title: SG1cMSB2 glucose t=8d 3-B

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description:
processed data file:
d8_SG1_MSB2_glucose_B_S208

data_processing:
Transcript quantification: Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PLoS genetics 11:e1005395, http://histo.ucsf.edu/downloads/ucsf_hc.01_1.G217B.transcripts.fasta).  Relative abundances (reported as TPM values) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and assembled transcripts using KALLISTO version 0.43.0.  Further analysis was restricted to transcripts with TPM ≥ 10 in at least one sample.  KALLISTO was invoked for each SAMPLE as:  kallisto quant -i ucsf_hc.01_1.G217B.idx -t 4 -b 100 \    --single --rf-stranded -l 250 -s 50 \    -o SAMPLE.kallisto SAMPLE.fastq.gz
Differentially expressed genes were identified by linear regression on four independent factors using LIMMA version 3.26.1.  Specifically, KALLISTO est_counts were rounded to the nearest integer and imported as counts per million (CPM) in a DGEList in R. Samples were TMM normalized with calcNormFactors and VOOM was used to estimate the mean/variance trend.  Samples were classified on four factors: batch (1 or 3), genotype (WT or msb2), media (GlcNAc or glucose), and time (0, 2d, 6d, or 8d). For each transcript, the observed counts were fit to a model assuming a mean transcript abundance plus independent corrections for each factor using lmFit. Shrinkage of the individual gene variances over the full data was applied with eBayes, and significantly differential genes were identified by extracting genes with a significantly non-zero genotype coefficient (at 5% FDR) with an effect size of at least 2x (absolute log2 fold change ≥ 1) using topTable.  The key processing steps in R were:  dge <- DGEList(counts)  dge <- calcNormFactors(dge)  time <- as.factor(time)  genotype <- as.factor(genotype)  media <- as.factor(media)  batch <- as.factor(batch)  d <- model.matrix(~time+genotype+media+batch)  v <- voom(dge, d)  fit <- lmFit(v, d)  fit <- eBayes(fit)  topTable(fit, coef="genotypeMSB2", n = 20000, lfc=1, p.value = .05)  The fit parameters and adjusted p-values from the LIMMA analysis are given, along with gene annotations and the input estimated counts from KALLISTO, in supplementary file Table_profiles.cdt (Excel and JavaTreeView compatible tab-delimited text).
Genome_build: http://histo.ucsf.edu/downloads/ucsf_hc.01_1.G217B.transcripts.fasta
Supplementary_files_format_and_content: All processed data files are tab-delimited text (generated as abundance.tsv by kallisto)

organism: Histoplasma ohiense

source_name: liquid culture

growth_protocol: G217B, msb2 (SG1), and msb2+MSB2 yeast cells were inoculated off of a plate into 5ml HMM liquid medium and incubated at 37C, shaking, with 5% CO2. Liquid cultures were passaged 1:25 after 48 hours into HMM media. They were passaged 1:25 again and expanded to 50ml into HMM liquid media with glucose or GlcNAc as carbon source. They were grown for another 48 hours at 37C, 5% CO2 after which time point 0 was taken. The cultures were then transferred to a room temperature shaker. Time points were taken after 2, 6, 8, and 10 days of growth at room temperature.

extract_protocol:
Histoplasma capsulatum cultures were collected by filtration with a disposable filtration apparatus either in Biosafety Level 2 laboratory for growth at 37°C or in the Biosafety Level 3 laboratory for growth at room temperature. At each time point, 10mL of fungal culture was passed through a disposable filter apparatus (Thermo Fisher), the cells were scraped off with a cell scraper, placed into a conical with 1mL trizol reagent (Qiazol) and flash frozen in liquid nitrogen. Samples were stored at -80°C until all time points were collected.  Total RNA was extracted from fungal cells using a trizol-based RNA extraction protocol. Frozen, resuspended pellets of cells were incubated at room temperature for 5 minutes to thaw. The lysate was bead beat followed by a chloroform extraction. The aqueous phase was then transferred to an Epoch RNA column where the filter was washed with 3M NaOAc and then with 10mM TrisCl in 80% EtOH. DNase (Purelink) treatment was used to remove any residual DNA and the filters were washed again with NaOAc and TrisCl before eluting the RNA in nuclease-free water. RNA quality was determined with a High Sensitivity DNA bioanalyzer chip from Agilent.  20ug of total RNA was purified for mRNA through polyA selection with Oligo-dT Dynabeads(Thermo Fisher) as described in the Thermo Scientific protocol. Ribosomal RNA depletion was confirmed with an RNA 6000 nano bioanalyzer chip from Agilent Technologies. Samples were acceptable for library preparation at 0-4% rRNA.
Libraries for RNAseq were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Individual libraries were uniquely barcoded with NEBNext Multiplex Oligos for Illumina sequencing platform (New England Biolabs). Average fragment size and presence of excess adapter was determined with High Sensitivity DNA bioanalyzer chip from Agilent Technologies. Libraries had an average fragment length of 300-500bp. The concentration of the individual libraries was quantified through Qubit dsDNA High Sensitivity Assay (Invitrogen). 5ng of each library was pooled into a final library and ran on a High Sensitivity DNA bioanalyzer chip to determine the average fragment size of the final pooled sample. Final library was submitted to the UCSF Center for Advanced Technology for sequencing on the Illumina HiSeq4000 sequencer.

tag: time

tag: replicate

value: B

tag: media

value: glucose

tag: batch


title: VUE_pt6 [Low]

status: Public on Sep 30 2019

type: RNA

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

country: USA

institute: Mayo Clinic

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Partek GS 6.4 software (St. Louis, MO) using GCRMA normalization algorithm

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Placenta

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

extract_protocol: Qiagen Rneasy FFPE kit used according to the manufacturer's protocol

tag: immune cell inflitration

value: Low

tag: disease

value: Villitis of unknown etiology


title: CoBFP233

type: SRA

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1233

library_source: transcriptomic

data_processing:
FASTQ files were checked for quality control metrics using FastQC (version 0.11.5) and RSeqQC (version 2.6.4)
Post-Quality control, raw reads were mapped to the reference genome using Hisat2 (version 2.1.0) proceeded by exon-counting using featureCounts (version 1.6.0)
Genome_build: Ensembl GRCz11, build 94
Supplementary_files_format_and_content: Tab-delimeted files containing the Ensembl gene id and the RLE normalized counts

organism: Danio rerio

source_name: Adult zebrafish heart_Uninjured_BFP

extract_protocol:
0.2% RNase inhibitor in Triton X-100 plus Dilute the oligo-dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo-dT primers and 90 µl of nuclease-free water to a tube and mix well. Cells were isolated in the lowest possible volume, possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer, 1 ul of oligo dT primeres and dNTP mix. Smart-seq2 (Picelli, S., et al. Nature Protocols 2014 )
Smart-seq2 (Picelli, S., et al. Nature Protocols 2014 )

tag: strain

tag: condition

value: Uninjured

tag: tissue

value: Adult zebrafish heart

tag: sorted cell population

value: BFP


title: VUE_pt6 [High]

value: High


title: Ch217

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1217

source_name: Adult zebrafish heart_Uninjured_RFP

value: RFP


title: VUE_pt5 [Low]


title: SG1cMSB2 glucose t=2d 3-B

state: CA

description:
processed data file:
d2_SG1_MSB2_glucose_B_S196

molecule: polyA RNA

tag: genotype


title: GAR020413B.B13.F2.19.PrimeView.071913

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Array hybridization were performed per recommended specifications

scan_protocol: Scanning were performed per recommended specifications

data_processing: Raw data in .CEL were processed using the R/Bioconductor package affy; background correction: normexp; quantile normalization: RMA

label_protocol: Biotin labeling per Affymetrix Protocol

extract_protocol:
Sample collection protocol: Blood samples were collected from COMET-IPF participants at study entry
Trizol extraction / Qiagen RNeasy Micro cleanup; Blood samples were collected from IPF patients enrolled in COMET cohort at study entry. PBMCs were isolated by Ficoll-Paque Plus (GE Healthcare Life Science, Pittsburgh, PA) and stored in TRIzol reagent (Thermo Fisher Sci., Waltham, MA). RNA was extracted following manufacturer’s protocol and was re-precipitated by sodium acetate/ethanol.

tag: age

tag: gender

value: M

tag: ethnicity

tag: smoker

tag: diagnosis

value: IPF

tag: follow-up time

value: PBMC


title: SG1cMSB2 glucose t=0d 3-B

description:
processed data file:
d0_SG1_MSB2_glucose_B_S190

tag: time


title: GAR020413B.B7.F1.19.PrimeView.071913


title: Ch225

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1225


title: VUE_pt5 [High]


title: SG1cMSB2 glucose t=8d 3-A

description:
processed data file:
d8_SG1_MSB2_glucose_A_S184

tag: replicate

value: A


title: CoBFP209

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1209


title: GAR020413B.B18.F3.19.PrimeView.071913


title: GAR020413B.B9.F1.21.PrimeView.071913


title: CICh195

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1195

source_name: Adult zebrafish heart_Cryoinjury_RFP

value: Cryoinjury


title: SG1cMSB2 glucose t=6d 3-A

description:
processed data file:
d6_SG1_MSB2_glucose_A_S178

tag: media


title: CICh193

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1193


title: VUE_pt4 [Low]


title: SG1cMSB2 glucose t=2d 3-A

description:
processed data file:
d2_SG1_MSB2_glucose_A_S172

tag: batch


title: GAR020413B.B2.20B.PrimeView.071913

value: Baseline


title: GAR020413B.B1.COMET.19.PrimeView.071913


title: GAR082812.37.COMET.18.FU3.PrimeView.100212

value: F


title: CICh192

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1192


title: VUE_pt4 [High]

tag: immune cell inflitration


title: GAR082812.36.COMET.18.FU2.PrimeView.100212


title: GAR082812.35.COMET.18.FU1.PrimeView.100212


title: GAR082812.34.COMET.18.PrimeView.100212


title: SG1cMSB2 glucose t=0d 3-A

description:
processed data file:
d0_SG1_MSB2_glucose_A_S166


title: VUE_pt3 [High]

tag: disease


title: CICh191

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1191

tag: strain


title: SG1 glucose t=8d 3-B

description:
processed data file:
d8_SG1_glucose_B_S207


title: CIMBFP190

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1190

source_name: Adult zebrafish heart_Cryoinjury_BFP

tag: condition


title: SG1 glucose t=6d 3-B

description:
processed data file:
d6_SG1_glucose_B_S201


title: VUE_pt2 [Low]


