title: Enterocyte BR#5

description:
SE.MATS.JCEC_StemVEnt.txt
DaPars_Output_StemVEnt_All_Prediction_Results.txt
MAJIQ_StemVEnt.txt

source_name: Enterocyte BR_colon

value: Sorted colon Enterocyte cell; Cd31-, Cd45-, Epcam+, Cd44low/-, Cd24-, live


title: 1GRKO_2_S22

status: Public on Jul 15 2020

type: SRA

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

country: USA

institute: MDI Biological Laboratory

library_source: transcriptomic

data_processing:
Fastq formatted read files were preprocessed with Trimmomatic version 0.36 with default options.
Fastq files were then aligned to the Zebrafish genome version 11, as presented in Ensembl version 93, using the STAR aligner version 2.6.1b.
The Ensembl transcriptome was preprocessed with a splice junction overhang of 100nt.
Following alignment, the resulting BAM files were preprocessed with RSEM version 1.3.0 for isoform and gene-level expression estimates.
The resulting gene-level expression values were merged into a single expression matrix with an in-house python script.
Further normalization was achieved using EDAseq version 2.18.0 using GC content data downloaded from Ensembl version 98 with EDAs built in scripts.
Counts were normalized with the data-within function using GC content and full normalization.
Additional normalization was accomplished with EDAseq using the following two commands: dataNorm <- betweenLaneNormalization(dataWithin, which=“full”) dataWithin <- withinLaneNormalization(edaData,“gc”, which=“full”)
Differential expression analysis was carried out in R version 3.6.1 with the DESeq2 version 1.24.0.  DESeq2 was also used to generate an rlog-matrix which was Z-transformed to normalize each gene across all samples.
The Z-transformed rlog matrix was then loaded into JMP version 13 and used for PCA after thresholding to an average rlog expression value of 7.5
DESeq2 output tables were filtered with the following restrictions for the identification of statistically significant differentially expressed genes: BaseMean >= 75 (average of 5 counts per sample), padj <= 0.05, |log2foldchange| >= 0.5, estimated standard error of the log2foldchange < 1.0.
GOrilla algorithm was used for Gene Ontology term enrichment analysis, data was visualized using REVIGO.  Venn diagrams were generated using Venny 2.1
Genome_build: GRCz11 Genome Reference Consortium Zebrafish Build 11
Supplementary_files_format_and_content: Tab-delimited text file includes normalized log2counts for each sample

molecule: total RNA

organism: Danio rerio

source_name: Whole embryo

growth_protocol: The AB wild-type strain was used for all genetic modifications. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of the MDI Biological Laboratory. Embryo culture and cortisol treatments were performed as previously described, with one difference: embryos were cultured in a diurnal light-dark cycle (14 hours light – 10 hours dark). Briefly, fertilized eggs were collected in the morning, disinfected and at ~4 hours post fertilization placed in dishes with either 1uM cortisol or vehicle (DMSO) added to embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.

extract_protocol:
At 3 hours zeitgeber time (post lights-on) on day 5 post-fertilization four biological replicates of cortisol-treated and control embryos were collected as follows.  For the first RNA-seq experiment, one by one, a dish of larvae corresponding to a single condition was removed from the incubator, and 8 larvae per replicate (4 replicates) were collected in a 1.5 mL tube with minimal water and immediately snap frozen in liquid nitrogen. All replicates from one condition were collected sequentially before moving on to the next condition. Total RNA was extracted using the Qiagen RNA-Easy Plus mini kit (Qiagen). For the second RNA-seq experiment, four replicates of n=10 larvae were collected from a single dish for each condition and immediately snap frozen in liquid nitrogen. Collection of 16 samples occurred over 22 minutes. RNA was prepared as described above on two different days. On the first day (experimental replicates 1 and 2) the lysis buffer was added to all 8 frozen samples before homogenization, while on the second day the lysis buffer was added to each sample which was then immediately homogenized. This difference in sample preparation likely accounts for the large variance between samples prepared on day 1 and day 2. RNA was sent to the Oklahoma State Genomics Facility for Illumina library preparation and single-end sequencing.
RNA libraries were prepared for sequencing using KAPA Library Kits compatible with Illumina RNA (polyA-selected) sequencing platform

treatment_protocol: To mutate nr3c1 and klf9 we used CRISPR-Cas9, injecting zygotes with multiple guide RNAs for each gene and mRNA encoding Cas9. Guide RNAs were designed using the CHOP-CHOP algorithm. To generate the GR369- mutant line fertilized wild-type AB embryos were injected at the 1 cell stage with 1-2 nL of a gRNA cocktail targeting nr3c1 exons 2 and 3 (final concentration 40 ng/µL for each gRNA, 230 ng/µL Cas9 mRNA, 0.1 M KCl, and 0.01% phenol red indicator dye). Individual whole injected larvae were screened for mutations of the targeted regions by high resolution melt analysis (HRMA) of PCR amplicons containing those regions43. Detected mutations were then verified by Sanger sequencing of a PCR amplicon containing the targeted region. F0 adults bearing mutations were identified by HRMA of DNA extracted from tailfin clips, and germline mutations were then identified by PCR and HRMA/sequencing of sperm. F0 males with germline mutations were outcrossed to AB females, and heterozygous progeny were screened via sequencing from tailfin clips. The GR369- mutation was identified and selected for by breeding over 2 additional generations to yield F3 homozygous progeny. Subsequent generations were maintained as heterozygotes for health and breeding purposes. To generate the klf9-/- mutant line fertilized wild-type AB embryos were injected at the 1-cell stage with <20% cell volume of injection mix consisting of 200ng/ul Cas9 mRNA, 100ng/ul guide RNA, 0.05% phenol red dye, and 0.2M KCl. Individual F0 larvae were screened with HRMA to confirm CRISPR efficacy. Larvae were placed into system and raised. Young adult fish were genotyped via HRMA using DNA extracted from fin clips, and mutations were confirmed by Sanger sequencing. F0 fish positive for mutation were outcrossed to wild-type (AB) fish. F1 offspring of this cross were screened by HRMA to confirm germline transmission, and Sanger sequencing identified the 2bp frame-shift mutation in one female founder. This female was out crossed with WT AB males. The resulting F2 fish were screened as young adults via fin clip and HRMA, and males positive for mutation were back crossed to the F1 founder female. Resulting F3 generation fish were screened via fin clip HRMA and sequenced to identify homozygous mutants as well as homozygous wild-type siblings. F3 generation was Mendelian 1:2:1 wild-type:heterozygote:homozygous-mutant ratio.

tag: tissue

value: whole embryo

tag: genotype

value: VBA minus

tag: agent

value: Cortisol


title: Enterocyte BR#2

city: Irvine

first: Amber

middle: Nicole

last: Habowski

state: CA

address: 240 Sprague Hall

department: MMG

institute: University of California, Irvine

data_processing:
Paired-end sequencing reads were trimmed of adapter sequences and analyzed for quality using Fastqc (version 0.11.7).
Data was aligned to the mouse genome (UCSC mm10 from Illumina iGenome) using STAR (version 2.5.2a), converted to bam files and merged (samtools 1.3)
Read counts were generated using HTSeq (version 0.6.1p1, with enthought_python version 7.3.2; option -s no).
Differential gene expression analysis was done in R studios (version 1.0.153) using DESeq2 (version 1.16.1; with cooksCutoff = FALSE option).
For Splicing: Merged bam files were sorted and indexed (samtools 1.3) for downstream analysis. Alternative splicing was investigated using rMATS Turbo was run (rMATS.4.0.1) with STAR 2.5.2a, Samtool 1.3, and enthought_python 7.3.2 comparing two cell types at a time using UCSC mm10 gtf. MAJIQ (v1.1) was also run for alternative splicing with anaconda 3-2.0.1 and recommended mm10 ensembl gff3 reference with type=strand-specific followed by VIOLA for visualization
For APA: DaPars (v0.9.1) was used for alternative polyadenylation analysis with recommended mm10 UCSC reference files and python 2.7.15, bedtools 2.25.0, R 3.4.1, and the following settings (Num_least_in_group1=1, Num_least_in_group2=1, Coverage_cutoff=30, FDR_cutoff=0.05, PDUI_cutoff=0.15, Fold_change_cutoff=0.32).
Genome_build: mm10
Supplementary_files_format_and_content: Counts files for Gene Expression; Splicing data from rMATS - SE only for cell type comparisons with stem; Alternative Polyadenylation data from DaPars - for cell comparison with stem.

organism: Mus musculus

extract_protocol:
Mouse colons (caecum to rectum) were removed, flushed, and linearized and then dissociated with EDTA and mechanical force. Populations of Epcam+ cells (See manuscript for details) were bulk sorted on a BD FACS Aria Fusion using a 100 µm nozzle (20 PSI) at a flow rate of 2.0 with a maximum threshold of 5000 events/sec. The sample chamber and collection tubes were kept at 4 °C. Following exclusion of debris and singlet/doublet discrimination, cells were gated as demonstrated in the paper supplement. Populations were sorted into TRIzol (Invitrogen # 15-596-018) for downstream RNA isolation and sequencing. RNA was extracted from TRIzol samples using a Direct-zol RNA Micro-Prep kit (Zymo #11-330M) and associated guidelines. Sorted samples of each cell type were pooled as needed at the start of RNA preparations to ensure a minimum of 2,500 cells per sample. RNA sample quality and concentration was evaluated using an Aligent Bioanalyzer on an RNA high sensitivity pico chip.
RNA samples were then pooled as needed to allow 1 ng library preps with Clontech Low Input Pico Kit (Takara #634940)

treatment_protocol: Wild Type mice - no treatment. Aged 5-7 weeks, Male.

tag: strain background

tag: genotype/variation

value: wild type

tag: age

value: 5-7 weeks

tag: Sex

value: male

value: Colon

tag: cell type


title: 1GRKO3_S15

value: VBA plus


title: 1GRKO_1_S21


title: Enterocyte BR#3


title: 0GRKO_4_S20

value: DMSO


title: Enterocyte BR#1


title: Tuft BR#3

description:
SE.MATS.JCEC_StemVTuft.txt
DaPars_Output_StemVTuft_All_Prediction_Results.txt
MAJIQ_StemVTuft.txt

source_name: Tuft BR_colon

value: Sorted colon Tuft cell; Cd31-, Cd45-, Epcam+, Ckit+, Cd24hi, live


title: 1GRKO1_S13


title: Tuft BR#4


title: 0GRKO4_S12


title: 1GRKO2_S14


title: Tuft BR#5


title: WT_veh2

data_processing:
Fastq formatted read files were preprocessed with Trimmomatic version 0.38 with default options.
Fastq files were then aligned to the Zebrafish genome version 11, as presented in Ensembl version 93, using the STAR aligner version 2.6.1b.
The Ensembl transcriptome was preprocessed with a splice junction overhang of 100nt.
Following alignment, the resulting BAM files were preprocessed with RSEM version 1.3.0 for isoform and gene-level expression estimates.
The resulting gene-level expression values were merged into a single expression matrix with an in-house python script.
Further normalization was achieved using EDAseq version 2.18.0 using GC content data downloaded from Ensembl version 98 with EDAs built in scripts.
Counts were normalized with the data-within function using GC content and full normalization.
Additional normalization was accomplished with EDAseq using the following two commands: dataNorm <- betweenLaneNormalization(dataWithin, which=“full”) dataWithin <- withinLaneNormalization(edaData,“gc”, which=“full”)
Differential expression analysis was carried out in R version 3.6.1 with the DESeq2 version 1.24.0.  DESeq2 was also used to generate an rlog-matrix which was Z-transformed to normalize each gene across all samples.
The Z-transformed rlog matrix was then loaded into JMP version 13 and used for PCA after thresholding to an average rlog expression value of 7.5
DESeq2 output tables were filtered with the following restrictions for the identification of statistically significant differentially expressed genes: BaseMean >= 75 (average of 5 counts per sample), padj <= 0.05, |log2foldchange| >= 0.5, estimated standard error of the log2foldchange < 1.0.
GOrilla algorithm was used for Gene Ontology term enrichment analysis, data was visualized using REVIGO.  Venn diagrams were generated using Venny 2.1
Genome_build: GRCz11 Genome Reference Consortium Zebrafish Build 11
Supplementary_files_format_and_content: Tab-delimited text file includes normalized log2counts for each sample

