflozin-treated

description: CRF318 C


title: scRNAseq: embryonic Day 12.5 mutant mouse r4 motor neurons

library_source: transcriptomic single cell

data_processing:
10x Cell Ranger mkfastq pipeline for fastq file generation
10x Cell Ranger count  pipeline for data filtering and alignment
Assembly: mm39
Supplementary files format and content: filtered feature bc matrix folder contains the barcodes.tsv, features.tsv, and matrix.mtx files. These files were used for downstream analysis

molecule: polyA RNA

extract_protocol:
Single cell suspensions of microdissected embryonic hindbrain tissue was performed using the Papain Dissociation System (Worthington). Isl1mn-GFPon cells were isolated using FACS, with the gates opened to GFP-negative cells at the conclusion of the sort to a total cell number of approximately 10,000-12,000
10x genomic Chromium Next GEM Single Cell 3' GEM-Library construction

tag: age


title: scRNAseq: embryonic Day 12.5 wildtype mouse r4 motor neurons


title: CRF119 vehicle control

description: CRF119 V


title: Zebrafish_3500 uM PFBS 1


title: 40Gy-3

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
All sequencing reads from RNA-seq were mapped to the porcine reference genome sequence (Sscrofa11.1) using hisat2-2.104. FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.15 using default parameters for gene expression levels. We used htseq-count6 to count reads on genes. Differential expression analysis was performed using DESeq27. Genes were considered differentially expressed if FPKM>1 in all sample and | log2(fold changes) | >= 1, q-value<=0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: Liver

extract_protocol:
Total RNA was extracted from pig livers using Trizol (Invitrogen) according to the manufacturer’s instructions.
Sequencing library was prepared from one microgram of total RNA using Illumina TruSeq RNA Sample Prep Kit. Paired-end 150 bp read length sequencing was performed on Illumina Hiseq 4000 sequencer.

value: Liver

tag: cell line

value: hepatocyte

value: WT


title: 40Gy-2


title: Zebrafish_700 uM PFBS 3


title: scRNAseq: embryonic Day 11.5 mutant mouse r4 motor neurons


title: CutnTag: Embryonic day 10.5 mutant mouse r4 motor neurons with NR2F1 antibody rep2


title: 40Gy-1


title: Zebrafish_700 uM PFBS 2


title: 30Gy-1


title: 30Gy-2


title: sg_WT_rep2


title: scRNAseq: embryonic Day 10.5 mutant mouse r4 motor neurons


title: Zebrafish_700 uM PFBS 1


title: 20Gy-2


title: Zebrafish_70 uM PFBS 3

value: 70 uM


title: 20Gy-3


title: 20Gy-1


title: Zebrafish_70 uM PFBS 2


title: Control-2 (irraditation)


title: scRNAseq: embryonic Day 10.5 wildtype mouse r4 motor neurons


title: scRNAseq: embryonic Day 9.5 wildtype mouse r4 motor neurons

value: Day 9.5


title: scRNAseq: embryonic Day 9.5 mutant mouse r4 motor neurons


title: Zebrafish_70 uM PFBS 1


title: sg_PC_rep1


title: Zebrafish_7 uM PFBS 3

value: 7 uM


title: 30Gy-3


title: scRNAseq: embryonic Day 11.5 wildtype mouse r4 motor neurons


title: Cultured MuSCs, MyoD-tdTomato High, rep2

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

country: Japan

institute: University of Tsukuba

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed for adaptor sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM39 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm39
Supplementary files format and content: Excel file of statistic test and expression data.

source_name: skeletal muscle

growth_protocol: Muscle stem cells (MuSCs) were cultured in growth medium containing 39% DMEM, 39% Ham's F12, 20% fetal bovine serum (FBS), 1% Ultraser G with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using TRIzoL (Qiagen). 187 to 800ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA library prep kit, and NEBNext Poly(A) mRNA Magnetic isolation module (Cat# E7770 and E7490; New England Biolabs) following manufacturer's protocols.

treatment_protocol:
Freshly isolated MuSCs from Pax7-YFP mice (QSCs) were not cultured.
MuSCs from MyoD-KI mice were cultured for 5 days, then MyoD-tdTomato low and high populations were sored by a flowcytometer.

value: skeletal muscle

value: muscle stem cells (MuSCs)

value: MyoD-tdTomato high

value: MyoD-KI

value: Culture for 5 days


title: Zebrafish_7 uM PFBS 2

value: AB (wild type)

value: Whole body

value: 120 hpf


title: Ruditapes decussatus_gills_MS93

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Sample of Ruditapes decussatus gills

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software
(no values/blank corresponds to missing spot; null corresponds to control spot not included in the normalization)

label: Cyanine 3

organism: Ruditapes decussatus

source_name: Gills of Ruditapes decussatus

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted using the QiAgen RNeasy Mini Kit protocol for tissue samples

tag: population

value: R. decussatus from South Mediterranean sea (Spain)

value: gills


title: Ruditapes decussatus_gills_MS84

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_MS52

description: Sample of Ruditapes decussatus gills


title: Zebrafish_7 uM PFBS 1


title: Cultured MuSCs, MyoD-tdTomato Low, rep3

value: MyoD-tdTomato low


title: Cultured MuSCs, MyoD-tdTomato High, rep1


title: Control-1 (irraditation)

value: Liver


title: Ruditapes decussatus_gills_MS46

description: Sample of Ruditapes decussatus gills


title: Cultured MuSCs, MyoD-tdTomato Low, rep2


title: Zebrafish_Control 2

value: Control


title: Ruditapes decussatus_gills_MS64

description: Sample of Ruditapes decussatus gills


title: Cultured MuSCs, MyoD-tdTomato Low, rep1


title: Cultured MuSCs, MyoD-tdTomato High, rep3


title: Zebrafish_Control 1


title: Ruditapes decussatus_gills_MN232

description: Sample of Ruditapes decussatus gills

value: R. decussatus from north Mediterranean sea (France)


title: Quiescent MuSCs, Pax7-YFP, rep3

value: Quiescent muscle stem cell

value: freshy isolated


title: Ruditapes decussatus_gills_MS2

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_MS28

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_MN209

description: Sample of Ruditapes decussatus gills


title: Quiescent MuSCs, Pax7-YFP, rep2


title: Ruditapes decussatus_gills_MN213

description: Sample of Ruditapes decussatus gills


title: Zebrafish_10 uM PFOS 3

value: 10 uM


title: Zebrafish_10 uM PFOS 2


title: Quiescent MuSCs, Pax7-YFP, rep1

value: skeletal muscle


title: Zebrafish_Control 3


title: Zebrafish_10 uM PFOS 1


title: Ruditapes decussatus_gills_AS552

description: Sample of Ruditapes decussatus gills

value: R. decussatus from South Atlantic (Portugal)


title: Zebrafish_5 uM PFOS 3

value: 5 uM


title: Ruditapes decussatus_gills_MN207

description: Sample of Ruditapes decussatus gills


title: 35_RNA-seq_FC1199_Sph_shSTAT3

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference genome assembly mm10 or hg19 using STAR mapping tool (Dobin et al, 2013l; PMID: 23104886).
Assembly: mm10 or hg19
Supplementary files format and content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

source_name: murine KPC cells

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: Treated with drugs as indicated.

value: KPC mice-derived FC1199 cells

tag: biological replicate


title: Zebrafish_5 uM PFOS 2


title: Ruditapes decussatus_gills_AS544

description: Sample of Ruditapes decussatus gills


title: 36_RNA-seq_FC1199_Sph_shSTAT3


title: Ruditapes decussatus_gills_AS536

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_MS37

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_MS38

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS534

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS539

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS540

description: Sample of Ruditapes decussatus gills


title: 34_RNA-seq_FC1199_Sph_shSTAT3


title: 33_RNA-seq_FC1199_Sph_shSTAT3


title: Ruditapes decussatus_gills_AS527

description: Sample of Ruditapes decussatus gills


title: Zebrafish_5 uM PFOS 1


title: Zebrafish_1 uM PFOS 3

value: 1 uM


title: 32_RNA-seq_FC1199_Sph_shCD109


title: Zebrafish_1 uM PFOS 2

value: AB (wild type)


title: Ruditapes decussatus_gills_AS523

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS504

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AN196

description: Sample of Ruditapes decussatus gills

value: R. decussatus from north Atlantic (Spain)


