title: Day 7 post-LCMV infection (PD1KO), biological rep3

city: Seattle

first: Surojit

last: Sarkar

address: 1100 Olive Way, Suite 100

department: Department of Pediatrics and Laboratory Medicine

institute: University of Washington School of Medicine

description: Gene expression data from FACS purified GP33-specific pdcd1 knockout CD8 T cells isolated at day 7 post-LCMV infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridized cRNA was detected using streptavidin coupled to phycoerythrin

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A .Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The .CEL files were analyzed using Genespring GX 11.5 software following RMA normalization.

source_name: In vivo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For Naive samples, Wild type CD8 T cells were isolated from the spleen of P14 mice and FACS purified. For Day 7 effector samples, wild type (WT) C57Bl6 mice were adoptively co-transferred with 5x10E4 Db-GP33-specific naive WT P14 CD8 T cells and 5x10E4 Db-GP33-specific naive PD1 KO P14 CD8 T cells, and then infected with LCMV Armstrong. At day 7 post-infection, all mice were sacrificed and splenocytes were isolated for FACS sorting of WT and PD1 KO P14 CD8 T cells from the same mice.  For Day 100 memory samples, wild type (WT) C57Bl6 mice were adoptively transferred with 5x10E4 Db-GP33-specific naive WT P14 CD8 T cells and then infected with LCMV Armstrong. At day 100 post-infection, all mice were sacrificed and splenocytes were isolated for FACS sorting of WT memory P14 CD8 T cells.

extract_protocol: Trizol extraction of total RNA  from FACS purified CD8 T cells was performed according to the manufacturer's instructions.

treatment_protocol: First, CD8 T cells were enriched from the mouse splenocytes using a negative isolation protocol using a magnetic bead based kit from Stem cell technologies. The purified CD8 T cells (~70% pure) were fluorescently labeled for CD8 and Thy 1.1 for Fluorescence Activated Cell Sorting (FACS). Finally, CD8+ Db-GP33-specific T cells were FACS purified up to >98% purity for the next step of mRNA isolation. At least 10E6 purified CD8+ Db-GP33-specific T cells were used for each replicate from three distinct experiments to serve as the individual biological replicates.

value: FACS purified GP33-specific CD8 T cells from spleen

tag: days post-lcmv infection

value: Day 7 Effector

value: P14 cells from pdcd1 knockout C57 Black 6 background

tag: age

value: 8-10 weeks


title: Animal 207

status: Public on Jul 29 2021

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

description: Gene expression data from progressor animal 207.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: lung homogenate

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Female DO (generations 15, 16, 21, 22, 34) and C57BL/6J mice were purchased from The Jackson Laboratory (Bar Harbor, ME) and housed in sterile BSL3 conditions at the New England Regional Biosafety Laboratory (Tufts University, Cummings School of Veterinary Medicine, North Grafton, MA).

extract_protocol: One lung lobe from each mouse was homogenized in TRIzol™ and stored at -80C until RNA extraction using Pure Link mini-kits (Life Technologies, Carlsbad, CA).

treatment_protocol: At 8-10-weeks old, mice were infected with aerosolized Mtb strain Erdman bacilli (~100 in experiments 1 and 2; ~25 in experiments 3, 4, 5) using a CH Technologies nose-only exposure system. All mice were weighed at least twice per week, and examined daily for lethargy, respiratory distress, and body condition.

tag: class

value: progressor


title: Animal 227

description: Gene expression data from controller animal 227.

value: controller


title: Animal 224

description: Gene expression data from controller animal 224.


title: Ptch1+/−/Tis21 wild-type replicate 3

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: mRNA profiling in GCPs of Patched1+/−/Tis21 wild-type replicate 3 at P7

hyb_protocol: Aliquots (750 ng) of Cy3- and Cy5-labeled cRNA targets were co-hybridized on Whole Mouse Genome Microarrays (Design ID 014868; Agilent Technologies).

scan_protocol: Microarrays were scanned at 5 μm resolution using a GenePix Personal 4100A microarray scanner and the GenePix Pro 6.0 acquisition and data extraction software (Molecular Devices).

data_processing:
Raw data were processed and analyzed by GeneSpring 11.5.1 (Agilent Technologies).
Raw signal values were thresholded to 1, log2 transformed, normalized to the 50th percentile, and baselined to the median of all samples. Genes with a corrected p-value of <0.05 (one-way ANOVA followed by the Benjamini and Hochberg false discovery rate and the Tukey's post hoc test) were considered differentially expressed.

source_name: GCPs isolated at P7

label_protocol: cRNAs labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. A reference cRNA, labeled with Cy5-CTP was synthesized from 1 μg of RNA from adult mouse brain.

growth_protocol: The Tis21 knockout mice were generated in the C57BL/6 (B6) strain by gene targeting of exon II of the Tis21 gene, while Patched1 heterozygous (Ptch1+/−) mice were previously created in CD1 background by replacing exons 6 and 7 of the gene with the neomycin-resistance gene cassette. The crossing of Ptch1+/− with Tis21−/− mice generated Ptch1+/−/Tis21+/− double heterozygous mice, which were interbred to obtain Ptch1+/−/Tis21+/+ and Ptch1+/−/Tis21−/−  genotypes; the progeny was further interbred for at least six generations to achieve isogenicity.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

tag: cell type

value: GCPs isolated from the external granular layer (EGL) of the cerebellum

tag: genotype

value: Post-natal day 7

source_name: Adult mouse brain

tag: tissue

value: Adult mouse brain


title: Ptch1+/−/Tis21 wild-type replicate 4

description: mRNA profiling in GCPs of Patched1+/−/Tis21 wild-type replicate 4 at P7


title: WT Memory, biological rep1

state: WA

description: Gene expression data from FACS purified GP33-specific WT CD8 T cells isolated at day 100 post-LCMV infection

value: Day 100 Memory

value: P14 cells from Wild Type C57 Black 6 background


title: Ptch1+/−/Tis21 knockout replicate 4

description: mRNA profiling in GCPs of Ptch1+/−/Tis21 knockout replicate 4 at P7


title: Day 7 post-LCMV infection (PD1KO), biological rep2


title: Ptch1+/−/Tis21 wild-type replicate 2

description: mRNA profiling in GCPs of Patched1+/−/Tis21 wild-type replicate 2 at P7


title: WT Memory, biological rep2


title: WT Memory, biological rep3


title: Animal 201

description: Gene expression data from progressor animal 201.


title: Ptch1+/−/Tis21 wild-type replicate 1

description: mRNA profiling in GCPs of Patched1+/−/Tis21 wild-type replicate 1 at P7


title: Ptch1+/−/Tis21 knockout replicate 3

description: mRNA profiling in GCPs of Ptch1+/−/Tis21 knockout replicate 3 at P7


title: Animal 222

description: Gene expression data from controller animal 222.


title: Ptch1+/−/Tis21 knockout replicate 2

description: mRNA profiling in GCPs of Ptch1+/−/Tis21 knockout replicate 2 at P7


title: Animal 220

description: Gene expression data from controller animal 220.


title: Day 7 post-LCMV infection (WT), biological rep3

description: Gene expression data from FACS purified GP33-specific WT CD8 T cells isolated at day 7 post-LCMV infection


title: Day 7 post-LCMV infection (WT), biological rep2


title: Day 7 post-LCMV infection (PD1KO), biological rep1


title: Ptch1+/+/Tis21 wild-type replicate 3

description: mRNA profiling in GCPs of Patched1+/+/Tis21 wild-type replicate 3 at P7


title: Ptch1+/+/Tis21 wild-type replicate 2

description: mRNA profiling in GCPs of Patched1+/+/Tis21 wild-type replicate 2 at P7


title: Animal 215

description: Gene expression data from controller animal 215.


title: Ptch1+/+/Tis21 wild-type replicate 1

description: mRNA profiling in GCPs of Patched1+/+/Tis21 wild-type replicate 1 at P7


title: Ptch1+/−/Tis21 knockout replicate 1

description: mRNA profiling in GCPs of Ptch1+/−/Tis21 knockout replicate 1 at P7


title: Tetep_Control BR2

type: SRA

city: New Delhi

first: Amolkumar

middle: U.

last: Solanke

state: Delhi

address: Pusa Campus

department: Rice Genetics

country: India

institute: National Institute for Plant Biotechnology

library_source: transcriptomic

data_processing:
CASAVA pipeline 1.7 was used for data processing, demultiplexing and Bcl conversion for all samples
The spliced read mapper Tophat v2.0.9 and Bowtie was used to map reads indiviually of each biological replicate(BR) in resistant and suceptible lines against O. sativa Japonica Group cultivar Nipponbare; MSU release 7.
Cufflink v2.1.1 was used to  assemble aligned reads into transcript. Cufflink measures abundance in fragments per kilobase of exon per million fragments mapped (FPKM).  Cuffdiff was used to quantify transcript using the merged transcript assembly obtained from cuffmerge and to detect differentially expressed genes.
Genome_build: O. sativa Japonica Group cultivar Nipponbare; MSU release 7.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa Indica Group

source_name: Panicle

growth_protocol: Growth conditions of 16 h light (115 μ Mol m–2 s–1) and 8 h dark photoperiod at 25 ± 2°C

extract_protocol:
Panicles from resistant and suceptible rice lines were collected at 0, 48, 72 and 96 hours  after M. oryza infection, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: M.oryzae Conidia concentration was adjusted to 105spores/ml

value: Panicle

tag: Stage

value: Milking seed stage

tag: treatment

value: 48 hours after water injection

value: Resistant


title: Ptch1+/+/Tis21 knockout replicate 2

description: mRNA profiling in GCPs of Ptch1+/+/Tis21 knockout replicate 2 at P7


title: Ptch1+/+/Tis21 knockout replicate 3

description: mRNA profiling in GCPs of Ptch1+/+/Tis21 knockout replicate 3 at P7


title: Animal 214

description: Gene expression data from controller animal 214.


title: WT Naïve, biological rep3

description: Gene expression data from FACS purified GP33-specific CD8 T cells isolated from WT Naïve P14 mice

value: Day 0 Naive


title: Ptch1+/+/Tis21 knockout replicate 1

description: mRNA profiling in GCPs of Ptch1+/+/Tis21 knockout replicate 1 at P7


title: Day 7 post-LCMV infection (WT), biological rep1


title: Animal 205

description: Gene expression data from controller animal 205.


title: Animal 208

description: Gene expression data from controller animal 208.


title: WT Naïve, biological rep2


title: GA_Day 14_Control 2

city: Tsukuba

first: Yuki

last: Yamauchi

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from control diet fed mice gastrocnemius musle on day 14 after denervation