value: wildtype


title: Tuft BR#2


title: Tuft BR#1


title: 0GRKO_3_S19


title: WT_veh1


title: 0GRKO3_S11


title: 0GRKO_2_S18


title: SecPDG BR#3

description:
SE.MATS.JCEC_StemVSecPDG.txt
DaPars_Output_StemVSecPDG_All_Prediction_Results.txt
MAJIQ_StemVSecPDG.txt

source_name: SecPDG BR_colon

value: Sorted colon SecPDG cell; Cd31-, Cd45-, Epcam+, Cd44hi, Cd24med, Ckitmed, live


title: SecPDG BR#4


title: 0GRKO1_S9


title: 0GRKO2_S10


title: Enterocyte BR#4


title: AbsPro BR#3

description:
SE.MATS.JCEC_StemVAbsPro.txt
DaPars_Output_StemVAbsPro_All_Prediction_Results.txt
MAJIQ_StemVAbsPro.txt

source_name: AbsPro BR_colon

value: Sorted colon AbsPro cell; Cd31-, Cd45-, Epcam+, Cd44med/hi, Cd24low, Ckit-, live


title: 0GRKO_1_S17


title: AbsPro BR#2


title: SecPDG BR#1


title: SecPDG BR#2


title: AbsPro BR#1


title: Upper layer bulk tissue Replicate 2

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description:
counttable_allsamples.tsv
UL-BULK-2

data_processing:
Basecalls performed using CASAVA software.
The reads were trimmed 5 nucleotides at the 5’ end. 45 nucleotide long reads were aligned to the mouse reference genome (Ensembl GRCm38) using TopHat2 v2.0.11. The multiple hit parameter was (-g) was set to 1 to exclude reads with multiple genomic alignments
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Read counts per gene were calculated using SAMtoools v0.1.19  and HTSeq v0.6.1p1 with default parameters. Count table was generated using DESeq2.

source_name: Cerebral Cortex

extract_protocol:
Microdissected cortical layer tissue were minced with a forceps and enzymatically dissociated with papain (20 U/mL) in dissociation buffer (glucose 22.5 mM, EDTA 0.5 mM, phenol red), L-cysteine (1 mM) and DNase (125 U/mL) for 80 min at 33oC. Tissue was then washed in inhibitor solution (dissociation buffer with ovomucoid (1.0 mg/mL)) and centrifuged for 5 min at 200 g. Supernatant was discarded, the tissue was resuspended in the inhibitor buffer and mechanically disrupted using a P1000 pipette. Dissociated cells were layered onto inhibitor buffer with concentrated ovomucoid (5 mg/mL) and centrifuged 5 min at 200 g. Finally, the cell pellet was resuspended in staining medium with DAPI. Aldh1l1-GFP+ and Aldh1l1-GFP- cells were sorted on a BD FACS Aria II and gated on forward/side scatter, live/dead by DAPI exclusion, and GFP, using GFP and DAPI controls to set gates for each experiment. Total RNA from FACS-purified cortical layer astrocytes and whole cortical layers was extracted with Trizol LS (Invitrogen) and purified using the RNeasy Kit (Qiagen).
cDNA was generated from full-length RNA using the NuGEN RNA-Seq V2 kit that employs the single primer isothermal amplification method to deplete ribosomal RNA, and sheared by Covaris to yield uniform size fragments. RNASeq libraries were generated using the NuGen Ultralow kit for adapters, barcoding, and amplification and purified using the Agencourt XP magnetic beads, quality controlled with an Agilent bioanalyzer, and quantified by qPCR. Five libraries were pooled per lane across three lanes for single end (SE50) sequencing ona. HiSeq4000.

value: Bulk tissue

tag: strain

value: SW


title: Upper layer non-astrocytes Replicate 2

description:
counttable_allsamples.tsv
UL-NEG-2


title: Stem BR#2

source_name: Stem BR_colon

value: Sorted colon stem cells; Cd31-, Cd45-, Epcam+, Cd44highest, Cd24low, Ckit-, live


title: Upper layer non-astrocytes Replicate 1

description:
counttable_allsamples.tsv
UL-NEG-1


title: Stem BR#1


title: Upper layer astrocytes Replicate 3

description:
counttable_allsamples.tsv
UL-GFP-3


title: Upper layer astrocytes Replicate 2

description:
counttable_allsamples.tsv
UL-GFP-2


title: Upper layer astrocytes Replicate 1

description:
counttable_allsamples.tsv
UL-GFP-1


title: Deep layer bulk tissue Replicate 2

description:
counttable_allsamples.tsv
DL-BULK-2


title: Deep layer bulk tissue Replicate 1

description:
counttable_allsamples.tsv
DL-BULK-1


title: Deep layer non-astrocytes Replicate 2

description:
counttable_allsamples.tsv
DL-NEG-2

value: Cortical cells excluding astrocytes


title: Upper layer bulk tissue Replicate 1

description:
counttable_allsamples.tsv
UL-BULK-1


title: Deep layer non-astrocytes Replicate 1

description:
counttable_allsamples.tsv
DL-NEG-1


title: Stem BR#3


title: Deep layer astrocytes Replicate 1

description:
counttable_allsamples.tsv
DL-GFP-1

value: Purified cortical astrocytes


title: Deep layer astrocytes Replicate 3

description:
counttable_allsamples.tsv
DL-GFP-3


title: Alkbh1KO-MFI-E10.5-2

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

data_processing:
Bases were called using illumina Casava1.8.2.
Paired-end reads were aligned to the mm9 genome (NCBI 37.67) using STAR 2.7.0f with 2-pass methodology.
Initial gene counts were performed using HTSeq 0.11.2 "htseq-count -f bam -r name -s reverse" using the Gencode VM1 comprehensive annotation.
Counts were filtered so that only genes with >10 counts in any of the samples were included for differential analysis.
Differential analysis was performed using DESeq2 1.24.0  using the following settings: "ref='WT',  'fitType = 'local'' , pAdjustMethod='fdr'. Genes with >2 fold change, and FDR <0.05 were considered differntialy regulated.
Genome_build: mm9 (NCBI 37.67), gencode vm1 comprehensive annotation
Supplementary_files_format_and_content: Filtered counts of individual samples.

molecule: polyA RNA

source_name: Maternal Fetal Interface

extract_protocol:
At 10.5 days post conception,whole maternal fetal interfaces were collected by excising the decidua and placenta from the embryo/myometrium. Samples were stored at -80 °C until homogenization and RNA extraction. Care was taken to reduce excess myometrial, perimetrium, amniotic sac, and umbilicus tissue. Tissues were lysed using the QIAzol lysis reagent (79306, Qiagen) in conjunction with the Tissuelyser II homogenization system (85300, Qiagen) as per the manufacturer’sinstructions.
RNA-seq libraries were constructed with Illumina Truseq stranded mRNA library prep kit and sequenced on an Illumina HiSeq 2000 instrument.

tag: gentoype

value: Alkbh1 Tm1a/Tm1a

tag: theiler stage


title: Deep layer astrocytes Replicate 2

description:
counttable_allsamples.tsv
DL-GFP-2


title: TMBIM6 KO HT1080, biological rep1

type: RNA

city: Jeonju

first: Hyun-Kyoung

last: Kim

address: 567 Baekje-daero, Deokjin-gu

department: Department of Pharmacology

country: South Korea

institute: Jeonbuk National University

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the array for 16 h at 45°C and 60 rpm according to the manufacturer’s protocol. After hybridization, the array was labeled with streptavidin/phycoerythrin, washed in GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChips were scanned using GeneChip Array scanner 3000 7G (Affymetrix).

data_processing: Image data were extracted from the scanned array using Command Console v.1.1 software (Affymetrix). The raw CEL file generated by the above procedure yielded expression intensity data that were analyzed with Expression Console v.1.1 software (Affymetrix). The Robust Multi-Average algorithm in the software was used for normalization.

label: biotin

organism: Homo sapiens

source_name: HT1080 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

growth_protocol: HT1080 cell was maintained in Dulbecco’s modified Eagle’s medium (DMEM high glucose) supplemented with 10% fetal bovine serum (FBS) (Life Technologies, Grand Island, NY, USA) and 100 U/ml penicillin-streptomycin at 37°C in a humidified 5% CO2 incubator.

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

treatment_protocol: No treatment

tag: cell line

value: fibrosarcoma cell

value: TMBIM6 KO


title: IR D3 KO sham

city: nagoya

first: Marie

last: Saka-Tanaka

state: aichi

address: furoutyou tikusaku

department: Department of  Molecular Medicine and Metabolism

country: Japan

institute: nagoya university

hyb_protocol: Following fragmentation, aRNA were hybridized on Mouse Genome 430 2.0 using Hybridization oven 640.   Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Chip Scanner 3000.

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 500.

source_name: WT kidney, sham day 3

label_protocol: Biotinylated aRNA were prepared according to Gene Chip 3' IVT Express Kit aRNA amplification procedure and Gene Chip 3' IVT Express KitUse Manual p/N 702646 Rev.1

extract_protocol: Total RNA was prepared using Sepasol(nacalai-tesque). Cleanup and concentration was performed by Rneasy MinElute Cleanup Kit.

value: kidney

value: Mincle KO

tag: gender

tag: treatment

value: sham; day 3


title: TMBIM6 KO HT1080, biological rep2


title: IR D3 KO IR

source_name: KO kidney, IRI day 3

value: male

value: renal ischemia–reperfusion injury; day 3


title: HT1080 wild type, biological rep2

value: wild type


title: IR D1 KO IR

source_name: KO kidney, IRI day 1

value: renal ischemia–reperfusion injury; day 1


title: IR D3  WT IR

source_name: WT kidney, IRI day 3

value: WT


title: IR D3 WT sham


title: WT-MFI-E10.5-1

value: Alkbh1 Tm1c/Tm1c


title: HT1080 wild type, biological rep1


title: Alkbh1KO-MFI-E10.5-1


title: WT-MFI-E10.5-2


title: Glomerular endothelial cells, AS brighttdT_2

first: Brendan

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description:
RUV_P7_v_P7_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
63P7
AS_bright_2

data_processing:
Quality Check: Fastqc, 0.11.5
Adapter Trimming: cutadapt, 1.18
Quality Trimming: trimmomatic, 0.38
Read Alignment/ Read Counts: STAR, 2.6.0c
RPKM and DE Analysis: RUVSeq (edgeR), 1.18
Genome_build: Gencode M16 (GRCm38.p5)
Supplementary_files_format_and_content: Spreadsheet, Raw Counts, RPKM, Statistics, Annotation

source_name: glomerular endothelial cells

extract_protocol:
Renal cortices were processed for mechanical and enzymatic digestion and glomeruli were isolated by a sieveing method. Isolated glomeruli were futher digested to obtain single cells.
Kapa low input RNA library kit

tag: reporter gene

value: TekCre^tdTomato

value: 4 month

value: glomerular endothelial cells


title: AGT2

city: Lubbock

first: Naima

last: Moustaid-Moussa

state: TX

address: 1301 Akron Street

department: Nutritional Sciences & Obesity Research Institute

institute: Texas Tech University

description:
Total miRNA
ID40

data_processing:
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
Total usable number of reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST; the abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text format, containing quantile normalized microRNA abundance