title: Ruditapes decussatus_gills_AN194

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS522

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS512

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AS525

description: Sample of Ruditapes decussatus gills


title: Zebrafish_1 uM PFOS 1

value: Whole body

value: 120 hpf


title: Ruditapes decussatus_gills_AN187

description: Sample of Ruditapes decussatus gills

value: gills


title: 30_RNA-seq_FC1199_Sph_shCD109


title: Zebrafish_0.1 uM PFOS 3


title: 29_RNA-seq_FC1199_Sph_shCD109


title: 28_RNA-seq_FC1199_Sph_shRen_rep2


title: Zebrafish_0.1 uM PFOS 2


title: Ruditapes decussatus_gills_AN169

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AN143

description: Sample of Ruditapes decussatus gills


title: Zebrafish_0.1 uM PFOS 1


title: 27_RNA-seq_FC1199_Sph_shRen_rep1


title: Zebrafish_Control 3


title: 31_RNA-seq_FC1199_Sph_shCD109


title: CLP_03_11

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

data_processing:
24 samples were sequenced using BGISEQ platform
HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Livers were removed,  and RNA was harvested using Qiagen RNA miniprep kit.
RNA libraries were prepared for sequencing using standard BGI protocols

value: liver

tag: Sex

value: male

value: water CLP


title: CLP_03_16

value: water sham


title: CLP_03_10

value: TAA CLP


title: Ruditapes decussatus_gills_AN123

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AN119

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AN132

description: Sample of Ruditapes decussatus gills


title: 26_RNA-seq_FC1199_Sph_Verteporfin_rep2

value: Verteporfin


title: Ruditapes decussatus_gills_AN193

description: Sample of Ruditapes decussatus gills


title: Ruditapes decussatus_gills_AN135

description: Sample of Ruditapes decussatus gills


title: CLP_03_09


title: 25_RNA-seq_FC1199_Sph_Verteporfin_rep1


title: Zebrafish_Control 1

value: Control


title: CLP_03_08

value: TAA sham


title: CLP_03_07


title: Zebrafish_Control 2


title: CLP_03_06


title: 24_RNA-seq_FC1199_Sph_DMSO_rep2

value: DMSO


title: CLP_03_04


title: CLP_03_03


title: CLP_03_02


title: 23_RNA-seq_FC1199_Sph_DMSO_rep1


title: CLP_03_15


title: 22_RNA-seq_FC1199_Sph_shTEAD2


title: WT zebrafish SHMO-treated group (bio rep 3)

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

institute: University of Verona

data_processing:
Raw reads  with  more  than  10%  of undetermined bases or more than 50 bases with a quality score <7 were discarded. Subsequently, reads were clipped from adapter sequences using Scythe software , and low-quality ends (Q score <20 on a 15-nt window) were trimmed with Sickle
Filtered reads were aligned to the Zebrafish reference genome GRCz11 using STAR aligner.
Gene  expression  quantification  has  been  performed  using  RSEM  and Zebrafish Ensembl  v104 annotation.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: whole body

growth_protocol: Zebrafish eggs were obtained from the natural spawning of adults of 8 months of age. Once collected, fertilized eggs were incubated at 28° C into petri dishes (Ø 10 cm) filled with 50 mL of egg water, with an initial stock density of 100 individuals per petri dish, for 5 days.

extract_protocol:
Total RNA was extracted from larvae 5 days old using the Quick RNA miniprep kit (ZymoResearch, Irvine, USA), according to the manufacturer’s instruction and checked for purity by NanophotometerTM Pearl-version 1.2 (IMPLEN, Westlake Village, CA), and integrity (RNA Integrity Number > 7) assessed using the RNA 6000 Pico Kit on a Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA-seq libraries were generated using the TruSeq stranded mRNA ligation kit (Illumina) from 350 ng ofRNA samples, after poly(A) capture and according to manufacturer’s instructions.

treatment_protocol: Embryos were microinjected into the yolk  at 4.7 hours post-fertilization with 4.6 nL of either Danieau saline solution or SMOs solutions. Sialylated human milk oligosaccharides and sialylated bovine milk oligosaccharides solutions were prepared with the corresponding purified SMOs fraction dissolved in the Danieau solution, with a concentration equal to 100 mmol/L.

value: whole body

tag: line

value: wild-type

value: AB

value: 5 days

value: microinjected with SHMO


title: WT zebrafish SHMO-treated group (bio rep 2)


title: CLP_03_01


title: WT zebrafish SHMO-treated group (bio rep 1)


title: 21_RNA-seq_FC1199_Sph_shTEAD2

value: KPC mice-derived FC1199 cells


title: ATTAC_lung_combination_24d_2

city: Washington

first: Gregory

middle: T

last: Gallanis

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

description:
ATTAC_counts.csv
ATTAC_CPM.csv

data_processing:
iIllumina multiplex analysis -> fastq
salmon alignment and quantification of fastq -> salmonquant file
salmonquant file -> raw counts table
edgeR normalization filtering statistical analysis of raw counts table -> fitted table (CPM)
Assembly: Grcm39 (lungs) GRCh38.p13 (HUVEC)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Palbociclib + AP residual effect (2)

extract_protocol:
Lungs were removed, preserved in RNA Later and stored at -80C until RNA collection. HUVEC cells were processed fresh after treatment. Total RNA from all tissues was harvested using the Rneasy kit (Qiagen). Sequencing results (fastq files) were provided by Novogene (Sacramento, CA) using Illumina Hiseq 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse experiment: A cohort of 24 female p16-INK-ATTAC mice were randomized into four groups (n=6 per group) for a 10-day treatment period: vehicle, AP20187 (AP) 2mg/kg every three days (four total doses) by intraperitoneal injection, palbociclib 150mg/kg daily by oral gavage (10 total doses), or combined palbociclib + AP. Following 10 days of treatment, three mice in each of groups were euthanized for analysis (“Immediate Effect” cohort). The remaining mice were treated with a 14-day holiday from palbociclib or with 14 days of continued AP 2mg/kg every three days (five additional doses) prior to collection (“Residual Effect” cohort). HUVEC experiment: Human umbilical vein endothelial cells were passaged once after cryorecovery, cultured for 24 hours, treated with 2µM palbociclib or water vehicle for 72 hours, and then collected for downstream processing.

value: lung

value: yes

tag: timepoint

value: Residual

value: F


title: ATTAC_lung_combination_24d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib + AP residual effect (1)


title: WT zebrafish SBMO-treated group (bio rep 3)

tag: treatment

value: microinjected with SBMO


title: WT zebrafish control group (bio rep 3)

value: non-microinjected


title: WT zebrafish SBMO-treated group (bio rep 1)


title: ATTAC_lung_combination_10d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib + AP immediate effect (3)

value: Immediate


title: WT zebrafish SBMO-treated group (bio rep 2)


title: 18_RNA-seq_FC1199_Sph_shRen_rep2


title: 19_RNA-seq_FC1199_Sph_shTEAD2


title: ATTAC_lung_combination_10d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib + AP immediate effect (2)


title: 20_RNA-seq_FC1199_Sph_shTEAD2


title: 17_RNA-seq_FC1199_Sph_shRen_rep1


title: WT zebrafish control group (bio rep 2)


title: ATTAC_lung_combination_24d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib + AP residual effect (3)


title: 16_RNA-seq_FC1199_Sph_invivo_rep3

value: KPC mice-derived FC1199 transplated tumors


title: ATTAC_lung_combination_10d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib + AP immediate effect (1)


title: 15_RNA-seq_FC1199_Sph_invivo_rep2


title: WT zebrafish control group (bio rep 1)


title: ATTAC_lung_palbociclib_24d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib residual effect (3)

value: no


title: 14_RNA-seq_FC1199_Sph_invivo_rep1


title: ATTAC_lung_palbociclib_24d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib residual effect (2)


title: ATTAC_lung_palbociclib_24d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib residual effect (1)


title: 13_RNA-seq_FC1199_Par_invivo_rep3


title: Lin-Sca-1hic-kit+, HDAC6 knockout 3

city: Tianjin

first: hanxiao

last: Yin

address: Weijin road 94

institute: nankai university

data_processing:
Trimmed reads were mapped to the mouse genome (GRCm39) using hisat2 (v2.2.1) with the following parameters: --no-unal --no-mix --no-discordant
samtools (v1.13) was further used to sort and set the index of highly mapped results and then transfer from sam format to bam format
FeatureCounts (v2.0.3) and DESeq2 were used to perform different gene expression analyses
Assembly: GRCm39
Supplementary files format and content: Read counts for every gene and every sample was calculated by featureCounts (v2.0.3)

source_name: bone marrow

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bone marrow

tag: cell type

value: hematopoietic stem/progenitor cells (LSK)

value: KO


title: ATTAC_lung_palbociclib_10d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib immediate effect (3)