title: SG1 glucose t=0d 3-B

description:
processed data file:
d0_SG1_glucose_B_S189


title: CICh177

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1177

tag: tissue


title: SG1 glucose t=2d 3-B

description:
processed data file:
d2_SG1_glucose_B_S195


title: CICh169

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1169

tag: sorted cell population


title: SG1 glucose t=6d 3-A

description:
processed data file:
d6_SG1_glucose_A_S177

tag: genotype


title: CICh49

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane149


title: SG1 glucose t=2d 3-A

description:
processed data file:
d2_SG1_glucose_A_S171


title: VUE_pt2 [High]


title: GAR082812.33.COMET.16.FU3.PrimeView.0928.12

tag: age


title: CICh189

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1189


title: GAR082812.30.COMET.16b.PrimeView.0928.12

tag: gender


title: CIMBFP41

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane141


title: GAR082812.29.COMET.13.FU3.PrimeView.092112

tag: ethnicity


title: VUE_pt3 [Low]


title: SG1 glucose t=0d 3-A

description:
processed data file:
d0_SG1_glucose_A_S165


title: GAR082812.32.COMET.16.FU2.PrimeView.0928.12

tag: smoker


title: VUE_pt1 [High]


title: VUE_pt1 [Low]


title: CICh17

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane117


title: SG1 glucose t=10d 2-B

description:
processed data file:
SG1_10_B_S31


title: GAR082812.31.COMET.16.FU1.PrimeView.0928.12

tag: diagnosis


title: GAR082812.28.COMET.13.FU2.PrimeView.092112

tag: follow-up time


title: GAR082812.27.COMET.13.FU1.PrimeView.092112


title: GAR082812.26.COMET.13.PrimeView.092112


title: SG1 glucose t=8d 2-B

description:
processed data file:
SG1_8d_B_S29

tag: time


title: SG1 glucose t=8d 3-A

description:
processed data file:
d8_SG1_glucose_A_S183

tag: replicate


title: CIMBFP73

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane173


title: CICh1

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane11


title: SG1 glucose t=6d 2-B

description:
processed data file:
SG1_6d_B_S27

tag: media


title: GAR020413.Comet.12.FU3.PrimeView.022013


title: CICh33

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane133


title: SG1 glucose t=0d 2-B

description:
processed data file:
SG1_0_B_S24

tag: batch


title: SG1 glucose t=8d 2-A

description:
processed data file:
SG1_8d_A_S28


title: SG1 glucose t=10d 2-A

description:
processed data file:
SG1_10_A_S30


title: SG1 glucose t=6d 2-A

description:
processed data file:
SG1_6d_A_S26


title: SG1 glucose t=2d 2-A

description:
processed data file:
SG1_2d_A_S25


title: SG1 glucose t=0d 2-A

description:
processed data file:
SG1_0_A_S23


title: GAR020413A.Comet.12.PrimeView.021513


title: G217B glucose t=8d 3-B

description:
processed data file:
d8_WT_glucose_B_S206


title: G217B glucose t=6d 3-B

description:
processed data file:
d6_WT_glucose_B_S200


title: G217B glucose t=2d 3-B

description:
processed data file:
d2_WT_glucose_B_S194


title: G217B glucose t=0d 3-B

description:
processed data file:
d0_WT_glucose_B_S188


title: SG1cMSB2 glucose t=6d 3-B

description:
processed data file:
d6_SG1_MSB2_glucose_B_S202


title: GAR020413.Comet.12.FU2.PrimeView.022013


title: GAR082812.25.COMET.11.FU3.PrimeView.092112


title: G217B glucose t=2d 3-A

description:
processed data file:
d2_WT_glucose_A_S170


title: G217B glucose t=0d 3-A

description:
processed data file:
d0_WT_glucose_A_S164


title: GAR020413G.2.22b.FU1.PrimeView.NL.100113


title: G217B glucose t=8d 3-A

description:
processed data file:
d8_WT_glucose_A_S182


title: GAR082812.20.COMET.9.FU1.PrimeView.091912


title: GAR082812.24.COMET.11.FU2.PrimeView.092112


title: G217B glucose t=10d 2-B

description:
processed data file:
G217B_10_B_S22


title: GAR082812.21.COMET.9.FU2.PrimeView.091912


title: GAR020413.Comet.8.FU3.PrimeView.022013


title: GAR020413G.4.22.FU3.PrimeView.NL.100113


title: GAR020413A.Comet.8.PrimeView.021513


title: GAR082812.22.COMET.11.PrimeView.092112


title: GAR082812.23.COMET.11.FU1.PrimeView.092112


title: G217B glucose t=6d 3-A

description:
processed data file:
d6_WT_glucose_A_S176


title: GAR020413.Comet.6.FU3.PrimeView.022013


title: GAR082812.19.COMET.9.PrimeView.091912


title: G217B glucose t=6d 2-B

description:
processed data file:
G217B_6d_B_S18


title: G217B glucose t=2d 2-B

description:
processed data file:
G217B_2d_B_S16


title: GAR020413.Comet.6.FU2.PrimeView.022013


title: GAR020413A.Comet.6.PrimeView.021513


title: GAR020413A.Comet.6.FU1.PrimeView.021513


title: G217B glucose t=10d 2-A

description:
processed data file:
G217B_10_A_S21


title: G217B glucose t=0d 2-B

description:
processed data file:
G217B_0_B_S14


title: GAR020413A.Comet.8.FU1.PrimeView.021513


title: GAR082812.18.COMET.5.FU2.PrimeView.091912


title: G217B glucose t=8d 2-A

description:
processed data file:
G217B_8d_A_S19


title: G217B glucose t=6d 2-A

description:
processed data file:
G217B_6d_A_S17


title: G217B glucose t=2d 2-A

description:
processed data file:
G217B_2d_A_S15


title: GAR082812.17.COMET.5.FU1.PrimeView.091912


title: GAR082812.15.COMET.4.FU3.PrimeView.011713


title: GAR082812.16.COMET.5.PrimeView.091912


title: GAR082812.14.COMET.4.FU2.PrimeView.011713


title: GAR020413A.Comet.12b.FU1.PrimeView.021513


title: G217B glucose t=0d 2-A

description:
processed data file:
G217B_0_A_S13


title: GAR082812.13.COMET.4.FU1.PrimeView.011713


title: SG1cMSB2 GlcNAc t=8d 3-B

description:
processed data file:
d8_SG1_MSB2_GlcNAc_B_S205

value: GlcNAc


title: NF10_Monolayer NPCs day 10_BPF

city: Beijing

first: Francesco

last: Faiola

address: 18 Shuangqing rd

country: China

institute: Research Center foe Eco-Environmental Sciences, Chinese Academy of Sciences

data_processing:
Base-calling was performed with the BGISEQ-500 software, version 0.3.8.1111
Raw reads were subjected to quality control, filtered into clean reads and aligned to the reference sequences with Bowtie2 (parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) and HISAT (parameters: -p 8 --phred64 --sensitive -I 1 -X 1000).
Gene quantification was performed with RSEM and expression levels calculated with the FPKM method.
To identify DEGs, FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1' were used as default thresholds to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample

organism: Mus musculus

source_name: Monolayer NPCs day 10 treated with BPF

extract_protocol:
RNA was extracted with Trizol and further purified with a Qiagen Rneasy Plus kit
RNA libraries were prepared for sequencing using standard protocols at BGI

tag: cell type

value: J1-derived NPCs

tag: day of differentiation

tag: treatment

value: BPF


title: GAR082812.10.COMET.3.FU2.PrimeView.011713


title: SG1cMSB2 GlcNAc t=6d 3-B

description:
processed data file:
d6_SG1_MSB2_GlcNAc_B_S199

value: B


title: NA10_Monolayer NPCs day 10_BPA

source_name: Monolayer NPCs day 10 treated with BPA

tag: strain

value: BPA


title: GAR082812.9.COMET.3.FU1.PrimeView.011713

tag: tissue


title: NS8_EBs Day 8_RA and_BPS

source_name: EBs Day 8 incubated for 4 days with RA and treated with BPS

value: J1-derived EBs

value: BPS


title: SG1cMSB2 GlcNAc t=8d 3-A

description:
processed data file:
d8_SG1_MSB2_GlcNAc_A_S181


title: SG1cMSB2 GlcNAc t=6d 3-A

description:
processed data file:
d6_SG1_MSB2_GlcNAc_A_S175


title: NC10_Monolayer NPCs day 10_DMSO

source_name: Monolayer NPCs day 10 treated with DMSO

value: DMSO


title: NA8_EBs Day 8_RA and_BPA

source_name: EBs Day 8 incubated for 4 days with RA and treated with BPA


title: NF8_EBs Day 8_RA and_BPF

source_name: EBs Day 8 incubated for 4 days with RA and treated with BPF


title: SG1cMSB2 GlcNAc t=2d 3-A

description:
processed data file:
d2_SG1_MSB2_GlcNAc_A_S169


title: SG1cMSB2 GlcNAc t=0d 3-A

description:
processed data file:
d0_SG1_MSB2_GlcNAc_A_S163


title: NC8_EBs Day 8_RA and_DMSO

source_name: EBs Day 8 incubated for 4 days with RA and treated with DMSO


title: GAR082812.8.COMET.3.PrimeView.011713


title: GS20_EBs Day 20_BPS

source_name: EBs Day 20 treated with BPS


title: NS10_Monolayer NPCs day 10_BPS

source_name: Monolayer NPCs day 10 treated with BPS


title: SG1cMSB2 GlcNAc t=2d 3-B

description:
processed data file:
d2_SG1_MSB2_GlcNAc_B_S193


title: GAR082812.12.COMET.4.PrimeView.011713


title: SG1cMSB2 GlcNAc t=0d 3-B

description:
processed data file:
d0_SG1_MSB2_GlcNAc_B_S187


title: SG1 GlcNAc t=6d 3-B

description:
processed data file:
d6_SG1_GlcNAc_B_S198


title: SG1 GlcNAc t=0d 3-B

description:
processed data file:
d0_SG1_GlcNAc_B_S186


title: SG1 GlcNAc t=2d 3-B

description:
processed data file:
d2_SG1_GlcNAc_B_S192


title: GF20_EBs Day 20_BPF

source_name: EBs Day 20 treated with BPF


title: GA20_EBs Day 20_BPA

source_name: EBs Day 20 treated with BPA


title: SG1 GlcNAc t=8d 3-A

description:
processed data file:
d8_SG1_GlcNAc_A_S180

source_name: liquid culture


title: GS12_EBs Day 12_BPS

source_name: EBs Day 12 treated with BPS


title: SG1 GlcNAc t=6d 3-A

description:
processed data file:
d6_SG1_GlcNAc_A_S174


title: GF12_EBs Day 12_BPF

source_name: EBs Day 12 treated with BPF


title: SG1 GlcNAc t=2d 3-A

description:
processed data file:
d2_SG1_GlcNAc_A_S168


title: SG1 GlcNAc t=0d 3-A

description:
processed data file:
d0_SG1_GlcNAc_A_S162


title: GC12_EBs Day 12_DMSO

source_name: EBs Day 12 treated with DMSO


title: Emu_HH18_hindlimb_rep3

city: Boston

first: John

last: Young

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: chromatin accessibility assay using Tn5 enzyme