source_name: Adipose tissue

extract_protocol:
Epididymal Adipose tissue was isolated after sacrifce, flash frozen in liquid nitrogen and stored in -80 degree celsius. RNA was harvested using Trizol reagent. with 1 ug of total RNA for the construction of sequencing libraries.
Small RNA libraries were prepared using the Illumina small RNA protocol (Illumina, Inc., San Diego, CA)

value: Adipose tissue

tag: diet

value: Chow diet

value: Agt Tg


title: Glomerular endothelial cells, AS dimtdT_2

description:
RUV_P6_v_P6_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
63P6
AS_dim_2


title: Glomerular endothelial cells, AS dimtdT_3

description:
RUV_P6_v_P6_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
64P6
AS_dim_3


title: AGT1

description:
Total miRNA
ID39


title: Glomerular endothelial cells, AS brighttdT_3

description:
RUV_P7_v_P7_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
64P7
AS_bright_3


title: Glomerular endothelial cells, AS brighttdT_1

description:
RUV_P7_v_P7_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
61P7
AS_bright_1


title: IR D1 WT IR

source_name: WT kidney, IRI day 1


title: AGT3

description:
Total miRNA
ID41


title: WT2

description:
Total miRNA
ID42


title: Tumor-1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent: 50 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner

data_processing: Feature extraction data processing, followed by quantile normalization, comBat batch effect correction and statistical analysis with limma - Bioconductor package in R

source_name: Gr-1bright neutrophils from tumor in skin

label_protocol: Agilent - Low RNA QuickAmp

extract_protocol: Papillomas, tumors and skin were treated enzymatically to dissociate tissues and isolate immune cells. Neutrophils were FACS-sorted to a purity >98% and mRNA extracted.

treatment_protocol: FVB/N mice were treated with DMBA at 6 and 13 weeks of age, together with the application twice weekly of PMA from week 1 to week 18-20.

value: tumor

value: FVB/N


title: WT1

description:
Total miRNA
ID38


title: Glomerular endothelial cells, WT brighttdT_1

description:
RUV_P7_v_P7_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
503P7
WT_bright_1


title: Glomerular endothelial cells, WT brighttdT_3

description:
RUV_P7_v_P7_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
522P7
WT_bright_3


title: Glomerular endothelial cells, WT brighttdT_2

description:
RUV_P7_v_P7_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
515P7
WT_bright_2


title: Glomerular endothelial cells, WT dimtdT_2

description:
RUV_P6_v_P6_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
515P6
WT_dim_2


title: Glomerular endothelial cells, AS dimtdT_1

description:
RUV_P6_v_P6_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
61P6
AS_dim_1


title: Glomerular endothelial cells, WT dimtdT_3

description:
RUV_P6_v_P6_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
522P6
WT_dim_3


title: Wt 6

city: Helsinki

first: Md. Rakibul

last: Hasan

address: Haartmaninkatu 8

department: Oral and maxillofacial diseases

country: Finland

institute: University of Helsinki

description:
chip.microarray006_Signal
replicate 3
Service provided: FIMM, University of Helsinki, Finland

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse calvaria

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted after lyse the calvaria with lysis buffer provided by QIAGEN RNeasy mini kit followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with nanodrop.

value: Wt

value: Embryonic day E15.5

value: Calvaria (excluding skin and brain)


title: Glomerular endothelial cells, WT dimtdT_1

description:
RUV_P6_v_P6_07May18_ManuallyFiltered_EdgeR_NoNormalization.csv
503P6
WT_dim_1


title: KE735TEK100

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

data_processing:
remove reads containing adapters
remove reads containing N>10% (N represents the base cannot be determined)
remove reads containing low quality (Qscore<=5) base which is over 50% of the total base
RNA-seq data were processed and interpreted with Genialis platform. An automated data analysis pipeline run in the Genilais platform consisted of the following: Sequence quality checks were performed on raw and trimmed reads with FastQC. Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the reference genome (UCSC GRCm 38) using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count , and differential gene expression analyses were performed with DESeq2. Lowly-expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Genome_build: GRCm 38

source_name: normal mammary gland PND100

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
Library construction was performed by Novogene. rRNA was removed using the Riob-Zero kit that leaves mRNA. mRNA is randomly fragmented and cDNA synthesized using mRNA template and random hexamer primers and custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase were added to initiated second strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double stranded DNA library was completed through size selection and PCR enrichment

treatment_protocol: mating mice were fed 20% ISP, 1% ISP, 20% casein or Teklad 2018 diets and mother's were maintained on this diet during lactation and pups were maintained on this diet after weaning and until the end of the study. At PND100, MTB-IGFIR mice fed the 20% ISP, 1%ISP and 20% casein diets were switched to the appropriate ISP or casein diet containing 100mg/kg of doxycycline until the end of the study.

tag: time of collection

value: mammary gland PND 100

value: FVB

value: Teklad 2018 standard diet


title: Wt 5

description:
chip.microarray005_Signal
replicate 2
Service provided: FIMM, University of Helsinki, Finland

tag: tissue


title: KW741TEK100


title: Wt 4

description:
chip.microarray004_Signal
replicate 1
Service provided: FIMM, University of Helsinki, Finland

tag: genotype


title: Papilloma-1

source_name: Gr-1bright neutrophils from papilloma in skin

value: papilloma


title: WT3

description:
Total miRNA
ID43

value: WT

value: male


title: Papilloma-2


title: Tumor-2


title: KW733TEK100


title: Rab23-/- 1

description:
chip.microarray001_Signal
replicate 1
Service provided: FIMM, University of Helsinki, Finland


title: Papilloma-3


title: Rab23-/- 3

description:
chip.microarray003_Signal
replicate 3
Service provided: FIMM, University of Helsinki, Finland


title: KW734TEK100


title: KW616CT

source_name: mammary tumor

value: tumor ~10% body weight

value: 20% (200g/kg) casein


title: Tumor-skin-2

source_name: Gr-1bright neutrophils from skin adjacent to tumor

value: skin


title: Tumor-skin-1


title: Rab23-/- 2

description:
chip.microarray002_Signal
replicate 2
Service provided: FIMM, University of Helsinki, Finland


title: NB06

city: Beijing

first: tao

middle: bo

last: zhang

address: No. 17 South Panjiayuan, Chaoyang District

country: China

institute: Cancer Hospital

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37°C GE Wash buffer 2 (Agilent p/n 5188-5326).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with the Agilent's Feature Extraction Software (v10.5)  using default parameters (protocol GE1_105_Dec08 and Grid 014850_D_20070207) to obtain background subtracted and spatially detrended processed signal intensities. The raw data was normalized by the GenespringGX Software (Agilent, version 11.5).

source_name: brain tissue

label_protocol: 500ng purified total RNA was reverse transcribed into cDNA, transcribed into cRNA and labeled with Cyanine-3 (Cy3) using the Agilent’s Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from frozen tissue using the mirVana miRNA Isolation kit (Ambion 1561) according to the manufacturer’s specifications, and purified by the RNeasy mini Kit (Cat No.74106, Qiagen, Germany). RNA integrity was detected using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: The brain tissue samples were rinsed with normal saline after surgical resection and divided into two parts, one of which was placed in liquid nitrogen immediately and then stored at -80°C until use, and the other was placed in formaldehyde solution and for hematoxylin-eosin stained to assess the percentage of tumor cells.

tag: history

value: normal

tag: grade

tag: idh1 mutation


title: Papilloma-skin-1

source_name: Gr-1bright neutrophils from skin adjacent to papilloma


title: NB07

tag: age


title: KW597CT


title: KW274CT


title: Papilloma-skin-2


title: KW206CT


title: Blood sample of patient_15 with Brugada syndrome

type: genomic

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

description: Hybridized to Illumina Omni1-Quad microarray

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol (BeadStation450 V3)

data_processing:
GenomeStudio v2010.1 software was used for data processing with the default settings suggested by the Illumina company. All the raw intensity for each probe including X and Y forms is provided in the 'signal_intensity.txt', which contains 2 x 1140419 = 2280838 data rows. Raw intensity data generated from Illumina GenomeStudio were imported into the Partek Genomic Suite software version 6.4 to calculate the copy numbers in order to performing copy number variation analyses. No additional normalization algorithms were utilized. Copy number segments were defined based on the following three criteria: (1) minimum consecutive genomic markers of ≥100, (2) statistical P-values between neighboring segments of ≤0.0001, and (3) signal-to-noise ratios (SNRs) of ≥0.3.
Log R Ratio (LRR) and B Allele Frequency (BAF) files were generated by Illumina GenomeStudio v2010.1.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Blood sample

label_protocol: standard Illumina protocol

extract_protocol: DNAs were extracted from peripheral blood lymphocytes using a modified proteinase K method (Qiagen, Hilden, Germany)

tag: implantable cardioverter-defibrillator (icd) treatment

value: Yes

value: blood


title: Melanoma, Verafinib, M20-3_S39

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description:
cells_fpkm.txt
M20-3

data_processing:
Mapping was carried out using Tophat.
Samtools and Cufflinks were used to generate FPKM values
To minimize the effects of dividing FPKM values by numbers close to 0 and stochastic nois, 0.1 was added to each FPKM values.
Genome_build: HG37
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: Melanoma, Verafinib

growth_protocol: Cells were grown in Roswell Park Memorial Institute (RPMI) medium supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
cell line RNA was  extracted using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated and 20 days of treatment with 2 µM vemurafenib

value: 2 µM Verafinib for 20 days


title: GBM784

value: M

value: A


title: GBME166


title: NB05


title: Blood sample of patient_11 with Brugada syndrome

value: No


title: Melanoma, Verafinib, M20-2_S38

description:
cells_fpkm.txt
M20-2


title: GBM792


title: Blood sample of patient_12 with Brugada syndrome


title: Blood sample of patient_6 with Brugada syndrome


title: Blood sample of patient_13 with Brugada syndrome


title: Blood sample of patient_2 with Brugada syndrome


title: Melanoma, untreated, M0-3_S36

description:
cells_fpkm.txt
M0-3

source_name: Melanoma, untreated

value: untreated


title: Blood sample of patient_14 with Brugada syndrome


title: GBME207


title: Melanoma, Verafinib, M20-1_S37

description:
cells_fpkm.txt
M20-1


title: Blood sample of patient_7 with Brugada syndrome


title: GBM770


title: Melanoma, untreated, M0-2_S35

description:
cells_fpkm.txt
M0-2


title: KW588S1T

value: 1% (10g/kg) isolated soy protein


title: Blood sample of patient_8 with Brugada syndrome


title: Blood sample of patient_16 with Brugada syndrome


title: Melanoma, untreated, M0-1_S34

description:
cells_fpkm.txt
M0-1


title: GBM776

value: F


title: Blood sample of patient_1 with Brugada syndrome


title: Blood sample of patient_5 with Brugada syndrome


title: KW611S1T

value: FVB


title: GBM746


title: GBM767


title: KW669S1T


title: KW550S1T


title: Melanoma, Verafinib, A20-3_S33

description:
cells_fpkm.txt
A20-3


title: GBM753


title: KW255S20T

value: 20% (200g/kg) isolated soy protein


title: Melanoma, Verafinib, A20-2_S32

description:
cells_fpkm.txt
A20-2


title: Melanoma, Verafinib, A20-1_S31

description:
cells_fpkm.txt
A20-1


title: GBM743


title: GBM718


title: KW239S20T


title: Blood sample of patient_4 with Brugada syndrome


title: Blood sample of patient_9 with Brugada syndrome


title: KW174S20T


title: Melanoma, untreated, A0-4_S30

description:
cells_fpkm.txt
A0-4


title: Blood sample of patient_10 with Brugada syndrome


title: KW534S20T


title: GBM712


title: Melanoma, untreated, A0-2_S28

description:
cells_fpkm.txt
A0-2


title: GBM708


title: GBM688


title: GBM711


title: GBM673


title: GBM692


title: GBM736


title: GBM672

value: O


title: GBM674

value: OA


title: GBM663


title: GBM662


title: GBM635


title: GBM623


title: GXA_3096

city: Freiburg

first: Vincent

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

country: Germany

institute: 4HF Biotec

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: All analyses were carried out using the “R” statistical computing environment and associated modules from Biobase (affy, simpleaffy, affyPLM). Gene expression signal values were extracted directly from the CEL files using robust multiarray average analysis algorithm (‘gcrma’ R package from Bioconductor; justGCRMA function with default parameters)

source_name: patient-derived tumor xenograft

label_protocol: standard Affymetrix protocol

growth_protocol: PDX were passaged from mouse to mouse until RNA extraction

extract_protocol: RNA were extracted from four pieces of snap frozen tumor xenografts from four individual xenografts of the same tumors in the same or different passages using the mirVana kit (Ambion) according to the manufacturer’s instructions. A DNAse digest was performed. Each RNA preparation was subjected to quality control using NanoDrop 2000 to control for purity and Bioanalyzer (Agilent) to control for RNA integrity. Only  the RNA samples with an integrity number (RIN)  between 6.5 and 10  and a ratio between 28s and 18 sRNA between 1.0 and 2.0, and the RNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.

