title: 4T1_ITGAV-gRNA1-UT-1

description:
ITGAV-gRNA-1 versus Control
20181220_4T1_ITGAV-gRNA1-UT-1_20181205_IDXE10_RV6429_S2

tag: genotype/variation


title: Genomic DNA from FF breast tumor tissue_18986

status: Public on Jan 01 2021

type: genomic

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

country: USA

institute: Roswell Park Comprehensive Cancer Center

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip (GPL13534) using standard Illumina protocol

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

data_processing:
The raw intensity IDAT files were extracted using GenomeStudio,and processed by the minfi R package. Only loci with a median detection p value <0.05 were retained for analysis, and only samples with detection p values < 1.0E-05 at more than 75% of CpG lici passed the performance criteria for inclusion. Probes containing SNPs and/or those that were ambiguously mapped were excluded from the analysis. The final dataset contained 276,108 CpG loci across 138 samples.
The signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Flash frozen breast tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a MasterPure DNA purification kit (Epicentre).

tag: gender

value: Female

tag: tissue

value: Flash frozen breast tumor tissue


title: ES2 parental cells replicate 2

type: SRA

city: Boston

first: Huy

last: Nguyen

state: Massachusetts

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

description:
ES2_parental_2
20191108_ES2_parental_2_KP7496_S18

library_source: transcriptomic

data_processing:
RNAseq analysis was performed using the VIPER snakemake pipeline (Cornwell et al., 2018)
Sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)
Differential gene expression testing was performed by DESeq2 (v1.22.1), and limma (v3.38.3)
Genome_build: hg19
Supplementary_files_format_and_content: raw gene counts for every gene and every sample; DESeq2 and limma results

molecule: total RNA

source_name: ES2 parental cells

extract_protocol:
Total RNA was prepared using a Qiagen kit according to the manufacturer’s instructions
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols. Uniquely dual-indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NovaSeq 6000 with paired-end 50bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: cell line

value: ES-2 (ATCC CRL-1978)

tag: tissue source

value: ovary

tag: treatment

value: untreated


title: Genomic DNA from FF breast tumor tissue_17758

description: Tumor


title: 256402110006_b1 - 9_5WT(2684)_S-_rep1 vs 13_5Mut(2684)_S-_rep1

type: RNA

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Role of sulfur and of the sulfate store in leaf metabolism.

hyb_protocol: 13_5Mut_S-_rep1 Cy5 / 9_5WT_S-_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Lathyrus oleraceus

source_name: 13_5Mut_S-_rep1 allele 2684

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: caulin leaf - Media:Perlite (2/3) and sand B3 (1L pot) Temperature: 18 °C Light:16h/day

treatment_protocol: Name:Sulfur deficiency - environmental treatment - sulfur concentration,sulfur:quantity 0mM .

value: cauline leaf

tag: cultivar

value: cameor

tag: genotype

value: PsSultr4 mutant

tag: harvest date

source_name: 9_5WT_S-_rep1 allele 2684

value: wildtype


title: Genomic DNA from FF breast tumor tissue_14503

description: Tumor


title: 256402110005_b3 - 26_6WT(2684)_S+_rep2 vs 30_6Mut(2684)_S+_rep2

hyb_protocol: 30_6Mut_S+_rep2 Cy5 / 26_6WT_S+_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 30_6Mut_S+_rep2 allele 2684

treatment_protocol: Name:Sulfur efficiency - environmental treatment - sulfur concentration,sulfur:quantity 0.3mM .

source_name: 26_6WT_S+_rep2 allele 2684


title: ES2 parental cells replicate 1

description:
ES2_parental_1
20191108_ES2_parental_1_KP7496_S17


title: 4T1_SOX4-gRNA2-UT-1

first: Archis

last: Bagati

state: MASSACHUSETTS

address: 450 brookline ave.

description:
SOX4-gRNA-2 versus Control
20181219_4T1_SOX4-gRNA2-UT-1_20181205_IDXC10_RV6428_S15

data_processing:
Statistics for differentially expressed genes were calculated using DESeq2 (version 3.5) (47) and Cufflinks (48).  Differential gene expression was analyzed using the DESeq2 (1.8.1) package in R using default settings (47). Principal component analyses were generated using the prcomp function in R and plotted with ggplot2. Human and mouse gene homologues were matched using the Mouse Genome Informatics annotation. Heatmaps were generated using the heatmap.2 function in R
Genome_build: hg19; mm9
Supplementary_files_format_and_content: Differential gene expression

organism: Mus musculus

growth_protocol: The base medium for this cell line is ATCC-formulated RPMI-1640 Medium, ATCC 30-2001. To make the complete growth medium, add the following components to the base medium: fetal bovine serum (ATCC 30-2020) to a final concentration of 10%.

extract_protocol:
Total RNA was extracted from control, SOX4 or ITGAV edited human BT549 and murine 4T1 cells cultured in complete RPMI media in biological triplicates.  RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen # 74134) following the manufacturer’s protocol. Total RNA was quality-checked using an Agilent BioAnalyzer 2000 instrument.  RNA with an integrity number of greater than 9.5 was used for subsequent analyses.
Libraries were prepared with TruSeq RNA Sample Prep Kit v2 (Illumina). Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for single-end 75bp sequencing using an Illumina NextSeq 500 instrument.