library_source: genomic

data_processing:
Sequencing and basecalling was carried out on NextSeq_2_1_0.
Raw ATAC-seq reads were trimmed using NGmerge (https://github.com/jsh58/NGmerge) with adapter mode (-a) and a minumum overlap of 20 bases (-e 20).
Trimmed reads were aligned to droNov1 for emu and galGal4 for chicken using Bowtie2.2.4 with -X 2000.
Mitochondrial reads were removed with removeChrom (https://github.com/jsh58/harvard/blob/master/removeChrom.py) .
ATAC-seq peaks were called using MACS2 (v 2.1.0) first on individual libraries and then on pools for each species and tissue.  Significant peaks were determined as described in the supplemental methods.
Homologous regions for emu peaks were identified using halLiftover (v2.1) as described in the supplementary methods.
Young_Grayson_2019_ATAC-seq_Matrix.txt was generated using bedtools annotate (v2.25.0).  Columns are as follows: Chromosome, Start, Stop, and Size all pertain the the galGal4 genomic position of the peak; geneName is the closest annotated gene to the peak; the next 6 columns are the Chicken (C) and Emu (E) strict peak calls for flank (K), forelimb (FL), and hindlimb (HL), where the value is the proportion of the entire peak region that is overlapped by that dataset; the next 18 columns are the individual libraries for each species and tissue as described for the strict datasets; the next 15 columns are the porportion of the entire peak region that overlaps with previously-published ChIP-seq datasets for chicken (Seki et al. 2017); CNEE is the porportion of overlap of the entire peak region with Conserved Non-Exonic Elements described in Sackton et al. 2019.
Genome_build: droNov1, galGal4
Supplementary_files_format_and_content: strict_(species)_(tissue)_annotate.txt files represent peaks that were present across all three biological replicates for a given species and tissue,

molecule: genomic DNA

organism: Dromaius novaehollandiae

source_name: embryonic HH18 hindlimb somatopleure

extract_protocol:
Tissue was dissected from each embryo in cold PBS.  Tissue was immediately transferred to 1x Trypsin in EDTA Solution (Sigma) for 10-15 minutes at room temperature. Following trypsinization, the tissue was transferred to a neutralizing culture media (DMEM (Gibco) with 10% FBS (Gibco) and 1% Pen Strep (Gibco)) and pipette-mixed until homogenized. Homogenate was filtered through 35µm nylon mesh filters and filtrate was taken immediately to cell counting.
50,000 live cells were utilized for ATAC-seq tagmentation as described in Buenrostro et al. (2015).  Following tagmentation clean-up, 11 cycles of PCR were carried out and PCR products were cleaned using the Minelute PCR Purification Kit (QIAGEN).

tag: developmental stage

value: hindlimb somatopleure


title: GS9_EBs Day 9_BPS

source_name: EBs Day 9 treated with BPS


title: SG1 GlcNAc t=8d 3-B

description:
processed data file:
d8_SG1_GlcNAc_B_S204

tag: genotype


title: SG1 GlcNAc t=10d 1-B

description:
processed data file:
SG1_10_B_S36


title: Emu_HH18_hindlimb_rep2


title: SG1 GlcNAc t=8d 1-B

description:
processed data file:
SG1_8_B_S34


title: GF9_EBs Day 9_BPF

source_name: EBs Day 9 treated with BPF


title: Emu_HH18_hindlimb_rep1


title: SG1 GlcNAc t=6d 1-B

description:
processed data file:
SG1_6_B_S32


title: GA9_EBs Day 9_BPA

source_name: EBs Day 9 treated with BPA


title: Emu_HH18_forelimb_rep3

source_name: embryonic HH18 forelimb somatopleure

value: forelimb somatopleure


title: SG1 GlcNAc t=2d 1-B

description:
processed data file:
SG1_2_B_S30


title: GC9_EBs Day 9_DMSO

source_name: EBs Day 9 treated with DMSO


title: SG1 GlcNAc t=0d 1-B

description:
processed data file:
SG1_0_B_S28


title: Emu_HH18_forelimb_rep2


title: GC20_EBs Day 20_DMSO

source_name: EBs Day 20 treated with DMSO


title: SG1 GlcNAc t=10d 1-A

description:
processed data file:
SG1_10_A_S35


title: Emu_HH18_forelimb_rep1


title: Emu_HH18_flank_rep3

source_name: embryonic HH18 flank somatopleure

value: flank somatopleure


title: GA12_EBs Day 12_BPA

source_name: EBs Day 12 treated with BPA


title: Emu_HH18_flank_rep2


title: SG1 GlcNAc t=6d 1-A

description:
processed data file:
SG1_6_A_S31


title: GA6_EBs Day 6_BPA

source_name: EBs Day 6 treated with BPA


title: GC6_EBs Day 6_DMSO

source_name: EBs Day 6 treated with DMSO


title: SG1 GlcNAc t=8d 1-A

description:
processed data file:
SG1_8_A_S33


title: SG1 GlcNAc t=2d 1-A

description:
processed data file:
SG1_2_A_S29


title: S4_EBs Day 4_BPS

source_name: EBs Day 4 treated with BPS


title: Emu_HH18_flank_rep1


title: SG1 GlcNAc t=0d 1-A

description:
processed data file:
SG1_0_A_S27


title: A4_EBs Day 4_BPA

source_name: EBs Day 4 treated with BPA


title: C4_EBs Day 4_DMSO

source_name: EBs Day 4 treated with DMSO


title: F4_EBs Day 4_BPF

source_name: EBs Day 4 treated with BPF


title: G217B GlcNAc t=6d 3-B

description:
processed data file:
d6_WT_GlcNAc_B_S197

source_name: liquid culture


title: G217B GlcNAc t=8d 3-B

description:
processed data file:
d8_WT_GlcNAc_B_S203


title: G217B GlcNAc t=2d 3-B

description:
processed data file:
d2_WT_GlcNAc_B_S191


title: S0_EBs day 0 (mESCs)_BPS

source_name: EBs day 0 (mESCs) treated with BPS

value: J1 ESCs


title: GS6_EBs Day 6_BPS

source_name: EBs Day 6 treated with BPS


title: F0_EBs day 0 (mESCs)_BPF

source_name: EBs day 0 (mESCs) treated with BPF


title: G217B GlcNAc t=0d 3-B

description:
processed data file:
d0_WT_GlcNAc_B_S185


title: GF6_EBs Day 6_BPF

source_name: EBs Day 6 treated with BPF


title: G217B GlcNAc t=8d 3-A

description:
processed data file:
d8_WT_GlcNAc_A_S179


title: C0_EBs day 0 (mESCs)_DMSO

source_name: EBs day 0 (mESCs) treated with DMSO


title: A0_EBs day 0 (mESCs)_BPA

source_name: EBs day 0 (mESCs) treated with BPA


title: G217B GlcNAc t=2d 3-A

description:
processed data file:
d2_WT_GlcNAc_A_S167


title: G217B GlcNAc t=0d 3-A

description:
processed data file:
d0_WT_GlcNAc_A_S161


title: G217B GlcNAc t=6d 3-A

description:
processed data file:
d6_WT_GlcNAc_A_S173


title: G217B GlcNAc t=8d 1-B

description:
processed data file:
G217B_8_B_S24


title: G217B GlcNAc t=10d 1-B

description:
processed data file:
G217B_10_B_S26


title: G217B GlcNAc t=6d 1-B

description:
processed data file:
G217B_6_B_S22


title: G217B GlcNAc t=2d 1-B

description:
processed data file:
G217B_2_B_S20


title: G217B GlcNAc t=0d 1-B

description:
processed data file:
G217B_0_B_S18


title: G217B GlcNAc t=10d 1-A

description:
processed data file:
G217B_10_A_S25


title: G217B GlcNAc t=2d 1-A

description:
processed data file:
G217B_2_A_S19


title: G217B GlcNAc t=6d 1-A

description:
processed data file:
G217B_6_A_S21


title: G217B GlcNAc t=0d 1-A

description:
processed data file:
G217B_0_A_S17


title: G217B GlcNAc t=8d 1-A

description:
processed data file:
G217B_8_A_S23


title: C4-2B MDVR Indocin

status: Public on Sep 29 2019

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Enzalutamide-resistant (MDVR), castration-resistant prostate cancer (CRPC) cell line treated with Indocin (20 uM)

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software (HCS) HD 3.4.0 and Real-Time Analysis (RTA) v2.7.7 software. The bcl2fastq conversion software was used for sample demultiplexing and FASTQ conversion.
FASTQ-formatted sequence data was analyzed using a standard TopHat-Cufflinks workflow. RNA-Seq sequence reads (FASTQ format) were aligned to the reference human genome assembly (Feb. 2009, GRCh37/hg19) using TopHat software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization.
Processed data are Cufflinks-Cufffnorm output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: Feb. 2009, GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the StringTie-Cuffnorm gene-level output files.

growth_protocol: Enzalutamide-resistant C4-2B (C4-2B MDVR) cells were maintained in RPMI 1640 medium [supplemented with 10% fetal bovine serum (FBS), 100 units per ml penicillin, and 0.1 mg per ml streptomycin] and containing 20 uM enzalutamide, and at 37°C in a humidified atmosphere containing 5% CO2 (v/v). C4-2B MDVR cultures were treated with Indocin (20 uM) or vehicle control (DMSO) for 3 days and then harvested for isolation of total cellular RNA.