tag: tissue


title: Lin-Sca-1hic-kit+, HDAC6 knockout 2


title: ATTAC_lung_palbociclib_10d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib immediate effect (2)


title: 12_RNA-seq_FC1199_Par_invivo_rep2

tag: strain


title: Lin-Sca-1hic-kit+, HDAC6 knockout 1


title: HRTPT 4.5As P10 #3

city: Grand Forks

first: Sandeep

middle: K

last: Singhal

state: NORTH DAKOTA

address: 1301 N Columbia Rd Stop 9037

department: Pathology

institute: University of North Dakota

hyb_protocol: affymetrix protocol

scan_protocol: affymetrix protocol

data_processing:
Quality of supplied RNA was checked using the nanodrop (Table 2) and determined to be of enough quality and quantity to proceed with processing onto the Clariom™ D microarray (Table 2). Samples were hybridized on to the Clariom™ D array using the GeneChip™ WT PLUS reagent kit as per the manufacturers protocol. Arrays were scanned using a GeneChip™ GCS 3000 scanner with autoloader. Data analysis was completed using Affymetrix Transcript Analysis console (TAC) and custom bioinformatic pipelines developed at Genome Explorations.
All 18 Clariom™ D microarrays passed the internal QC for running the arrays (Table 2). All samples were run together as a single batch to avoid potential batch effects.

label: biotin

source_name: HRTPT cells exposed to 4.5 µM iAS for 11 serial passages

label_protocol: affymetrix protocol

extract_protocol: The isolation and serum-free culture conditions for the HRTPT cells has been previously described.10, 11 Confluent cultures of HRTPT cells were exposed to 4.5 µM iAS for 24 hrs and then subcultured at a 1:3 ratio in the continued presence of iAS until confluent. Following confluence, the cells were serially sub cultured again in the present of iAS until confluent. This was repeated for 10 serial passages. Additional cultures of iAS-exposed cells at passage 8 were subcultured into iAS-free growth media and continued in iAS-free media for 11 additional passages.

value: HRTPT Cell lines

tag: passages


title: HRTPT 4.5As P10 #2


title: HRTPT DF12 P11 #3

source_name: HRTPT Cells After Recovery from Exposure to iAS 11 serial passages


title: HRTPT DF12 P11 #2


title: HRTPT DF12 P11 #1


title: 11_RNA-seq_FC1199_Par_invivo_rep1

source_name: murine KPC cells


title: Lin-Sca-1hic-kit+, control 3

value: WT


title: HRTPT DF12 P2 #3

source_name: HRTPT Cells After Recovery from Exposure to iAS 2 serial passages


title: HRTPT 4.5As P10 #1


title: Lin-Sca-1hic-kit+, control 2


title: 10_490_Sph_rep2

value: KPC mice-derived NB490 cells


title: ATTAC_lung_palbociclib_10d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Palbociclib immediate effect (1)


title: ATTAC_lung_AP20187_24d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: AP20187 Residual effect (3)


title: HRTPT DF12 P2 #2


title: Lin-Sca-1hic-kit+, control 1


title: 9_490_Sph_rep1


title: ATTAC_lung_AP20187_24d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: AP20187 Residual effect (2)


title: ATTAC_lung_AP20187_10d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: AP20187 Immediate effect (3)


title: 7_490_Par_rep1


title: 8_490_Par_rep2


title: ATTAC_lung_AP20187_24d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: AP20187 Residual effect (1)


title: HRTPT DF12 P2 #1


title: ATTAC_lung_AP20187_10d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: AP20187 Immediate effect (2)


title: Ruditapes decussatus_gills_AS555

description: Sample of Ruditapes decussatus gills

source_name: Gills of Ruditapes decussatus

value: R. decussatus from South Atlantic (Portugal)

value: gills


title: ATTAC_lung_AP20187_10d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: AP20187 Immediate effect (1)

value: lung


title: 5_RNA-seq_FC1199_Sph_rep1

value: KPC mice-derived FC1199 cells


title: ATTAC_lung_vehicle_24d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Vehicle residual effect (3)

value: Residual


title: 4_RNA-seq_FC1199_Spheroid_rep2


title: ATTAC_lung_vehicle_24d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Vehicle residual effect (2)

value: F


title: HRTPT 4.5As P8 #1

source_name: HRTPT cells exposed to 4.5 µM iAS for 8 serial passages


title: HRTPT 4.5As P8 #2


title: HRTPT 4.5As P8 #3


title: ATTAC_lung_vehicle_24d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Vehicle residual effect (1)


title: HRTPT 4.5 As P3 #3

source_name: HRTPT cells exposed to 4.5 µM iAS for 3 serial passages


title: 3_RNA-seq_FC1199_Spheroid_rep1


title: 2_RNA-seq_FC1199_Par_rep2


title: A549_NE_01

city: Zhengzhou

first: Jie

last: Zhao

state: China

address: 1th Jianshe road, Zhengzhou, Henan, PR China

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
The sequencing data was filteed with SOAP nu:ke (v1.5.2) by(1) Removing'eads containing sequencing adapter;(2) Removing reads whose low quality base ratio (base quality less than or equal to 5)is more than 20%; (3) Removing reads whose unknown base ('N' base)ratio is more than 5%afterwa ds clean reads were obtained and stored in FASTQ format.The clean reads were mappe d to the reference genome using HISAT2(v2.0.4). Bowtie (.2.2.5) wa. appied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM(v1.2.12).
The differential expression analysis was performed using the limma voom (v3.36.1).
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: The DEGs between NC and ADO group in PBMCs.
Supplementary files format and content: The DEGs between NC and NE group in A549.

growth_protocol: The cells were separately maintained in DMEM/RPMI1640 with 10% FBS (Thermo Fisher Scientific, USA) and 1% penicillin–streptomycin (Thermo Fisher Scientific, USA), which were cultured at 37°C, 5% CO2 and saturated humidity.

extract_protocol:
Total RNA was extracted by Trizol method
Oligo(dT)-attached magnetic beads were used to purified mRNA.Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature.Then First-strand cDNA was generated using random hesamer-primed reverse transcription,followed bya second-strand cDNA synthesis.afterwards,A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads,then dissolved in EB solutionThe product was validated on the Agilent Technologies 2100 bioanalyzer for quality control.The double stranded PCR products from previous slep were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA(ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNAnanoball(DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform(BGI-Shenzhen,China).

treatment_protocol: PBMCs were treated with 30 uM ADO for 24 h; A549 was treated with 10uM NE for 24h.

value: lung adenocarcinoma cell

tag: time

value: 10uM Norepinephrine


title: 1_RNA-seq_FC1199_Par_rep1


title: ATTAC_lung_vehicle_10d_2

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Vehicle immediate effect (2)

value: Immediate


title: 6_RNA-seq_FC1199_Sph_rep2


title: HRTPT 4.5 As P3 #1


title: A549_NC_02

value: Dimethyl sulfoxide


title: ATTAC_lung_vehicle_10d_1

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Vehicle immediate effect (1)

value: no


title: 12_ChIP-seq_H3K27ac_FC1199_Sph_Verteporfin

data_processing:
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Assembly: mm9 or hg19
Supplementary files format and content: bigWig files were generated using makeBigwig.pl script of HOMER suite.

source_name: murine KPC cells

extract_protocol:
Lysates were prepared from 5-10 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02; PerkinElmer) according to the manufacturer's instructions.