tag: cell type

value: murine TNBC cells


title: 256402110005_b4 - 30_6Mut(2684)_S+_rep2 vs 26_6WT(2684)_S+_rep2

hyb_protocol: 26_6WT_S+_rep2 Cy5 / 30_6Mut_S+_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from FF breast tumor tissue_9862

description: Tumor


title: Genomic DNA from FF breast tumor tissue_16533

description: Tumor


title: Genomic DNA from FF breast tumor tissue_17098

description: Tumor


title: scVDJ-CMVCTLs #3 TCR

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

country: Japan

institute: Jichi Medical University Saitama Medical Center

description:
human TCR
1500 CMV-CTLs were sorted

data_processing:
Library strategy: VDJ-seq
demultiplexed reads were processed (filtering low quality reads, mapping, counting) by Cell Ranger ver. 3.0.2 (10x Genomics)
Loupe Cell Browser (ver.4.0.0) and Loupe VDJ Browser (ver.3.0.0)
Genome_build: Ensembl/GRCh38
Supplementary_files_format_and_content: cloupe or vloupe formats for Loupe Browser provided by 10x Genomics

source_name: CTLs in peripheral blood

extract_protocol:
An input volume of cells was adjusted as 1,000 cells were estimated to be recovered.
Individual cell beads in emulsion with single cells (GEMs) were generated with 10x Genomics Chromium Single Cell A Chip (10x GENOMICS) and Chromium Single Cell 5' Library & Gel Bead Kit (10x GENOMICS) on Chromium Controller (10x GENOMICS) followed by RT within each GEMs. Simultaneously, human TCR regions were enriched with specific primers from the cDNA above using Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10x GENOMICS).
sc-VDJ-RNA-seq

tag: cmv reactivation

value: no

tag: donor cmv

value: positive

tag: sampling time


title: 4T1_SOX4-gRNA1-UT-2

description:
SOX4-gRNA-1 versus Control
20181219_4T1_SOX4-gRNA1-UT-2_20181205_IDXB10_RV6428_S14


title: 4T1_SOX4-gRNA2-UT-2

description:
SOX4-gRNA-2 versus Control
20181220_4T1_SOX4-gRNA2-UT-2_20181205_IDXD10_RV6429_S1


title: scVDJ-CMVCTLs #4 TCR

description:
human TCR
2300 CMV-CTLs were sorted


title: 4T1_ITGAV-gRNA4-UT-1

description:
ITGAV-gRNA-2 versus Control
20181220_4T1_ITGAV-gRNA4-UT-1_20181205_IDXG10_RV6429_S4

value: ITGAV-edited


title: 256402110005_b1 - 25_5WT(2684)_S+_rep1 vs 29_5Mut(2684)_S+_rep1

hyb_protocol: 29_5Mut_S+_rep1 Cy5 / 25_5WT_S+_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 29_5Mut_S+_rep1 allele 2684

source_name: 25_5WT_S+_rep1 allele 2684


title: scVDJ-CMVCTLs #14 TCR

description:
human TCR
5000 CMV-CTLs were sorted

value: One-episode

value: negative


title: 256402110004_b4 - 24_4Mut(4693)_S+_rep4 vs 20_4WT(4693)_S+_rep4

hyb_protocol: 20_4WT_S+_rep4 Cy5 / 24_4Mut_S+_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 20_4WT_S+_rep4 allele 4693

source_name: 24_4Mut_S+_rep4 allele 4693


title: 256402110005_b2 - 29_5Mut(2684)_S+_rep1 vs 25_5WT(2684)_S+_rep1

hyb_protocol: 25_5WT_S+_rep1 Cy5 / 29_5Mut_S+_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from FF breast tumor tissue_17690

description: Tumor


title: 4T1_ITGAV-gRNA1-UT-2

description:
ITGAV-gRNA-1 versus Control
20181220_4T1_ITGAV-gRNA1-UT-2_20181205_IDXF10_RV6429_S3


title: Genomic DNA from FF breast tumor tissue_11296

description: Tumor


title: scVDJ-CMVCTLs #3 GEX

description:
5' gene expression
1500 CMV-CTLs were sorted

data_processing:
demultiplexed reads were processed (filtering low quality reads, mapping, counting) by Cell Ranger ver. 3.0.2 (10x Genomics)
Loupe Cell Browser (ver.4.0.0) and Loupe VDJ Browser (ver.3.0.0)
Genome_build: Ensembl/GRCh38
Supplementary_files_format_and_content: cloupe or vloupe formats for Loupe Browser provided by 10x Genomics


title: 4T1_LacZ-UT-1

description:
Control
20181219_4T1_LacZ-UT-1_20181205_IDXG9_RV6428_S11

value: control


title: 256402110004_b3 - 20_4WT(4693)_S+_rep4 vs 24_4Mut(4693)_S+_rep4

hyb_protocol: 24_4Mut_S+_rep4 Cy5 / 20_4WT_S+_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256402110004_b1 - 19_3WT(4693)_S+_rep3 vs 23_3Mut(4693)_S+_rep3

hyb_protocol: 23_3Mut_S+_rep3 Cy5 / 19_3WT_S+_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 23_3Mut_S+_rep3 allele 4693

source_name: 19_3WT_S+_rep3 allele 4693


title: scVDJ-CMVCTLs #4 GEX

description:
5' gene expression
2300 CMV-CTLs were sorted


title: Genomic DNA from FF breast tumor tissue_14439

description: Tumor


title: scVDJ-CMVCTLs #14 GEX

description:
5' gene expression
5000 CMV-CTLs were sorted


title: Genomic DNA from FF breast tumor tissue_18033

description: Tumor


title: siNTC-rep3

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling was done with Illumina's FASTQ Generation software bcl2fastq2 Conversion v2.19 and overall sequencing quality was determined with FastQC
Reads (FASTQ files) were mapped to whole genome mm10 using Bowtie2 with default settings.
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed and differentially expressed genes were called using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: A matrix file (csv format) containing Ensembl gene ID, gene symbol, gene description and raw read counts for all genes of all samples.
Supplementary_files_format_and_content: A differential expression file (csv format) containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for the comparisons of all genes.