tag: passage


title: GBM659


title: GBM626


title: GXA_3083


title: GBM615


title: GBM671


title: GBM598

value: AO


title: GXA_3087


title: GBM633


title: GBM601


title: GXA_3080


title: GBM639


title: GXA_3079


title: GBM648


title: GXA_3084


title: GBM610


title: GXA_3095


title: GXA_3069


title: nontreat 4

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: AML cells from PBS-treated mice 21 days after AML cell transfer

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: AML cells were isolated using an SH800 cell sorter (Sony) from three untreated and three cytarabine-treated mice 21 days after AML cell injection.

value: murine acute myeloid leukemia (AML) cells (C1498)


title: nontreat 3


title: GBM596

value: AOA


title: GXA_3067


title: GBM595


title: GBM592


title: AraC 4

description: AML cells from cytarabine-treated mice 21 days after AML cell transfer


title: nontreat 2


title: GBM577


title: GBM590


title: GXA_3057


title: GXA_3044


title: AraC 5


title: GBM566


title: GBM583


title: GBM579


title: AraC 1


title: GXA_3063


title: GBM562


title: GBM544


title: Blood sample of patient_3 with Brugada syndrome

value: male


title: GBM552


title: GBM548


title: GXA_3054


title: GXA_3052


title: GBM558


title: GBM543


title: GBM542


title: GXA_3040


title: GBM571


title: Aurothioglucose/Hyperoxia_3

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

data_processing:
RNA-seq FASTQ files were aligned using Bowtie2 to mouse refernce genome mm10.
Normalized gene expressions were generated using Cufflinks.
Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the raw gene counts and calculate differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: text file of RNA raw counts

extract_protocol:
RNA was isolated from BAL fluid removed lungs (n=3/group). Total RNA was used to generate amplified cDNA with the Ovation RNA-Seq System V2 kit (NuGEN, Redwood City, CA)
Sequencing library was prepared using the Nextera XT DNA Sample Preparation 16 Kit
RNA-Seq was preformed using paired end 75bp rapid flow cell on a HiSeq 2500 sequencing platform.

treatment_protocol: Day 0 Neonatal C57/Bl6 mice were intraperitoneally injected with 25 mg/kg of aurothioglucose or saline, followed by >95% oxygen exposure for 72hrs or room air.

tag: strain

tag: agent

value: Aurothioglucose

tag: protocol

value: Hyperoxia


title: GXA_3039


title: Aurothioglucose/Hyperoxia_1


title: GBM528


title: GBM589


title: Saline/Hyperoxia_3

value: Saline


title: GBM522


title: GXA_3038


title: Aurothioglucose/Hyperoxia_2


title: Saline/Hyperoxia_2


title: Aurothioglucose/Room_Air_3

value: Romm Air


title: Saline/Hyperoxia_1


title: GBM514


title: GXA_3037


title: GBM508


title: GBM519


title: GBM523


title: Melanoma, untreated, A0-3_S29

description:
cells_fpkm.txt
A0-3

tag: cell line


title: GBM513

tag: gender


title: Aurothioglucose/Room_Air_2


title: Aurothioglucose/Room_Air_1


title: GXA_3029


title: GBM500


title: GXA_3023


title: GBM490


title: GXA_3036


title: GBM484


title: GBM492

value: M


title: GBM485


title: GBM498


title: Saline/Room_Air_3


title: Saline/Room_Air_1


title: GXA_3012


title: GBM489


title: GBM476

value: AA


title: GBM455


title: GXA_3011


title: iUB d6

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Genome_build: The sequence reads were mapped to refdata-cellranger-GRCh38-3.0.0, downloaded on 7th Nov 2018
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Ureteric bud organoid

growth_protocol: hiPSC colonies grown without feeder cells were plated at a density of 2.5 × 104 cells/cm2 in 4-well culture plates in Stem Fit AK02N medium with 10 mM Y-27632 and 0.125 mg/cm2 iMatrix-511 silk. After 24 h, the cells were treated with Essential 6 medium containing 100 ng/ml Activin A and 3 mM CHIR99021. After 21 h, the cells were treated with Essential 6 medium containing 200 ng/ml FGF8, 0.1 mM TTNPB, 1 mM A83-01 and 0.1 mM LDN193189 for 2 days. Then the cells were replated at a density of 1 × 105 cells/cm2 in Matrigel-coated 24-well culture plates in Essential 6 medium containing the same 4 factors and 10 mM Y-27632 and incubated for an additional 24 h to induce anterior intermediate mesoderm (AIM). AIM cells were treated with Essential 6 medium containing 1 mM CHIR99021, 0.1 mM LDN193189, 200 ng/ml FGF8, 100 ng/ml GDNF and 0.1 mM TTNPB for 2 days to induce nephric duct (ND) leader cells. For differentiation toward epithelialized ND aggregates, ND leader cells were dissociated into single cells by pipetting after treatment with Accutase for 3 min, seeded onto low-attachment 96-well plates at density of 1 × 104 cells/well, and treated with the same medium and factors plus 10 mM Y-27632 for 2 days.

extract_protocol:
Single cells were directory lyzed in droplets generated by Chromium controlor.
Sequencing libraries were generated using Chromium Single Cell 3’ Reagent Kits v2 accoding to the manifacturer's instruction.
single cell RNA-seq

treatment_protocol: Unwanted cells were separated from ND aggregates by pipetting. The ND aggregates were treated with Essential 6 medium containing 1 mM CHIR99021, 0.1 mM LDN193189, 200 ng/ml FGF1, 200 ng/ml FGF8, 100 ng/ml GDNF, 0.1 mM TTNPB, 50 ng/ml EGF and 2% Matrigel for 6 days to constitute induced ureteric bud (iUB) organoids.

tag: cell type

value: iPSC-derived ureteric bud


title: GXA_3027


title: INPUT

city: Krakow

first: Klaudia

last: Skrzypek

address: Wielicka 265

department: Department of Transplantation

country: Poland

institute: Jagiellonian University Medical College

library_source: genomic

data_processing:
Quality assessment of the reads was performed using the FastQC tool (v0.11.7). Reads containing adapters were filtered using the Trim Galore tool (v0.5.0). Mapping of reads to the human reference genome GRCh38 from the Ensembl database was done using the BWA-MEM software (v. 2.1.0). The aligned reads were filtered out more than once. Subsequently, the analysis using the MASC2 callpeak tool (v. 2.1.2) with default parameters (minimum FDR 0.05) was performed. The detected transcription factor binding sites were noted using the HOMER annotatePeaks.pl tool (v4.10) and a GTF file from the Ensembl database.
Genome_build: Human reference genome GRCh38 from the Ensembl database
Supplementary_files_format_and_content: Excel peak file

source_name: RH30 rhabdomyosarcoma cells

growth_protocol: RH30 cells were cultured in DMEM high-glucose medium (Lonza Group Ltd., Basel, Switzerland) supplemented with 10% fetal bovine serum (FBS, EURx, Gdansk, Poland) and 50 g/ml gentamicin (Lonza) at 37°C, 5% CO2 and 95% humidity.

extract_protocol:
ChIP was performed using SimpleChip Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. For ChIP assays 10 µg of goat antibody against SNAIL (R&D Systems, cat. AB-108-C) was used. After immunoprecipitation, the DNA was isolated using spin columns from the kit. Input sample was also analyzed.
Chip-Seq analysis was performed using the Intelliseq sp. z o. o. (Cracow, Poland) company service in cooperation with Novogene Co., Lt d using Illumina high-throughput sequencer. RNA libraries were prepared for sequencing using standard Illumina protocols. Paired-end sequencing libraries were sequenced by Illumina high-throughput sequencer by the Novogene company.

tag: antibody

value: input sample


title: GBM505

value: A


title: KO_ZT7_Coc_rep3

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Basecalling performed using RTA version 1.18.64
Demultiplexing performed using CASAVA version 1.8.2
Alignment to reference assembly mm10 with Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: FPKM value for each gene in tsv format

source_name: ventral striatum

extract_protocol:
Total RNA was harvested using Trizol reagent from frozen ventral striatum tissue punches
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cocaine was dissolved in saline solution and intraperitoneally injected at a dose of 20 mg/kg. Saline solution was injected instead of cocaine in saline-treated mice.

value: ventral striatum

tag: time of harvest

tag: treatment at zt3

value: cocaine


title: GXA_3005


title: KO_ZT7_Coc_rep1

tag: tissue


title: GBM482


title: GBM441

value: F


title: GBM469


title: Saline/Room_Air_2


title: GXA_3013


title: GBM461


title: GBM438


title: K562_K27me3_Xlink_rep2_(20190927_SH_Hs_K27me3_X_0918)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag for H3K27me3 in crosslinked nuclei from 120000 K562 cells

data_processing:
Library strategy:  CUT&TAG
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19.bed.gz).