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45°C on GeneChip  Mus musculus Genome Array (MG-430 PM). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) [https://www.gsea-msigdb.org/gsea/index.jsp]
RMA

source_name: gastrocnemius muscle in denervated mice fed the control diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: After a week of acclimatization, the mice were randomly divided into two groups: fed either control or maslinic acid (0.27% content) diets. After 1 week, the sciatic nerve of both legs was cut and a 5-mm piece was excised under anesthesia. During the development of disuse muscle atrophy, the mice continued to receive the control or maslinic acid diet until the end of the experiment. On days 14 after surgery, the mice were anesthetized and the gastrocnemius muscle was excised, weighed, quickly frozen in liquid nitrogen, and stored at -80℃ until needed for analyses.

extract_protocol: Total RNA of gastrocnemius muscle was isolated using Isogen reagent (Nippon Gene Co., Ltd., Tokyo, Japan) and then purified using the RNeasy Mini Kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Seven-week-old male ICR mice were housed under conventional conditions (24°C ± 1°C, 50% ± 10% relative humidity with a 12 h light/dark cycle). The mice were fed the AIN-93G diet and were provided ad libitum access to the diet and water for 24 h.

tag: sample type

value: gastrocnemius muscle, male ICR mice, 14 days after denervation


title: Tetep_Control BR1


title: Mouse cuSCC 21

city: Tampa

first: Michael

middle: B.

last: Mann

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

description: Biomaterial Collected By: Michael B. Mann, Ph.D., H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA

hyb_protocol: Samples were hybridized with GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) and scanned at the University of Otago Genomics & Bioinformatics Facility Microarray Core.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processeded in R (version 2.15, www.r-project.org) using the rma function of the affy package (quantile normalization, no background correction). Subsequent data analysis and statistical evaluations were performed with customized R scripts (version 2.15, http://www.r-project.org/).

molecule: polyA RNA

label_protocol: RNA was labelled using a Affymetrix 3' IVT Express kit Cat # 901229 using 100ng of total RNA for each sample. Labelling was preformed according to manufacturer's instructions

growth_protocol: Aging mice until spontaneous skin mass formation.

extract_protocol: RNA was extracted using a NORGEN Bioteck Animal Tissue RNA Purification kit Cat #25700 according to manufacturer's instructions

treatment_protocol: Flash Frozen tissues were collected at necropsy and stored at -80ºC until RNA isolation was performed.

tag: tumor id

tag: Sex

value: F

value: Skin, tumor

tag: diagnosis

value: Squamous Cell Carcinoma, cutaneous

tag: disease stage

value: terminal

tag: zmiz1 insertion

value: N


title: GA_Day 14_Maslinic acid 2

description: Gene expression data from maslinic acid diet fed mice gastrocnemius musle on day 14 after denervation

source_name: gastrocnemius muscle in denervated mice fed the maslinic acid diet


title: GA_Day 14_Control 3


title: Tetep_96hpi BR2

value: 96 hours after M.oryzae infection


title: Tetep_96hpi BR1


title: GA_Day 14_Control 1


title: GA_Day 14_Maslinic acid 3


title: GA_Day 14_Maslinic acid 1


title: Tetep_72hpi BR1

value: 72 hours after M.oryzae infection


title: Tetep_48hpi BR2

value: 48 hours after M.oryzae infection


title: Animal 211

description: Gene expression data from controller animal 211.

value: controller


title: HP2216_Control BR2

value: Susceptible


title: Animal 198

description: Gene expression data from controller animal 198.


title: Tetep_48hpi BR1


title: WT Naïve, biological rep1

value: FACS purified GP33-specific CD8 T cells from spleen

value: P14 cells from Wild Type C57 Black 6 background

value: 8-10 weeks


title: HP2216_Control BR1

value: Panicle

value: Milking seed stage

value: 48 hours after water injection


title: Mouse cuSCC 19

institute: H. Lee Moffitt Cancer Center and Research Institute

value: Y


title: HP2216_96hpi BR1


title: Animal 204

description: Gene expression data from controller animal 204.


title: HP2216_96hpi BR2


title: Tetep_72hpi BR2

value: Resistant


title: HP2216_72hpi BR1


title: HP2216_48hpi BR2


title: HP2216_48hpi BR1


title: Animal 218

description: Gene expression data from controller animal 218.


title: Mouse cuSCC 20

value: F

value: Skin, tumor


title: Mouse cuSCC 16

value: Squamous Cell Carcinoma, cutaneous

value: terminal


title: Animal 217

description: Gene expression data from controller animal 217.


title: Mouse cuSCC 18


title: bulk_RNA-Seq_V577_Ep cells (replicate 3)

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: Sample 6

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
For sc-RNA-Seq additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files, count tables, matrix, barcodes and gene name files

growth_protocol:
Sample 1-6: KP cells were injected I.V. into syngeneic mouse to form orthotopic lung tumor, tumor formation was confirmed by MRI
Sample 7-10: KP cells were injected I.V. into syngeneic mouse to form orthotopic lung tumor, tumor formation was confirmed by MRI

extract_protocol:
Sample 1-6: Tumor nodules were harvested from the treated mice, and dissociated into single cell suspensions. Epcam+ tumor cells were sorted out, total RNA were extracted
Sample 1-6: Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 machine using 150bp paired end reads.
Sample 1-6: Bulk RNA-Seq
Sample 7-10: Tumor nodules were harvested from the treated mice, and dissociated into single cell suspensions. Magnetic bead based live cell enrichment was performed on the single cell suspension. Cell suspensions from different mice within each treatment code were hashtagged and pooled.
Sample 7-10: Libraries were prepared using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1
Sample 7-10: 10X scRNA-Seq

treatment_protocol:
Sample 1-6: Tumor-bearing mice were treated with respective treatments for 11 days
Sample 7-10: Tumor-bearing mice were treated with respective treatments for 11 days

tag: hto

value: Epcam+ tumor cells

value: Vehicle


title: Animal 213

description: Gene expression data from controller animal 213.


title: bulk_RNA-Seq_V555_Ep cells (replicate 2)

description: Sample 5


title: bulk_RNA-Seq_V549_Ep cells (replicate 1)

description: Sample 4


title: Mouse cuSCC 15

value: M


title: Animal 206

description: Gene expression data from controller animal 206.

value: controller


title: Animal 200

description: Gene expression data from controller animal 200.


title: Mouse cuSCC 17

value: N


title: Animal 202

description: Gene expression data from controller animal 202.


title: bulk_RNA-Seq_S597_Ep cells (replicate 3)

description: Sample 3


title: bulk_RNA-Seq_S544_Ep cells (replicate 1)

description: Sample 1


title: Animal 199

description: Gene expression data from controller animal 199.


title: NB-1 treated with 5-aza-dC

type: genomic

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

institute: National Cancer Center

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: The data were analyzed using GenomeStudio Methylation Module Software (v1.9.0). Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

growth_protocol: NB-1 cell line was maintained in RPMI1640 medium with 10% FBS.

extract_protocol: High-quality DNA was extracted by the phenol/chloroform method.

treatment_protocol: Cells were seeded on Day 0. On Days 1, 2, and 3, the medium was replaced with a medium containing 0.3 µM of 5-aza-dC. On Day 4, the cells were collected for genomic DNA extraction.

tag: cell line


title: bulk_RNA-Seq_S595_Ep cells (replicate 2)

description: Sample 2


title: Animal 197

description: Gene expression data from controller animal 197.


title: NB-1 treated with mock

value: mock


title: Mouse cuSCC 14


title: Animal 196

description: Gene expression data from controller animal 196.


title: Mouse cuSCC 11


title: Mouse cuSCC 12


title: Animal 194

description: Gene expression data from controller animal 194.


title: Mouse cuSCC 13


title: Mouse cuSCC 10


title: Mouse cuSCC 9


title: Animal 253

description: Gene expression data from non-infected animal 253.

value: non-infected


title: Mouse cuSCC 8


title: Animal 252

description: Gene expression data from non-infected animal 252.


title: Mouse cuSCC 6

description: Biomaterial Collected By: Michael B. Mann, Ph.D., H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA


title: Animal 195

description: Gene expression data from controller animal 195.


title: Mouse cuSCC 3


title: Mouse cuSCC 4


title: Mouse cuSCC 5


title: Animal 249

description: Gene expression data from non-infected animal 249.


title: Animal 251

description: Gene expression data from non-infected animal 251.


title: Animal 250

description: Gene expression data from non-infected animal 250.


title: Mouse cuSCC 7


title: Mouse cuSCC 2


title: Sample_O3_33_ILC2

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Base-calling: Illumina  software
Aligned to the mm10 genome (Gencode, release M23) using STAR (v2.7.3a)
Quantification using htseq-count function from HTSeq framework (v0.9.1)
Differential expression analysis was done using DESeq function from DeSeq2
See detailed methods in Goldberg et al., Cell Metabolism 2021
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated file with raw gene counts

source_name: sorted ILC2

extract_protocol:
Total RNA was extracted with RLT buffer
Bulk RNA libraries were prepared for sequencing using standard Illumina protocols.
101bp paired-end sequencing

tag: strain

tag: developmental stage

value: old

value: visceral adipose tissue (VAT)


title: Sample_O2_33_ILC2


title: WaGa_DOXneg_3

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Genome_build: GRCh38.74
Supplementary_files_format_and_content: WaGa_Cuff_Gene_Counts.csv

growth_protocol: WaGa cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 2 mM glutamine.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline.

value: WaGa

value: Merkel cell carcinoma

tag: tag

value: puromycin resistance

value: vehicle


title: WaGa_DOXpos_2

value: 500 ng/ml doxycycline


title: WaGa_DOXpos_3


title: WaGa_DOXneg_2


title: Sample_O1_33_ILC2


title: WaGa_DOXneg_1


title: WaGa_DOXpos_1


title: Wt 40DAP Replicate 2b

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Seeds were sterilized, grown and transformed according to Boisson-Dernier et al (2001). Germinated and transformed roots seeds were cultivated with Fahräeus medium, with appropriated antibiotics, with sixteen hours of photoperiod, at 20°C.

extract_protocol: Roots total RNA was extract with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommandations.