molecule: polyA RNA

source_name: differentiated adipocytes

extract_protocol:
Total RNA was isolated by using the RNeasy Mini Kit (Qiagen) including on-column DNaseI digestion. mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were generated with 1 µg of purified mRNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter). The quality, quantity and the size of the cDNA libraries were determined with the Fragment Analyzer (Thermo Fisher Scientific, previously Advanced Analytical Technologies). Libraries were sequenced on a NextSeq500 System (Illumina).

treatment_protocol: Differentiated adipocytes were transfected with siRNA following detachment with Accutase using Dharmafect-Duo transfection reagent (Dharmacon) on Matrigel-coated culture plates. A ratio of 2.1 ul per cm^2 duofect, 1.25 nM per cm^2 siRNA and 16.4x10^4 per cm^2 cells was used for transfection. Cells were used for experiments 48 hours after transfection.

value: adipocytes

tag: sirna transfection

value: siRNA non-targeting control


title: 256402110004_b2 - 23_3Mut(4693)_S+_rep3 vs 19_3WT(4693)_S+_rep3

hyb_protocol: 19_3WT_S+_rep3 Cy5 / 23_3Mut_S+_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: siNTC-rep4


title: NC-shRNA-U251-3

city: Shanghai

first: Fengjiao

last: LI

address: 131 Dong'an Rd., Xuhui District

country: China

institute: Fudan University

data_processing:
nova s6000
Purify and Fragment mRNA; Synthesize First Strand cDNA; Synthesize Second Strand cDNA; Adenylate 3' Ends; Ligate Adapters; Enrich DNA Fragments;  sequcence
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Skewer , then mapped to hg38 whole genome using HISAT2, different gene expression using DEGseq
Genome_build: hg38
Supplementary_files_format_and_content: different gene expression between ETV6-siRNA-U251 and NC-siRNA-U251

source_name: Glioblastoma Cell Line

growth_protocol: ETV6-shRNA transfected U251 cells and NC(non-specific control)-shRNA transfected U251 cells were culture

extract_protocol:
Total RNA was extracted from control or shRNA transfected U251 cells by the miRNeasy mini kit (QIAGEN). On column DNase digestion was then performed using RNase free DNase set (QIAGEN).
1 µg of total RNA was used for RNA sequencing library preparation using SMARTer Stranded Total RNA Sample Prep kit (Clontech). Libraries prepared from 3 negative control and 3 siETV6 transfected U251 cells were sequenced.

value: human malignant glioblastoma multiforme


title: 4T1_LacZ-UT-2

description:
Control
20181219_4T1_LacZ-UT-2_20181205_IDXH9_RV6428_S12


title: Genomic DNA from FF breast tumor tissue_10834

description: Tumor

value: Female

value: Flash frozen breast tumor tissue


title: 256402110003_b4 - 22_2Mut(4693)_S+_rep2 vs 18_2WT(4693)_S+_rep2

hyb_protocol: 18_2WT_S+_rep2 Cy5 / 22_2Mut_S+_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 18_2WT_S+_rep2 allele 4693

source_name: 22_2Mut_S+_rep2 allele 4693


title: 256402110003_b3 - 18_2WT(4693)_S+_rep2 vs 22_2Mut(4693)_S+_rep2

hyb_protocol: 22_2Mut_S+_rep2 Cy5 / 18_2WT_S+_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NC-shRNA-U251-2


title: siNTC-rep1


title: Genomic DNA from FF breast tumor tissue_8785

description: Tumor

source_name: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_16722

description: Tumor


title: 4T1_SOX4-gRNA1-UT-1

description:
SOX4-gRNA-1 versus Control
20181219_4T1_SOX4-gRNA1-UT-1_20181205_IDXA10_RV6428_S13


title: NC-shRNA-U251-1


title: 256402110003_b2 - 21_1Mut(4693)_S+_rep1 vs 17_1WT(4693)_S+_rep1

hyb_protocol: 17_1WT_S+_rep1 Cy5 / 21_1Mut_S+_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 17_1WT_S+_rep1 allele 4693

source_name: 21_1Mut_S+_rep1 allele 4693


title: Genomic DNA from FF breast tumor tissue_14677

description: Tumor


title: Genomic DNA from FF breast tumor tissue_20376

description: Tumor


title: siNTC-rep2


title: siERK3-rep4

value: siRNA targeting ERK3


title: ETV6-shRNA-U251-3


title: ETV6-shRNA-U251-2


title: ETV6-shRNA-U251-1


title: siERK3-rep3


title: 256402110003_b1 - 17_1WT(4693)_S+_rep1 vs 21_1Mut(4693)_S+_rep1

hyb_protocol: 21_1Mut_S+_rep1 Cy5 / 17_1WT_S+_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cauline leaf


title: 256402110002_b4 - 8_4Mut(4693)_S-_rep4 vs 4_4WT(4693)_S-_rep4

hyb_protocol: 4_4WT_S-_rep4 Cy5 / 8_4Mut_S-_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4_4WT_S-_rep4 allele 4693

value: cameor

source_name: 8_4Mut_S-_rep4 allele 4693


title: Genomic DNA from FF breast tumor tissue_9648

description: Tumor


title: 256402110002_b3 - 4_4WT(4693)_S-_rep4 vs 8_4Mut(4693)_S-_rep4

hyb_protocol: 8_4Mut_S-_rep4 Cy5 / 4_4WT_S-_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: PsSultr4 mutant