tag: antibody

value: H3K27ac (ab4729, Abcam)

value: Verteporfin


title: A549_NC_01


title: 11_ChIP-seq_H3K27ac_FC1199_Sph_DMSO

value: DMSO


title: PBMC_ADO_02

source_name: peripheral blood mononuclear cells (PBMCs)

value: 30 uM adenosine


title: PBMC_ADO_01

value: peripheral blood mononuclear cells (PBMCs)


title: A549_NE_02


title: HRTPT 4.5 As P3 #2

value: HRTPT Cell lines


title: HRTPT Control #2

source_name: Control HRTPT cells

value: Control


title: 10_ChIP-seq_H3K27ac_FC1199_Sph_shTEAD2


title: ATTAC_lung_vehicle_10d_3

description:
ATTAC_counts.csv
ATTAC_CPM.csv

source_name: Vehicle immediate effect (3)

tag: genotype


title: 9_ChIP-seq_H3K27ac_FC1199_Sph_shTEAD2


title: KO_H3K27me3 chipseq_rep2

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

description: CHIP-seq

data_processing:
ATAC-seq reads were mapped to the mm10 genome assembly using Bowtie version 1.1.1,allowing two mismatches, after adapter sequences were removed using trimgalore version0.6.6.
RNA-seq reads were mapped to the mm10 genome assembly using TopHat version 2.1.1 with the default configurations after adapter sequences were removed using trimgalore version 0.6.6.
peaks were called using MACS 1.4.2 (Zhang et al., 2008)  with the following setting: a p value (1.0E-05).
Gene expression values (RPKM: Reads Per Kilobase exon per Million mapped reads) were calculated using Partek Genomics Suite 7.18.
scRNA-seq reads were processed with CellRanger ver. 3.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
For clustering, filtering, variable gene selection, dimensionality reduction of scRNA(single cell RNA) are performed using the Seurat ver.3.4.0 (Butler et al., 2018).
The pseudotemporal Analyses of scRNA(single cell RNA) was performed using Monocle v.3.0.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include barcodes,gene names, and UMI counts  for each Sample; peak bed files

source_name: KO

growth_protocol: FACS-purified MuSCs from the hindlimbs of wild-type (WT) or Ezh1-/- mice were collected and immediaetly processed for bulk RNA-seq, bulk ATAC-seq, chIP-seq, scRNA-seq

extract_protocol:
RNA was extracted using Trizol.  ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013). For ChIP cells were  crosslinked in 1% formaldehyde and  lysed in RIPA buffer prior to immunoprecipitation.
For RNA-seq, poly (A)+ mRNA libraries were generated  using NEBNext Ultra II RNA library preparation kit for Illumina (NEB #E7490). For chIPSeq libraries were generated with  using NEBNext Ultra II DNA library preparation kit for Illumina (NEB#E7645L). Single-cell RNA-seq libraries were prepared using a Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (P/N 1000121, 10x Genomics).

treatment_protocol: Tibialis anterior (TA) muscles of WT and Ezh1-/- mice were injured twice with notexin (NTX). MuSC were FACS isolated 3 days after second injury and used for scRNA-seq analysis of regenerating cells.

value: KO


title: PBMC_NC_02


title: KO_Input chipseq_rep2

description: CHIP-seq

value: none (input)


title: HRTPT Control #1


title: PBMC_NC_01


title: HRTPT Control#3


title: 8_ChIP-seq_H3K27ac_FC1199_Sph_shRen

value: KPC mice-derived FC1199 cells


title: 6_ChIP-seq_H3K4me1_FC1199_Sph

value: H3K4me1 (ab8895, Abcam)


title: 5_ChIP-seq_H3K4me1_FC1199_Par


title: 7_ChIP-seq_H3K27ac_FC1199_Par_Flag-TEAD2


title: 4_ChIP-seq_H3K27ac_FC1199_Sph


title: WT_Input chipseq_rep1

description: CHIP-seq

source_name: WT

value: WT


title: KO_Input chipseq_rep1

description: CHIP-seq


title: 2_ChIP-seq_H3K4me3_FC1199_Sph

value: H3K4me3 (ab8580, Abcam)


title: WT_H3K27me3 chipseq_rep2

description: CHIP-seq


title: QSC_KO- scRNAseq_rep1

description: scRNA-seq


title: QSC_WT- scRNAseq_rep1

description: scRNA-seq


title: 3_ChIP-seq_H3K27ac_FC1199_Par


title: 1_ChIP-seq_H3K4me3_FC1199_Par


title: WT_H3K27me3 chipseq_rep1

description: CHIP-seq


title: ac4C,mRNA,IgG

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
The output file of novaseq is removed by cutadapt
Clean reads were mapped to the mouse reference genome (mm10) using STAR
The mapping files containing the reads matching the mouse genome were used HTseq to calculate gene expression values of CDS, and raw read counts
Converts raw reads count to TPM by R, then the translation efficiency is calculated
Signal tracks were visualized by Integrative Genomics Viewer (IGV)
Assembly: mm10
Supplementary files format and content: bw, txt
Supplementary files format and content: bw, txt

source_name: Mouse ovary

extract_protocol:
Mice were sacrifised on the indicated times and total RNA were extracted from WT and Nat10-ZcKO at GV and MII oocytes for ribo-seq;Mice were sacrifised on the indicated times and total RNA were extracted from WT GV oocytes for acRIP-seq
Ribo-seq libraries,briefly, the oocytes were directly lysed in the lysis buffer. Then RNase treatment by RNaseI. Extract RNA by Trizol. End repair, 3' ployadenylation and the full-legnth first-strand cDNA was generated using the riboRT primer, along with the TSO primer. The PCR products were amplified.PCR Library purification using selection beads.Library was performed according to the m6A acRIP-seq method. Briefly, the oocytes were directly lysed in the lysis buffer. acRIP-seq libraries, fragment RNA and incubate with beads with ac4C antibody or IgG antibody. Extract RNA by Trizol. End repair, 3' ployadenylation and the full-legnth first-strand cDNA was generated using the riboRT primer, along with the TSO primer. The PCR products were amplified.PCR Library purification using selection beads.

value: Mouse ovary

value: GV

value: oocytes

value: anti-IgG


title: MII,ZcKO,rep3

data_processing:
The output file of novaseq is removed by cutadapt
Clean reads were mapped to the mouse reference genome (mm10) using STAR
The mapping files containing the reads matching the mouse genome were used HTseq to calculate gene expression values of CDS, and raw read counts
Converts raw reads count to TPM by R, then the translation efficiency is calculated
Signal tracks were visualized by Integrative Genomics Viewer (IGV)
Assembly: mm10
Supplementary files format and content: bw, txt
Supplementary files format and content: bw, txt
Library strategy: ribo-seq

value: MII

value: Rnase I


title: MII,ZcKO,rep2


title: WT_Input chipseq_rep2

description: CHIP-seq


title: KO_H3K27me3 chipseq_rep1

description: CHIP-seq


title: ac4C,mRNA,IP


title: MII,WT,rep2


title: MII,WT,rep1


title: MII,ZcKO,rep1


title: GV,ZcKO,rep3


title: 1_ATAC-seq_FC1199_Par

data_processing:
Raw reads were mapped to the reference mouse (mm9) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Assembly: mm9

extract_protocol:
Nuclear extract were prepared from 50,000 single cell dissociated of cell lines, incubated with Tn5 transposase, and purified with Qiagen MinElute kit for library construction.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit, as described in Corces et al, 2017 (PMID: 28846090).


title: GV,ZcKO,rep1


title: QSC_WT_bulk ATACseq_rep1

description: bulk ATAC-seq


title: GV,ZcKO,rep2


title: pre-WT-M15_S12

city: Los Angeles

first: Brent

middle: L

last: Fogel

state: CA

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

description: miR-142-3p-null_PrefrontalCortex-seq_RPKM.csv

data_processing:
Sequence reads were aligned to the mouse mm10 reference genome and RefSeq GTFusing the Spliced Transcripts Alignment to a Reference (STAR).
Mapped reads were counted with HTSeq.
RPKM were calculated using a custom script in R based on the GenomicFeatures library and rtracklayer library.
Assembly: mm10
Supplementary files format and content: comma separated text files include RPKM values for each sample

source_name: prefrontal cortex

extract_protocol:
Following immunoprecipitation, ribosomal-bound RNA was isolated using the Nucleospin miRNA isolation kit (Clontech) allowing purification of large and small RNA species. Bulk RNA from miR-142-null and heterozygote mice as well as rTg4510 mice was generated by fresh dissection of the frontal cortex (rTg4510) or prefrontal cortex (miR-142-null), homogenization in lysis buffer and RNA isolation using the Nucleospin miRNA isolation kit. RNA quality was measured using an Aligent Bioanalyzer generating RINs between 6.1-9.5 for all samples.
RNA-sequencing was carried out using either the NuGEN RNA amplification with RiboZero treatment with 50 bp paired end reads (M dataset) or the Illumina TruSeq Stranded RNA library kit with RiboZero Gold treatment with 75 bp paired end reads (T and P datasets).