treatment_protocol: Binary vector pK7GW2D (Karimi et al, 2002) containing the full-lenght GUS gene was introduced in Arqua1 strain of Agrobacterium rhizogenes by a freeze-thaw method. Thirty hours age old apex roots were cut and scrapped on fourty eight hours age old transformed ARqua1 culture before being placed on culture medium

value: seeds

tag: genetic background

value: wild-type

tag: phenotype

value: development stage

tag: age

value: 40 days after flowering

tag: harvest date


title: NF3185 40DAP Replicate 1

tag: tissue

tag: genotype


title: NF3185 40DAP Replicate 2

tag: treatment


title: Sample_A3_33_ILC2

value: adult

tag: cell type


title: HP2216_72hpi BR2

value: Panicle

tag: Stage

value: Milking seed stage

value: 72 hours after M.oryzae infection

value: Susceptible


title: Sample_A2_33_ILC2


title: Wt 40DAP Replicate 1b


title: Mouse cuSCC 1

tag: tumor id

tag: Sex

value: M

value: Skin, tumor

tag: diagnosis

value: Squamous Cell Carcinoma, cutaneous

value: terminal

value: Y


title: NF3185 24DAP Replicate 2

value: 24 days after flowering


title: Wt 24DAP Replicate 2b


title: DL5216B

city: BETHESDA

first: Benura

last: Azeroglu

state: Maryland

address: National Cancer Institute, NIH, Building 37, Room 1108 37 Convent Drive

institute: NIH

library_source: genomic

data_processing:
Alignment: reads were mapped to bespoke reference sequence (DL5216_in_lab_reference_genome) using the default parameters of software Bowtie 2 (Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods, 9, 357-359).
Count data was extracted from each de-duplicated alignment file (in .bam format) using HTSeq software (Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2)) and the distribution of reads along the E. coli genome was visualized using the Integrated Genome Browser.
Genome_build: DL5216_in_lab_reference_genome.fasta
Supplementary_files_format_and_content: bedgraph

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

value: lacZY::XXX mhpA::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX- rph+ cynX X- codBX- prpEX- mhpCX-

tag: antibody

value: anti-RecA


title: Wt 24DAP Replicate 1b

value: seeds


title: NF3185 16DAP Replicate 2

value: 16 days after flowering


title: NF3185 24DAP Replicate 1

value: development stage


title: Sample_A1_33_ILC2

value: visceral adipose tissue (VAT)


title: DL5216A


title: IRX3_WT_1

city: Beijing

first: Jingfei

last: Yao

state: State / Province

address: yiheyuan street

country: China

institute: Peking university

data_processing:
bcl2fq used for basecalling.
Sequenced reads were trimmed by Trimmomatic, then mapped to mm10 whole genome using HISAT2 (v2.1.0)
Reads Per Kilobase of exon model per Million mapped reads (RPKM) and Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated by StringTie (v1.3.5)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BMDM

growth_protocol: The macrophage precursors were differentiated in DMEM supplemented with 10% FBS, 20 nM M-CSF and 1% P/S on Bacteriological Petri Dishes (Falcon) at 37℃ in a humidiﬁed 5% CO2  incubator for 7 days.

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

treatment_protocol: 100ng/ml LPS for 4h

value: BMDM

tag: overexpression

value: LPS 4 h


title: IRX3_S361A_1

tag: strain


title: IRX3_S389A_1


title: IRX3_S361A_3


title: IRX3_S389A_3


title: IRX3_S361A_2


title: IRX3_WT_2


title: IRX3_S389A_2


title: IRX3_WT_3


title: GFP_3

value: GFP


title: GFP_2


title: rPHGDH S55A-2 rep1

city: Shanghai

first: Ke

last: Zheng

address: No. 1630 East Road

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using Seqtk.
Spliced mapping algorithm of Hisat2 (version 2.0.4) was used to mapping Genome for the pretreated reads, and the default parameters were used. The adopted genomic version is GRCH38.
Stringtie (version 1.3.0) was used to count Fragments from each gene after Hisat2 comparison, and then normalized with TMM (mean of M values). Finally, Perl script was used to calculate the FPKM value of each gene.
Differential genes between samples were analyzed by edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel worksheets include FPKM values and count values for each Sample ...

source_name: pancreatic cancer cells SW1990

growth_protocol: SW1990 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cDNA microarray analysis was performed for cells cultured in the glucose-free DMEM for 24 h.

value: spleen metastasis of pancreatic adenocarcinoma

tag: cell line

value: glucose deprivation


title: WT rPHGDH-2 rep1


title: WT rPHGDH-2 rep3


title: rPHGDH S55A-2 rep2


title: WT rPHGDH-2 rep2


title: rPHGDH S55A-2 rep3


title: T cell NP W250S rep3

city: New Haven

first: Carrie

last: Lucas

state: CT

address: 300 George Street

institute: Yale University

description:
Elf4 W250S Non-Pathogenic Th17 RNA-seq CPM
3996_NP_274_303_S30_L004

data_processing:
ATAC-seq: base trimming, alignment via BWA, peak calling with MACS2, annotated with mm10, differential analysis with GSA, filtered by FC > 2 (Partek 10.0.21.0411)
RNA-seq Th17: Alignment - Bowtie 2, Assembly: mm10, Differential analysis: DEseq2(R), Filter: 0.05 FDR, 2 FC, normalized CPM (Partek 10.0.21.0411)
RNA-seq BMDM: Alignment - Bowtie 2, Assembly: mm10, Differential analysis: DEseq2(R), Filter: 0.05 FDR, 2 FC, normalized CPM (Partek 10.0.21.0411)
Genome_build: mm10
Supplementary_files_format_and_content: T cell RNA-seq: normalized reads CPM
Supplementary_files_format_and_content: T cell ATAC-seq: annotated peaks MACS2
Supplementary_files_format_and_content: BMDM RNA-seq: normalized reads CPM

source_name: Non-Pathogenic Th17 Cell

extract_protocol:
T-cell RNA-seq: RNA was isolated from whole cells using RNeasy kit (Cat. # 74104)
T-cell ATAC-seq: DNA isolation was performed by GeneWiz
RNA-seq BMDM: RNA was isolated from whole cells using RNeasy kit (Cat. # 74104)
T cell RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
T-cell ATAC-seq: DNA libraries were repared for sequencing using standard Illumina protocols
RNA-seq BMDM: Libraries were prepared for sequencing using standard illumina protocols for RNA-seq

value: Elf4 W250S

tag: time point

value: 48 hours

value: Differentiated with IL-6, TGF-beta

value: Non-Pathogenic Th17 Cell


title: GFP_1


title: NF6003 40DAP Replicate 2

tag: genetic background

value: 40 days after flowering


title: rPHGDH S371A-1 rep3


title: Wt 16DAP Replicate 1b

value: wild-type

tag: phenotype


title: Wt 16DAP Replicate 2b

tag: age


title: NF6003 40DAP Replicate 1

tag: harvest date


title: T cell NP WT rep3

description:
Elf4 W250S Non-Pathogenic Th17 RNA-seq CPM
3995_NP_188_362_S27_L004

value: WT


title: NF6003 40DAP Replicate 3

tag: tissue


title: NF3185 16DAP Replicate 1

tag: genotype


title: T cell NP W250S rep2

description:
Elf4 W250S Non-Pathogenic Th17 RNA-seq CPM
3994_NP_286_291_S29_L004

tag: treatment


title: T cell NP WT rep1

description:
Elf4 W250S Non-Pathogenic Th17 RNA-seq CPM
3992_NP_239_338_S25_L004

tag: cell type


title: T cell NP W250S rep1

description:
Elf4 W250S Non-Pathogenic Th17 RNA-seq CPM
3989_NP_176_374_S28_L004


title: WT rPHGDH-1 rep3


title: T cell P W250S 48 hours rep3

description:
Elf4 W250S Pathogenic Th17 RNA-seq CPM
3996_P_251_326_S24_L004

source_name: Pathogenic Th17 Cell

value: Differentiated with IL-6, IL-23 IL-1b

value: Pathogenic Th17 Cell


title: rPHGDH S371A-1 rep2


title: T cell NP WT rep2

description:
Elf4 W250S Non-Pathogenic Th17 RNA-seq CPM
3993_NP_227_350_S26_L004


title: T cell P WT 48 hours rep1

description:
Elf4 W250S Pathogenic Th17 RNA-seq CPM
3992_P_189_361_S19_L004


title: T cell P WT 48 hours rep3

description:
Elf4 W250S Pathogenic Th17 RNA-seq CPM
3995_P_287_290_S21_L004


title: T cell P WT 48 hours rep2

description:
Elf4 W250S Pathogenic Th17 RNA-seq CPM
3993_P_177_373_S20_L004


title: Wt 40DAP Replicate 3a

value: seeds


title: WT rPHGDH-1 rep2


title: T cell P W250S 48 hours rep1

description:
Elf4 W250S Pathogenic Th17 RNA-seq CPM
3989_P_275_302_S22_L004


title: Wt 40DAP Replicate 2a

value: development stage


title: T cell P W250S 48 hours rep2

description:
Elf4 W250S Pathogenic Th17 RNA-seq CPM
3994_P_263_314_S23_L004


title: T cell W250S 0 hours rep3

description:
Elf4 W250S Naive CD4 RNA-seq CPM
3988_228_349_S18_L004

source_name: Naive CD4 T cell

value: 0 hours

value: Naive CD4 T cell


title: T cell WT W250S 0 hours rep3

description:
Elf4 W250S Naive CD4 RNA-seq CPM
3979_264_313_S15_L004


title: T cell W250S 0 hours rep1

description:
Elf4 W250S Naive CD4 RNA-seq CPM
3980_252_325_S16_L004


title: T cell W250S 0 hours rep2

description:
Elf4 W250S Naive CD4 RNA-seq CPM
3985_240_337_S17_L004


title: WT rPHGDH-1 rep1


title: T cell WT W250S 0 hours rep2

description:
Elf4 W250S Naive CD4 RNA-seq CPM
3978_276_301_S14_L004


title: NF6003 32DAP Replicate 3

value: 32 days after flowering


title: NF6003 32DAP Replicate 1


title: Wt 32DAP Replicate 3


title: T cell WT W250S 0 hours rep1

description:
Elf4 W250S Naive CD4 RNA-seq CPM
3977_288_289_S13_L004


title: T cell WT 0 hours rep 3

description:
Elf4 KO Naive CD4 RNA-seq CPM
WT3_255_322_S3_L002


title: muscle stem cells, 27 month old, rep 4

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
mtDNA
S20

data_processing:
Data was processed using an in-house mtDNA workflow (https://git.biohpc.swmed.edu/CRI/mtDNASeq).
Sequences were checked and trimmed for quality control using FastQC 0.11.8 and TrimGalore 0.6.4.
Reads were mapped to the Mus musculus mitochondrial genome GRCm38 using MapSplice2 2.2.1. Paired-und reads were de-duplicated (Picard 2.23.1) and qualidy filtered (SAMtools 1.9.0).
Per-base sequencing depth and point mutations were assessed using bam-readcount 0.8.0.
To avoid false positives and mtDNA-derived nuclear pseudogenes, variants were called when detected on both strands with >50 supporting reads, and greater than 0.5% allelic frequency.
Large deletions were determined using the non-canonical junction detection mode of MapSplice2. Junction coordinates for the deletion were extracted by regtools 0.5.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files for each sample containing position and strand-specific read counts.