title: siERK3-rep1

value: wildtype


title: Pro-BMPs replicate 3

first: Anaïs

last: Wanet

state: MA

address: 3 Blackfan circle

department: Hematology Oncology

institute: BIDMC

data_processing:
Raw fq files had optical duplicates removed using clumpify with the flags "dedupe spany addcount."  Next, Adaptor trimming was performed using BBDuk with the flags "ref=/.../bbmap/resources/adapters.fa ktrim=l hdist=2 ".  Next, reads were trimmed using trimmomatic with the flags "-phred33 LEADING:28 SLIDINGWINDOW:4:26 TRAILING:28 MINLEN:20"
After read cleanup, reads were aligned to mm38.89 using STAR with the flags " --outFilterScoreMinOverLread 0.1 --outFilterMatchNminOverLread 0.1 --outFilterMultimapNmax 2  --outSAMprimaryFlag AllBestScore --outSAMtype BAM SortedByCoordinate".  BamCoverage maps were generated using bamCoverage using default parameters.  Read distributions were calcualted using read_distribution.py from the RSeQC suite of tools.
Counts tables were generated using htseq-count with the flags " --stranded=no --idattr=gene_id --format=bam".  EnsembleID gtf generated for mm38.89 from the UCSC genome browser portal was used as input for htseq.
Raw counts were processed further in R on a workflow based around the tutorial "https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html"
Genome_build: mm38.89
Supplementary_files_format_and_content: text file with normalized counts

source_name: Bone marrow

extract_protocol:
Each population was FACS-sorted (double sorting) into TRIzol. RNA was isolated according to manufacturer's protocol. RNA integrity was analyzed using BioAnalyzer (Agilent) and ≥ 8.4 for all samples.
Libraries were prepared using SmartSeq v4 (Takara) and Nextera XT DNA library kit (Illumina)

value: bone marrow

tag: strain

tag: facs phenotype

value: B220- CD3- Ter119- CD11b- Gr1- c-Kit+ Sca1- CD34+ CD16/32+ CDH1+ FceRIa-

value: Pro-BMPs


title: siERK3-rep2


title: Pro-BMPs replicate 2


title: Natural2_Dneg4

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

source_name: Cryopreserved PBMC

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by  1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cryopreserved PBMCs were thawed and washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. After counting, cells were resuspended in PBS + 2% FCS prior to scRNAseq library generation

value: PBMC

tag: subject

tag: study day


title: Natural2_D180


title: 256402110002_b1 - 3_3WT(4693)_S-_rep3 vs 7_3Mut(4693)_S-_rep3

hyb_protocol: 7_3Mut_S-_rep3 Cy5 / 3_3WT_S-_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 7_3Mut_S-_rep3 allele 4693

source_name: 3_3WT_S-_rep3 allele 4693


title: Natural2_Dneg5


title: 256402110002_b2 - 7_3Mut(4693)_S-_rep3 vs 3_3WT(4693)_S-_rep3

hyb_protocol: 3_3WT_S-_rep3 Cy5 / 7_3Mut_S-_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from FF breast tumor tissue_17110

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip (GPL13534) using standard Illumina protocol

tag: gender


title: 256402110001_b4 - 6_2Mut(4693)_S-_rep2 vs 2_2WT(4693)_S-_rep2

hyb_protocol: 2_2WT_S-_rep2 Cy5 / 6_2Mut_S-_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 2_2WT_S-_rep2 allele 4693

tag: tissue

source_name: 6_2Mut_S-_rep2 allele 4693


title: Genomic DNA from FF breast tumor tissue_18549

description: Tumor


title: 256402110001_b1 - 1_1WT(4693)_S-_rep1 vs 5_1Mut(4693)_S-_rep1

hyb_protocol: 5_1Mut_S-_rep1 Cy5 / 1_1WT_S-_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 5_1Mut_S-_rep1 allele 4693

source_name: 1_1WT_S-_rep1 allele 4693


title: Natural1_D180


title: 256402110001_b2 - 5_1Mut(4693)_S-_rep1 vs 1_1WT(4693)_S-_rep1

hyb_protocol: 1_1WT_S-_rep1 Cy5 / 5_1Mut_S-_rep1 Cy3 : 20pmol. (Hybridation_CAGE_proto.doc)


title: 256402110001_b3 - 2_2WT(4693)_S-_rep2 vs 6_2Mut(4693)_S-_rep2

hyb_protocol: 6_2Mut_S-_rep2 Cy5 / 2_2WT_S-_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from FF breast tumor tissue_17731

description: Tumor


title: Natural1_Dneg2


title: Pre-BMPs replicate 2

value: B220- CD3- Ter119- CD11b- Gr1- c-Kit+ Sca1- CD34+ CD16/32+ CDH1- FceRIa+

value: Pre-BMPs


title: Pre-BMPs replicate 1


title: Genomic DNA from FF breast tumor tissue_11466

description: Tumor


title: Pre-BMPs replicate 3


title: SB505124:24hr, treatment, replicate 4

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM SB505124 and tissues were collected at 24 hours post amputation.
SB.T24hr-4

hyb_protocol: Microarray hybridization using an Ambystoma Affymetrix array (Huggins et al., 2012) was performed by the University of Kentucky Microarray Core Facility.

scan_protocol: Affymetrix Command Console was used according to manufacturer's instructions

data_processing: GeneChips were normalized using the affy R package (Gautier et al 2004) Affymetrix Expression Console software to accomplish robust multichip averaging (RMA) (Irizarry et al., 2003).

label: biotin

organism: Ambystoma mexicanum

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 24hpa. Samples were treated with SB505124.