value: prefrontal cortex


title: QSC_KO_bulk RNAseq_rep3

description:
bulk RNA-seq
BulkRNA_RPKM.xlsx
BulkRNA_ANOVA.xlsx


title: rag1_rescue_mCherry_g19_1

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
scRNA-seq libraries were aligned with STARsolo (Kaminow et al., 2021) using a custom two-pass strategy. First, an annotated chimeric GRCh38 and GRCm38 reference was generated using Ensembl 102 human and mouse annotations with the addition of mCherry and EGFP. STARsolo was run with parameters: twopassMode = basic, limitSjdbInsertNsj = 3000000, and soloUMIfiltering = MultiGeneUMI. BAM files were then split by species and cross-species multimapping reads were assigned to both human or mouse BAMs. FASTQ files were re-generated from either the mouse or human BAM files andre-aligned to a single species reference.
Human data were imported into R using Seurat(Butler et al.,2018). Cells were filtered (Unique genes > 250 and percent mitochondrial genes < 15). Cells were then further filtered for appropriate expression of mCherry or EGFP. These filtered cells were used to construct the submitted processed data counts matices.
Assembly: GRCh38 and GRCm38 both with ensembl 102
Supplementary files format and content: Sparse (10x compatable) matrices containing filtered cells

organism:
Homo sapiens
Mus musculus

source_name: Mouse Human Chimera

extract_protocol:
Mice were euthanized with euthasol, transcardially perfused with sterile Hank’s Balanced Salt Solution (HBSS) containing magnesium chloride and calcium chloride, and the brain removed. The brains were immersed in ice-cold sterile HBSS for about 5 minutes to facilitate the microdissection. Under a dissecting microscope, the striata from each mouse was dissected and placed in sterile HBSS on ice. The striatal tissues were transferred to a Petri dish containing sterile HBSS without magnesium chloride and calcium chloride, chopped into small pieces using sterile disposable scalpels, transferred into a sterile tube, and then incubated in a papain/DNase dissociation solution at 37°C for 50 minutes. Ovomuccoid dissolved in EBSS was then added to inactivate the papain. The tissue was triturated by repeated pipetting in order to achieve a single cell suspension. The cells were then pelleted, resuspended into MEM, and filtered for flow cytometry. Single cell suspensions were isolated based on their expression of mCherry, EGFP, or the lack of reporter expression on a BD FACSAria Fusion. To exclude dead cells, 4′,6-diamidino-2-phenylindole (DAPI) was added at 1 µg/mL.
Libraries were constructed according to the manufacturer instructions for the 10x chromium controller (v3.1 chemistry).

value: striatal

tag: transplant

value: Adult

tag: animal

tag: phlorophore

value: mCherry

tag: paradigm

value: HD Rescue

tag: library


title: rag1_rescue_GFP_g20_1

tag: cell line

value: HD

value: Neonatal

value: eGFP


title: GV,WT,rep3


title: rag1_Rescue_Ctrl_G20_eGFP_Pos

value: Alone


title: QSC_KO_bulk RNAseq_rep1


title: pre-WT-F13_S9


title: pre-WT-M15_S11


title: GV,WT,rep2

value: WT


title: pre-WT-F13_S8


title: rag1_Rescue_Ctrl_G19_mCherry_Pos


title: 2_ATAC-seq_FC1199_Sph

value: KPC mice-derived FC1199 cells


title: QSC_WT_bulk RNAseq_rep2


title: QSC_WT_bulk RNAseq_rep1


title: QSC_KO_bulk ATACseq_rep1

description: bulk ATAC-seq


title: rag1_Rescue_Ctrl_G20_eGFP_Neg

value: Mouse


title: GV,WT,rep1

value: Mouse ovary

value: GV


title: pre-HET-F13_S10


title: QSC_WT_bulk RNAseq_rep3


title: SMG-3

city: Shenzhen

first: yue

last: xiong

address: Xueyuan Avenue 1068

institute: SIAT

data_processing:
Illumina Novaseq 6000 for transcriptome sequencing
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(v2.0) (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped using Hisat2 (v 2.1.0) and quality evaluated by RSeQC（V 3.0.1)
Read count extraction and normalization were performed using Hisat2 (v 2.1.0)
Assembly: AnimalTFDB 3.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: NCTC 1469

growth_protocol: NCTC 1469 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NR604-VAHTS® Fast mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Under normal gravity or random positioning machine culture system for 6 days

value: NCTC 1469

value: hepatocytes


title: rag1_Rescue_Ctrl_G19_mCherry_Neg


title: pre-HET-M14_S6


title: QSC_KO_bulk RNAseq_rep2


title: SMG-2

value: random positioning machine culture system


title: pre-HET-M14_S5

value: prefrontal cortex


title: SMG-1


title: NG-3

value: normal gravity


title: G19_control_rescue_mCherry_1

value: striatal

value: WT Rescue


title: pre-HET-M14_S3


title: NG-2


title: NG-1


title: G19_rescue_mCherry_alone

value: mCherry


title: pre-KO-M14_S7


title: Mixed_Rescue_mCherry_G19_1_10X

value: G19(tagged and untagged)

value: Adult

value: HD Rescue


title: Control ERW_4 (Cy3green) vs ERW_4 (Cy5red)

city: Turin

first: Massimo

middle: E

last: Maffei

address: Via Quarello 15/a

department: Life Sciences and Systems Biology

institute: University of Turin

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). The raw microarray data are subjected to background subtraction and lowess normalization.

organism: Arabidopsis thaliana

source_name: whole seedling

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: were placed on bi-partite squared Petri dish containing in the upper part half-strength Murashige–Skoog medium (MS medium) and in the lower part a nutrient agar II

extract_protocol: A. thaliana seedling were collected at different times of E. amylovora mVOCs exposure and immediately frozen in liquid nitrogen and stored at -80 °C

treatment_protocol: Total RNA extracted following manufacturer's instructions

tag: cultivar

tag: agent

value: Control

tag: organ

value: roots and shoots

value: E. amylovora mVOC


title: G19_control_rescue_eGFP_1

value: WT

value: eGFP


title: 542-8mo-mutant_S40

source_name: frontal cortex

value: frontal cortex


title: WD2_Liver, replicate 2, snRNA-seq

city: Richmond

first: Nicholas

middle: J

last: Koelsch

state: Virginia

address: 1810 East Cary Street Apt MG02

department: Microbiology & Immunology

institute: Virginia Commonwealth University

data_processing:
All aligned data files were provided by the Singulomics Corporation, in which they analyzed the sequencing results with mouse reference genome mm10 using CellRanger v6.1.1
All analyses were conducted by using the filtered matrix files containing the data through Rstudio for processing with various packages.
Assembly: mm10
Supplementary files format and content: The matrix.mtx.gz file contains raw read counts for each gene (rows) in each cell (columns) in a tab-delimited file.
Supplementary files format and content: The barcode.tsv.gz file contains column names for the matrix file.
Supplementary files format and content: The features.tsv.gz file contains row names for the matrix file.

molecule: nuclear RNA

source_name: Liver

growth_protocol: Feeding mice either a standard chow diet, or providing mice with a high-fat diet coupled with sugar water

extract_protocol:
after they reached the end of the time course for the study, the livers of these mice were resected, snap-frozen in liquid nitrogen, and subjected to snRNA-seq
The Singulomics corporation constructed 3' single cell gene expression libraries (Next GEM v3.1) using the 10X Genomics Chromium system.

value: Liver

value: 129A1/SvIm and C57BL/6J cross mice

tag: Sex

value: male

tag: time on_diet

value: 40 weeks

tag: disease state

value: Pre-Tumor (Pre-T)

tag: treatment

value: Western Diet


title: WD1_Liver, replicate 1, snRNA-seq

tag: tissue

tag: strain


title: pre-KO-F14_S1

value: prefrontal cortex


title: WDT2_Tumor, replicate 2, snRNA-seq

value: 48 weeks

value: Post-Tumor (Post-T)


title: pre-KO-M14_S2


title: WDT1_Tumor, replicate 1, snRNA-seq


title: pre-KO-M14_S4


title: Rescue_eGFP_G20_2

value: striatal

value: HD

value: Neonatal


title: Rescue_mCherry_G19_2

value: Adult

value: mCherry

value: HD Rescue


title: 540-8mo-mutant_S38


title: 524-8mo-control_S37


title: normal weight sample - rep 3

city: Caserta

first: Gilda

last: Cobellis

address: Viale Abramo Lincoln

institute: University of Campania "Luigi Vanvitelli"

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by using cutadapt software (version 2.5).
The tool sRNAbench was used to obtain the miRNA expression profiling respect to miRBase database (version22 - GRCh38 - GCA_000001405.15).
Reads that had a sum read count less than 10 were excluded, in all samples used.
the DESeq2 (version 1.36.0) algorithm was used to detected the differentially expressed miRNA.
Assembly: HG38-miRbase 22
Supplementary files format and content: Matrix table with raw miRNA counts for every sample
Supplementary files format and content: tab-delimited text files include normalized values (median of ratio of miRNA counts) for each Sample.