extract_protocol:
Total cellular RNA was isolated from C4-2B MDVR cells treated with Indocin (20 uM) or DMSO vehicle control using the TRIzol Reagent (Invitrogen).
Indexed, directional RNA-seq libraries were prepared using the KAPA Stranded mRNA-Seq Library Kit (Kapa Biosystems) according to the manufacturer’s standard protocol.

treatment_protocol: C4-2B MDVR cultures were treated with either Indocin (20 uM) or vehicle control (DMSO) for 3 days.

value: cell culture

value: Indocin (20 uM)


title: A549 NSCLC cell line_VECTOR

city: Guangzhou

first: Han

last: Tian

state: Guangdong

address: No.74, Zhongshan Er Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

data_processing:
Bustard software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG38 whole genome using bowtie2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using HTseq.
Genome_build: HG38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each samples were attached.

source_name: A549 cell line, NSCLC

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: NSCLC

tag: cell line

value: VECTOR control


title: A549 NSCLC cell line_NICD1

value: NICD1 overexpression


title: C4-2B MDVR DMSO (Indocin Control)

description: Enzalutamide-resistant (MDVR), castration-resistant prostate cancer (CRPC) cell line treated with DMSO


title: M397 DR29 Day30_RNA-seq

status: Public on Sep 23 2019

city: Los Angeles

first: Xiang

last: Lu

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

institute: University of California, Los Angeles

description:
Reversible RPKM values.txt
dr29.D30

data_processing:
For UCLA samples, we are uncertain about the precise base calling procedures; For COH RNA-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.1.8.4; For COH ChIP-Seq / ATAC-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.2.18
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).  For unstranded counts (with anti-sense, AS, genes removed), strand was to "no" for "Unstranded" counts / FPKM (and strand was set to "reverse" for "Stranded" counts / FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

growth_protocol: M-series patient derived cell lines used in this study were generated under UCLA institutional review board approval # 11–003254. Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2 in RPMI 1640 with L-glutamine (Life Technologies), supplemented with 10% fetal bovine serum (Omega), and 0.2% antibiotics (MycoZapTM Plus-CL from Lonza). The cell lines were tested for mycoplasma and were periodically authenticated to its early passage using GenePrint 10 System (Promega).

extract_protocol:
total RNA was extracted from cell pellets using RNeasy Mini Kit (Qiagen).
for UCLA Samples: Libraries were prepared using the IlluminaTruSeq RNA sample preparation kit, for COH RNA-Seq 160607 Batch Samples: TruSeq unstranded polyA kit, for COH RNA-Seq 160916+160930 Batch Samples: KAPA stranded polyA kit

treatment_protocol: BRAF inhibitor (vemurafenib) from Selleck Chemicals LLC, were dissolved in DMSO at designated concentrations before applying to cell culture media. Cells were plated in 10cm tissue culture plate at 60% confluency and treated with certain drugs for the specified numbers of days. M397 cells were treated with 3uM of vemurafenib for 59days and at day29, drug were removed and cells were cultured with normal medium for another 35days.

value: Patient-derived melanoma cell line M397

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 30 days

tag: library strandedness

value: unstranded

tag: facility

value: COH


title: M397 DR29 Day35_RNA-seq

description:
Reversible RPKM values.txt
dr29.D35

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 35 days


title: M397 Day59_RNA-seq

description:
Reversible RPKM values.txt
D59

value: M397 Cells treated with BRAF inhibitor 59 days


title: M397 DR29 Day4_RNA-seq

description:
Reversible RPKM values.txt
dr29.D4

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 4 days


title: M397 DR29 Day10_RNA-seq

description:
Reversible RPKM values.txt
dr29.D10

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 10 days


title: M397 Day38_RNA-seq

description:
Reversible RPKM values.txt
D38

value: M397 Cells treated with BRAF inhibitor 38 days


title: M397 DR29 Day15_RNA-seq

description:
Reversible RPKM values.txt
dr29.D15

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 15 days


title: M397 Day33_RNA-seq

description:
Reversible RPKM values.txt
D33

value: M397 Cells treated with BRAF inhibitor 33 days


title: M397 Day29_RNA-seq

description:
Reversible RPKM values.txt
D29

value: M397 Cells treated with BRAF inhibitor 29 days


title: M397 Day0_RNA-seq

description:
Reversible RPKM values.txt
Control

value: M397 Cells untreated with BRAF inhibitor


title: M397 Day13_RNA-seq

description:
Reversible RPKM values.txt
D13

value: M397 Cells treated with BRAF inhibitor 13 days


title: M397 Day21_RNA-seq

description:
Reversible RPKM values.txt
D21

value: M397 Cells treated with BRAF inhibitor 21 days


title: M397 Day8_RNA-seq

description:
Reversible RPKM values.txt
D8

value: M397 Cells treated with BRAF inhibitor 8 days


title: M263_ATAC-seq

data_processing:
For UCLA samples, we are uncertain about the precise base calling procedures; For COH RNA-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.1.8.4; For COH ChIP-Seq / ATAC-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.2.18
ChIP-seq and ATAC-seq Reads were aligned to hg19 with bowtie2
Peaks were called on the merged set of bam files using MACS2
Differential accessibility or enrichment of histone mark were measured using diffReps/DESeq2
Differentially accessible or enrichmental regions were called if the absolute log value of the fold change was more than 1 at an FDR <0.05
RNA-seq reads were aligned against the human genome (hg19) using TopHat2. Read counts were quantified using htseq-count (Anders et al., 2015), with UCSC known gene annotations (Hsu et al., 2006) with anti-sense (AS) genes removed.  Fold-change values were calculated from Fragments Per Kilobase per Million reads(FPKM) (Warden et al., 2013) normalized expression values, which were also used for visualization (following a log2 transformation). Aligned reads were counted using GenomicRanges (Lawrence et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, bigwig files. To visualize peaks in each sample, bed graph file was generated using MACS2 with following parametes: --nomodel, --broad, --bdg, --SPMR. Then the generated bed graph file was converted into bigwig file by bedGraphToBigWig tool. For RNA-seq, tab-delimited text files include RPKM values for each sample.

extract_protocol:
Briefly, cells were cultured to ~80% confluency in a petri dish containing 10 mL of growth media, and then fixed in 1% formaldehyde by adding 275 μl of 37% formaldehyde for 10 minutes to cross-link protein–DNA complexes at room temperature. The unreacted formaldehyde was quenched by adding Glycine to a final concentration 0.125 M. Gently swirl dish to mix. The nuclear pellet was isolated with Cell Lysis Buffer. The pellet was resuspended with 500 μl SDS Lysis Buffer containing 1X Protease Inhibitor Cocktail II before sonication for 4 min (10 s on, 30 s off, 10% strength in a Bioruptor to yield DNA fragments of 0.2-1.0 kb in length. The lysates were cleared by centrifugation (12,000g for 10 min at 4 °C) and diluted tenfold in ChIP dilution buffer to decrease the concentration of SDS. After keeping 10% of the sample as input, 500 μl supernatant was incubated overnight at 4 °C with antibody and 20 μL of fully resuspended protein A/G magnetic beads. The washing, elution, reverse cross-linking, and purification steps were performed according to manufacturer’s description. ChIPed Eluted DNA was quantified by Qubit dsDNA HS Assay Kit.  As for ATAC-seq, the previous published protocol (Buenrostro et al., 2015) were used for cell lysis, tagmentation and DNA purification. For RNA-seq, total RNA was extracted from cell pellets using RNeasy Mini Kit (Qiagen).
ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Kapa, Cat KK 8700) according to the manufacturer's protocol. Briefly, 5-10 ng of immunoprecipitated DNA was underwent end-repaired, A tailing and adaptor ligation. A 10 cycles of PCR was performed to produce the final sequencing library. As for ATAC, the Tn5 treated DNA was amplified with a 5-cycle PCR in 50µl reaction volume. The tubes were removed from thermocycler and used 5 µl of partially amplified library to perform qPCR to determine how many additional PCR cycles were needed. For the samples in this study, an additional 4-5 cycles of PCR was performed on the remaining 45ul of each partially amplified product. 1.8X AmpurXP beads purification was used for the final PCR cleanup. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit, and quantified with qPCR. For RNA-seq, sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, USA) with minor modifications.

value: Patient-derived melanoma cell line M263

value: Untreated M263 cells


title: M381_ATAC-seq

value: Patient-derived melanoma cell line M381

value: Untreated M381 cells


title: M249_ATAC-seq

value: Patient-derived melanoma cell line M249

value: Untreated M249 cells


title: M397 DR29 Day17_RNA-seq

description:
Reversible RPKM values.txt
dr29.D17

value: Patient-derived melanoma cell line M397

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 17 days

value: unstranded

value: COH


title: M262_ATAC-seq

value: Patient-derived melanoma cell line M262

value: Untreated M262 cells


title: M233_ATAC-seq

value: Patient-derived melanoma cell line M233

value: Untreated M233 cells


title: M229_ATAC-seq

value: Patient-derived melanoma cell line M229

value: Untreated M229 cells


title: M229K27_H3K27ac_ChIPSeq

tag: chip antibody

value: H3K27ac (Millipore, 17-683)


title: M249K27_H3K27ac_ChIPSeq


title: M262K27_H3K27ac_ChIPSeq


title: M263K27_H3K27ac_ChIPSeq

value: Patient-derived melanoma cell line M263


title: M233K27_H3K27ac_ChIPSeq


title: M381K27_H3K27ac_ChIPSeq


title: M263K4_H3K4me3_ChIPSeq

value: Untreated M263 cells

value: H3K4me3 (Millipore, 07-473)


title: M381K4_H3K4me3_ChIPSeq

value: Patient-derived melanoma cell line M381

value: Untreated M381 cells


title: M397 Day3_RNA-seq

description:
Reversible RPKM values.txt
D3

value: M397 cells treated with BRAF inhibitor 3 days


title: M262K4_H3K4me3_ChIPSeq


title: M249K4_H3K4me3_ChIPSeq

value: Patient-derived melanoma cell line M249

value: Untreated M249 cells


title: M229K4_H3K4me3_ChIPSeq


title: mKidney_EC_Tbx3_KO_S1

status: Public on Sep 20 2019

city: New York City

first: Balvir

last: Kunar

state: New York

address: 1300 York Ave

department: Regenerative Medicine; Physiology, Biophysics, & Systems Biology

institute: Weill Cornell Medical College

description:
CTRL1_S3_L001
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.MM10.GENES.FPKM.tsv

data_processing:
Base calling and sequencing reads de-multiplexing were performed using bcl2fastq v2.17.
Sequencing reads were checked for quality (FastQC v0.11.5), and trimmed/filtered using BBtools.
Read alignment to the transcriptome sequence reference of the UCSC mm10 or hg38 genome build were performed using STAR v2.5.3a.
Aligned files were sorted and indexed with samtools v1.50.
Gene counts were quantified using the Python package HTSeq v0.9.1.
Counts were imported to R v3.4.0, batch corrected and normalized with the EdgeR package.
Mapped reads were assembled into transcripts, and abundance measures (FPKM values) quantified using Cufflinks v2.2.1.
Genome_build: mm10; hg38
Supplementary_files_format_and_content: Tab-delimited data-matrix with GENE_ID, GENE_DESCRIPTION, and SAMPLE_NAMES. All numerical inputs represent FPKM values.