label_protocol: Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: The use of pre-feeding stage axolotls does not require a protocol approved by the Institutional Animal Care and Use Committee (IACUC) at University of Kentucky, however embryos used in this study were treated according to the same ethical standards that apply to feeding axolotls. Rearing water (40% modified Holtfretter's solution) was changed three times per week.

extract_protocol: The tissue samples were maintained at 4 C in RNA later prior to RNA isolation using first the Trizol method and then a Qiagen minikit with on-the-column DNAse treatment of DNA.

treatment_protocol: Developmental stage 42 (Bordzilovskaya et al 1989) axolotl embryos were manually hatched by removing the egg jelly and membrane, anesthetized in 0.02% benzocaine, and administered tail amputations with a razor blade to remove 2 mm (~20% of the body length) of the distal tail tip. After amputation, animals were placed into microtiter plates containing rearing water (40% modified Holtfreter’s Solution) and 0.001% DMSO (controls) or rearing water with the chemical treatment.

value: distal tip of embryonic tail

tag: time (hpa)


title: Subject5_D28


title: Pro-BMPs replicate 1


title: Natural1_Dneg3


title: Genomic DNA from FF breast tumor tissue_12488

description: Tumor


title: Genomic DNA from FF breast tumor tissue_17614

description: Tumor


title: Subject5_D14


title: SB505124:24hr, treatment, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM SB505124 and tissues were collected at 24 hours post amputation.
SB.T24hr-3


title: DN-GMPs replicate 2

value: B220- CD3- Ter119- CD11b- Gr1- c-Kit+ Sca1- CD34+ CD16/32+ CDH1- FceRIa-


title: Subject5_D10


title: SB505124:24hr, treatment, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM SB505124 and tissues were collected at 24 hours post amputation.
SB.T24hr-2


title: Genomic DNA from FF breast tumor tissue_10387

description: Tumor


title: Genomic DNA from FF breast tumor tissue_16053

description: Tumor


title: DN-GMPs replicate 1


title: SB505124:24hr, treatment, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM SB505124 and tissues were collected at 24 hours post amputation.
SB.T24hr-1


title: Basophils replicate 3

value: B220- CD4- CD8a- Ter119- Sca1- c-Kit- CD49b+ FceRIa+

value: Basophils


title: Subject5_D8


title: SB505124:24hr, control, replicate 4

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
SB.C24hr-4

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 24hpa. Samples were treated with DMSO.

value: Control


title: Subject5_D6


title: Genomic DNA from FF breast tumor tissue_20298

description: Tumor

value: Female

value: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_10444

description: Tumor


title: Subject5_D4


title: Basophils replicate 2


title: Basophils replicate 1


title: Subject5_D2


title: SB505124:24hr, control, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
SB.C24hr-3


title: Genomic DNA from FF breast tumor tissue_11909

description: Tumor


title: Amel_embryo_55-70h_male_rep2

city: Düsseldorf

first: Oksana

last: Netschitailo

address: Universitätsstraße 1

department: Evolutionary Genetics

institute: Heinrich-Heine University

description:
M3b
T3_male2

data_processing:
Sequencing was performed using an Illumina HiSeq2500 instrument
Reads that passed Illumina pipeline quality filtering criteria were mapped to a reference genome
Mapping was then performed using Tophat v.2.2.1 (Trapnell et al., 2012), with Bowtie v2.2.6 (Langmead et al., 2010) . A reference annotation (ref_Amel_4.5_top_level) was supplied in gtf format with the -G option.
The reference sequence for mapping was the Assembly v.4.5 from ncbi (ftp://ftp.ncbi.nih.gov/genomes/genbank/invertebrate/Apis_mellifera/all_assembly_versions/GCA_000002195.1_Amel_4.5/GCA_000002195.1_Amel_4.5_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/)
BAM files were used to generate FPKM values in xls format using Cufflinks version 2.2.1 (Trapnell et al,. 2012)
Genome_build: Amel_4.5
Supplementary_files_format_and_content: fpkm values for mapped and assembled reads

organism: Apis mellifera

extract_protocol: Total RNA was isolated from pools of 30 (55-70 h old embryos), 60 (25-40 h old embryos) or 100 (10-15 h old embryos) from three different mothers . 250 µl Trizol were added to each pool and the tissue was homegenized using a pestle. After incubation for 5 min at room temperature 50 µl chloroform were added. The solution was mixed for 30 sec and centrifuged for 15 min on 13,000 rpm at 4°C. The upper phase was transferred into a new tube and 100 µl 70% ethanol were added, mixed and transfered to a purification column (Qiagen RNeasy Mini Kit, Qiagen). The purification was performed accoring to protocol with an included on-column DNaseI treatment (10 µl DNase and 70 µl buffer RDD; RNAse-Free DNase Set, Qiagen) for 15 minutes.

treatment_protocol: Wildtype male and female embryos were collected 5-15 h after egg deposition in feral honeybee colonies using a Jenter egg collection box (Jenter Queen Rearing Kit, Karl Jenter GmbH). The embryos were kept in an incubator at 34°C and 90% relative humidity until they were 10-15 h, 25-40 h or 55-70 h old, frozen in liquid nitrogen and stored at -80°C.

value: Apis mellifera carnica

tag: age of embryo

tag: Sex

value: male

value: whole embryos


title: Genomic DNA from FF breast tumor tissue_14467

description: Tumor


title: SB505124:24hr, control, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
SB.C24hr-2

tag: treatment


title: Geldanamycin:24hr, treatment, replicate 4

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM geldanamycin and tissues were collected at 24 hours post amputation.
GDM.24hr-GDM4