source_name: CUT&TAG

extract_protocol:
CnT_Protocols_io_v2.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: H3K27me3 Cell Signaling Technology cat# 9733

value: K562 human immortalised myelogenous leukemia cell line


title: GXA_3002


title: GBM446

value: O


title: GBM434


title: GBM440

value: OA


title: GBM459


title: KO_ZT7_Coc_rep2

tag: genotype


title: KO_ZT7_Saline_rep2

value: saline


title: K562_K27me3_Native_rep2_(20190927_SH_Hs_K27m3_N_0918)

description: CUT&Tag for H3K27me3 in nuclei from 120000 K562 cells


title: GBM412

tag: history


title: GBM433

tag: grade


title: GBM415

tag: idh1 mutation


title: SNAIL IP

value: SNAIL antibody


title: KO_ZT7_Saline_rep1


title: GBM474

tag: age

value: AO


title: GBM411


title: GBM406

value: AOA


title: GBM418


title: KO_ZT23_Coc_rep3


title: KO_ZT23_Coc_rep2


title: GBM407


title: KO_ZT23_Saline_rep3


title: KO_ZT23_Coc_rep1


title: KO_ZT7_Saline_rep3


title: GBM405


title: K562_IgG_Xlink_(20190927_SH_Hs_IgG_1x_0924)

value: Guinea pig anti-rabbit Antibodies-Online ABIN101961


title: KO_ZT23_Saline_rep2


title: WT_ZT23_Coc_rep3

value: wild type


title: GBM399

value: M


title: GBM398


title: WT_ZT23_Coc_rep2


title: GBM395


title: GBM402


title: WT_ZT23_Coc_rep1


title: GBM387


title: GBM379


title: WT_ZT23_Saline_rep3


title: KO_ZT23_Saline_rep1


title: GBM391


title: WT_ZT23_Saline_rep2


title: GBM364


title: GBM365


title: GBM393


title: GBM378


title: GBM403


title: GBM353

value: AA


title: GBM354


title: GBM348


title: GBM352


title: GBM396


title: WT_ZT23_Saline_rep1


title: GBM357


title: KO_ZT19_Coc_rep2


title: GBM323


title: KO_ZT19_Coc_rep1


title: KO_ZT19_Coc_rep3


title: KO_ZT19_Saline_rep3


title: KO_ZT19_Saline_rep2


title: KO_ZT19_Saline_rep1


title: GBM334


title: GBM331


title: WT_ZT19_Coc_rep3


title: GBM321


title: GBM296


title: GBM291


title: GBM315


title: GBM317


title: GBM316


title: GBM329


title: WT_ZT19_Coc_rep2


title: GBM285


title: GBM312


title: GBM314


title: GBM273


title: GBM281


title: WT_ZT19_Saline_rep3


title: GBM275


title: GBM266


title: WT_ZT19_Saline_rep2


title: WT_ZT19_Saline_rep1


title: GBM259


title: GBM271


title: WT_ZT19_Coc_rep1


title: THP-1_AML_exposed_to_osteoblasts_2

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: readcount files were generated using featureCounts.

source_name: THP-1 AML cell-line

extract_protocol: RNA isolation, and cDNA preparation were carried out following standard protocols. Total RNA from cortical bone (femurs of 8-10-week old mice, cleaned, flushed and centrifugated 20 seconds at 10.000g’s to remove bone marrow) was extracted using TRIzol (Invitrogen) followed by RNA clean-up using PureLink RNA Mini Kit (Ambion, Invitrogen). mRNA was reversed transcribed using random hexamers RNA-to-cDNA kit (Takara).

value: THP-1 AML cell-line


title: osteoblasts_untreated_1

source_name: Osteoblasts cells

value: Osteoblasts cells


title: KO_ZT15_Saline_rep2

value: ventral striatum


title: osteoblasts_untreated_2


title: KO_ZT15_Coc_rep3

value: cocaine


title: osteoblasts_co-cultured_with_THP-1_AML_2


title: GBM260

value: F


title: GBM253

value: A


title: THP-1_AML_untreated_2


title: GBM258


title: osteoblasts_co-cultured_with_THP-1_AML_1


title: KO_ZT15_Coc_rep2


title: GBM282


title: GBM447


title: GBM232


title: GBM249


title: GBM231


title: GBM191


title: THP-1_AML_untreated_1


title: KO_ZT15_Saline_rep3


title: KO_ZT15_Coc_rep1


title: THP-1_AML_exposed_to_osteoblasts_1


title: KO_ZT15_Saline_rep1


title: WT_ZT15_Coc_rep3


title: WT_ZT15_Coc_rep2


title: WT_ZT15_Saline_rep3


title: WT_ZT15_Coc_rep1


title: WT_ZT15_Saline_rep1


title: WT_ZT15_Saline_rep2


title: KO_ZT11_Coc_rep3


title: TBPH_706_rep6

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: TBPH treated 706 mg/kg R. norvegicus sample

hyb_protocol: The amplified RNA (aRNA) was fragmented then hybridized to Affymetrix Rat Genome 230 2.0 arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Affymetrix Scanner 3000 7G

data_processing:
Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized separately for each chemical.
RMA expression measures from R/affy package

organism: Rattus norvegicus

source_name: liver, TBPH 706 mg/kg

label_protocol: Microarray expression analysis was performed using total RNA isolated from liver samples. RNA meeting the following acceptance criteria were used for microarray expression analysis: RNA samples with a concentration ≥ 35 ng/μL and purity between l.80 to 2.20 and an RNA integrity number (RIN) ≥ 7.0. The RNA was amplified through cDNA synthesis, in vitro transcription and biotin labeling using GeneChip® 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA). One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

growth_protocol: At the start of the study, the animals were 7 weeks of age. The animals were given NTP-2000 diet (Zeigler 117 Brothers, Gardners, PA) and tap water ad libitum. The animal studies were conducted according to the guidelines of the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC) and approved by the local Animal Care and Use Committee.

extract_protocol: Necropsy was conducted after five days of dosing (one day after the last dose). At necropsy, the remaining left lobe of the liver was processed for RNA isolation. Tissue was placed in a cryotube containing RNAlaterTM and stored at 2-8 °C overnight. After overnight storage the RNAlaterTM was removed and the samples stored at -60 °C to -80 °C until processed for RNA isolation for use in microarray analysis. RNA was extracted from frozen samples using a Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA) with a deoxyribonucleic acid (DNA) digestion step. The concentration and purity of each RNA sample was calculated from UV absorbance readings (A260 and A280) obtained using a NanoDrop Spectrophotometer (ND-1000, NanoDrop Products; Thermo Scientific, Wilmington, DE). All samples were also evaluated for RNA integrity using an Agilent RNA 6000 Nano Chip kit with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: TBPH (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver TBPH at doses of 0, 0.07, 0.71, 7.06, 70.6 or 706 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.

value: Sprague Dawley

value: male

tag: treatment

value: liver


title: TBPH_706_rep2


title: TBPH_706_rep4


title: TBPH_706_rep5


title: TBPH_70.6_rep4

description: TBPH treated 70.6 mg/kg R. norvegicus sample

source_name: liver, TBPH 70.6 mg/kg


title: TBPH_7.06_rep6

description: TBPH treated 7.06 mg/kg R. norvegicus sample

source_name: liver, TBPH 7.06 mg/kg


title: TBPH_706_rep1


title: TBPH_706_rep3


title: TBPH_70.6_rep3


title: TBPH_70.6_rep5


title: TBPH_70.6_rep6


title: TBPH_70.6_rep1


title: TBPH_7.06_rep3


title: KO_ZT11_Coc_rep2


title: TBPH_7.06_rep5


title: TBPH_7.06_rep4


title: TBPH_7.06_rep2


title: KO_ZT11_Coc_rep1


title: TBPH_7.06_rep1


title: TBPH_0.71_rep5

description: TBPH treated 0.71 mg/kg R. norvegicus sample

source_name: liver, TBPH 0.71 mg/kg


title: KO_ZT11_Saline_rep2

value: saline


title: TBPH_0.71_rep3


title: KO_ZT11_Saline_rep3


title: TBPH_70.6_rep2


title: TBPH_0.71_rep4


title: WT_ZT11_Coc_rep2


title: TBPH_0.71_rep6


title: WT_ZT11_Coc_rep1


title: TBPH_0.07_rep6

description: TBPH treated 0.07 mg/kg R. norvegicus sample

source_name: liver, TBPH 0.07 mg/kg


title: WT_ZT11_Saline_rep2


title: TBPH_0.71_rep1


title: KO_ZT11_Saline_rep1


title: TBPH_0.07_rep2


title: TBPH_0.07_rep5


title: TBPH_0.07_rep1


title: WT_ZT11_Coc_rep3


title: TBPH_0.71_rep2


title: TBPH_Veh_rep4

description: R. norvegicus TBPH vehicle control sample

source_name: liver, TBPH vehicle control


title: WT_ZT11_Saline_rep1


title: TBBPA.DBPE_943_rep6

description: TBBPA.DBPE treated 943 mg/kg R. norvegicus sample

source_name: liver, TBBPA.DBPE 943 mg/kg

treatment_protocol: TBBPA.DBPE (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver TBBPA.DBPE at doses of 0, 0.1, 0.94, 9.4, 94.3 or 943 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: TBPH_Veh_rep3


title: WT_ZT11_Saline_rep3


title: TBPH_0.07_rep3


title: TBPH_Veh_rep5


title: TBBPA.DBPE_943_rep5


title: TBPH_0.07_rep4


title: WT_ZT7_Coc_rep3


title: TBPH_Veh_rep2


title: TBBPA.DBPE_943_rep2


title: TBPH_Veh_rep1


title: TBPH_Veh_rep6


title: GBM351

source_name: brain tissue


title: TBBPA.DBPE_943_rep1


title: TBBPA.DBPE_943_rep3


title: TBBPA.DBPE_94.3_rep6

description: TBBPA.DBPE treated 94.3 mg/kg R. norvegicus sample

source_name: liver, TBBPA.DBPE 94.3 mg/kg


title: TBBPA.DBPE_94.3_rep5


title: WT_ZT7_Coc_rep2


title: TBBPA.DBPE_94.3_rep4


title: TBBPA.DBPE_943_rep4


title: WT_ZT7_Coc_rep1


title: WT_ZT7_Saline_rep3


title: WT_ZT7_Saline_rep2


title: WT_ZT7_Saline_rep1


title: KO_ZT3_Saline_coc_rep3

value: saline/cocaine


title: KO_ZT3_Saline_coc_rep2


title: KO_ZT3_Saline_coc_rep1


title: WT_ZT3_Saline_coc_rep2


title: WT_ZT3_Saline_coc_rep1


title: TBBPA.DBPE_94.3_rep3


title: TBBPA.DBPE_9.4_rep2

description: TBBPA.DBPE treated 9.4 mg/kg R. norvegicus sample

source_name: liver, TBBPA.DBPE 9.4 mg/kg


title: TBBPA.DBPE_9.4_rep6


title: TBBPA.DBPE_9.4_rep4


title: TBBPA.DBPE_9.4_rep5


title: DP_histone_ChIP_Input

first: Kazuko

last: Miyazaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Institute for Life and Medical Sciences, Kyoto University

data_processing:
Illumina bcl2fastq software used for basecalling (HiSeq 2500, NovaSeq 6000,Illumina HiSeq X Ten).
ATAC-seq and ChIP-seq trimmed reads were mapped to the mm9 reference genome using Bowtie2 (version 1.2.7). Hi-C reads were trimmed from the 3’ end of sequences to GATC (MboI restriction enzyme site) and aligned to the mouse reference genome mm9 using bowtie2.
Tags mapped to unique DNA sequences of ATAC-seq, ChIP-seq and Hi-C were analyzed using HOMER (Lin et al., 2012, Heinz et al., 2018)
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq : Tab-delimited BED files containing peak positions for each ATAC-seq or ChIP-seq experiment. Hi-C: Tab-delimited Text files containing PC1 values for each experiment.

source_name: DP cells purified by MACS (CD4+CD8+CD69–TCRb– )

growth_protocol: For proB cell culture, B cells were enriched by B220-MACS column from total bone marrow cells. Then, B cells were cultured in PRMI 1640 with 10% fetal bovine serum, 2mg/ml sodium bicarbonate, 1 mM sodium pyruvate, 0.1mM nonessential amino acid solution, 5x10-5M 2-Mercaptoethanol, 100µg/ml streptomycine and 100U/ml penicillin in the presence of IL-7 and stem cell factor.