source_name: endothelial cell

extract_protocol:
At least 100 ng of total RNA from both freshly harvested and cultured cells was isolated (phenol-chloroform separation of TRIzol LS) and purified using Qiagen’s RNeasy Mini Kit.
RNA library preps were prepared and multiplexed using Illumina’s TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as input for high-throughput sequencing via Illumina’s HiSeq 4000 producing 51 bp paired-end reads.

treatment_protocol: All cell populations were purified via FACS. Purity mask was applied.

value: Tbx3 fl/fl; Luisa.Cre+

value: kidney

value: endothelial cell

tag: culture status

value: freshly isolated from tissue


title: mKidney_EC_Tbx3_Control_S2

description:
BDR_127_S66_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.MM10.GENES.FPKM.tsv

value: Tbx3 fl/fl; Luisa.Cre-


title: mKidney_EC_Tbx3_KO_S2

description:
CTRL2_S4_L001
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.MM10.GENES.FPKM.tsv


title: mKidney_EC_Tbx3_KO_S3

description:
CTRL3_S5_L001
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.MM10.GENES.FPKM.tsv


title: mKidney_EC_Tbx3_Control_S3

description:
BDR_134_S70_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.MM10.GENES.FPKM.tsv


title: hKidney_Cortex_CD34+_EC_S1

description:
BDR_129_S67_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

value: kidney (Cortex)

value: endothelial cell (CD34+)


title: mKidney_EC_Tbx3_Control_S1

description:
BDR_125_S65_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.MM10.GENES.FPKM.tsv


title: hKidney_Medulla_CD34-_EC_S1

description:
BDR_132_S68_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

value: kidney (Medulla)

value: endothelial cell (CD34-)


title: hKidney_Glomeruli_EC_S2

description:
HUMAN_GLAM_EC_S27_L006
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

value: kidney (Glomeruli)


title: hKidney_Glomeruli_EC_S1

description:
BDR_133_S69_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_ALL++_S2

description:
DB6_ALL_1_S31_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

value: ALL++

value: umbilical cord

value: HUVEC

value: cultured


title: HUVEC_PBX1++_S3

description:
DB11_PBX1_2_S36_L006
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_PRDM1++_S3

description:
DB10_PRDM1_2_S35_L006
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_ALL++_S1

description:
DB_6_S76_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_PBX1++_S1

description:
DB_5_S75_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_PBX1++_S2

description:
DB5_PBX1_1_S30_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_PRDM1++_S2

description:
DB4_PRDM1_1_S29_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: M233K4_H3K4me3_ChIPSeq

value: Patient-derived melanoma cell line M233

value: Untreated M233 cells

value: H3K4me3 (Millipore, 07-473)


title: HUVEC_PRDM1++_S1

description:
DB_4_S74_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: G217B glucose t=8d 2-B

description:
processed data file:
G217B_8d_B_S20

tag: time

value: B

value: glucose


title: HUVEC_TBX3++_S3

description:
DB8_TBX3_2_S33_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

value: endothelial cell


title: HUVEC_TBX3++_S1

description:
DB_2_S72_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_GATA5++_S1

description:
DB_3_S73_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_GATA5++_S3

description:
DB9_GATA5_2_S34_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_TBX3++_S2

description:
DB2_TBX3_1_S27_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: HUVEC_GATA5++_S2

description:
DB3_GATA5_1_S28_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: Methylome B73 leaf

status: Public on Sep 19 2019

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

institute: University of Georgia

data_processing:
MethylC-seq: analysis was performed by Methylpy 1.3
RNA-seq: analysis was performed by hisat2 v2.0.5 and StringTie v1.3.3b
ChIP-seq: analysis was performed by bowtie1.1.1
DAP-seq:  analysis was performed by bowtie2.2.8 and GEM v2.5
ATAC-seq: analysis was performed by bowtie1.1.1
HiC-seq: analysis was performed by HiC-pro v2.8.0 and Juicertools v0.7.0
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt for column headers
Supplementary_files_format_and_content: RNA tab delimited text file, see "RNA_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ChIP bed file, see "ChIP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: DAP bed file, see "DAP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ATAC tbed file, see "ATAC_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: HiC tab delimited text file, see "HiC_column_header_descriptions.txt" for column headers

organism: Zea mays

source_name: B73 leaf

growth_protocol:
There are two separate growth protocols—one for the second leaf and one for the ear primordia.  For both samples, plants were grown from seed collected from field-grown ears grown during the summer of 2017 in Athens, Georgia.
Second leaf protocol: kernels were sown in Sungro Horticulture professional growing mix (Sungro Horticulture Canada Ltd., 52130 RR 65, P.O. Box 189, Seba Beach, AB T0E 2B0 Canada) approximately 0.5 inches below the soil surface.  Soil was saturated with tap water and placed under a 50/50 mixture of 4100K (Sylvania Supersaver Cool White Delux F34CWX/SS, 34W) and 3000K (GE Ecolux w/ starcoat, F40CX30ECO, 40W) light.  The photoperiod was 16 hours of light, eight hours of dark.  The temperature was approximately 25°C during light hours. The relative humidity was approximately 54%.  Seedlings were grown for approximately six days and harvested from four to six hours after photoperiod dawn.  Seedlings were harvested when the V1 leaf had emerged two to three centimeters above the apical tip of the coleoptile. The seedlings were cut approximately three millimeters above the coleoptile-mesocotyl boundary, excluding the shoot apical meristem, and the V2 leaf was removed from within the sheath of the V1 leaf.  Only the inner V2 leaves were used for experiments.
Ear primordia protocol: Plants were grown in greenhouse or field conditions.  Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

extract_protocol:
MethylC-seq: prepared as previously described in (Urich et al. 2015).
RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol.
ChIP-seq: ChiP-seq was performed following the methods of (Zhang et al. 2007).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.
DAP-seq: DAP-seq experiments involving maize ARF samples were processed according to (Galli et al. 2018). All other TFs were processed according to (Bartlett et al. 2017) with the exception that 1ug of pIX-HALO-TF plasmid DNA was used for protein expression and 1ug of adapter ligated library prepared from B73 ear genomic DNA was used for DNA binding.
ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).
Hi-C libraries were prepared following the HiChIP protocol described in (Mumbach et al. 2016) with modifications described in the text.

tag: line

value: 7-day-old 2nd leaf


title: HUVEC_ALL++_S3

description:
DB12_ALL_2_S37_L006
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: CTCF_ChIP_Seq_ZF1d_Rescue

status: Public on Sep 12 2019

city: New York

first: Ricardo

last: Saldana-Meyer

state: NY

address: 522 First Avenue

department: Biochemistry and Molecular Pharmacology

institute: NYUMC - HHMI

data_processing:
Raw sequencing files were aligned against the mouse reference genome (GRCm38/mm10) using Bowtie2 (version 2.3.4.1) (parameters: -N 1 -k 1 -q -x). Ambiguous reads were filtered to use uniquely mapped reads in the downstream analysis. PCR duplicates were removed using Picard-tools (version 1.88). MACS version 2.0.10 was used to call narrow peaks (parameters: -g 1.87e9 --qvalue 0.01).
supplementary_files_format_and_content:bigWigs or peaks called by MACS on bed format
Genome_build: mm10

growth_protocol: E14Tga2 ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent)

extract_protocol:
Cells were fixed with 1% Formaldehyde. Nuclei were isolated and chromatin was fragmented. Chromatin immunoprecipitation (ChIP) was performed and the libraries were prepared using the eluted DNA from ChIP
Kapa Library Prep Kit following the manufacturer’s instructions

treatment_protocol: Rescue cell lines were also grown with 500mM of indole-3-acetic acid (IAA, chemical analog of auxin) in the medium.

value: embryonic stem cells

tag: antibody

value: Anti-CTCF antibody - ChIP Grade, ab70303


title: CTCF_ChIP_Seq_ZF10d_Rescue


title: HUVEC_Vehicle.Control_S2

description:
DB1_EV_1_S26_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

value: Control


title: CTCF_ChIP_Seq_Mock

treatment_protocol: Nuclei were permeabilized with 0.05% Tween-20 in PBS for 10 min at 4C, washed once and resuspended in PBS and finally incubated with RNase A (1 mg/ml) or a mock reaction for 30 minutes


title: CTCF_ChIP_Seq_Rnase_Treatment


title: CTCF_ChIP_Seq_Transcriptional_Inhibition, 4h

treatment_protocol: Cells were incubated with DMSO or a combination of DRB and Triptolide for 1 or 4 hours


title: HUVEC_Vehicle.Control_S1

description:
DB_1_S71_L008
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv


title: CTCF_ChIP_Seq_WT_Rescue


title: CTCF_ChIP_Seq_Transcriptional_Inhibition, 1h


title: CTCF_ChIP_Seq_Transcriptional_Inhibition, DMSO


title: HTP85B2_WBC

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQC (v0.11.5) was used to assess sequence data quality
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.05) tool from ea-utils
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.1.1, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.5)
Reads were coordinate sorted and duplicates were marked using Picard (v2.9.4)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.8.0) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts and RPKM for each sample

source_name: white blood cells

extract_protocol:
Qiagen RLT Extraction
Strand-specific libraries were prepared by Novogene

tag: Sex

value: Male

value: WBC

tag: age

tag: karyotype

tag: library type

value: strand-specific


title: HTP332A_WBC

tag: cell type


title: HTP84A2_WBC


title: HTP351A_WBC


title: HTP322B_WBC


title: HTP328A_WBC

value: Female


title: HUVEC_Vehicle.Control_S3

description:
DB7_EV_2_S32_L005
Manuscript_Kidney.Vascular.Specialization_Bulk-RNA-Seq_Data.HG38.GENES.FPKM.tsv