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 24hpa. Samples were treated with Geldanamycin.

value: 1uM Geldanamycin


title: Subject5_D0


title: SB505124:24hr, control, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
SB.C24hr-1


title: Genomic DNA from FF breast tumor tissue_18873

description: Tumor


title: Genomic DNA from FF breast tumor tissue_9038

description: Tumor


title: Amel_embryo_55-70h_male_rep1

description:
M3a
T3_male1


title: Subject3_D28


title: Geldanamycin:24hr, treatment, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM geldanamycin and tissues were collected at 24 hours post amputation.
GDM.24hr-GDM2


title: Genomic DNA from FF breast tumor tissue_14843

description: Tumor


title: Subject3_D14


title: Genomic DNA from FF breast tumor tissue_9781

description: Tumor


title: Geldanamycin:24hr, treatment, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM geldanamycin and tissues were collected at 24 hours post amputation.
GDM.24hr-GDM1


title: Geldanamycin:24hr, treatment, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 1uM geldanamycin and tissues were collected at 24 hours post amputation.
GDM.24hr-GDM3


title: DN-GMPs replicate 3

value: bone marrow


title: Amel_embryo_25-40h_male_rep1

description:
M2a
T2_male1


title: Subject3_D10


title: Amel_embryo_10-15h_male_rep2

description:
M1b
T1_male2


title: Genomic DNA from FF breast tumor tissue_14045

description: Tumor


title: Amel_embryo_10-15h_male_rep1

description:
M1a
T1_male1


title: Genomic DNA from FF breast tumor tissue_12151

description: Tumor


title: Genomic DNA from FF breast tumor tissue_14496

description: Tumor


title: Subject3_D8


title: Genomic DNA from FF breast tumor tissue_13882

description: Tumor


title: Amel_embryo_55-70h_female_rep2

description:
W3b
T3_female2

value: female


title: Subject3_D2


title: Geldanamycin:24hr, control, replicate 4

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
GDM.24hr-C4


title: Amel_embryo_55-70h_female_rep1

description:
W3a
T3_female1


title: Subject3_D6


title: Romidepsin:0hpa, control, replicate 3

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated by romidepsin for 1 minute post amputation, then placed in 10uM Romidepsin. Tail samples were collected at 3 hours post amputation.
R.Day0-4_031717

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 0hpa. Samples were not treated.

value: Control (DMSO)


title: Geldanamycin:24hr, control, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
GDM.24hr-C3


title: Subject3_D0

value: PBMC


title: Romidepsin:0hpa, control, replicate 2

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated by romidepsin for 1 minute post amputation, then placed in 10uM Romidepsin. Tail samples were collected at 3 hours post amputation.
R.Day0-3_031717


title: Amel_embryo_25-40h_female_rep2

description:
W2b
T2_female2


title: Geldanamycin:24hr, control, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
GDM.24hr-C1


title: Geldanamycin:24hr, control, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were not treated and collected at 24 hours post amputation.
GDM.24hr-C2


title: Subject3_D4


title: Genomic DNA from FF breast tumor tissue_11184

description: Tumor

source_name: Flash frozen breast tumor tissue


title: Amel_embryo_25-40h_female_rep1

description:
W2a
T2_female1


title: Subject2_D28


title: Romidepsin:0hpa, control, replicate 1

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated by romidepsin for 1 minute post amputation, then placed in 10uM Romidepsin. Tail samples were collected at 3 hours post amputation.
R.Day0-2_031717


title: Amel_embryo_10-15h_female_rep2

description:
W1b
T1_female2


title: Genomic DNA from FF breast tumor tissue_18136

description: Tumor


title: Genomic DNA from FF breast tumor tissue_14069

description: Tumor


title: Subject2_D15


title: Amel_embryo_10-15h_female_rep1

description:
W1a
T1_female1


title: Subject2_D10


title: Genomic DNA from FF breast tumor tissue_16296

description: Tumor


title: Genomic DNA from FF breast tumor tissue_9025

description: Tumor


title: Romidepsin:3hpa, treatment, replicate 3

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated with Romidepsin. Tail samples were collected at 3 hours post amputation.
3hrR3_110917

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 3hpa. Samples were treated with Romidepsin.

value: 10uM Romidepsin 3hrs


title: Genomic DNA from FF breast tumor tissue_17785

description: Tumor


title: Amel_embryo_25-40h_male_rep2

description:
M2b
T2_male2


title: Frog2 Explant Mid Neurula

city: Notre Dame

first: Paul

last: Huber

state: Indiana

address: 251 Nieuwland Science Hall

department: Chemistry & Biochemistry

institute: University of Notre Dame

data_processing:
Illumina Real Time Analysis (RTA) v2 was used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xla.v91 genome and .gff3 file using Tophat/bowtie2
Fragments Per Kilobase Million (FPKM) were calculated and differentially compared using Cufflinks/Cuffdiff. FPKMs were also converted in Transcripts Per Million (TPM)
Genome_build: bowtie2  Xla.v91.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Xenopus laevis

source_name: Xenopus explant

extract_protocol: D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo.

tag: developmental stage

value: Stage 17

value: Explanted Tissue

tag: age

value: 18 hours


title: Frog3 Explant Mid Neurula


title: Genomic DNA from FF breast tumor tissue_15980

description: Tumor


title: Subject2_D6

tag: cell type


title: Frog1 Explant Mid Neurula


title: Romidepsin:3hpa, treatment, replicate 2

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated with Romidepsin. Tail samples were collected at 3 hours post amputation.
3hrR2_110917

value: distal tip of embryonic tail


title: Romidepsin:3hpa, treatment, replicate 1

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated with Romidepsin. Tail samples were collected at 3 hours post amputation.
3hrR1_110917


title: Romidepsin:3hpa, control, replicate 3

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated with DMSO. Tail samples were collected at 3 hours post amputation.
3hrC3_110917