source_name: Muscle stem cells

growth_protocol: Animals were maintained on a standard chow dite, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
Skeletal muscle was dissected and digested with Collagenase II and Dispse at 37C for 30 minutes. Mononucleated cells were collected through a 70micron cell strainer. MuSCs were FACS purified as CD34+, CD31/CD45/DAPI/Sca1- populations. Total DNA was purified using the QIAamp DNA Micro Kit (Qiagen #56304).
mtDNA sequences were enriched using the Repli-G Mitochondrial DNA kit (Qiagen 151023). Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina FC-131-1096) following manufacturer instructions.

treatment_protocol: No treatments were performed on these animals.

value: Muscle stem cells, purified from mouse skeletal muscle

value: 27 months


title: muscle stem cells, 27 month old, rep 1

description:
mtDNA
S17


title: muscle stem cells, 18 month old, rep 4

description:
mtDNA
S16

value: 18 months


title: T cell KO 0 hours rep3

description:
Elf4 KO Naive CD4 RNA-seq CPM
KO3_192_358_S6_L002

value: Elf4 KO


title: muscle stem cells, 27 month old, rep 3

description:
mtDNA
S19


title: muscle stem cells, 18 month old, rep 3

description:
mtDNA
S15


title: muscle stem cells, 27 month old, rep 2

description:
mtDNA
S18


title: T cell WT 0 hours rep 2

description:
Elf4 KO Naive CD4 RNA-seq CPM
WT2_267_310_S2_L002


title: NF6003 32DAP Replicate 2


title: T cell WT 0 hours rep1

description:
Elf4 KO Naive CD4 RNA-seq CPM
WT1_279_298_S1_L002


title: T cell KO 0 hours rep1

description:
Elf4 KO Naive CD4 RNA-seq CPM
KO1_243_334_S4_L002


title: T cell KO 0 hours rep2

description:
Elf4 KO Naive CD4 RNA-seq CPM
KO2_231_346_S5_L002


title: muscle stem cells, 18 month old, rep 2

description:
mtDNA
S14


title: T cell KO 0 hours rep4

description:
Elf4 KO Naive CD4 RNA-seq CPM
KO4_180_370_S7_L002


title: BMDM WT 16 hours LPS rep3

description:
BMDM normalized CPM RNA sequencing LPS timecourse
29

source_name: BMDM 7 days M-CSF

value: 16 hours

value: LPS 100ng/ml

value: BMDM


title: BMDM WT 16 hours LPS rep2

description:
BMDM normalized CPM RNA sequencing LPS timecourse
28


title: BMDM KO 16 hours LPS rep3

description:
BMDM normalized CPM RNA sequencing LPS timecourse
30


title: Wt 32DAP Replicate 2


title: NF6003 24DAP Replicate 2

value: 24 days after flowering


title: BMDM KO 16 hours LPS rep2

description:
BMDM normalized CPM RNA sequencing LPS timecourse
27


title: muscle stem cells, 18 month old, rep 1

description:
mtDNA
S13


title: Wt 24DAP Replicate 3a

value: wild-type


title: NF6003 24DAP Replicate 1


title: NF6003 24DAP Replicate 3


title: Wt 32DAP Replicate 1


title: muscle stem cells, 12 month old, rep 4

description:
mtDNA
S12

value: 12 months


title: BMDM WT 16 hours LPS rep1

description:
BMDM normalized CPM RNA sequencing LPS timecourse
25

value: WT


title: BMDM KO 0 hours rep3

description:
BMDM normalized CPM RNA sequencing LPS timecourse
14


title: BMDM KO 0 hours rep2

description:
BMDM normalized CPM RNA sequencing LPS timecourse
11


title: BMDM WT 0 hours rep2

description:
BMDM normalized CPM RNA sequencing LPS timecourse
12


title: BMDM WT 0 hours rep3

description:
BMDM normalized CPM RNA sequencing LPS timecourse
13


title: BMDM KO 0 hours rep1

description:
BMDM normalized CPM RNA sequencing LPS timecourse
10


title: muscle stem cells, 12 month old, rep 1

description:
mtDNA
S9


title: muscle stem cells, 12 month old, rep 2

description:
mtDNA
S10


title: muscle stem cells, 12 month old, rep 3

description:
mtDNA
S11


title: BMDM WT 0 hours rep1

description:
BMDM normalized CPM RNA sequencing LPS timecourse
9


title: BMDM KO 16 hours LPS rep1

description:
BMDM normalized CPM RNA sequencing LPS timecourse
26


title: Wt 24DAP Replicate 1a


title: muscle stem cells, 6 month old, rep 4

description:
mtDNA
S8

value: 6 months


title: BMDM KO 4 hours LPS rep3

description:
BMDM normalized CPM RNA sequencing LPS timecourse
6

value: 4 hours


title: T cell KO ATAC rep3

description:
Elf4 Naive CD4 ATAC-seq Annotated Quantified Peaks
5398


title: BMDM WT 4 hours LPS rep2

description:
BMDM normalized CPM RNA sequencing LPS timecourse
4


title: muscle stem cells, 6 month old, rep 3

description:
mtDNA
S7


title: muscle stem cells, 6 month old, rep 2

description:
mtDNA
S6


title: rPHGDH S371A-1 rep1

value: spleen metastasis of pancreatic adenocarcinoma

value: glucose deprivation


title: BMDM WT 4 hours LPS rep3

description:
BMDM normalized CPM RNA sequencing LPS timecourse
5


title: NF6003 16DAP Replicate 3

value: seeds

value: development stage

value: 16 days after flowering


title: T cell WT ATAC rep3

description:
Elf4 Naive CD4 ATAC-seq Annotated Quantified Peaks
5397

value: 0 hours

value: Naive CD4 T cell


title: NF6003 16DAP Replicate 1


title: Wt 24DAP Replicate 2a


title: NF6003 16DAP Replicate 2


title: Wt 16DAP Replicate 3a


title: Wt 16DAP Replicate 2a


title: muscle stem cells, 6 month old, rep 1

description:
mtDNA
S5

value: Muscle stem cells, purified from mouse skeletal muscle


title: BMDM WT 4 hours LPS rep1

description:
BMDM normalized CPM RNA sequencing LPS timecourse
1


title: T cell KO ATAC rep2

description:
Elf4 Naive CD4 ATAC-seq Annotated Quantified Peaks
5396

value: Elf4 KO


title: muscle stem cells, 2 month old, rep 4

description:
mtDNA
S4

value: 2 months


title: ChAT-eGFPpos_IWAT_macrophages_3

city: Ann Arbor

first: Shanshan

last: Liu

state: Michigan

address: 210 Washtenaw Avenue

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
Reads were trimmed using CutAdapt v2.3 (Martin, EMB-net.journal, 2011)
Trimmed reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin, Bioinformatics 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, BMC Bioinformatics, 2011)
FastQC (Andrews, 2010) (v0.11.8) was run on .bam files in a post-alignment step, including both aligned and un-aligned reads, to ensure data quality.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: IWAT macrophages

growth_protocol: ChAT-eGFP mice were housed in 12h light/dark cycle with ad libitum access to water and chow food

extract_protocol:
IWAT was harvested and digested to yield the stromal vascular fraction (SVF). SVF cells were stained with fluorescently-conjugated antibodies and ChAT-eGFP+ or ChAT-eGFP- macrophages (live CD45+ CD11b+ CD64+ Ly6G- SiglecF- NK1.1- CD3- CD19-) were isolated by FACS. Cells were sorted directly into NEBNext Lysis Buffer containing RNase inhibitor then flash frozen.
Library preparation was undertaken using the NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB #E6420) according to manufacturer’s instructions. Quality control assessment on prepared libraries was performed using Agilent TapeStation. Paired end (150 bp) sequencing was performed on an Illumina NovaSeq (S4).

treatment_protocol: ChAT-eGFP mice were housed at 4oC for 4h prior to harvest

value: IWAT

value: Macrophages

tag: mouse genotype

value: ChAT-eGFP (Jax 007902)

tag: mouse treatment

value: 4 degrees C, 4h


title: Wt 40DAP Replicate 1a

value: wild-type

value: 40 days after flowering


title: ChAT-eGFPpos_IWAT_macrophages_2


title: T cell WT ATAC rep2

description:
Elf4 Naive CD4 ATAC-seq Annotated Quantified Peaks
5395

value: WT


title: Wt 16DAP Replicate 1a


title: BMDM KO 4 hours LPS rep1

description:
BMDM normalized CPM RNA sequencing LPS timecourse
2

value: 4 hours

value: LPS 100ng/ml

value: BMDM


title: BMDM KO 4 hours LPS rep2

description:
BMDM normalized CPM RNA sequencing LPS timecourse
3


title: T cell KO ATAC rep1

description:
Elf4 Naive CD4 ATAC-seq Annotated Quantified Peaks
5344


title: shSOX9 II_(HG-U133_Plus_2)

city: Donsotia-San Sebastian

first: charles

last: lawrie

address: Paseo Mikeletegi, 83- planta 3

department: Oncology

country: Spain

institute: Biodonostia Research Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix TAC v.4.0

source_name: GNS166 glioblastoma cell line

label_protocol: standard Affymetrix protocol

growth_protocol: Cells  harboring the pLKO.1-sh-hSOX9-1 plasmid or pLKO.1 puro empty vector in biological triplicate. RNA extracted and gene expression with U133plus2.0 microarrays

extract_protocol: 0.5 μg of RNA (trizol total RNA)

value: SOX9 shRNA


title: muscle stem cells, 2 month old, rep 2

description:
mtDNA
S2


title: shSOX9 I_(HG-U133_Plus_2)


title: ChAT-eGFPpos_IWAT_macrophages_1


title: shSOX9 III_(HG-U133_Plus_2)