tag: tissue

value: umbilical cord


title: HTP338B_WBC


title: HTP288B_WBC


title: HTP326A_WBC


title: HTP310A_WBC


title: HTP206B_WBC


title: WT-CCR6 rep3

status: Public on Sep 11 2019

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

description: DNA - accessability. Illumina FC-121-1030

data_processing:
ChIP-seq reads were aligned ot the mm9 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: mm19
Supplementary_files_format_and_content: bigwig

source_name: NKp46- CCR6+ ILC3

extract_protocol: ATAC-seq were processed as per manufacturers instructions (Illumina FC-121-1030)

value: Nr1d1 WT


title: KO-DN rep3

source_name: NKp46- CCR6- ILC3


title: KO-CCR6 rep3


title: HTP0208B_WBC

data_processing:
FASTQC (v0.11.5) was used to assess sequence data quality
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.05) tool from ea-utils
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.1.1, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-unstranded) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.5)
Reads were coordinate sorted and duplicates were marked using Picard (v2.9.4)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.8.0) with the following options (--stranded=no –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts and RPKM for each sample

extract_protocol:
Qiagen RLT Extraction
Unstranded libraries were prepared by Novogene

tag: preparation

value: unstranded


title: HTP0125B_WBC


title: HTP0315A_WBC


title: HTP0314B_WBC


title: HiC_Retina_Adult-Rep4

status: Public on Sep 05 2019

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description:
hic_Retina_Adult.inter_30.hic
Proc.HiC_Retina_Adult.tgz

data_processing:
Basecalls performed using CASAVA
All HiC data have been processed by the Juicer pipeline (version 1.5) against mouse genome mm9. We confirmed the data were reproducible before merging the files from technical or biological replicates using  HiC-spector (version 201706028 from github).
All 5 samples had more than 4.9 billion contacts and 3 samples had >7.5 billion contacts providing a resolution less than 1 kb. Stable loops were identified using HiCCUPS from Juicer at 5kb and 10kb resolution. The highest quality (MAPQ > 30), 370~640 loops were called from each sample and those that were less than 3 Mb were included in the visualization online.
Using Juicebox tools from Juicer pipeline, we extracted contact matrixes from .hic file created by Juicer and call TADs or Loops as below. File name suffix "HiCCUPS.loops": Loops called using HiCCUPS (default parameters and "--ignore_sparsity") come with Juicer pipeline(Durand, Cell Syst, 2016). File name suffix "ArrowHead.5000_blocks": TADs called using Arrowhead(default parameters and "--ignore_sparsity") come with Juicer pipeline(Durand, Cell Syst, 2016). File name suffix "DOM.DC.NONE.100K.bed": TADs called using DomainCaller(Dixon, Nature, 2012. Default parameters using matlab2017b) at 100kb resolution on raw contacts. File name suffix "DOM.DC.VC_SQRT.100K.bed": TADs called using DomainCaller(Dixon, Nature, 2012. Default parameters using matlab2017b) at 100kb resolution on VC_SQRT(Rao, 2014, Cell) normalized contacts. File name suffix "NONE.100K.bed": TADs called using Armatus(Filippova, Algorithms Mol Biol, 2014. Parameters "-m -g 0.2 -s 0.1") at 100kb resolution on raw contacts. File name suffix "KR.100K.bed": TADs called using Armatus(Filippova, Algorithms Mol Biol, 2014. Parameters "-m -g 0.2 -s 0.1") at 100kb resolution on Knight-Ruiz (Rao et al, 2014, Cell) normalized contacts. File name suffix "VC_SQRT.100K.bed": TADs called using Armatus(Filippova, Algorithms Mol Biol, 2014. Parameters "-m -g 0.2 -s 0.1") at 100kb resolution on VC_SQRT (Rao et al, 2014, Cell) normalized contacts. File name suffix "100K.VCS-KR.vote.bed": TADs merged "VC_SQRT.100K.bed" and "KR.100K.bed" after removing TADs called in "KR.100K.bed" overlapping TADs called in "VC_SQRT.100K.bed"
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: HiC file version: 8; multiple bed files instructed in README.txt.

source_name: retina

extract_protocol:
In situ Hi-C protocol was performed using retinal cells, with minor modification to the original protocol (Rao et al., 2014).  Two to five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature, then digested with 125 units of MboI overnight followed by labeling with biotinylated nucleotides and proximity ligation.
After reverse crosslinking, ligated DNA was purified and sheared to 300-500 bp using a Covaris LE220.
The DNA fragments containing ligation junctions were pulled down with streptavidin beads followed by Illumina compatible library construction and paired end sequencing.

tag: strain

value: retina

tag: developmental stage

value: postnatal day 21


title: HiC_Retina_Adult-Rep3


title: HTP0303A_WBC


title: HiC_Retina_Adult-Rep1


title: HiC_Retina_Adult-Rep2


title: WT-DN rep3

tag: genotype


title: HTP302B_WBC


title: HiC_Retina_P0-Rep2

description:
hic_Retina_P0.inter_30.hic
Proc.HiC_Retina_P0.tgz

value: postnatal day 0


title: HiC_Retina_P0-Rep1


title: HTP348A_WBC


title: HiC_Retina_E14.5-Rep2

description:
hic_Retina_E14.5.inter_30.hic
Proc.HiC_Retina_E14.tgz

value: embryonic day 14.5


title: HiC_Retina_NRLGFPpositive

description:
hic_Retina_NRLGFPnegative.inter_30.hic
Proc.HiC_Rod_GFPpos.tgz

value: Nrl-GFP mice

value: purified rod photoreceptors (NRL GFP+)


title: HiC_Retina_NRLGFPnegative

description:
hic_Retina_GFPnegative.inter_30.hic
Proc.HiC_Retina_GFPneg.tgz

value: purified rod photoreceptors (NRL GFP-)


title: HiC_Retina_E14.5-Rep1


title: Titration_B1

status: Public on Sep 01 2019

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

data_processing:
The reads with a low quality score (Q30) were discarded, hereafter read duplicates were removed with Clumpify (BBMap v.37.93) .The libraries were trimmed using cutadapt (v.1.16)16 to remove 3 nucleotides of the 5’ end of read 2. To enable a fair comparison, we started data-analysis from an equal number of reads by subsampling to 1 million trimmed and deduplicated reads. To assess the quality of the data, the reads were mapped using STAR (v.2.5.3)17 on the hg38 genome including the full ribosomal DNA (45S, 5.8S and 5S) and mitochondrial DNA sequences. The parameters of STAR were according to the ENCODE project.
Genes were quantified by Kallisto (v.0.43.1) using Ensembl (v.91) extended with the ERCC spike and Sequin spike sequences.
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv for kallisto

source_name: PFP

extract_protocol:
RNA isolation was performed using the miRNeasy Serum/Plasma Kit (Qiagen) starting from 200µl volume.
Sequencing libraries were generated using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Pico v2, total RNA, Takara, 634413). Compared to the manufacture’s protocol, the fragmentation step was adapted to 4 min at 94°C, hereafter the option to start from highly degraded RNA was followed.

tag: kit

value: SMARTer

tag: biofluid

value: platelet-poor plasma


title: Titration_E1


title: Titration_D2


title: Titration_B2


title: HiC_Retina_Adult-Rep5


title: Titration_D1


title: Titration_C1


title: Titration_E2


title: CM_rep2

source_name: conditioned medium

value: conditioned medium


title: CM_rep1


title: Titration_A1


title: CM_EV_rep2

source_name: conditioned medium EV

value: conditioned medium EV


title: urine_EV_rep1

source_name: urine EV

value: urine EV


title: urine_EV_rep2


title: PRP_EV_rep2

source_name: PRP EV

value: platelet-rich plasma EV


title: urine_rep1

source_name: urine

value: urine


title: CM_EV_rep1


title: PRP_EV_rep1


title: Titration_A2


title: urine_rep2


title: PRP_rep2

source_name: PRP

value: platelet-rich plasma


title: PRP_rep1


title: HTP204A_WBC

value: Male

value: WBC

value: strand-specific


title: PFP_rep2_donor2


title: PFP_rep1_donor2


title: PFP_rep1_donor1


title: PFP_rep2_donor1


title: PRP_rep1_donor2


title: Titration_C2


title: PRP_rep2_donor1


title: PRP_rep1_donor1


title: N32

status: Public on Aug 15 2019

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

description: normal serum

data_processing:
Map reads with STAR version 2.5.1b
Count reads for each gene with HTSeq-count
Calculate gene expression in TPM
[UMI index files]  UMI index is part of adaptor ligated to cDNA molecules during library construction, it is used together with mapping location of the reads to identify PCR duplicates. UMI indices for cancer samples (C1_index.fastq to C96_index.fastq) were in the base 9 - base 16 (8 bases) of the 16 bases index read, while UMI indices for the normal samples (N1_index.fastq.gz to N32_index.fastq.gz) were in the base 1 - base 8 (8 bases) of the 8 bases index read.
Genome_build: Hg38/Ensembl
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: cancerTPM.txt: tab-deliminated TPM
Supplementary_files_format_and_content: normalTPM.txt: tab-deliminated TPM
Supplementary_files_format_and_content: metaData.xlsx: age and gender metadata

source_name: serum

extract_protocol: Sequencing libraries were constructed with SILVER-seq from serum.

tag: gender

tag: condition

value: normal serum

tag: equivalent serum volume used (ul)

tag: rna extration (y/n)

value: N

tag: library construction method

value: SILVER-seq


title: N29

description: normal serum

value: Female


title: N27

description: normal serum


title: Thirtymonth 2

status: Public on Aug 21 2019

city: Xinyang

first: Yun

last: Ma

address: Shihe

institute: Xinyang Normal University

description: mRNA、lncRNA、circRNA

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14)
Linear transcripts assembly and abundance estimation were performed using CuffLinks analyzed by LC-Bio (Hangzhou, China). The assembled transcripts were mapped to the reference annotation using a program named Cuffcompare in the Cufflinks site to derive novel genes.
The transcript abundances were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Supplementary_files_format_and_content: FPKM

organism: Bubalus bubalis

source_name: thirtymonth adipose tissue

growth_protocol: Six adipose samples from Xinyang buffalo of two developmental states (6Month and 30Month old) were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer. The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries.
Then the rRNA depleted RNA samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with a Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) and sequenced by Illumina HiSeq 3000 (LC Sciences, USA) on a 125 bp paired-end run.