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 3hpa. Samples were treated with DMSO.


title: Genomic DNA from FF breast tumor tissue_18713

description: Tumor


title: Subject2_D8


title: Romidepsin:3hpa, control, replicate 2

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated with DMSO. Tail samples were collected at 3 hours post amputation.
3hrC2_110917


title: Subject2_D4


title: Genomic DNA from FF breast tumor tissue_19011

description: Tumor


title: Frog3 Explant Early Neurula

value: Stage 14

value: 16 hours


title: Genomic DNA from FF breast tumor tissue_18475

description: Tumor

value: Female


title: Frog2 Explant Early Neurula


title: Subject2_D0


title: Frog1 Explant Early Neurula


title: Frog3 Explant Gastrula

value: Stage 11

value: 11 hours


title: Subject2_D2


title: Genomic DNA from FF breast tumor tissue_14302

description: Tumor

value: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_12777

description: Tumor


title: Romidepsin:1MPA, treatment, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated by romidepsin for 1 minute post amputation, then placed in DMSO. Tail samples were collected at 3 hours post amputation.
D3_051118

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 24hpa. Samples were treated with Romidepsin.

value: Rom 1MPA


title: Frog2 Explant Gastrula


title: calcified bicuspid aortic valve + XCT790 [TN-2955_39_S47_L003]

city: San Francisco

first: Christina

last: Theodoris

state: California

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

data_processing:
Sequencing quality was assessed with FASTQC
Reads were aligned to the hg19 transcriptome and genome using Tophat
Unmapped (-F 4) and low-quality reads with MAPQ score below 30 (-q 30) were removed using Samtools
Duplicate reads were removed using Picard MarkDuplicates
Differential expression was analyzed using Useq
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: aortic valve endothelial cells

growth_protocol: Valve leaflets were washed with PBS and incubated for 10 minutes at 37°C with 0.2% collagenase solution (Collagenase type IV, ≥160 units/mg, Worthington Biochemical Corporation, USA). Then, the valve tissue was vortexed for 1 minute to isolate ECs, and the supernatant was collected and centrifuged for 5 minutes at 300g. The pellet of cells was washed with DMEM and plated onto a 3 cm2 culture dish covered with 0.2% gelatin (Sigma-Aldrich, USA) in Endothelial Cell Medium (ECM) (ScienCell, USA) and incubated at 37°C. Two days later, ECs were washed with PBS, and culture medium was changed.

extract_protocol:
Trizol reagent per protocol
NUGEN Ovation RNA-Seq System V2 per kit protocol

treatment_protocol: AV ECs were exposed to 10μM DMSO or XCT790 renewed with EC media (ScienCell #1001) changes on alternating days for 7 days

tag: agent

tag: aortic valve anatomy

value: bicuspid

tag: disease

value: calcified


title: calcified bicuspid aortic valve + XCT790 [TN-2955_47_S55_L003]


title: Genomic DNA from FF breast tumor tissue_12472

description: Tumor


title: Frog1 Explant Gastrula


title: Genomic DNA from FF breast tumor tissue_13913

description: Tumor


title: calcified bicuspid aortic valve + XCT790 [TN-2955_35_S43_L003]


title: Romidepsin:1MPA, treatment, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated by romidepsin for 1 minute post amputation, then placed in DMSO. Tail samples were collected at 3 hours post amputation.
D2_051118


title: calcified bicuspid aortic valve + XCT790 [TN-2955_45_S53_L003]


title: Romidepsin + CoCl2:1MPA, treatment, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were co-treated with 10uM Romidepsin and 7.5mM CoCl2 for 1 minute post amputation, and then placed in DMSO until 3 hours post amputation. Tail tissues were collected at 3 hours post amputation.
C3_051118

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 3hpa. Samples were treated with CoCl2 and Romidepsin.

value: 10uM Romidepsin cotreated with 7.5uM CoCl2


title: Romidepsin:3hpa, control, replicate 1

description:
Data previously published in Voss et al. 2019 (GSE118515). RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated with DMSO. Tail samples were collected at 3 hours post amputation.
3hrC1_110917

value: Control (DMSO)


title: Romidepsin:1MPA, treatment, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Samples were treated by romidepsin for 1 minute post amputation, then placed in DMSO. Tail samples were collected at 3 hours post amputation.
D1_051118


title: calcified bicuspid aortic valve + XCT790 [TN-2955_29_S37_L003]


title: Frog3 Explant Blastula

value: Stage 8

value: 5 hours


title: Genomic DNA from FF breast tumor tissue_16012

description: Tumor


title: Frog2 Explant Blastula


title: calcified bicuspid aortic valve + XCT790 [TN-2955_25_S33_L003]


title: Frog1 Explant Blastula


title: calcified bicuspid aortic valve + XCT790 [TN-2955_22_S30_L003]


title: Frog3 Explant 32Cell

value: Stage 6

value: 3 hours


title: Romidepsin + CoCl2:1MPA, treatment, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were co-treated with 10uM Romidepsin and 7.5mM CoCl2 for 1 minute post amputation, and then placed in DMSO until 3 hours post amputation. Tail tissues were collected at 3 hours post amputation.
C2_051118


title: calcified bicuspid aortic valve + XCT790 [TN-2955_18_S26_L003]


title: Genomic DNA from FF breast tumor tissue_14051

description: Tumor


title: Romidepsin + CoCl2:1MPA, treatment, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were co-treated with 10uM Romidepsin and 7.5mM CoCl2 for 1 minute post amputation, and then placed in DMSO until 3 hours post amputation. Tail tissues were collected at 3 hours post amputation.
C1_051118


title: Genomic DNA from FF breast tumor tissue_15878

description: Tumor


title: CoCl2:60-90MPA, treatment, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Animals were treated with 7.5mM CoCl2 for 60-90 MPA, and tissues were collected at 3 hours post amputation.
B3_051118