title: T cell WT ATAC rep1

description:
Elf4 Naive CD4 ATAC-seq Annotated Quantified Peaks
5342


title: muscle stem cells, 2 month old, rep 3

description:
mtDNA
S3


title: ChAT-eGFPneg_IWAT_macrophages_4


title: Spleen, 2YP

city: Chengdu

first: hu

last: chen

state: Sichuan

address: 211 huimin road

institute: sichuan agriculture university

description: mRNA derived from spleen tissue of fish oil diet postprandial feed

data_processing:
The de novo assembly was performed on cleaned reads using Trinity (Grabherr et al., 2011). Before assembly, raw reads were trimmed by removing adaptor sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 bp were all trimmed. The resulting high-quality sequences were used in subsequent assembly. Briefly, the raw reads were assembled into the unique sequences of transcripts in Inchworm via greedy K-mer extension (k-mer 25).
After mapping of reads to Inchworm contig bundles, Chrysalis incorporated reads into de Bruijn graphs. Butterfly then processed the individual graphs in parallel, reporting full-length transcripts and paralogous genes. After assembly, the open reading frame (ORF) of each unisequence was predicted by using Trinity software. Unisequences were used for BLAST search and annotation against the NR, NT, STRING (http://string-db.org/) (Franceschini et al., 2013), COG (http://www.ncbi.nlm.nih.gov/COG/), KEGG (http://www.genome.jp/kegg/) databases using an E-value cut-off of 10-5 (Camacho et al., 2009). Functional annotation by gene ontology (GO, http://www.geneontology.org) terms was analysed by using BLAST2GO software (NCBI) (Conesa et al., 2005).
Supplementary_files_format_and_content: TPMs

organism: Acipenser dabryanus

source_name: spleen

growth_protocol: Forty Yangtze sturgeon (approximate initial weight 358.64 ± 37.1 g) were randomly sorted into 2 round fish pond (2 m in diameter, 2.5 m3) and fed the different fat sources diets once daily at 16:00. The feeding trial lasted for 7 weeks. At the termination of the feeding trial, six individual from each pond (fish oil diet longterm feed, FOLF; soybean oil diet longterm feed, SOLF), were caught and sampled 1 hour before feeding (15:00). After feeding for 1 hour, another 6 fish from each different group (fish oil diet postprandial feed, FOPF; soybean oil diet postprandial feed, SOPF) were captured and sampled.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
Total RNA was extracted from liver using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. RNA samples were digested using DNase I to remove potential genomic DNA and stored at -80℃. RNA was quantified and quality was assessed by NanoDrop Spectrophotometer 2000c (NanoDrop Technologies, Wilmington, DE, USA) and 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and all samples were standardised to 500 ng/μl. Three samples from per group at each time point were used for RNA library construction which OD ratios of 260/280 and 260/230 greater than 1.8 and RNA Integrity Number (RIN) greater than 8. RNA-seq library preparation and sequencing were carried out by Annoroad Gene Technology Co., Ltd (Beijing, China), forty five sequencing libraries were constructed using a TruSeq™ RNA Sample Preparation Kit (Illumina) according to the manufacturer’s directions. The next step was KAPA quantifcation and dilution, after which the library was sequenced on an Illumina HiSeq.2500 with 125-bp paired-end reads. After removing adaptor sequences, ambiguous N nucleotides (those an N ratio <5%) and low quality sequences (reads with <50% bases of quality value), the remaining clean reads were assembled using Trinity sofware

treatment_protocol: Fish were collected from each tank, the fish were anesthetized with MS-222, after weighting fish were killed by cutting the spine, and immediately dissected for sampling their liver. All the samples were immediately frozen in liquid nitrogen, and stored at -80℃ until use.

value: spleen

tag: developmental stage

tag: feeding protocol

value: fish oil diet postprandial feed


title: Spleen, 2DP

description: mRNA derived from spleen tissue of soybean oil diet postprandial feed

value: soybean oil diet postprandial feed


title: MGHU3-shPLK4

city: Shen Zhen

first: Haiyan

last: Sun

state: Guang Dong

address: 47 Youyi Road, Luohu District

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads 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%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI, which known and novel, coding transcripts were included
Then expression level of gene was calculated by RSEM (v1.2.12). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test .
Genome_build: GRCh38
Supplementary_files_format_and_content: differential expression

source_name: bladder carcinoma cell line

growth_protocol: 5637 and MGHU3 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% PS,respectively.

extract_protocol:
Magzol Reagent (Magen, China)
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 hexamer-primed reverse transcription, followed by a 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 solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).

treatment_protocol: bladder cancer cells (5637 and MGHU3) were grown on 100 mm culture dishes and cultured overnight.Then cells were treated with vehicle or shPLK4 for 24h before harvested for RNA-seq analysis.

value: wild type

value: PLK4 knockdown


title: MGHU3-shNC

description: CTL

value: no treatment


title: pLKO II_(HG-U133_Plus_2)

value: vector only control


title: ChAT-eGFPneg_IWAT_macrophages_2

value: IWAT

value: Macrophages


title: pLKO I_(HG-U133_Plus_2)


title: muscle stem cells, cox10-/-, rep 3 [S7]

data_processing:
Data was processed using the BICF RNASeq Analysis Workflow (ssh://git@git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq.git) provided by the UTSouthwestern Bioinformatics Core Facility.
Reads were trimmed (trimgalore), and aligned to the reference genome using HiSAT2.
Readcounts were calculated using featureCounts.
Differential expression analysis was performed using DeSeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files including logCPM counts for each sample.

source_name: muscle stem cells, cox10-/-

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
Skeletal muscle was dissected and digested with Collagenase II and Dispse at 37C for 30 minutes. Mononucleated cells were collected through a 70micron cell strainer. MuSCs were FACS purified as CD34+, CD31/CD45/DAPI/Sca1- populations. Total RNA was purified using the RNeasy Micro Kit (Qiagen #74004).
Libraries were constructed using the SMARTer stranded pico input total RNA-seq kit (Takara, #63411) following manufacturer instructions.

treatment_protocol: Single dose of tamoxifen (200mg/kg) was adminstered by intraperitoneal injection.

value: Muscle stem cells, purified from mouse skeletal muscle


title: Spleen, 1YP

description: mRNA derived from spleen tissue of fish oil diet longterm feed

value: fish oil diet longterm feed


title: muscle stem cells, cox10-/-, rep 2 [S6]


title: Spleen, 1DP

description: mRNA derived from spleen tissue of soybean oil diet longterm feed

value: soybean oil diet longterm feed


title: 5637-shPLK4


title: ChAT-eGFPneg_IWAT_macrophages_1

value: ChAT-eGFP (Jax 007902)

value: 4 degrees C, 4h


title: muscle stem cells, 2 month old, rep 1

description:
mtDNA
S1

value: 2 months


title: 5637-shNC

description: shctl


title: muscle stem cells, cox10-/-, rep 1 [S5]


title: Liver, 2YG

description: mRNA derived from liver tissue of fish oil diet postprandial feed

source_name: liver

value: liver


title: Liver, 2DG

description: mRNA derived from liver tissue of soybean oil diet postprandial feed


title: muscle stem cells, wild-type, rep 4 [S4]

source_name: muscle stem cells, wild-type

value: wild-type


title: HB 53 Background

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description:
nuclei RNA
single-cell RNA-seq from nuclei with 10x genomics

data_processing:
FASTQ files were aligned to GRh38 reference genome and processed with Cell Ranger version 3.1.0 to obtain the unique molecular identifier (UMI).
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.gz: filtered UMI count data matrix
Supplementary_files_format_and_content: raw_feature_bc_matrix.gz: all UMI count data matrix

source_name: Background Liver

growth_protocol: Background liver and tumor samples from patients with HB were collected under conditions appropriate for characterization and further generation of PDXs with institutional review board approval

extract_protocol:
Background liver, tumor and PDX tissues (25-30 mg each) were pulverized with liquid nitrogen and nuclei prepared, sorted and counted as described by Wu et. al. with addition of 0.04% BSA/PBS in the final buffer
3'v3 assay, 10x genomics, Novaseq6000 instrument

treatment_protocol: PDX tumors were grown in NSG mice to generate in vivo HB tumor models

value: Background liver adjacent to hepatoblastoma


title: muscle stem cells, cox10-/-, rep 4 [S8]


title: ChAT-eGFPneg_IWAT_macrophages_3


title: HB 53 Hepatoblastoma

source_name: Hepatoblastoma

value: Hepatoblastoma


title: muscle stem cells, wild-type, rep 3 [S3]


title: HB 30 PDX

source_name: PDX

value: PDX


title: muscle stem cells, wild-type, rep 2 [S2]


title: Liver, 1YG

description: mRNA derived from liver tissue of fish oil diet longterm feed


title: HB 30 Hepatoblastoma


title: muscle stem cells, wild-type, rep 1 [S1]


title: HB 17 PDX


title: Brain, 2YN

description: mRNA derived from brain tissue of fish oil diet postprandial feed

source_name: brain

value: brain

value: fish oil diet postprandial feed


title: HB 17 Hepatoblastoma


title: HB 17 Background


title: Brain, 2DN

description: mRNA derived from brain tissue of soybean oil diet postprandial feed

value: soybean oil diet postprandial feed


title: Brain, 1YN

description: mRNA derived from brain tissue of fish oil diet longterm feed


title: CD11c+CD11bneg (rep 3)

city: lebanon

first: Jennifer

last: Vella

address: 1 medical center drive

institute: Dartmouth College

data_processing:
Fastq files were aligned to the mm10 genome using bowtie2 and normalized to obtain Transcripts Per Kilobase Million (TPM) for each RNA-seq sample using the software RSEM
Genome_build: mm10

source_name: lymphocyte

growth_protocol: Cells were harvested from C57BL/6 mice 40 days after B16F10 tumors were resected

extract_protocol:
Skin was minced and incubated in 2 mg/mL Collagenase Type IV (Worthington Biochemical Corporation), 0.2 mg/mL DNase I (Sigma-Aldrich), and 2% FBS in HBSS at 37°C for 25 minutes with a magnetic stir bar. Remaining skin fragments were mechanically dissociated in RPMI-1640 containing 10% FBS and 2mM EDTA. 2 mice were pooled prior to staining, for a total of 3 experimental samples. Single cell suspensions were prepared for each tissue and stained with anti-mouse CD8a-PerCP/Cynine5.5 (clone 53-6.7; Biolegend; #100773), anti-mouse CD11c-Alexa Fluor 647 (clone N418; Biolegend; #117314), anti-mouse CD11b-Alexa Fluor 488 (clone M1/70; Biolegend; #101219), anti-mouse CD45.2- Alexa Fluor 488 (clone 104; Biolegend; #109821).
Libraries were generated from 10ng cDNA using the Nextera DNA Flex library prep kit (Illumina). Libraries underwent quality control by Fragment Analyzer (Agilent) and Qubit (ThermoFisher) to determine the size distribution and the quantity of the libraries. Libraries were sequenced on a NextSeq 500 (Illumina).