extract_protocol: ATAC-seq : ATAC-seq was performed as described (Buenrostro et al., 2013) with modifications. Cells were lysed, then treated with Tn5 transposase (Nextera DNA Sample Preparation Kit). After the treatment, the tagmentated DNA was cleaned up and purified with DNA Clean & Concentrator kit (Zymo Research).  The purified DNA were amplified with determined cycles of PCR based on the amplification curve, then were size-selected using Ampure XP beads. Hi-C : in situ Hi-C was performed as described (Rao et al., 2014).  DP and cultured proB cells from control and deletion mutant mice were fixed with 1% formaldehyde/FACS buffer for 10 minutes at room temperature. Cells were lysed and chromatin was digested overnight using MboI. The fragment overhangs generated by the restriction enzyme were filled in with biotin-14-dATP by Klenow fragment, then proximity ligation was performed.  Biotinylated DNA was sonicated to 300-500 bp on a Covaris M220. The biotinylated DNA was captured on Dynabeads MyOne Streptavidin T1 beads. After washing the beads, ends of sheared DNA were repaired and added A-tail according to the protocol. NEBNext Multiplex Oligos for Illumina (NEB) were ligated and the beads were washed.  Libraries were amplified by PCR and size selected using ProNex (Promega). As to CD4SP cells, Tethered Conformation Capture (TCC) was performed as described (Kalhor et al. 2012).  CD4SP cells were fixed with 1% formaldehyde/FACS buffer for 10 minutes at room temperature. Cells were lysed and chromatin was digested overnight using MboI.  ChIP-seq : Cells were fixed in 1% formaldehyde/PBS . The reactions were quenched by 1.5M glycine and cells were washed with PBS and pelleted. Pelleted cells were lysed and chromatin was sonicated by Covaris M220.  Diluted sheared chromatin was immunoprecipitated with each antibody which is pre-bound to Dynabead Protein G magnetic microbeads overnight at 4 °C. Samples were washed, eluted and reverse cross-linked  65°C overnight. Samples were next treated with RNase A and proteinase K and purified using DNA Clean & Concentrator kit (Zymo Research). Samples were ligated to NEBNext Multiplex Oligos for Illumina (NEB) and multiplex amplified by PCR. Amplified ChIP DNA was selected by size.

tag: cell

value: DP cells purified by MACS

value: Wild type

value: Thymus

tag: chip antibody


title: TBBPA.DBPE_0.94_rep6

description: TBBPA.DBPE treated 0.94 mg/kg R. norvegicus sample

source_name: liver, TBBPA.DBPE 0.94 mg/kg

tag: strain


title: TBBPA.DBPE_94.3_rep1


title: TBBPA.DBPE_0.94_rep4


title: TBBPA.DBPE_9.4_rep1


title: TBBPA.DBPE_0.94_rep3


title: TBBPA.DBPE_Veh_rep6

description: R. norvegicus TBBPA.DBPE vehicle control sample

source_name: liver, TBBPA.DBPE vehicle control


title: TBBPA.DBPE_0.1_rep3

description: TBBPA.DBPE treated 0.1 mg/kg R. norvegicus sample

source_name: liver, TBBPA.DBPE 0.1 mg/kg


title: TBBPA.DBPE_0.94_rep1


title: TBBPA.DBPE_9.4_rep3


title: TBBPA.DBPE_0.1_rep6


title: TBBPA.DBPE_94.3_rep2


title: TBBPA.DBPE_0.1_rep5


title: TBBPA.DBPE_Veh_rep5


title: TBBPA.DBPE_0.94_rep5


title: TBBPA.DBPE_0.1_rep4


title: TBBPA.DBPE_0.1_rep1


title: WT_ZT3_Saline_coc_rep3

source_name: ventral striatum

value: wild type


title: TBBPA.DBPE_0.1_rep2


title: DP_factor_ChIP_Input


title: HiC_WT_CD4SP

source_name: CD4SP cells (CD4+CD8-Tcrb+)

value: CD4SP cells


title: TBBPA.DBPE_0.94_rep2


title: TBB_550_rep6

description: TBB treated 550 mg/kg R. norvegicus sample

source_name: liver, TBB 550 mg/kg

treatment_protocol: TBB (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver TBB at doses of 0, 0.05, 0.55, 5.50, 55 or 550 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: TBBPA.DBPE_Veh_rep2


title: HiC_Cont_proB

source_name: cultured proB cells (CD19+B220+IgM–IgD–CD25–Kit+)

value: cultured proB cells

value: Bone marrow


title: HiC_R1Bdel-R2Bdel_proB


title: HiC_Cont_DP

source_name: DP cells (CD4+CD8+CD5–CD69–TCRb– )

value: DP cells


title: ATAC_CD4SP_2


title: ATAC_CD4SP_1


title: ATAC_CD4SP_3


title: TBBPA.DBPE_Veh_rep4


title: ATAC_R1pro_Ebox_mut_proB


title: TBBPA.DBPE_Veh_rep3


title: TBB_5.50_rep4

description: TBB treated 5.50 mg/kg R. norvegicus sample

source_name: liver, TBB 5.50 mg/kg


title: TBB_55_rep5

description: TBB treated 55 mg/kg R. norvegicus sample

source_name: liver, TBB 55 mg/kg


title: TBBPA.DBPE_Veh_rep1


title: TBB_5.50_rep3


title: TBB_5.50_rep5


title: ATAC_R1pro_Ebox_Cont_proB


title: TBB_550_rep5


title: TBB_550_rep3


title: TBB_55_rep2


title: TBB_55_rep6


title: TBB_550_rep1


title: TBB_55_rep3


title: TBB_55_rep1


title: TBB_5.50_rep6


title: TBB_5.50_rep2


title: ATAC_R1pro_Ebox_Cont_DN3

source_name: DN3a cells (CD4–CD8–LinnegCD44–CD25+CD28– )

value: DN3a cells


title: ATAC_R-TEn-p1-Ebox_Mut_DP_2


title: TBB_550_rep4


title: TBB_550_rep2


title: TBB_55_rep4


title: HiC_R-TEn-del_DP

value: R-TEnd/d


title: ATAC_R-TEn-p1-Ebox_Cont_DP_2


title: ATAC_R-TEn-p1-Ebox_Mut_DP_1


title: ATAC_R1pro_Ebox_mut_DN3


title: ATAC_EHdKO_DP_2


title: TBB_0.55_rep5

description: TBB treated 0.55 mg/kg R. norvegicus sample

source_name: liver, TBB 0.55 mg/kg


title: TBB_5.50_rep1


title: TBB_0.55_rep6


title: TBB_0.55_rep4


title: TBB_0.55_rep2


title: TBB_0.55_rep1


title: ATAC_R-TEn-p1-Ebox_Cont_DP_1


title: TBB_0.05_rep6

description: TBB treated 0.05 mg/kg R. norvegicus sample

source_name: liver, TBB 0.05 mg/kg


title: TBB_0.55_rep3


title: ATAC_EHCont_DP_2


title: ATAC_EHCont_DP_1


title: TBB_0.05_rep3


title: TBB_0.05_rep4


title: TBB_0.05_rep5


title: TBB_0.05_rep1


title: TBB_0.05_rep2


title: TBB_Veh_rep5

description: R. norvegicus TBB vehicle control sample

source_name: liver, TBB vehicle control


title: TBB_Veh_rep4


title: ATAC_R1Bdel-R2Bdel_preB_2

value: preB cells


title: PBDE47_485_rep4

description: PBDE47 treated 485 mg/kg R. norvegicus sample

source_name: liver, PBDE47 485 mg/kg

treatment_protocol: PBDE47 (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver PBDE47 at doses of 0, 0.0485, 0.485, 4.85, 48.5 or 485 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: PBDE47_485_rep6


title: TBB_Veh_rep1


title: TBB_Veh_rep2


title: PBDE47_485_rep3


title: ATAC_Cont_preB_1


title: ATAC_R1Bdel-R2Bdel_proB_2

value: proB cells


title: ATAC_R1Bdel-R2Bdel_preB_1


title: PBDE47_485_rep2

value: Sprague Dawley


title: ATAC_Cont_preB_2


title: ATAC_EHdKO_DP_1


title: PBDE47_485_rep5

value: male


title: PBDE47_485_rep1

value: liver


title: ATAC_Cont_proB_2


title: PBDE47_48.5_rep4

description: PBDE47 treated 48.5 mg/kg R. norvegicus sample

source_name: liver, PBDE47 48.5 mg/kg


title: ATAC_R1Bdel-R2Bdel_proB_1


title: PBDE47_4.85_rep6

description: PBDE47 treated 4.85 mg/kg R. norvegicus sample

source_name: liver, PBDE47 4.85 mg/kg


title: PBDE47_48.5_rep2


title: PBDE47_48.5_rep6


title: PBDE47_48.5_rep1


title: TBB_Veh_rep3


title: ATAC_Cont_proB_1


title: ATAC_Cont_DN3_2


title: PBDE47_48.5_rep3


title: PBDE47_4.85_rep1


title: ATAC_Cont_DN3_1


title: PBDE47_4.85_rep3


title: ATAC_R-TEn-del_DN3_2


title: PBDE47_4.85_rep2


title: ATAC_R-TEn-del_DN3_1


title: PBDE47_0.485_rep6

description: PBDE47 treated 0.485 mg/kg R. norvegicus sample

source_name: liver, PBDE47 0.485 mg/kg


title: ATAC_Cont_DP_1


title: PBDE47_4.85_rep5


title: PBDE47_0.485_rep1


title: PBDE47_0.485_rep2


title: PBDE47_0.0485_rep5

description: PBDE47 treated 0.0485 mg/kg R. norvegicus sample

source_name: liver, PBDE47 0.0485 mg/kg


title: PBDE47_4.85_rep4


title: PBDE47_48.5_rep5


title: PBDE47_0.485_rep3


title: PBDE47_0.0485_rep4


title: PBDE47_0.485_rep4


title: PBDE47_0.0485_rep6


title: PBDE47_Veh_rep3

description: R. norvegicus PBDE47 vehicle control sample

source_name: liver, PBDE47 vehicle control


title: ATAC_R-TEn-del_DP_2


title: PBDE47_0.0485_rep2


title: PBDE47_Veh_rep6


title: PBDE47_0.0485_rep1


title: PBDE47_0.0485_rep3


title: PBDE47_Veh_rep2


title: HCDBCO_541_rep5

description: HCDBCO treated 541 mg/kg R. norvegicus sample

source_name: liver, HCDBCO 541 mg/kg

treatment_protocol: HCDBCO (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver HCDBCO at doses of 0, 0.05, 0.54, 5.41, 54.1 or 541 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: ATAC_R-TEn-del_DP_1


title: PBDE47_Veh_rep4


title: HCDBCO_541_rep6


title: ATAC_Cont_DP_2


title: STAP-1 KO CML LSCs.