source_name: Extracellular vesicles from serum

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (TRIzol Reagent, Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer’s instructions.
Total RNA was used for sequencing library preparation using NEXTFLEX Small RNA-Seq Kit v3 (Perki-nElmer) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and Qubit fluorometer (Invitrogen Co.), then pooled such that each index-tagged sample was present in equimolar amounts. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 550 Dx System (Illumina) in a 1x75 single-end format.

value: Extracellular vesicles from serum

tag: condition

value: Normal Weight

tag: patient diagnosis

value: breast cancer


title: normal weight sample - rep 1


title: CD1_Liver, replicate 1, snRNA-seq

value: Liver

value: 129A1/SvIm and C57BL/6J cross mice

value: Control

value: Chow Diet


title: normal weight sample - rep 2


title: Control ERW_1 (Cy3green) vs ERW_1 (Cy5red)

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.

value: roots and shoots

value: E. amylovora mVOC


title: G19_rescue_EGFP_alone

tag: genotype

value: WT

tag: transplant

value: eGFP

value: Alone


title: Control ERW_3 (Cy3green) vs ERW_3 (Cy5red)

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: control healthy sample - rep 3

value: Untreated-Control

value: healthy control (no cancer)


title: CD2_Liver, replicate 2, snRNA-seq

value: male

value: 40 weeks


title: 522-8mo-control_S36

value: frontal cortex


title: Control ERW_2 (Cy3green) vs ERW_2 (Cy5red)

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: 541-8mo-mutant_S39


title: T56_Exp3_RV16_plus_PI_200_S84_L004

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

description:
count.matrix.txt
count.matrix.vst.txt

data_processing:
Raw sequencing reads were trimmed using skewer (v0.2.2) with the following parameters: end-quality=15, mean-quality=25, min=30.
Read alignment to the human reference genome GRCh38 was performed using HISAT2 (v2.1.0) with default parameters.
Gene quantification was performed using htseq-count (v0.9.1) and GRCh38 Ensemble v84 gene transcript model with the following parameters: stranded=reverse, a=20, mode=intersection-nonempty.
Raw count data were filtered for all genes with at least 6 counts in at least 10% of samples and then variance stabilized using the variance stabilizing transformation (VST) function implemented in DESeq2.
Assembly: Hg38
Supplementary files format and content: "count.matrix.raw.txt" - tab-delimited text file with raw counts for all seqeunced samples and genes
Supplementary files format and content: "count.matrix.vst.txt" - tab-delimited text file with VST-normalized counts for all sequenced samples and filtered genes

source_name: Differentiated human tracheal airway epithelial ALI cultures

growth_protocol: Primary AECs were isolated by the National Jewish Health (NJH) Live Cell Core from human lung specimens that were obtained from de-identified donors whose lungs were not suitable for transplantation by the International Institute for the Advancement of Medicine (Edison, NJ) and Donor Alliance of Colorado. The NJH Institutional Review Board (IRB) approved the research on lung cells (HS-3209), and the use and collection of cells and tissues by NJH Live Cell Core (HS-2240). Cells were differentiated and maintained using air-liquid interface (ALI) culture. We routinely performed three individual experiments using primary tracheal epithelial cells, obtained from four different non-smoking donors. Tracheal epithelial cells were expanded on collagen coated plates (Corning) initially using tracheal epithelial cell growth media (BEGM bullet kit from LONZA, (Walkersville, MD, USA)), and subsequently, cultured at ALI in 24-well plates with transwell inserts (Corning, ME, USA). After shift to ALI conditions, the cultures undergo differentiation for 14-16 days. H1-HeLa cells were ob-tained from Dr. Wai-Ming Lee (University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin) and cultured in DMEM/F12 medium (GIBCO, NY, USA) supplemented with 1% glutamine, 15mM HEPES, 1% penicillin and streptomycin (GIBCO, NY, USA), and 10% heat-inactivated bovine growth serum ((BGS), Cyti-va HyClone, Utah).

extract_protocol:
RNA extractions from cultured cells were performed by the RNeasy Mini kit (Qi-agen, Hilden, Germany).
Library preparation and RNA sequencing were conducted at National Jewish Health (Seibold Laboratory). RNA-seq libraries were generated on 81 ALI samples (3 replicates for 3 donors for 9 treatments). KAPA mRNA Hyper Prep (Roche) whole-transcriptome libraries were constructed on the Beckman Coulter FXP automation system with 500 ng RNA input per sample, and Illumina Dual Index Adapters (IDT Technologies) were used to barcode samples using 10 cycles of amplification. Barcoded libraries were pooled and sequenced on an Illumina NovaSeq 6000 system using 150bp paired end reads.

treatment_protocol: To examine anti-RV effects of the phospholipids, palmitoyl-oleoyl-phosphatidylglycerol (POPG) and phosphatidylinositol (PI) with inhibitory effects against the RV-A16 virus or the control lipid palmitoyl-oleoyl-phosphatidylcholine (POPC), unilamellar liposomes perpared by bath sonicatin were added to cells apically and incubated for 16 h at the concentration of 10 mg/ml (POPG), 4 mg/ml (PI) and 20 mg/ml (POPC). Subsequently, the virus, RV-A16, which was obtained from the ATCC (ATCC# VR-283), propagated in H1-HeLa cells and purified by ultracentrifugation, was added at a multiplicity of infection (moi) of 0.02 plaque-forming units (pfu) per cell for 4 h at 35 °C. Unbound virions were removed by washing with Dulbecco's phos-phate-buffered saline (DPBS) three times and the epithelial cells were next incubated for 48 hr at 35 °C either with, or without phospholipids in apical media. At 48 h, apical media was harvested. Ultimately, we generated three replicate ALI samples from each of three tracheal donors (T22, T51, T56) treated in each of the following ways: (1) mock (i.e., Control), (2) lipid only (PI, POPG, or PC), (3) RV-A16 infection alone at 4hr or 48hr (RV-A16_4hr, RV-A16_48h, respectively), or (4) lipid pretreatment followed by RV-A16 infection (RV-A16+PI, RVA-16+POPG, RV-A16+PC).

tag: cell type

value: Tracheal airway epithelial cultures

tag: donor

tag: phospholipid treatment

value: PI

tag: virus treatment


title: WTWT_M_Tibia_2182

city: Montreal

first: Ghalib

last: Bardai

state: Quebec

address: 1003 Boulevard Decarie

department: Clinical Laboratories

country: Canada

institute: Shriners Hospital for Children

data_processing:
Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads. Between 31 million and 57 million 100-base paired-end reads were generated per sample
Analysis of paired-end sequencing reads was performed using GenPipes. Read pairs were aligned to GRCm38 by the RNA-seq aligner STAR. Aligned RNA-seq reads were assembled into transcripts, and their relative abundance was estimated using Cufflinks and Cuffdiff.
Differential expression analysis was conducted using DESeq. Significantly differentially expressed genes were defined as those with an adjusted p value <0.05 as determined by DESeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Tibia

growth_protocol: Male mice were euthanized at the age of 8 weeks. Tibia shafts were dissected, the bone marrow was flushed out and the bones were immediately immersed in RNAlater (Thermo Fisher) and stored at −80°C until processing.

extract_protocol:
After mincing with scissors, the bones were homogenized in 5 mL of TRIzol™ (Thermo Fisher) for 15 s with a tissue mincer equipped with a 5-mm stainless steel generator probe. The total RNA was extracted using the phenol-chloroform method.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). cDNA synthesis was achieved with the NEBNext Modules (New England Biolabs). The remaining steps of the library preparation were done  using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

value: Tibia

value: WT,WT


title: WTWT_M_Tibia_2179


title: control healthy sample - rep 1

value: Extracellular vesicles from serum


title: RPF_Liver_tRNA_IV_replicate2

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description: Ribosome-protected fragments

data_processing:
Library strategy: Ribo-seq (ribosome profiling)
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Genome read mapping using STAR (2.5.4b), parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1
Read counting using HTSeq, version 0.9.1
Genome_build: Homo sapiens Ensemble build GRCh38.p13
Genome_build: Mus musculus Ensemble build GRCm38
Supplementary_files_format_and_content: tab-delimited text files include unique read counts per gene per kilobase and million mapped reads RPKM for each sample

source_name: Intravenous administration (IV) of suppressor tRNA

growth_protocol: CFBE41o- cells were grown in Dulbecco´s Modified Essential Medium (DMEM). CFBE41o-cells were co-transfected in triplicate with 25 ng PTC-FLuc or WT-FLuc plasmids and 100 ng each tRNA variant using lipofectamine 3000 (Thermo Fisher Scientific)

extract_protocol:
The whole organs were pulverized in liquid nitrogen and lysed by grinding in 360 µL 10 mM Tris-HCl (pH 7.4) supplemented with 5 mM MgCl2, 100 mM KCL, 1% NP-40, 2mM DTT, 100 µg/mL cycloheximide topped with 40µL of 10% sodium deoxycholate. Lysate from each animal organ were used to produce an independent library. re flash frozen and immediately lysed by grinding in 10mM Tris-HCL pH 7.4, 5mM MgCl2, 100mM KCL, 1% NP-40, 2% sodium deoxycholate.The lysates from three animals each were pooled.
Isolation of mRNA-bound ribosome complexes, RNase I digestion-derived ribosome-protected fragments (RPFs), RNA-size selection and generation of the cDNA libraries was performed as described (Guo et al, 2010; doi: 10.1038/nature09267 )

treatment_protocol: Two mice were i.v. dosed with LUNAR1 co-formulated with 0.3 mg/kg R208X-aLuc mRNA and 0.6 mg/kg tS, and in two mice LUNAR2 co-formulated with 0.35 mg/kg tSA1T5::UGA suppressor with an anticodon to pair to UGA PTC with 0.35 mg/kg PTC-Cre mRNA (S69X-S82X) were i.t. administered. Six hours post treatment the mice were anesthetized and liver or lung, respectively, extracted and flash frozen. Mice treated with PBS for the same duration served as negative control.