value: Skin

value: 40 days post tumor resection


title: CD11c+CD11b+ (rep 3)


title: CD8 T cells (rep 3)


title: CD8 T cells (rep 2)


title: CD11c+CD11b+ (rep 2)


title: Liver, 1DG

description: mRNA derived from liver tissue of soybean oil diet longterm feed


title: UDI0047=17-unt10

description: comparison of tumor and background liver to PDX tumor over multiple passages

data_processing:
https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/0471142727.mb0421s106
Trimmimatic to trim FastQ files
HiSat2 aligner for alignment
kallisto for expression count
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM .xls represents gene expression level using transcript per million

source_name: control PDX

extract_protocol:
RNA was extracted from tissues using the Qiagen Rneasy Plus kit
TruSeq polyA-stranded library preps from Illumina, sequenced with Paired-End, 100bp parameters on the NovaSeq 6000 instrument

treatment_protocol: PDX tumors were grown in NSG mice to generate in vivo HB tumor models. Irinotecan treatment at 1 and 10mg/kg was used for a small subset of PDX tumors.

tag: sample

value: HB pdx

value: control treated


title: UDI0048=17-irinotecan1-1L

source_name: chemo treated PDX

value: irinotecan 1 mg/kg


title: IH exosome-3

city: Zhengzhou

first: Jie

last: Ren

address: No.1 Jianshe East Road, Erqi District

institute: The Fifst Affilated Hospital of Zhengzhou University

description: miRNA Gene expression data from exosomes isolated fromA549 cells under IH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48℃ on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

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

data_processing: SAM (Significance Analysis of Microarray) R package was used to analyze differential genes.

source_name: IH exosomes

label_protocol: Biotin-labeled proprietary 3DNA dendrimer was attached to the poly A tail of RNA under ligase guidance.

growth_protocol: A549 cells were maintained at 37 ℃ with 5% CO2 in 4ml RPMI-1640 medium containing; 10% fetal bovine serum, 10 U/ml penicillin and 10 μg/ml streptomycin.

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

treatment_protocol: When the A549 confluency reached 80%, the cells were collected and treated to IH (30 min 5% O2 followed by 30 min 21% O2 balanced in 5% CO2, 1 cycle/h) or RA (21% O2 balanced in 5% CO2) for 48h. 30ml of the cell culture was collected and centrifuged at 300×g for 10 min, 2000×g for 10 min, and 10000×g for 30 min to remove residual cells and debris. The exosomes were then resuspended and collected by centrifugation at 100,000 g for 70 min

tag: cell

value: exosome isolated from A549 cell

tag: condition

value: intermittent hypoxia (IH)


title: CD11c+CD11bneg (rep 2)

tag: strain


title: UDI0046=17-unt1


title: IH exosome-1


title: IH exosome-2


title: UDI0045=18-F2

value: HB liver tumor PDX passage 2


title: CD8 T cells (rep 1)


title: pLKO III_(HG-U133_Plus_2)

value: vector only control


title: CD11c+CD11b+ (rep 1)


title: UDI0044=18-F1

value: HB liver tumor PDX passage 1


title: Brain, 1DN

description: mRNA derived from brain tissue of soybean oil diet longterm feed

value: soybean oil diet longterm feed


title: RA exosome-3

description: miRNA Gene expression data from exosomes isolated fromA549 cells under RA

source_name: RA exosomes


title: IH A549 cells-3

description: miRNA Gene expression data from A549 cells under IH

source_name: IH A549 cells

value: A549 cell

value: room air (RA）


title: RA exosome-2


title: UDI0043=18-F0

value: HB liver tumor PDX primary implant


title: CD11c+CD11bneg (rep 1)


title: UDI0018=17-irinotecan10-1L

value: irinotecan 10mg/kg


title: RA exosome-1


title: IH A549 cells-1


title: IH A549 cells-2


title: RA A549 cells-2

description: miRNA Gene expression data from A549 cells under RA

source_name: RA A549 cells


title: Tumor sample 9

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using STAR with default parameters.
RSEM was used to quantify gene expression levels
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastrointestinal stromal

extract_protocol:
Total RNA was collected using TRIzol Reagent (Invitrogen); then, rRNAs were removed by using the RiboMinus Eukaryote Kit (QIAGEN, Valencia, CA, USA). We next prepared the RNA-seq libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Beverly, MA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastrointestinal stromal

tag: disease

value: Gastrointestinal stromal tumor

tag: group

value: Imatinib resistant patient


title: UDI0017=17-irinotecan1-1R


title: Tumor sample 7


title: AM4h_21

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: AMX/MPLA 4h

hyb_protocol: One color Agilent-074809 SurePrint G3 Mouse GE v2 8x60K  60-mer oligonucleotide Microarrays  were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: lung

label_protocol: manufacturer's instructions

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Lungs were perfused with PBS prior to sampling. Lung  total RNAs were extracted with the Nucleospin RNA II kit (Macherey Nagel, Germany).

tag: agent

value: Amoxicillin trihydrate (AMX)

tag: time point

value: Six-to-eight weeks

tag: Sex

value: female

value: BALB/cJRj

tag: immunostimulant agent

value: MPLA


title: Tumor sample 6

tag: tissue


title: RA A549 cells-1


title: AF2h_5

description: AMX/FliC 2h

tag: age

value: FliC


title: UDI0019=17-irinotecan10-1L1R

value: HB pdx

tag: treatment


title: RA A549 cells-3


title: Adjacent normal sample 10

value: Normal gastrointestinal stromal


title: UDI0042=18T

source_name: HB tumor

value: HB liver tumor


title: UDI0040=17-F5

value: HB liver tumor PDX passage 5


title: Tumor sample 10


title: UDI0041=18B

source_name: Background liver

value: liver adjacent to hepatoblastoma


title: A8h_25

description: AMX/mock 8h

value: mock


title: Adjacent normal sample 9


title: A4h_13

description: AMX/mock 4h


title: A2h_1

description: AMX/mock 2h


title: UDI0038=17-F3

value: HB liver tumor PDX passage 3


title: A4h_15

description: AMX/mock 4h


title: AM2h_9

description: AMX/MPLA 2h


title: Adjacent normal sample 8


title: AM8h_32

description: AMX/MPLA 8h


title: UDI0039=17-F4

value: HB liver tumor PDX passage 4


title: AF4h_18

description: AMX/FliC 4h


title: AF4h_17

description: AMX/FliC 4h


title: AF2h_7

description: AMX/FliC 2h


title: Adjacent normal sample 7

value: Gastrointestinal stromal


title: e9.5_rep2_ATAC

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Reads were mapped to the mouse mm9 genome using Bowtie v1.1.0 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Accessible regions were identified using MACS v1.4 (PMID: 18798982) with the following parameters: --gsize=mm --bw=150 --nomodel --nolambda --shiftsize=75.
Evidences from biological replicates were combined using MSPC (PMID: 25957351), using the following parameters -r biological -s 1E-10 -W 1E-6.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of replicated regions (MACS + MSPC)

source_name: embryonic forelimb bud

growth_protocol: WT embryos were used. The day the vaginal plug was detected is defined as embryonic day 0.5 (E0.5)

extract_protocol:
For the earlier stage (E9.75), each replicate contains a pair of forelimbs from a E9.5 WT embryo with the attached portion of trunk. For the E10.5 embryonic stage, each replicate consists of a pair of forelimbs from a E10.5 WT embryo. For both stages, two biological replicates were processed independently by following the protocol of Buenrostro et al., 2013  (https://www.nature.com/articles/nmeth.2688)
The ATAC libraries were prepared by the Genomic Facility Basel – ETH Zurich, by amplifiying the transposed DNA fragments with the KAPA HiFI HotStart ReadyMix kit followed by sequencing on an Illumina NextSeq 500.

value: NMRI

value: gestational day e9.5

value: forelimb buds with the attached trunk


title: UDI0037=17-F2

value: HB liver tumor PDX passage 2


title: AM2h_10

description: AMX/MPLA 2h

value: Amoxicillin trihydrate (AMX)

value: Six-to-eight weeks

value: female


title: e9.5_rep1_ATAC


title: UDI0036=17-F1

value: HB liver tumor PDX passage 1


title: Adjacent normal sample 6

value: Imatinib resistant patient


title: e10.5_rep2_ATAC

value: gestational day e10.5

value: forelimb and hindlimb buds


title: UDI0034=17T

value: HB liver tumor


title: UDI0035=17-F0

value: HB liver tumor PDX primary implant


title: Tumor sample 4

value: Gastrointestinal stromal tumor

value: Imatinib sensitive patient


title: e9.5_rep2_Smad4

description:
Chromatin IP against Smad4-Flag
smad4_e9.5.bed

data_processing:
Reads were mapped to the mouse mm9 genome using Bowtie v1.1.0 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained. Reads were trimmed using fastx_trimmer (-l 63), a tool part of the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) (v0.0.13).
Peak calling was performed using MACS v1.4 (PMID: 18798982) with the following parameters: --gsize=mm --bw=300 --nomodel --shiftsize=100 --pvalue=1e-2. Each IP was compared to experiment-matched input DNA.
Evidences from these replicates were combined using MSPC (PMID: 25957351), with the following parameters -r biological -s 1E-5 -W 1E-2.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of replicated peaks (MACS + MSPC)

source_name: embryonic forelimb bud, Smad4 ChIP

growth_protocol: The Smad4-Flag allele was generated by inserting a 3xFlag epitope in Smad4 3’UTR coding region. The day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5).