description: STAP-1 KO CML stem cells

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a  75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks ver.2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: STAP-1 KO CML LSCs

extract_protocol:
Total RNA samples were prepared by miRNeasy-Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
Each cDNA was generated using a Clontech SMART-Seq v4 Ultra® Low Input RNA Kit for Sequencing (Takara Clontech,Mountain View, CA, USA). Each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA) according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: STAP-1 KO

value: Chronic Myeloid Leukemic Stem Cells (LSCs)


title: WT CML LSCs

description: WT CML stem cells

source_name: WT CML LSCs


title: PBDE47_0.485_rep5

tag: gender


title: KW556Reg

data_processing:
reads trimmed from 3' end to have a phred score of at least 30
illumina sequencing adapaters removed from the reads and all reads required to have length of at least 32bp
trimming and clipping performed using Trimmomatic
Genome_build: GRCm38

source_name: normal mammary gland PND55

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
mRNA stranded library preparation (NEB) was performed by Genome Quebec Innovation Centre

treatment_protocol: mating mice were fed 20% ISP, 1% ISP, 20% casein or Teklad 2018 diets and mother's were maintained on this diet during lactation and pups were maintained on this diet after weaning and until the end of the study

tag: time of collection

value: postnatal day (PND) 55

value: FVB

tag: diet

value: Teklad 2018 standard diet


title: KW572Reg


title: KW538Reg


title: KW549Reg


title: KW527Cas

value: 20% (200g/kg) casein


title: HCDBCO_541_rep2


title: PBDE47_Veh_rep5


title: KW526Cas


title: KW571Reg


title: KW525Cas


title: HCDBCO_54.1_rep2

description: HCDBCO treated 54.1 mg/kg R. norvegicus sample

source_name: liver, HCDBCO 54.1 mg/kg


title: HCDBCO_54.1_rep3


title: HCDBCO_541_rep1


title: HCDBCO_54.1_rep1


title: HCDBCO_5.41_rep6

description: HCDBCO treated 5.41 mg/kg R. norvegicus sample

source_name: liver, HCDBCO 5.41 mg/kg


title: HCDBCO_5.41_rep5


title: HCDBCO_541_rep4


title: HCDBCO_541_rep3


title: HCDBCO_5.41_rep4


title: HCDBCO_54.1_rep5


title: PBDE47_Veh_rep1


title: HCDBCO_54.1_rep6


title: HCDBCO_5.41_rep3


title: HCDBCO_5.41_rep1


title: HCDBCO_54.1_rep4


title: KW524Cas


title: KW517Cas


title: HCDBCO_5.41_rep2


title: HCDBCO_0.54_rep6

description: HCDBCO treated 0.54 mg/kg R. norvegicus sample

source_name: liver, HCDBCO 0.54 mg/kg


title: HCDBCO_0.54_rep5


title: KW523Soy10

value: 1% (10g/kg) isolated soy protein


title: HCDBCO_0.54_rep2


title: KW522Soy10


title: HCDBCO_0.05_rep6

description: HCDBCO treated 0.05 mg/kg R. norvegicus sample

source_name: liver, HCDBCO 0.05 mg/kg


title: KW425Soy10


title: KW423Soy10


title: KW505Soy10


title: KW405Soy200

value: 20% (200g/kg) isolated soy protein


title: HCDBCO_0.54_rep4


title: KW393ASoy200


title: HCDBCO_0.05_rep4


title: HCDBCO_0.05_rep5


title: KW391ASoy200


title: HCDBCO_0.54_rep1


title: KW390ASoy200


title: HCDBCO_0.54_rep3


title: HBCD_641_rep5

description: HBCD treated 641 mg/kg R. norvegicus sample

source_name: liver, HBCD 641 mg/kg

treatment_protocol: HBCD (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver HBCD at doses of 0, 0.06, 0.641, 6.41, 64.1 or 641 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: HCDBCO_Veh_rep4

description: R. norvegicus HCDBCO vehicle control sample

source_name: liver, HCDBCO vehicle control


title: HCDBCO_Veh_rep5


title: HCDBCO_Veh_rep1


title: HBCD_641_rep3


title: HBCD_641_rep4


title: HBCD_641_rep2


title: HCDBCO_Veh_rep6


title: HCDBCO_0.05_rep2


title: HCDBCO_Veh_rep3


title: HCDBCO_Veh_rep2


title: HCDBCO_0.05_rep3


title: HCDBCO_0.05_rep1


title: KW392ASoy200


title: HHDM_5

city: Winnipeg

first: Christopher

last: Pascoe

state: MB

address: 602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba

department: Physiology & Pathophysiology

institute: University of Manitoba

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the mouse genome using STAR v2.5
read count tables were generated from bam files using htseq-count v.2.5
Significance and fold changes calculated in R using DEseq2 package with Likelihood Ratio Test
Genome_build: Ensebml GRCm38
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

source_name: Left lung post lavage

extract_protocol:
Lungs were lavaged with 2x 1mL of saline and then removed. The left lung was placed into RNAlater (Qiagen) and stored at 4 degrees Celcius for 24 hours after which time it was flash frozen in liquid nitrogen and stored at -80 degrees celcius.
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

value: BALB/c

value: Left Lung

tag: exposure

value: HDM containing high endotoxin abundance


title: HBCD_641_rep1


title: HHDM_4


title: HHDM_3


title: HBCD_64.1_rep6

description: HBCD treated 64.1 mg/kg R. norvegicus sample

source_name: liver, HBCD 64.1 mg/kg


title: HHDM_2


title: HBCD_641_rep6


title: HBCD_64.1_rep2


title: HBCD_64.1_rep4


title: HBCD_64.1_rep5


title: HBCD_64.1_rep3


title: HHDM_1


title: LHDM_5

value: HDM containing low endotoxin abundance


title: LHDM_3


title: HBCD_6.41_rep5

description: HBCD treated 6.41 mg/kg R. norvegicus sample

source_name: liver, HBCD 6.41 mg/kg


title: LHDM_2


title: LHDM_1


title: Control_5

value: Control


title: HBCD_6.41_rep3


title: HBCD_6.41_rep6


title: HBCD_6.41_rep2


title: Control_4


title: HBCD_6.41_rep4


title: HBCD_64.1_rep1


title: LHDM_4


title: Control_3


title: HBCD_0.641_rep6

description: HBCD treated 0.641 mg/kg R. norvegicus sample

source_name: liver, HBCD 0.641 mg/kg


title: HBCD_0.641_rep2


title: HBCD_0.641_rep1


title: HBCD_0.06_rep4

description: HBCD treated 0.06 mg/kg R. norvegicus sample

source_name: liver, HBCD 0.06 mg/kg


title: HBCD_0.06_rep3


title: HBCD_Veh_rep6

description: R. norvegicus HBCD vehicle control sample

source_name: liver, HBCD vehicle control


title: HBCD_Veh_rep4


title: HBCD_0.641_rep4


title: HBCD_Veh_rep5


title: HBCD_0.641_rep5


title: HBCD_6.41_rep1


title: HBCD_0.06_rep6


title: HBCD_0.06_rep5


title: HBCD_0.06_rep2


title: HBCD_0.06_rep1


title: Control_2


title: HBCD_0.641_rep3


title: Control_1


title: decaBDE_959_rep6

description: decaBDE treated 959 mg/kg R. norvegicus sample

source_name: liver, decaBDE 959 mg/kg

treatment_protocol: decaBDE (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver decaBDE at doses of 0, 0.1, 0.959, 9.59, 95.9 or 959 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: Testis, metformin treatment, rep2

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

institute: Peking University

data_processing:
HCS2.2.58 and RTA v1.18 software was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, including those containing more than 10% of unknown nucleotides or more than 50% of low-quality (Q-value no larger than 20%) bases. Then they were filtered against rRNA database to remove potential rRNA contamination.
Reads that passed the above filtration and quality control were mapped to GRCm38 genome (Ensembl release 84), by using TopHat2 software (version 2.1.1) with custom parameters -g 1 -r 50 --mate-std-dev 80 --no-coverage-search --phred64-quals --keep-fasta-order
Gene abundances were quantified by RSEM software (version 1.2.19) with recommended command line parameters by Trpnell C, et al Nature protocol, 2012, 7(3): 562-578. The gene expression level was normalized by using Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method, where the number of fragments mapped to the specific gene was normalized by the total number of fragments that mapped to reference genes and the number of bases on this specific gene.
Genome_build: GRCm38 genome (Ensembl release 84)
Supplementary_files_format_and_content: Single tab-delimited text file that includes FPKM values (i.e. normalized gene expression levels) for all samples.

source_name: Testis

growth_protocol: Male 14-week-old C57BL/6 mice were housed in standard cages in a temperature- and humidity-controlled environment, on a 12-h light/dark cycle, with regular feeding and free access to water. All animal care and experimental protocols complied with the Declaration of Helsinki, Animal Management Rules of the Ministry of Health of the People’s Republic of China and the guide for the Care and Use of the Laboratory Animals of Peking University. The protocol was approved by the Peking University Animal Ethics Committee.

extract_protocol:
Tissues were harvested, flash frozen on dry ice. Total RNA was extracted by using Qiagen RNeasy kit, prepared with Illumina TruSeq Stranded Total RNA Library Prep kit under the manufacturer's guideline.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For treatment group, the mice were treated with 300mg/kg (10mL/kg) metformin through gavage administration, for 30 days. For control group, the mice were treated with double distilled water through gavage administration, for 30 days.

value: Testis

value: 14 weeks

tag: Sex


title: Testis, metformin treatment, rep3

tag: tissue

value: male

value: 300mg/kg (10mL/kg) metformin through gavage administration, for 30 days


title: Testis, metformin treatment, rep1


title: Testis, control, rep3

value: double distilled water through gavage administration, for 30 days


title: HBCD_Veh_rep2

value: Sprague Dawley

value: liver


title: Testis, control, rep2


title: Testis, control, rep1


title: HBCD_Veh_rep1


title: decaBDE_959_rep5


title: decaBDE_959_rep3


title: HBCD_Veh_rep3


title: decaBDE_959_rep2


title: Stomach, metformin treatment, rep2

source_name: Stomach

value: Stomach


title: decaBDE_9.59_rep3

description: decaBDE treated 9.59 mg/kg R. norvegicus sample

source_name: liver, decaBDE 9.59 mg/kg


title: Stomach, metformin treatment, rep1


title: decaBDE_959_rep4


title: decaBDE_95.9_rep6

description: decaBDE treated 95.9 mg/kg R. norvegicus sample

source_name: liver, decaBDE 95.9 mg/kg


title: decaBDE_95.9_rep5


title: decaBDE_95.9_rep4


title: Stomach, control, rep3


title: decaBDE_9.59_rep6


title: decaBDE_95.9_rep3


title: decaBDE_95.9_rep2


title: Stomach, metformin treatment, rep3


title: decaBDE_9.59_rep2


title: decaBDE_959_rep1


title: Stomach, control, rep2


title: decaBDE_9.59_rep4


title: decaBDE_9.59_rep1


title: decaBDE_9.59_rep5


title: decaBDE_0.959_rep6

description: decaBDE treated 0.959 mg/kg R. norvegicus sample

source_name: liver, decaBDE 0.959 mg/kg


title: decaBDE_95.9_rep1


title: Stomach, control, rep1


title: Skeletal muscle, metformin treatment, rep3

source_name: Skeletal muscle

value: Skeletal muscle


title: Skeletal muscle, metformin treatment, rep2


title: Skeletal muscle, metformin treatment, rep1


title: Skeletal muscle, control, rep3


title: Skeletal muscle, control, rep2


title: Skeletal muscle, control, rep1


title: Liver, metformin treatment, rep3

source_name: Liver

value: Liver


title: Liver, metformin treatment, rep2


title: Liver, metformin treatment, rep1


title: decaBDE_0.959_rep4


title: decaBDE_0.1_rep6

description: decaBDE treated 0.1 mg/kg R. norvegicus sample

source_name: liver, decaBDE 0.1 mg/kg


title: decaBDE_0.959_rep2


title: Liver, control, rep3


title: decaBDE_0.1_rep4


title: decaBDE_0.959_rep5


title: decaBDE_Veh_rep6

description: R. norvegicus decaBDE vehicle control sample

source_name: liver, decaBDE vehicle control


title: decaBDE_Veh_rep5


title: decaBDE_Veh_rep2


title: decaBDE_0.1_rep5


title: decaBDE_0.1_rep1


title: decaBDE_0.959_rep1


title: decaBDE_0.1_rep2


title: decaBDE_Veh_rep3


title: decaBDE_0.959_rep3


title: DBDPE_970_rep1

description: DBDPE treated 970 mg/kg R. norvegicus sample

source_name: liver, DBDPE 970 mg/kg

treatment_protocol: DBDPE (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver DBDPE at doses of 0, 0.1, 0.97, 9.71, 97.1 or 970 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: decaBDE_0.1_rep3