value: Liver

value: Liver - whole organ

value: Balb/C

value: suppressor tRNA administered


title: WTWT_M_Tibia_2173


title: 504-8mo-control_S35


title: over weight - obese sample - rep 6

value: Obese-Over Weight

value: breast cancer


title: over weight - obese sample - rep 5


title: T56_Exp3_RV16_4h_S56_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Control


title: SostKoOI_M_Tibia_2195

value: Col1a1Jrt/+ Sost-/-


title: T56_Exp3_RV16_plus_PC_1000_S91_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: RPF_Liver_tRNA_IV_replicate1

description: Ribosome-protected fragments


title: RPF_Liver_Ct_IV

description: Ribosome-protected fragments

source_name: control untreated

value: Untreated


title: WTWT_M_Tibia_2189

value: male


title: over weight - obese sample - rep 4


title: RPF_Lung_tRNA_IT_replicate2

description: Ribosome-protected fragments

source_name: Intratracheal administration (IT) of suppressor tRNA

value: Lung

value: Lung - whole organ


title: over weight - obese sample - rep 3


title: SostKoOI_M_Tibia_2183


title: T56_Exp3_PI_200_S112_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures

value: PI


title: T56_Exp3_POPG_500_S105_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG


title: RPF_Lung_tRNA_IT_replicate1

description: Ribosome-protected fragments


title: T56_Exp3_PC_1000_S98_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: SostKoOI_M_Tibia_2168

value: Tibia


title: SostKoOI_M_Tibia_2167


title: over weight - obese sample - rep 1

value: Extracellular vesicles from serum


title: RPF_Lung_Control

description: Ribosome-protected fragments


title: T56_Exp3_RV16_plus_POPG_500_S77_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: OI_M_Tibia_2187


title: OI_M_Tibia_2181


title: control healthy sample - rep 2

value: Untreated-Control

value: healthy control (no cancer)


title: T56_Exp3_RV16_0_2_S70_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: OI_M_Tibia_2175


title: OI_M_Tibia_2174


title: T56_Exp3_CONT_S63_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T56_Exp2_RV16_plus_PI_200_S104_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: over weight - obese sample - rep 2


title: Zambia, early, rep3

city: Planegg-Martinsried

first: Amanda

last: Glaser-Schmitt

address: Grosshaderner Str. 2

department: Biology

institute: LMU München

data_processing:
Reads were mapped using NextGenMap in paired-end mode. Ambiguous read pairs were discarded.
Assembly: Flybase release version 6.21
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

organism: Drosophila melanogaster

source_name: larval fat body

growth_protocol: Larval staging was performed at 25°C. First instar larvae were density controled with 250 larvae per vial and allowed to develop on medium supplemented with 5% bromophenol blue (Carl Roth). Early and late larvae were identified based on the color of their guts. White prepupae were identified by pupariation formation and cessation of wriggling.

extract_protocol:
RNA was extracted with the Rneasy Plus Universal kit (Qiagen).
Genewiz (Leipzig, Germany) performed ribosomal depletion and library prep.

treatment_protocol: Female larvae were washed in PBS and fat bodies were dissected in cold PBS and stored in RNA/DNA shield (Zymo Research) at -80°C until RNA extraction.

value: larval fat body

tag: developmental stage

value: early wandering 3rd instar larvae

tag: population

value: Zambia


title: Zambia, late, rep3

value: late wandering third instar larvae


title: Zambia, prepupal, rep3

value: white prepupae


title: FloxCre_HFD_2

city: Cleveland

first: Ernest

last: Chan

address: 10900 Euclid Ave, Robbins E211

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: mm10
Supplementary files format and content: TSV text file containing FPKM for all samples and genes

source_name: Adipose tissue

growth_protocol: MBOAT7 Flox and ASKO genotype on C57Bl6/J Background

extract_protocol:
Mice were euthanized, and perfused with saline. The adipose tissue was removed and  flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NovaSeq 6000

treatment_protocol: Chow (Teklad, TD:130104) or HFD (Research Diets, D12492) feeding for 20 weeks

value: Adipose tissue

value: HFD

value: Flox Adiponectin Cre (ASKO)

tag: strain background


title: FloxCre_HFD_3


title: FloxCre_HFD_0


title: Zambia, early, rep2


title: Zambia, late, rep2


title: Zambia, prepupal, rep1


title: FloxCre_HFD_1


title: T56_Exp2_RV16_0_2_S90_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Control


title: T56_Exp2_POPG_500_S124_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T56_Exp2_PI_200_S130_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Zambia, late, rep1


title: T56_Exp2_RV16_4h__S76_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T56_Exp2_RV16_plus_POPG_500_S97_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Zambia, early, rep1


title: T56_Exp2_RV16_plus_PC_1000_S111_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PC


title: Flox_HFD_3

value: Flox


title: T56_Exp2_CONT_S83_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures


title: Zambia, prepupal, rep2


title: Flox_HFD_2


title: Netherlands, prepupal, rep3

value: Netherlands


title: T56_Exp1_T56_PI_200_S69_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI


title: Flox_HFD_1


title: Netherlands, late, rep3


title: T56_Exp1_RV16_plus_POPG_500_S117_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG


title: Netherlands, early, rep3


title: T56_Exp1_RV16_plus_PI_200_S123_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: FloxCre_Chow_3

value: Chow


title: T56_Exp2_PC_1000_S118_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T56_Exp1_RV16_plus_PC_1000_S129_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Netherlands, prepupal, rep2


title: Netherlands, late, rep2


title: FloxCre_Chow_1


title: FloxCre_Chow_2


title: Netherlands, prepupal, rep1


title: Netherlands, early, rep2


title: FloxCre_Chow_0


title: Flox_Chow_3


title: T56_Exp1_PC_1000_S55_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T56_Exp1_RV16_0_2_S110_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: T56_Exp1__OPG_500_S62_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Netherlands, late, rep1


title: T56_Exp1_CONT_S103_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Flox_Chow_2


title: Flox_Chow_1


title: Flox_HFD_0


title: Netherlands, early, rep1


title: MU26, late, rep2

growth_protocol: Larval staging was performed at 25°C. First instar larvae were density controled with 250 larvae per vial and allowed to develop on medium supplemented with 5% bromophenol blue (Carl Roth). Late wandering larvae were identified based on the color of their guts.

extract_protocol:
RNA was extracted with the Rneasy Plus Universal kit (Qiagen).
Novogene (Hong Kong) performed poly-A selection and library prep.

value: late wandering 3rd instar larvae

tag: isofemale strain

value: Germany


title: T51_Exp3_RV16_plus_POPG_500_S54_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: AKU seven days withdrawal condition, biological rep3