extract_protocol:
Chromatin immune-precipitation were performed as previously described (PMID:    25453830) with some modifications. About 80 Smad43xF/3xF embryos at E9.75 (forelimbs with attached trunk) or 100 Smad43xF/3xF embryos E10.5 (forelimbs/hindlimbs) were dissected per replicate. Samples were cross-linked with 11% formaldehyde at RT for 5 min as described in PMID 25453830. Protein G Dynabeads (Invitrogen) were incubated overnight at 4°C with 2 µg of M2 anti-FLAG antibody. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp. The chromatin was then incubated with the beads for 6hrs at 4°C. Immuno-complexes were washed and the protein/DNA complexes were eluted in an Elution buffer (1% SDS, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) at 65°C overnight. Samples were treated for 1hr at 37°C with RNase A and then with Proteinase K for 2hrs at 55°C. The DNA was purified on QIAquick columns (Qiagen) and the quality was assessed on the Advanced Analytical fragment Analyzer.
The ChIP-seq libraries were peformed using the KAPA Hyper prep Kit. Samples were sequenced by the Genomic Facility Basel – ETH Zurich on an Illumina Illumina NextSeq 500

tag: genotype

tag: chip antibody

value: M2 anti-FLAG antibody (Sigma F1804)


title: A2h_3

description: AMX/mock 2h

value: BALB/cJRj

value: mock


title: Tumor sample 3

value: Gastrointestinal stromal


title: e9.5_rep1_Smad4

value: NMRI

value: gestational day e9.5

value: forelimb buds with the attached trunk


title: Tumor sample 2


title: AM8h_33

description: AMX/MPLA 8h

value: Amoxicillin trihydrate (AMX)

value: Six-to-eight weeks

value: MPLA


title: AM4h_23

description: AMX/MPLA 4h

value: female


title: A8h_26

description: AMX/mock 8h


title: Tumor sample 5


title: UDI0083=HB18-F4

value: HB liver tumor PDX passage 4


title: UDI0084=HB18-F3

value: HB liver tumor PDX passage 3


title: e10.5_rep2_Smad4

description:
Chromatin IP against Smad4-Flag
smad4_e10.5.bed

value: gestational day e10.5

value: forelimb and hindlimb buds


title: Tumor sample 1

value: Gastrointestinal stromal tumor


title: AM8h_34

description: AMX/MPLA 8h


title: Adjacent normal sample 5

value: Normal gastrointestinal stromal

value: Imatinib sensitive patient


title: UDI0082=HB18-F5

value: HB liver tumor PDX passage 5


title: e10.5_rep1_Smad4

value: M2 anti-FLAG antibody (Sigma F1804)


title: e10.5_rep1_ATAC


title: AF4h_19

description: AMX/FliC 4h

value: BALB/cJRj

value: FliC


title: UDI0033=17B

source_name: Background Liver

value: liver adjacent to hepatoblastoma


title: e9.5_rep2_input

description: Input DNA

source_name: embryonic forelimb bud, ChIP input

value: NMRI

value: gestational day e9.5

value: forelimb buds with the attached trunk


title: AM4h_24

description: AMX/MPLA 4h

value: Amoxicillin trihydrate (AMX)

value: Six-to-eight weeks

value: MPLA


title: s4_120h

city: Santa Barbara

first: Eyal

last: Karzbrun

state: CA

address: UCSB

department: Physics

institute: UCSB

data_processing:
Cell Ranger counts pipeline (version 3.1.0)
The supplementary file (allsamples_aggr_matrix.mtx.gz) was was generated by running the Cell Ranger aggr pipeline (version 3.1.0) consecutively to Cell Ranger counts
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: gene expression matrices

source_name: iPSC-derived neural tube

extract_protocol:
Chromium Single Cell Kit v3.1 (10x Genomics)
single-cell RNA seq

tag: timepoint


title: s3_72h


title: Adjacent normal sample 4

value: Gastrointestinal stromal


title: A2h_4

description: AMX/mock 2h

value: female

value: mock


title: Adjacent normal sample 3


title: e9.5_rep1_input

description: Input DNA


title: e10.5_rep2_input

description: Input DNA

value: gestational day e10.5

value: forelimb and hindlimb buds


title: e10.5_rep1_input

description: Input DNA


title: Adjacent normal sample 1

value: Normal gastrointestinal stromal

value: Imatinib sensitive patient


title: s1_24h


title: SacPom_plus_plus_1

status: Public on Jul 28 2021

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description:
Ribosome profiling
processed data file: Pombe_supplementary_count_table.txt

data_processing:
Library strategy: Ribo-Seq
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13.
Processed yeast reads were mapped to tRNA, rRNA, snRNA and snoRNA; reads from human samples were mapped to rRNA using bowtie version 1.2.1.1.
Residual reads were uniquely mapped to non-dubious ORFs (hg38; SacCer3; C_albicans_SC5314_version_A22;Pombe_ASM294v2) extended by 18 nt into the UTRs.
Genome_build: hg38 (GRCh38); SacCer3 (R64); C_albicans_SC5314_version_A22 (ASM18296v3); Pombe_ASM294v2 (ASM294v2)
Supplementary_files_format_and_content: *_count_table.txt: Tab-delimited text files include raw counts for each sample.

organism: Schizosaccharomyces pombe

source_name: Yeast

growth_protocol: HEK 293T cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37C. Yeast cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4–0.5) at 30C, 200 revolutions per minute in yeast extract peptone dextrose (YPD).

extract_protocol:
For HEK 293T cells, total RNA is extracted using phenol:chloroform method. For yeast, total RNA is extracted using the hot-acid-phenol method.
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

treatment_protocol: (+/+) samples are pre-treated with CHX and lyzed in buffer containing CHX; (-/+) samples are lyzed in buffer containing CHX WITHOUT CHX pre-treatment; (-/-) samples are lyzed without CHX pre-treatment in buffer devoid of CHX.

value: Pre-treated with CHX, lyzed in buffer containing CHX


title: SacPom_plus_plus_2


title: Male medaka pituitary scRNA-seq

city: Oslo

first: Khadeeja

last: siddique

address: Karl Staaffs vei 75, house 7

country: Norway

institute: Norwegian University of Life sciences (NMBU))

data_processing:
CellRanger (10X Genomics) version 3.0.2 was used for fastq demultiplexing and alignment.
Quantification,  quality control, normalization and additional analysis by dropEst, DoubletFinder and Seurat R packages.
Genome_build: Hd-rR medaka reference genome (ASM223467v1, Ensembl release 94)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: the barcode, gene, expression matrix file of each sample
Supplementary_files_format_and_content: Tab-separated data files include barcode, cell types, total RNA counts and UMAP dimensions  for each sample
Supplementary_files_format_and_content: Tab-separated files include top 5 differentially expressed genes with cell types, average gene counts  for each sample
Supplementary_files_format_and_content: Matrix tables with raw gene counts  (exon, intron and spanning data) for each sample, which can be transcriptional dynamics analysis (RNA velocity).

organism: Oryzias latipes

source_name: Transgenic line expressing GFP under the control of the pituitary-specific lhb promoter

extract_protocol:
Pituitaries were collected from 24 female and 23 male adult medaka of approximately 8 months old. pituitaries cells were dissociated as described in Ager-Wick, E. et al (2018). Briefly, fresh pituitaries were put in an Eppendorf tube with modified PBS (phosphate buffered saline, pH 7.75, 0.05% bovine serum albumin) and kept on ice until processing. Pituitaries were treated with 0.1% w/v trypsin type II S for 30 minutes at 26 °C, with 0.1% w/v trypsin inhibitor type I S for 20 minutes at 26 °C, and subsequently mechanically dissociated using a glass pipette.
10x Genomics Chromium Single Cell 3′ Reagents Kit v2

value: Adult

value: Male

value: Pituitary

value: d-rR lhb:GFP


title: A9-RKI_WT

city: St. Louis

first: Joseph

middle: C

last: Corbo

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description:
index: GGAGTCC
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_RKIWTvshomozygous.txt
DE_transcripts_RKIWTvshomozygous.txt

data_processing:
Reads were aligned to the Ensembl release 76 assembly with STAR v2.0.4b.
Gene counts were obtained with Subread:featureCount v1.4.5.
Transcript counts were generated with Sailfish v0.6.3.
Sequencing performance was assessed with RSeQC v2.3.
Counts were imported and TMM normalization size factors were calculated in EdgeR.
Limma and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were generated with Voom.
Generalized linear models were used to test for differential expression. Adjusted (FDR-corrected) p-values were calculated.
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: Processed data files linked to Series record:
[all.gene_counts_annot.txt]: read counts for all samples, gene-level
[all.transcript_counts_annot.txt]: read counts for all samples, transcript-level
[all.gene_RPKM_annot.txt]: RPKM values for all samples, gene-level
[all.transcript_RPKM_annot.txt]: RPKM values for all samples, transcript level
[DE_genes_LC1KOvsWT.txt]: Differential expression analysis, gene-level, LC1 KO vs. LC1 WT
[DE_genes_RKIWTvshomozygous.txt]: Differential expression analysis, gene-level, rs77910749 knock-in homozygous vs. wild-type
[DE_transcripts_LC1KOvsWT.txt]: Differential expression analysis, transcript-level, LC1 KO vs. LC1 WT
[DE_transcripts_RKIWTvshomozygous.txt]: Differential expression analysis, transcript-level, rs77910749 knock-in homozygous vs. wild-type

source_name: brain homogenate

extract_protocol:
E14.5 embryos were harvested in cold HBSS with calcium and magnesium, and whole brains were rapidly dissected and stored in TRIzol (Invitrogen) at -80 degrees Celsius. Tail tissue was saved from each embryo for genotyping. Sex-matched, litter-matched wild-type and mutant embryos were used. RNA was extracted with TRIzol, DNase-treated, and purified with RNeasy Mini (Qiagen).
RNA libraries were prepared for sequencing using the Illumina oligo-dT kit according to manufacturer's protocol.

value: embryonic day 14.5 (E14.5)

value: Wild-type for rs77910749

value: brain


title: A2-RKI_WT

description:
index: CCATCAT
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_RKIWTvshomozygous.txt
DE_transcripts_RKIWTvshomozygous.txt

value: male


title: 73-LC1_WT

description:
index: AGTTATG
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_LC1KOvsWT.txt
DE_transcripts_LC1KOvsWT.txt

value: wild-type


title: A10-RKI_homozygous

description:
index: TGGCATA
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_RKIWTvshomozygous.txt
DE_transcripts_RKIWTvshomozygous.txt

value: Homozygous for rs77910749 knock-in


title: AM2h_11

description: AMX/MPLA 2h

value: Amoxicillin trihydrate (AMX)

value: Six-to-eight weeks

value: female

value: BALB/cJRj

value: MPLA


title: A4h_16

description: AMX/mock 4h

value: mock


title: A16-RKI_WT

description:
index: GTAAAAA
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_RKIWTvshomozygous.txt
DE_transcripts_RKIWTvshomozygous.txt


title: A8h_27

description: AMX/mock 8h


title: 6-LC1_WT

description:
index: CCGGCAG
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_LC1KOvsWT.txt
DE_transcripts_LC1KOvsWT.txt


title: GPI-negative clone 4

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital, University of Bonn

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Wegneretal.GEO.counts.csv

source_name: undifferentiated BLaER1 cells

growth_protocol: Undifferentiated BLaER1 cells were cultured in RPMI-1640 medium containing 10 % FCS, 100 U/ml penicillin, and 100 µg/ml streptomycin

extract_protocol:
1x10^6 cells were resuspended in 500 µl TRIzol Reagent (Thermo Fisher Scientific) and their total RNA was purified according to the manufacturer’s instructions.
Libraries of sequences close to the 3' end of polyadenylated RNA were generated with a QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen).
3' mRNA-Seq