value: adipose tissue

value: thirty months


title: Thirtymonth 1

description: mRNA、lncRNA、circRNA


title: N21

description: normal serum


title: N23

description: normal serum


title: Thirtymonth 3

description: mRNA、lncRNA、circRNA


title: N20

description: normal serum


title: N25

description: normal serum


title: N28

description: normal serum


title: N19

description: normal serum


title: N30

description: normal serum


title: N17

description: normal serum


title: N16

description: normal serum


title: N15

description: normal serum


title: N10

description: normal serum


title: N11

description: normal serum


title: N9

description: normal serum


title: N31

description: normal serum


title: N24

description: normal serum


title: N8

description: normal serum


title: N7

description: normal serum


title: N3

description: normal serum


title: N2

description: normal serum


title: N26

description: normal serum


title: N18

description: normal serum


title: N5

description: normal serum


title: N4

description: normal serum


title: C96

description: breast cancer serum (without recurrence)


title: C92

value: breast cancer serum (without recurrence)


title: C95


title: C93


title: C94


title: C90


title: N12

description: normal serum


title: C89


title: N13

description: normal serum


title: N1

description: normal serum


title: C87


title: C86


title: C84


title: C83


title: C88


title: N6

description: normal serum


title: C82


title: C77


title: C79


title: C74


title: C73


title: C76


title: C70


title: C67


title: C78


title: C64


title: C65


title: C66


title: C72


title: C80


title: C62


title: C69


title: C59


title: C60


title: C81


title: C71


title: C58


title: C61


title: C75


title: C57


title: C56


title: C68


title: C55


title: C91


title: N22

description: normal serum


title: PRP_rep2_donor2

value: SMARTer


title: C52


title: C53


title: C63


title: C51


title: C50


title: C49


title: C48


title: C46


title: C44


title: C47


title: C43


title: N14

description: normal serum


title: C41


title: C40


title: C39


title: C37


title: C38


title: C36


title: C35


title: C54


title: C34


title: C32


title: C33


title: C28

description: breast cancer serum (with recurrence)

value: breast cancer serum (with recurrence)


title: C45


title: C31


title: C25

description: breast cancer serum (with recurrence)


title: C26

description: breast cancer serum (with recurrence)


title: C30


title: C27

description: breast cancer serum (with recurrence)


title: C24

description: breast cancer serum (with recurrence)


title: C20

description: breast cancer serum (with recurrence)


title: C18

description: breast cancer serum (with recurrence)


title: C29


title: C21

description: breast cancer serum (with recurrence)


title: C17

description: breast cancer serum (with recurrence)


title: C42


title: C23

description: breast cancer serum (with recurrence)


title: C19

description: breast cancer serum (with recurrence)


title: C22

description: breast cancer serum (with recurrence)


title: C16

description: breast cancer serum (with recurrence)


title: C85


title: C14

description: breast cancer serum (with recurrence)


title: C13

description: breast cancer serum (with recurrence)


title: C12

description: breast cancer serum (with recurrence)


title: C11

description: breast cancer serum (with recurrence)


title: C9

description: breast cancer serum (with recurrence)


title: C10

description: breast cancer serum (with recurrence)


title: C7

description: breast cancer serum (with recurrence)


title: C8

description: breast cancer serum (with recurrence)


title: C6

description: breast cancer serum (with recurrence)


title: C5

description: breast cancer serum (with recurrence)


title: C3

description: breast cancer serum (with recurrence)


title: C2

description: breast cancer serum (with recurrence)


title: C1

description: breast cancer serum (with recurrence)


title: C15

description: breast cancer serum (with recurrence)


title: EC_014_HPAEC ChIP-seq Input

status: Public on Aug 08 2019

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
Sequenced reads were mapped to the human genome using BWA version 0.7.15 with default parameters.
Genome_build: hg19 (also hg38 for BAM and BigWig)
Supplementary_files_format_and_content: BigWig files were generated both with and without the total read normaization (RPM) by DROMPA+ verision 1.1.2.
Supplementary_files_format_and_content: Peak files (BED) with the total read normalization were generated by DROMPA version 3.7.0.

source_name: Pulmonary Artery Endothelial cells

growth_protocol: Purified ECs were cultured in VascuLife VEGF Endothelial Cell Culture Medium (Lifeline Cell Technology, Frederick, MD) with 250 pg/mL VEGF. Cells were maintained at 37°C in a humidified 5% CO2 incubator and the medium was changed every 3 days.

extract_protocol:
Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed.
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: adult

value: Caucasian

value: female

value: Cessation of life

tag: disease

value: Disease type AND/OR category unknown

value: pulmonary artery endothelial cell

value: ChIP-Seq

tag: molecule

value: genomic DNA

value: ChIP-Seq Input


title: EC_025_HPAEC ChIP-seq Input

value: male

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_028_HUAEC ChIP-seq H3K27ac

source_name: Umbilical Artery Endothelial cells

value: newborn

value: umbilical artery endothelial cell

value: Histone H3K27ac

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_025_HPAEC ChIP-seq H3K4me3

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: Histone H3K4me3


title: EC_014_HPAEC ChIP-seq H3K27ac

value: year

value: adult

value: Caucasian

value: female


title: EC_035_HUAEC ChIP-seq H3K27ac

value: Cessation of life

value: Disease type AND/OR category unknown

value: ChIP-Seq


title: EC_035_HUAEC ChIP-seq H3K4me3

value: genomic DNA


title: EC_014_HPAEC ChIP-seq H3K4me3

value: pulmonary artery endothelial cell

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_028_HUAEC ChIP-seq H3K4me3

value: newborn

value: male

value: umbilical artery endothelial cell


title: IMR90 ChIP-seq H3K4me3

source_name: IMR90 cells

value: Cell Line

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_039_HUVEC ChIP-seq H3K4me3

source_name: Umbilical Vein Endothelial cells

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: Arabic

value: endothelial cell of umbilical vein


title: EC_039_HUVEC ChIP-seq H3K27ac

value: year

value: Histone H3K27ac


title: EC_028_HUAEC ChIP-seq Input

value: Caucasian

value: Cessation of life

value: Disease type AND/OR category unknown

value: ChIP-Seq Input


title: EC_039_HUVEC ChIP-seq Input

value: ChIP-Seq

value: genomic DNA

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_040_HUVEC ChIP-seq H3K27ac

value: newborn

value: male


title: EC_040_HUVEC ChIP-seq H3K4me3

value: Histone H3K4me3

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: C4

description: breast cancer serum (with recurrence)

tag: age

value: Female

value: breast cancer serum (with recurrence)

value: N

value: SILVER-seq


title: EC_162_HRAEC ChIP-seq Input

source_name: Renal Artery Endothelial cells

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: adult

value: Asian

value: female

value: kidney blood vessel cell


title: EC_029_HUVEC ChIP-seq H3K4me3

value: Caucasian

value: Cessation of life

value: Disease type AND/OR category unknown

value: endothelial cell of umbilical vein

value: ChIP-Seq

value: genomic DNA

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_029_HUVEC ChIP-seq Input

value: newborn

value: male

value: ChIP-Seq Input


title: EC_029_HUVEC ChIP-seq H3K27ac

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: Histone H3K27ac

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_160_HRAEC ChIP-seq Input

value: The University of Tokyo

value: year

value: adult

value: Asian


title: EC_162_HRAEC ChIP-seq H3K27ac

value: female

value: Cessation of life

value: kidney blood vessel cell


title: EC_160_HRAEC ChIP-seq H3K27ac

value: Disease type AND/OR category unknown

value: ChIP-Seq


title: EC_160_HRAEC ChIP-seq H3K4me3

value: genomic DNA

value: Histone H3K4me3

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_025_HPAEC ChIP-seq H3K27ac

value: Caucasian

value: male

value: pulmonary artery endothelial cell


title: IMR90 ChIP-seq Input

value: Cell Line

value: Epigenome and transcriptome database for human vascular endothelial cells

value: ChIP-Seq Input


title: EC_158_HRAEC ChIP-seq Input

value: Primary Cell

value: The University of Tokyo

value: year


title: EC_162_HRAEC ChIP-seq H3K4me3

value: adult

value: Asian

value: female

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_040_HUVEC ChIP-seq Input

value: newborn

value: Cessation of life

value: Disease type AND/OR category unknown

value: endothelial cell of umbilical vein

value: ChIP-Seq


title: EC_158_HRAEC ChIP-seq H3K27ac

value: male

value: kidney blood vessel cell

value: genomic DNA

value: Histone H3K27ac

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_150_HRAEC ChIP-seq Input

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: ChIP-Seq Input


title: EC_154_HRAEC ChIP-seq H3K4me3

value: The University of Tokyo

value: year

value: adult

value: Histone H3K4me3


title: EC_154_HRAEC ChIP-seq Input

value: Asian


title: EC_146_HRAEC ChIP-seq Input

value: Cessation of life


title: EC_156_HRAEC ChIP-seq H3K27ac

value: Disease type AND/OR category unknown

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_146_HRAEC ChIP-seq H3K4me3

value: ChIP-Seq


title: EC_116_HGSVEC ChIP-seq H3K4me3

source_name: Great Saphenous Vein Endothelial cells

value: male

value: vein endothelial cell


title: EC_154_HRAEC ChIP-seq H3K27ac

value: kidney blood vessel cell

value: genomic DNA


title: EC_116_HGSVEC ChIP-seq H3K27ac

value: Histone H3K27ac

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_146_HRAEC ChIP-seq H3K27ac

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells


title: EC_156_HRAEC ChIP-seq Input

value: The University of Tokyo

value: ChIP-Seq Input


title: EC_150_HRAEC ChIP-seq H3K4me3

value: year

value: adult


title: EC_116_HGSVEC ChIP-seq Input

value: Asian


title: EC_158_HRAEC ChIP-seq H3K4me3

value: Cessation of life

value: Histone H3K4me3


title: EC_112_HGSVEC ChIP-seq H3K4me3

value: Disease type AND/OR category unknown

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_112_HGSVEC ChIP-seq H3K27ac