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-cosmetology (IVTD)

country: Belgium

institute: Vrije Universiteit Brussel

description: Gene expression data from liver tissue of AKU mice after seven days NTBC therapy discontinuation

hyb_protocol: 5.5 μg fragmented aRNA was hybridized to Affymetrix Mouse Gene 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, quantile normalization and summarization were done with Robust Multi-array Analysis algorithm using Transcriptome Analysis Console (TAC) 4.0.2 (Applied Biosystems)

source_name: AKU liver after seven days NTBC therapy withdrawal

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip Whole Transcriptome PLUS Reagent Kit  following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Unless specified otherwise, all mice received continuous NTBC treatment (8 mg/l) through their drinking water. Mice were fed with irradiated LabDiet® 5LJ5 chow ad libitum, which is a low-tyrosine and low-phenylalanine diet that acts as a surrogate for the protein-restricted diet of HT1 patients. All mouse caring, breeding and experimental procedures were performed in accordance with the ethical standards of the Vrije Universiteit Brussel and National Rules on Animal Experimentation. Mice were group-housed in individual ventilated cages (IVC) in a temperature (19 – 23 °C) and humidity (30 – 70% relative humidity) regulated environment with a 14/10-hour light/dark cycle under continuous NTBC treatment (8 mg/l) administered through their drinking water. Cage environment was enriched with cardboard shelters, nesting material and wooden sticks.

extract_protocol: Total RNA was extracted from all samples using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions. The isolated RNA was quantified at 260 nm using a Nanodrop spectrophotometer (Thermo Scientific). Total RNA was reverse transcribed into cDNA using iScriptTM cDNA Synthesis Kit (Bio-Rad) followed by cDNA purification with the Genelute PCR clean up kit (Sigma-Aldrich).

treatment_protocol: At the age of 11 weeks, NTBC therapy was discontinued for seven consecutive days for the FAH and AKU 7 days withdrawal group whereas it was administered continuously for the FAH and AKU control group.

tag: gender

value: male

value: liver

tag: age

value: 12 weeks

value: AKU


title: AKU seven days withdrawal condition, biological rep2

tag: disease state

tag: treatment

value: after seven days NTBC therapy discontinuation


title: AKU control condition, biological rep3

description: Gene expression data from liver tissue of AKU mice under NTBC treatment

source_name: AKU liver under continuous NTBC therapy

tag: tissue

value: NTBC treatment (control)


title: AKU seven days withdrawal condition, biological rep1


title: T56_Exp1_RV16_4h__S96_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: Flox_Chow_0

department: PQHS

value: Adipose tissue


title: AKU control condition, biological rep2


title: MU26, late, rep1

value: larval fat body


title: T51_Exp3_RV16_plus_PI_200_S61_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: KO rep2

city: wuhan

first: Jianfei

last: Liang

address: No. 237, Luoyu Road, Hongshan District,

institute: wuhan university

data_processing:
Raw sequencing data processed by Trim_Galore (v.0.6.6) for removing adapters and  low-quality base pairs. Reads were aligned with bowtie2 (v.2.3.5.1) to GRCm38  reference genome. Read counts were generated by featureCounts (v.2.0.1)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Genome_build: GRCm38

source_name: dental progenitor cells

extract_protocol:
RNA was extracted from freshly CD45-Ter119-Tie2- progenitor cells sorted by FACS from lower incisors using TRIzol reagent (Takara 9109)
RNA was reverse transcribed with oligo dT primers and template-switching oligos, followed by amplification by 14 PCR cycles with ISPCR oligos. The PCR program was as follows: 98°C for 3 min; 14 cycles of 98°C for 20 s, 67°C for 15 s, and 72°C for 6 min; 72°C for 5 min; and a 4°C hold. The amplified cDNAs were purified using AMPure XP beads (Beckman A63880) to abolish primer dimers. After purification, 50 ng cDNAs were fragmented using the TruePrep DNA Library Prep Kit (Vazyme, TD501).

tag: strain

value: dental pulp

value: post natal day30


title: KO rep1


title: T51_Exp3_RV16_plus_PC_1000_S68_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures

value: PC


title: MU17, late, rep1


title: MU14, late, rep3


title: MU17, late, rep2


title: T51_Exp3_RV16_0_2_S128_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Control


title: WT rep1

value: Ptipf/f;


title: T51_Exp3_RV16_4h_S122_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: WT rep2


title: T51_Exp3_POPG_500_S75_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: POPG


title: FAH seven days withdrawal condition, biological rep2

description: Gene expression data from liver tissue of FAH mice after seven days NTBC therapy discontinuation

source_name: FAH liver after seven days NTBC therapy withdrawal

value: FAH


title: AKU control condition, biological rep1


title: MU14, late, rep1

value: late wandering 3rd instar larvae

value: Germany


title: FAH seven days withdrawal condition, biological rep3

value: male

value: liver


title: T51_Exp3_PI_200_S82_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: PI


title: T51_Exp3_PC_1000_S89_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: MU12, late, rep2


title: T51_Exp3_CONT_S116_L004

description:
count.matrix.txt
count.matrix.vst.txt


title: MU12, late, rep1


title: WT_R2_60

city: Sevilla

first: Javier

last: Avalos

address: Faculty of Biology, Av. Reina Mercedes s/n

department: Genetics

country: Spain

institute: University of Seville

description: Re-analysis of GSM4832047

data_processing:
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Tophat 2.1.1 (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (Roberts, 2011; doi:10.1093/bioinformatics/btr355. http://cole-trapnell-lab.github.io/cufflinks/)
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the RNAseq quantitation pipeline with the improved mRNA annotation generated by Cuffmerge, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which needs raw counts for quantitation, was used to compare among conditions.
Assembly: FMJU01
Supplementary files format and content: Processed data are described in a single tab-delimited text file that includes raw counts for all samples, indicating probe, chromosome, start and end positions, and feature. Transcripts with no equivalent in FFUJ annotation are indicated as "null"

organism: Fusarium fujikuroi

source_name: Wild type 60 min illumination, replicate 2

growth_protocol: the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, the Petri dishes were either kept in the dark or illuminated for 15, 60, or 240 min.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols
400 bp libraries

treatment_protocol: Illumination was provided by a set of four fluorescent tubes (Philips TL-D 18 W/840) at a distance of 60 cm, yielding a light intensity of 7 W/m2.

value: wild strain FKMC1995

value: wild type

value: mycelium

value: 60 min illumination


title: WT_R3_60

description: Re-analysis of GSM4832051

source_name: Wild type 60 min illumination, replicate 3


title: WT_R3_0

description: Re-analysis of GSM4832049

source_name: Wild type dark, replicate 3

value: dark


title: MU10, late, rep2

value: larval fat body


title: MU14, late, rep2


title: WT_R2_0

description: Re-analysis of GSM4832045

source_name: Wild type dark, replicate 2


title: T51_Exp2_T51_CONT_S53_L004

description:
count.matrix.txt
count.matrix.vst.txt

value: Tracheal airway epithelial cultures


title: FAH control condition, biological rep3

description: Gene expression data from liver tissue of FAH mice under NTBC treatment

source_name: FAH liver under continuous NTBC therapy

value: 12 weeks

value: NTBC treatment (control)


title: MS53D3-071717-D3_ActEcoli

city: Cincinnati

first: Shouxiong

last: Huang

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati College of Medicine

data_processing:
Sequence reads aligned to the genome and converted to intensity counts
edgeR to identify differentially expressed genes between Act and InAct subsets with defined fold change (>4 folds) and p-values (<0.05).
Supplementary files format and content: tab-delimited text files include intensity counts for each Sample

source_name: blood

growth_protocol: human peripheral blood mononuclear cells were sorted using magnetic-conjugated anti-Va7.2 antibody and grew with RPMI1640 complete medium, and were further co-cultured with bacterial-incubated human MR1-overexpressed K562 cells for 16 hours.

extract_protocol:
mirVana kit (ThermoFisher)
NEBNext Ultra Directional RNA Library Prep 185 kit (New England BioLabs)

treatment_protocol: Cultured cells were sorted into two populations labeled by Va7.2+CD161+CD4-CD8+CD69+CD26++ (Act subset) and Va7.2+CD161+CD4-CD8+CD69+/-CD26+/- (InAct subset).

value: blood

tag: cell line

value: mononuclear cells

value: MAIT

tag: agent

value: ActEcoli


title: MS40D2-062317-D2_InActEcoli

value: InActEcoli


title: MS54D3-071717-D3_InActEcoli


title: MU10, late, rep1

value: late wandering 3rd instar larvae

value: Germany


title: MS51D3-071717-D3_Listeria

value: Listeria


title: WT_R1_60

description: Re-analysis of GSM4832043

source_name: Wild type 60 min illumination, replicate 1

value: wild strain FKMC1995

tag: genotype


title: FAH control condition, biological rep2

value: male

value: liver

value: FAH


title: FAH seven days withdrawal condition, biological rep1

value: after seven days NTBC therapy discontinuation


title: FAH control condition, biological rep1


title: WT_R1_0

description: Re-analysis of GSM4832041

source_name: Wild type dark, replicate 1

value: wild type

value: mycelium

value: dark


title: MS39D2-062317-D2_ActEcoli

tag: cell type