tag: cell line

value: WT

tag: gpi-anchored protein expression

value: no


title: GPI-negative clone 3


title: 7-LC1_KO

description:
index: GATGGCC
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_LC1KOvsWT.txt
DE_transcripts_LC1KOvsWT.txt

value: LC1 knockout


title: AF2h_8

description: AMX/FliC 2h

value: FliC


title: A18-RKI_homozygous

description:
index: CTGCAAT
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_RKIWTvshomozygous.txt
DE_transcripts_RKIWTvshomozygous.txt


title: 22-LC1_KO

description:
index: ACGCGGG
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_LC1KOvsWT.txt
DE_transcripts_LC1KOvsWT.txt


title: s2_48h


title: 26-LC1_WT

description:
index: CGCTACA
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_LC1KOvsWT.txt
DE_transcripts_LC1KOvsWT.txt


title: GPI-negative clone 2


title: Adjacent normal sample 2

city: Shanghai

value: Gastrointestinal stromal

value: Normal gastrointestinal stromal

value: Imatinib sensitive patient


title: GPI-positive clone 1

value: yes


title: GPI-positive clone 2


title: GPI-positive clone 3


title: 71-LC1_KO

description:
index: ATGTTCT
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_LC1KOvsWT.txt
DE_transcripts_LC1KOvsWT.txt

value: embryonic day 14.5 (E14.5)

value: brain


title: A1-RKI_homozygous

description:
index: TGACTCT
all.transcript_counts_annot.txt
all.gene_RPKM_annot.txt
all.transcript_RPKM_annot.txt
DE_genes_RKIWTvshomozygous.txt
DE_transcripts_RKIWTvshomozygous.txt

value: male

value: Homozygous for rs77910749 knock-in


title: Female medaka pituitary scRNA-seq

value: Adult

value: Female

value: Pituitary

value: d-rR lhb:GFP


title: GPI-negative clone 1


title: E15 4h replicate 3

city: Prague

first: Helena

last: Líbalová

address: Videnska 1083

department: Department of Nanotoxicology and Molecular Epidemiology

country: Czech Republic

institute: Institute of Experimental Medicine CAS

description:
replicate 3
SAMPLE 6

hyb_protocol: 900 ng of biotinylated cRNA targets was hybridized to HumanHT-12 v4 Beadchips. The steps of hybridization and the subsequent washing, staining and drying of the beadchips were performed according to standard instructions from Illumina.

scan_protocol: The hybridized beadchips were scanned on the Illumina iScan according to standard scanning protocol.

data_processing: Bead level data were summarized by GenomeStudio Software v2 (Illumina, USA) and processed in R statistical environment. Normalization was performed using the quantile method in the Lumi package.

source_name: lung epithelial cells

label_protocol: Biotinylated complementary RNA (cRNA) was prepared from 500 ng of total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturer’s instructions.

growth_protocol: Human bronchial epithelial cells BEAS-2B (ATCC, USA) were cultivated in basal medium (BEBM, Lonza), supplemented with the standardized set of growth factors (BEGM™ BulleKit™, Lonza) as recommended by the manufacturer. Cultivation flasks and plates were coated with BEBM containing fibronectin, collagen and bovine serum albumin.

extract_protocol: BEAS-2B cells exposed to PM extracts were lysed and the total RNA was extracted using NucleoSpin RNA II Isolation Kit (Macherey-Nagel, Germany), according to the manual. High-purity RNA was obtained and the concentration was quantified with Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, USA). The integrity of RNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA) and Agilent RNA 6000 Nano Kit. Samples with RNA Integrity Number (RIN) > 9 were used for further analysis.

treatment_protocol: Cells for treatments were seeded in three separate wells with an independent cell population. Next day, cells were treated with E0 or E15 PM extracts (both in concentration 50 μg PM/mL) and incubated for 4h or 24h. The control cells were incubated with the extract of blank non-exposed filter for the same time intervals (4 and 24h). Cells were grown at 37°C and 5% CO2.

value: lung

tag: cell type

value: epithelial cells

value: organic extract of PM from E15

tag: dose (ug pm/ml)

tag: time of exposure (hour)


title: E0 4h replicate 3

description:
replicate 3
SAMPLE 3

value: organic extract of PM from E0


title: E15 4h replicate 1

description:
replicate 1
SAMPLE 4


title: Tumor sample 8

tag: disease

value: Gastrointestinal stromal tumor

value: Imatinib resistant patient


title: E0 4h replicate 2

description:
replicate 2
SAMPLE 2


title: E15 4h replicate 2

description:
replicate 2
SAMPLE 5


title: E0 24h replicate 3

description:
replicate 3
SAMPLE 12


title: Blank 4h replicate 1

description:
replicate 1
SAMPLE 7

value: organic extract of non-exposed filter


title: Blank 24h replicate 3

description:
replicate 3
SAMPLE 18


title: E0 4h replicate 1

description:
replicate 1
SAMPLE 1


title: E15 24h replicate 2

description:
replicate 2
SAMPLE 14


title: Blank 24h replicate 2

description:
replicate 2
SAMPLE 17


title: Blank 4h replicate 3

description:
replicate 3
SAMPLE 9


title: E0 24h replicate 1

description:
replicate 1
SAMPLE 10


title: E15 24h replicate 1

description:
replicate 1
SAMPLE 13


title: Blank 24h replicate 1

description:
replicate 1
SAMPLE 16


title: E15 24h replicate 3

description:
replicate 3
SAMPLE 15


title: Blank 4h replicate 2

description:
replicate 2
SAMPLE 8


title: E0 24h replicate 2

description:
replicate 2
SAMPLE 11


title: SAMPLE 41_B22_RO_G

city: New York

first: Yingjie

last: Zhu

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: The extracted material was sent to Helixio (Saint-Beauzire, France), where it was hybridized with gene arrays (Human SurePrint, Agilent Technologies France, Les Ullis, France)

scan_protocol: not provided

data_processing: Limma package was applied to process Agilent microarray data and identify differentially expressed genes between progressive tumors and tumors with pathological complete response. Background correction was performed on expression intensities before normalization by the parameter of “expnorm”. Median value was taken when a gene has multiple probes. Then, “cyclicloess” method, which applies loess normalization to all possible pairs of arrays, was used to normalize corrected intensities. The probes have been filtered for those close to background and without gene name.

source_name: breast

label_protocol: not provided

extract_protocol: Nucleic acids were extracted from frozen tumor tissue (pre-NAT samples) using AllPrep DNA/RNA mini kit (Qiagen France SAS, Courtaboeuf, France) according to the manufacturer’s protocol.

tag: Stage

value: IIA

tag: tissue type

value: frozen tumor tissue


title: SAMPLE 33_B69_AZ_C


title: SAMPLE 36_B76_GE_L


title: SAMPLE 32_B32_DE_G


title: SAMPLE 24_E12_SEG_BR


title: SAMPLE 31_B67_VI_M


title: SAMPLE 39_B61_SC_G


title: SAMPLE 29_E27_GRA_OK

value: IIB


title: SAMPLE 28_E25_ROY_CA


title: SAMPLE 38_B63_MO_N


title: SAMPLE 34_B96_SC_M


title: SAMPLE 30_B4_MU_V


title: SAMPLE 40_B64_GI_C


title: SAMPLE 37_B57_AR_F


title: SAMPLE 21_B30_PU_S


title: SAMPLE 23_B95_BE_E


title: SAMPLE 26_E22_CRO_MA


title: SAMPLE 35_B46_SA_S


title: SAMPLE 22_B42_TH_I


title: SAMPLE 25_E16_DAL_CH


title: SAMPLE 20_E51_TRE_EM


title: SAMPLE 17_E23_GUT_NA


title: SAMPLE 13_E13_VEY_CL


title: SAMPLE 16_E21_GIL_CH


title: SAMPLE 18_E28_LAS_MA


title: SAMPLE 14_B23_HA_F


title: SAMPLE 12_B60_PF_A


title: SAMPLE 19_E26_SAV_MI


title: SAMPLE 27_E29_DUV_PA


title: SAMPLE 15_E55_CON_BE


title: N4_5-8_5D

city: Seoul

first: Jaewon

last: Kim

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system  control and base calling through an integrated primary analysis software called RTA (Real Time  Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Raw reads were trimmed first by fastx_toolkit (version 0.0.14). After trimming, the reads were mapped to the mouse genome (mm10, GRCm38.97 from Ensembl) using STAR software (version 2.6.0c).
Transcript abundance was estimated at the gene level by RSEM version 1.3.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Nox4-/-#5-8 iPSCs

growth_protocol: WT and Nox4-/- iPSCs were maintained on MEF feeder cells treated with mitomycin C in DMEM supplemented with 15% FBS, 0.1mM MEM nonessential amino acid , 2mM GlutaMAX , 1mM sodium pyruvate, 1% Penicillin/streptomycin , 0.1mM β-mercaptoethanol and 1000units/ml LIF.

extract_protocol:
For library construction, DNA/RNA is extracted from a sample. After performing quality control  (QC), qualified samples proceed to library construction. RNA-seq was performed on the Illumina TruSeq (Stranded mRNA LT Sample Prep Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and Nox4-/- iPSC colonies were harvested using TrypLE and suspended in mouse ES medium without LIF. The single cells were cultured in hanging drop (3x103/20μl) to form EB. After 3 days, aggregated cells were plated onto gelatin-coated 12-well plates and cultured for 0, 3,5,7 and 10 days.

value: Nox4 kockout

tag: time-series


title: N4_5-8_14D


title: N4_5-23_0D


title: N4_5-23_3D


title: N4_5-8_7D


title: N4_5-8_0D


title: N4_5-23_14D


title: N4_5-23_7D


title: N4_5-8_3D


title: N4_5-23_5D


title: SAMPLE 11_B24_FAY_SO


title: SAMPLE 9_B92_ME_F

value: IIIA


title: SAMPLE 2_B52_GE_C


title: SAMPLE 4_B53_SC_A


title: SAMPLE 8_E54_DIO_MI


title: SAMPLE 5_B62_PA_L


title: SAMPLE 6_B65_DE_C


title: SAMPLE 10_B89_RA_M


title: SAMPLE 3_B72_FAL_SA


title: SAMPLE 1_B87_DR_D


title: WT_20d_7D

source_name: WT#20D-17 iPSCs

value: wild type


title: WT_20d_3D


title: WT_1-4_7D

source_name: WT#1-4 iPSCs


title: WT_1-4_3D


title: WT_1-4_5D


title: WT_20d_14D


title: WT_20d_0D


title: WT_20d_5D


title: WT_1-4_14D


title: WT_1-4_0D