value: male

value: ChIP-Seq


title: EC_112_HGSVEC ChIP-seq Input

value: vein endothelial cell


title: EC_089_HGSVEC ChIP-seq Input

value: genomic DNA


title: EC_089_HGSVEC ChIP-seq H3K4me3


title: EC_089_HGSVEC ChIP-seq H3K27ac

value: Histone H3K27ac


title: EC_059_HENDC ChIP-seq H3K27ac

source_name: Endocardial cells

value: Native American

value: female

value: endocardial cell

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_042_HENDC ChIP-seq H3K27ac

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: Caucasian


title: EC_042_HENDC ChIP-seq H3K4me3

value: year

value: adult

value: Cessation of life


title: EC_059_HENDC ChIP-seq H3K4me3

value: Disease type AND/OR category unknown

value: Histone H3K4me3

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_023_HENDC ChIP-seq Input

value: child

value: African American

value: ChIP-Seq

value: ChIP-Seq Input


title: EC_042_HENDC ChIP-seq Input

value: male

value: genomic DNA


title: EC_150_HRAEC ChIP-seq H3K27ac

value: Asian

value: kidney blood vessel cell

value: Histone H3K27ac

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_156_HRAEC ChIP-seq H3K4me3

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo


title: EC_023_HENDC ChIP-seq H3K27ac

value: year

value: female

value: Cessation of life

value: endocardial cell


title: EC_061_HCoAEC ChIP-seq H3K4me3

source_name: Coronary Artery Endothelial cells

value: adult

value: Native American

value: Disease type AND/OR category unknown

value: endothelial cell of coronary artery

value: Histone H3K4me3

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_034_HCoAEC ChIP-seq H3K4me3

value: child

value: Caucasian

value: male

value: ChIP-Seq

value: genomic DNA


title: EC_023_HENDC ChIP-seq H3K4me3

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: African American

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_061_HCoAEC ChIP-seq Input

value: The University of Tokyo

value: year

value: female

value: Cessation of life

value: ChIP-Seq Input


title: EC_026_HCoAEC ChIP-seq Input

value: adult

value: Disease type AND/OR category unknown

value: endothelial cell of coronary artery


title: EC_034_HCoAEC ChIP-seq Input

value: child


title: EC_034_HCoAEC ChIP-seq H3K27ac

value: Caucasian

value: Histone H3K27ac

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_026_HCoAEC ChIP-seq H3K27ac

value: male

value: ChIP-Seq

value: genomic DNA


title: EC_055_HCCaEC ChIP-seq Input

source_name: Common Carotid Artery Endothelial cells

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: endothelial cell of artery


title: EC_015_HCoAEC ChIP-seq Input

value: The University of Tokyo

value: year

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_052_HCCaEC ChIP-seq Input

value: Asian

value: Cessation of life

value: ChIP-Seq Input


title: EC_026_HCoAEC ChIP-seq H3K4me3

value: adult

value: Disease type AND/OR category unknown

value: endothelial cell of coronary artery

value: Histone H3K4me3


title: EC_055_HCCaEC ChIP-seq H3K4me3

value: Caucasian

value: female

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_052_HCCaEC ChIP-seq H3K27ac

value: male

value: ChIP-Seq

value: genomic DNA

value: Histone H3K27ac


title: EC_059_HENDC ChIP-seq Input

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: Native American

value: endocardial cell


title: EC_052_HCCaEC ChIP-seq H3K4me3

value: year

value: Asian

value: Cessation of life

value: endothelial cell of artery

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_055_HCCaEC ChIP-seq H3K27ac

value: adult

value: Caucasian

value: Disease type AND/OR category unknown


title: EC_047_HCCaEC ChIP-seq Input

value: male

value: ChIP-Seq Input


title: EC_047_HCCaEC ChIP-seq H3K27ac

value: ChIP-Seq

value: genomic DNA

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_047_HCCaEC ChIP-seq H3K4me3

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: Histone H3K4me3


title: EC_046_HCCaEC ChIP-seq Input

value: The University of Tokyo


title: EC_045_HCCaEC ChIP-seq Input

value: year


title: EC_046_HCCaEC ChIP-seq H3K4me3

value: Asian


title: EC_061_HCoAEC ChIP-seq H3K27ac

value: Native American

value: female

value: Cessation of life

value: endothelial cell of coronary artery

value: Histone H3K27ac


title: EC_046_HCCaEC ChIP-seq H3K27ac

value: adult

value: Disease type AND/OR category unknown

value: endothelial cell of artery

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: EC_045_HCCaEC ChIP-seq H3K27ac

value: male

value: ChIP-Seq

value: genomic DNA


title: EC_045_HCCaEC ChIP-seq H3K4me3

value: Primary Cell

value: Epigenome and transcriptome database for human vascular endothelial cells

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_015_HCoAEC ChIP-seq H3K27ac

value: The University of Tokyo

value: year

value: Caucasian


title: EC_015_HCoAEC ChIP-seq H3K4me3

value: female

value: Histone H3K4me3


title: EC_038_HCCaEC ChIP-seq Input

value: Asian

value: Cessation of life

value: ChIP-Seq Input


title: EC_038_HCCaEC ChIP-seq H3K27ac

value: adult

value: Disease type AND/OR category unknown

value: Histone H3K27ac


title: IMR90 ChIP-seq H3K27ac

value: Cell Line

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: CP-764-MLUNG-2237-140211_UNC15-SN850_0351_AC3KCTACXX_TTAGGC_L001

status: Public on Aug 06 2019

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Quality-control-passed reads were aligned to the mouse reference genome (GRCm38) using STAR
Aligned reads were sorted and indexed using SAMtools and translated to transcriptome coordinates then filtered for indels, large inserts, and zero mapping quality using UBU v1.0
Transcript abundance estimates for each sample were performed using SALMON 70.
Raw SALMON read counts for all RNAseq samples were normalized to a fixed upper quartile
Supplementary_files_format_and_content: RNAseq normalized gene counts from primary, metastatic and normal lung/mmammary gland tissues were log2 transformed and genes were filtered for those expressed in 70% of samples using the cluster 3.0 software.

source_name: Mouse Lung tissue

growth_protocol: We used primary tumors and metastases using a lentiviral-based signaling reporter system in conjunction with the basal-like p53-null syngeneic mouse models of TNBC. Tumors were collected as indicated in the methods section.

extract_protocol:
Cell line lysate was prepared using QIAshredder tubes (QIAGEN). RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. Isolated RNA was quantified using a NanoDrop® Spectrophotometer.
mRNA libraries were made from total RNA using the Illumina TruSeq mRNA sample preparation kit
Samples were equenced on an Illumina HiSeq 2000/2500 using a 2x50bp configuration with an average of 136 million read pairs per sample

treatment_protocol: All RNA was purified from tissue chunks of 3 primary tumors, 3 lung metastases, 8 normal lung and 12 normal mammary gland tissues following the manufacturer’s protocol (PicoPure RNA Isolation Kit, ThermoFisher Scientific)

value: Mouse Lung tissue


title: CP-765-MLUNG-2238-140211_UNC15-SN850_0351_AC3KCTACXX_TGACCA_L001


title: CP-1938-FVB5-Lung_ACAGTG_S10_L004


title: EC_031_HAoEC ChIP-seq Input

source_name: Aortic Endothelial cells

value: Primary Cell

value: African/American

value: male

value: aortic endothelial cell

value: ChIP-Seq

value: genomic DNA


title: EC_060_HAoEC ChIP-seq Input

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: Native American

value: female


title: EC_038_HCCaEC ChIP-seq H3K4me3

value: adult

value: Asian

value: Cessation of life

value: endothelial cell of artery

value: Histone H3K4me3

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: CP-1936-BalbC6-Lung-170223_UNC18-D00493_0399_ACAJD6ANXX_CTTGTA_S44_L007

value: Mouse Lung tissue


title: EC_013_HAoEC ChIP-seq H3K4me3

value: Primary Cell

value: Caucasian

value: Disease type AND/OR category unknown

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: CP-1939-FVB6-Lung_ATGTCA_S11_L004


title: EC_013_HAoEC ChIP-seq Input

value: aortic endothelial cell

value: ChIP-Seq

value: genomic DNA

value: ChIP-Seq Input


title: EC_031_HAoEC ChIP-seq H3K27ac

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: African/American

value: male

value: Histone H3K27ac


title: CP-1937-FVB4-Lung-170223_UNC18-D00493_0399_ACAJD6ANXX_AGTTCC_S45_L007


title: EC_013_HAoEC ChIP-seq H3K27ac

value: adult

value: female

value: Cessation of life


title: EC_060_HAoEC ChIP-seq H3K4me3

value: Primary Cell

value: Native American

value: Histone H3K4me3

value: Protein G Seprarose beads (GE Healthcare Bio-Sciences AB, Sweden)


title: EC_031_HAoEC ChIP-seq H3K4me3

value: Disease type AND/OR category unknown

value: aortic endothelial cell

value: Antibodies were used in combination with Protein G Sepharose beads (GE Healthcare Bio-Sciences AB, Sweden). The prepared DNA was quantified using Qubit (Life Technologies/Thermo Fisher Scientific) and more than 10 ng of DNA was processed. Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).


title: CP.763.MMG.172238.131212_UNC12.SN629_0341_BC2RKJACXX_CGATGT_L008

source_name: Mouse mammary gland tissue

value: Mouse mammary gland tissue


title: CP-1935-BalbC5-Lung-170223_UNC18-D00493_0399_ACAJD6ANXX_AGTCAA_S46_L007

value: Mouse Lung tissue


title: CP-1934-BalbC4-Lung-170223_UNC18-D00493_0399_ACAJD6ANXX_GAGTGG_S48_L008


title: CP.762.MMG.172237.131212_UNC12.SN629_0341_BC2RKJACXX_ATCACG_L008


title: CP.1648.Atish.N2.C9HRJANXX_TGACCA_131596_S29_L004


title: CP-1884-T2-LM3819-ST_ACAGTG_L001

source_name: Orthotopic breast cancer spontaneous metastasis model

value: Metastatic mouse breast tumor


title: CP.1647.Atish.N1.C9HRJANXX_CGATGT_131595_S28_L004


title: CP-1885-T2-LM3820-ST_GCCAAT_L001


title: CP-1883-T2-LM3817-ST_TGACCA_L001


title: CP-1881-T2-3819PRIM-ST_CGATGT_S10_L004

source_name: Primary breast tumors impanted at orthotopic and subcutaneous site

value: Orthotopic mouse breast tumor


title: CP-1882-T2-3820PRIM-ST_TTAGGC_S12_L004


title: EC_060_HAoEC ChIP-seq H3K27ac

value: Epigenome and transcriptome database for human vascular endothelial cells

value: The University of Tokyo

value: year

value: ChIP-Seq

value: genomic DNA


title: CP-1880|T2-3817PRIM-ST_ATCACG_S11_L004