title: Liver, control, rep2


title: DBDPE_970_rep6


title: decaBDE_Veh_rep4


title: DBDPE_970_rep2


title: DBDPE_97.1_rep4

description: DBDPE treated 97.1 mg/kg R. norvegicus sample

source_name: liver, DBDPE 97.1 mg/kg


title: DBDPE_97.1_rep2


title: DBDPE_970_rep5


title: DBDPE_97.1_rep5


title: decaBDE_Veh_rep1


title: Liver, control, rep1


title: DBDPE_97.1_rep6


title: DBDPE_970_rep3


title: DBDPE_970_rep4


title: Kidney, metformin treatment, rep3

source_name: Kidney

value: Kidney


title: Kidney, metformin treatment, rep1


title: Kidney, metformin treatment, rep2


title: DBDPE_9.71_rep6

description: DBDPE treated 9.71 mg/kg R. norvegicus sample

source_name: liver, DBDPE 9.71 mg/kg


title: Kidney, control, rep3


title: Kidney, control, rep1


title: DBDPE_97.1_rep1


title: Heart, metformin treatment, rep3

source_name: Heart

value: Heart


title: Heart, metformin treatment, rep2


title: Heart, metformin treatment, rep1


title: DBDPE_97.1_rep3


title: DBDPE_9.71_rep5


title: DBDPE_9.71_rep2


title: DBDPE_0.97_rep4

description: DBDPE treated 0.97 mg/kg R. norvegicus sample

source_name: liver, DBDPE 0.97 mg/kg


title: Kidney, control, rep2


title: DBDPE_0.97_rep5


title: DBDPE_9.71_rep1


title: DBDPE_0.97_rep1


title: DBDPE_0.97_rep3


title: DBDPE_9.71_rep4


title: DBDPE_0.97_rep6


title: DBDPE_0.1_rep6

description: DBDPE treated 0.1 mg/kg R. norvegicus sample

source_name: liver, DBDPE 0.1 mg/kg


title: DBDPE_9.71_rep3


title: DBDPE_0.1_rep3


title: Heart, control, rep2


title: DBDPE_0.1_rep4


title: Heart, control, rep1


title: DBDPE_Veh_rep6

description: R. norvegicus DBDPE vehicle control sample

source_name: liver, DBDPE vehicle control


title: DBDPE_0.97_rep2


title: DBDPE_Veh_rep5


title: DBDPE_0.1_rep2


title: DBDPE_0.1_rep5


title: Heart, control, rep3


title: DBDPE_Veh_rep4


title: DBDPE_0.1_rep1


title: Eyeball, metformin treatment, rep2

source_name: Eyeball

value: Eyeball


title: DBDPE_Veh_rep3


title: Eyeball, metformin treatment, rep1


title: Eyeball, control, rep3


title: Eyeball, control, rep1


title: Eyeball, metformin treatment, rep3


title: Brown adipose tissue, metformin treatment, rep2

source_name: Brown adipose tissue

value: Brown adipose tissue


title: Brown adipose tissue, metformin treatment, rep3


title: DBDPE_Veh_rep2


title: BTBPE_680_rep1

description: BTBPE treated 680 mg/kg R. norvegicus sample

source_name: liver, BTBPE 680 mg/kg

treatment_protocol: BTBPE (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver BTBPE at doses of 0, 0.07, 0.69, 6.88, 68 or 680 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.


title: BTBPE_68_rep3

description: BTBPE treated 68 mg/kg R. norvegicus sample

source_name: liver, BTBPE 68 mg/kg


title: BTBPE_680_rep6


title: BTBPE_680_rep5


title: BTBPE_680_rep2


title: BTBPE_680_rep3


title: BTBPE_680_rep4


title: BTBPE_68_rep5


title: BTBPE_68_rep4


title: DBDPE_Veh_rep1


title: BTBPE_6.88_rep2

description: BTBPE treated 6.88 mg/kg R. norvegicus sample

source_name: liver, BTBPE 6.88 mg/kg


title: BTBPE_6.88_rep6


title: BTBPE_6.88_rep5


title: BTBPE_6.88_rep4


title: BTBPE_68_rep2


title: BTBPE_68_rep1


title: Eyeball, control, rep2


title: BTBPE_6.88_rep3


title: Brown adipose tissue, metformin treatment, rep1


title: Brown adipose tissue, control, rep2


title: Brown adipose tissue, control, rep3


title: Brown adipose tissue, control, rep1


title: Brain, metformin treatment, rep3

source_name: Brain

value: Brain


title: BTBPE_0.69_rep6

description: BTBPE treated 0.69 mg/kg R. norvegicus sample

source_name: liver, BTBPE 0.69 mg/kg


title: BTBPE_0.69_rep3


title: BTBPE_0.69_rep5


title: BTBPE_0.69_rep4


title: BTBPE_6.88_rep1


title: Brain, control, rep3


title: Brain, metformin treatment, rep2


title: Brain, metformin treatment, rep1


title: BTBPE_0.07_rep5

description: BTBPE treated 0.07 mg/kg R. norvegicus sample

source_name: liver, BTBPE 0.07 mg/kg


title: Brain, control, rep1


title: Aorta, metformin treatment, rep3

source_name: Aorta

value: Aorta


title: Aorta, metformin treatment, rep2


title: Act_minus_NP (BR-78)

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 2.20.0.422.
Mapping to the reference genome (GRCh38), and calcutating the gene expression values were perfomed by CellRanger 2.1.0 CellRanger count.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx files contain genewise UMI counts for all cells in a sparse matrix format; genes.tsv files contain Ensembl gene IDs and gene symbols as Tab-separated text format; barcode.tsv files contain the 10X cell barcodes used to identify cells.

source_name: Mesonephric nephron progenitor

growth_protocol: hiPSC colonies grown on SNL feeder cells were first treated by an enzymatic method with CTK dissociation solution for 3 min to remove SNL cells, dissociated into single cells by gentle pipetting after treatment with Accutase for 6 min and seeded on Matrigel-coated 24-well plates at a density of 2.5 × 104 cells/cm2 with Primate Repro FF2 medium, 4 ng/ml bFGF, 10 µM Y-27632 and 500 U/ml Penicillin and Streptomycin (PS). On culture day 2, the cells were treated in serum-free differentiation medium consisting of DMEM/F12 Glutamax medium, B27 supplement minus vitamin A, and 500 U/ml PS (hereafter called basal medium) supplemented with 1 µM CHIR99021, 10 nM retinoic acid, 1 ng/ml BMP4 and 100 ng/ml bFGF to induce CDX1+ cells. For differentiation towards intermediate mesoderm (IM) and metanephric nephron progenitor (NP) cells, CDX1+ cells were cultured with 3 μM CHIR99021, 100 ng/ml bFGF and 1 ng/ml BMP7. After 12 h, the medium was switched to basal medium containing 3 μM CHIR99021, 100 ng/ml bFGF, 1 ng/ml BMP7 and 10 μM A83-01.

extract_protocol:
Sequencing libraries were generated from cells directly.
isolation of single cells and preparation of library with cell barcode were conducted using ddSEQ platform (Bio-Rad Laboratories) and SureCell WTA 3′ Library Prep Kit (Illumina)
scRNA-seq

treatment_protocol: For induction of metanephric NP-like cells, the medium was changed at Stage 4, to basal medium containing 3 μM CHIR99021, 100 ng/ml bFGF, 1 ng/ml BMP7, 10 ng/ml activin A and 30 μM Y-27632. At Stage 5, the medium was changed to basal medium containing 200 ng/ml FGF9, 0.1 μM RA and 25 ng/ml NOGGIN. At Stage 6, the medium was switched to basal medium containing 200 ng/ml FGF9 and 1 µM CHIR99021. Subsequently, the culture medium was refreshed every day. For induction of mesonephric NP-like cells, cells were cultured as the same protocol described above, but activin A was lacked in Stage 4 culture medium.

tag: cell type

value: iPSC-derived projenitor

tag: cell line

value: 4A6 iPSC

tag: activin

value: minus


title: BTBPE_0.07_rep6

value: male


title: BTBPE_0.69_rep2


title: BTBPE_0.07_rep1


title: BTBPE_0.69_rep1


title: BTBPE_Veh_rep6

description: R. norvegicus BTBPE vehicle control sample

source_name: liver, BTBPE vehicle control


title: Brain, control, rep2

value: 14 weeks


title: Aorta, metformin treatment, rep1

value: 300mg/kg (10mL/kg) metformin through gavage administration, for 30 days


title: WTDIV143

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

data_processing:
Alignment to mouse genome using Salmon (salmon-0.11.1-linux_x86_64) for single end reads.
Trim first column of Salmon output data to contain ENSMUST transcript identifiers. This was done using the Galaxy platform.
Created a file to convert ENSMUST identifiers to GeneID using Galaxy
Normalize count values and idnetify differentially expressed genes using DeSeq2. This was done using the Galaxy Platform.
Export Data and evaluate in R to create visuals.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Counts as computed from TPM values of all data in the experiment, done using Galaxy DeSeq2. File is CSV format.

source_name: Dorsal Root Ganglia

growth_protocol: Embryonic neurons were cultured in Neurobasal with added B27, Pen/Strep, FDU (anti-mitotic) and NGF for 14 days, with media changes on Day 5 and Day 10.

extract_protocol:
Trizol (Invitrogen) was used to extract total RNA according to the manufacturer's instructions.
250-300bp insert library prepared according to Illumina instructions

treatment_protocol: A subset of mutant neurons received lentivirus that re-expressed Tmem184b (and a Venus fluorescent reporter) using a CMV promoter. Virus transduction efficiency was verified by Venus expression.

value: DRG neurons

tag: days in culture

tag: transduced with virus


title: WTDIV142

tag: age


title: WTDIV144


title: BTBPE_0.07_rep2

value: Sprague Dawley

tag: treatment

value: liver


title: Act_plus_NP (BR-77)

source_name: Metanephric nephron progenitor

value: plus


title: BTBPE_0.07_rep3


title: BTBPE_Veh_rep4


title: BTBPE_Veh_rep3


title: BTBPE_Veh_rep5


title: BTBPE_Veh_rep2


title: BTBPE_Veh_rep1


title: Aorta, control, rep3

value: double distilled water through gavage administration, for 30 days


title: WTDIV141


title: DU145 cells, mut_rep2

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

country: Italy

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

description:
DU145 cells treated with SPOP mutation
200796230064_H

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v4. Raw expression data were log2-transformed and normalized using the robust spline normalization method.

label: Biotin

source_name: DU145 cells

label_protocol: Biotinylated cRNA were prepared with Illumina RNA TotalPrep amplification kit (Ambion)

growth_protocol: 0.25 x 10e6 cells/ml of DU145 cells in 2 ml of RPMI 10% FBS medium without antibiotics per well (in a 6-well plate) so that they were 90% confluent at the time of transfection

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: DU145 cells were transfected with 50mg of plasmids expressing wt or mutated SPOP combined 1:1 with Lipofectamine 2000 and resuspended in a total of 500ml of Optimem Medium (amounts per well)

value: DU145 cells

tag: genotype

value: SPOP mutation


title: DU145 cells, wt_rep2

description:
DU145 cells treated with SPOP wild type
200796230064_B

value: SPOP wild type


title: DU145 cells, mut_rep1

description:
DU145 cells treated with SPOP mutation
200796230064_G


title: DU145 cells, wt_rep3

description:
DU145 cells treated with SPOP wild type
200796230064_C


title: DU145 cells, wt_rep1

description:
DU145 cells treated with SPOP wild type
200796230064_A


title: mutd14fg

tag: strain

value: Tmem184b gene trap homozygous (C57BL/6 background)


title: Aorta, control, rep2