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 3hpa. Samples were treated with CoCl2.

value: 7.5 uM 60-90MPA CoCl2


title: Genomic DNA from FF breast tumor tissue_17271

description: Tumor


title: CoCl2:60-90MPA, treatment, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Animals were treated with 7.5mM CoCl2 for 60-90 MPA, and tissues were collected at 3 hours post amputation.
B2_051118

value: distal tip of embryonic tail


title: Frog2 Explant 32Cell

value: Explanted Tissue


title: calcified bicuspid aortic valve + XCT790 [TN-2955_16_S24_L003]


title: CoCl2:60-90MPA, treatment, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm regenerating axolotl embryo tail tip tissues. Animals were treated with 7.5mM CoCl2 for 60-90 MPA, and tissues were collected at 3 hours post amputation.
B1_051118


title: Genomic DNA from FF breast tumor tissue_9281

description: Tumor


title: Genomic DNA from FF breast tumor tissue_10561

description: Tumor


title: Frog1 Explant 32Cell


title: Genomic DNA from FF breast tumor tissue_17385

description: Tumor


title: CoCl2:0-30MPA, treatment, replicate 3

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 7.5mM CoCl2 for 0-30 MPA, and tissues were collected at 3 hours post amputation.
A3_051118

value: 7.5uM 0-30MPA CoCl2


title: calcified bicuspid aortic valve + XCT790 [TN-2955_08_S16_L003]


title: Frog2 Explant 16Cell

value: Stage 5

value: 2 hours 45 mins


title: calcified bicuspid aortic valve + XCT790 [TN-2955_11_S19_L003]


title: Genomic DNA from FF breast tumor tissue_11665

description: Tumor

value: Female


title: calcified bicuspid aortic valve + XCT790 [TN-2955_03_S11_L003]


title: Frog3 Explant 16Cell


title: Frog1 Explant 16Cell


title: GRO-Seq 3CBEsD_LPS_3

first: Frederick

middle: W

last: Alt

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

data_processing:
Library strategy: GRO-Seq
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples

source_name: Splenic mature B cells

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with the buffer (10 mM Tris-HCl pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, protease inhibitors and Rnase inhibitor). The permeabilized cells were resuspended in 100 ml of storage buffer (10 mM Tris-HCl pH 8.0, 25% (V/V) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT) for nuclear run-on with 2X run-on mix (5 mM Tris-HCl PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, RNase inhibitor, 1% sarkosyl) at 37o for 5 min. RNA was extracted by Trizol and followed by hybrolyzation with NaOH at a final concentration of 0.2 N on ice for 18 min. After quenching with ice-cold Tris-HCl PH6.8 at a final concentration of 0.55 M and exchanging buffer via Bio-Rad P30 columns, the RNA was incubated with Br-dU antibody-conjugated beads (Santa Cruz biotechnology, sc-32323-ac) for 1 hr. The enriched run-on samples were incubated with RppH (NEB, M0356S) and hydroxyl repair with T4 PNK (NEB, M0201S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA
Half of the cDNA was subjected to making Groseq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318).

treatment_protocol: Primary splenic B cells  were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4 or LPS +anti-IgD-dextran for 48 hrs.

value: AID-deficient splenic mature B cells

tag: activation

value: LPS/alphaIgD-dextran

tag: genotype

tag: molecule

value: Run-on RNA


title: GRO-Seq 3CBEsD_LPS_2

tag: strain


title: calcified bicuspid aortic valve + DMSO [TN-2955_44_S52_L003]

value: DMSO

value: bicuspid

value: calcified


title: calcified bicuspid aortic valve + DMSO [TN-2955_46_S54_L003]


title: Frog3 Explant 8Cell

value: Stage 4

value: 2 hours 15 mins


title: Frog2 Explant 8Cell


title: Genomic DNA from FF breast tumor tissue_13922

description: Tumor

value: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_18664

description: Tumor


title: CoCl2:0-30MPA, treatment, replicate 1

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 7.5mM CoCl2 for 0-30 MPA, and tissues were collected at 3 hours post amputation.
A1_051118


title: calcified bicuspid aortic valve + DMSO [TN-2955_38_S46_L003]


title: GRO-Seq 3CBEsD_LPS_1


title: GRO-Seq 3CBEsD_IL4_3


title: GRO-Seq 3CBEsD_IL4_2


title: Genomic DNA from FF breast tumor tissue_16855

description: Tumor


title: Frog1 Explant 8Cell


title: CoCl2:0-30MPA, treatment, replicate 2

description:
RAW microarray data quantified from three pooled samples of 12, 1.0 mm non-regenerating axolotl embryo tail tip tissues. Animals were treated with 7.5mM CoCl2 for 0-30 MPA, and tissues were collected at 3 hours post amputation.
A2_051118


title: calcified bicuspid aortic valve + DMSO [TN-2955_34_S42_L003]


title: Frog3 Progeny Mid Neurula

source_name: Xenopus embryo

value: Stage 17

value: Fluorescent Descendant

value: 18 hours


title: GRO-Seq 3CBEsD_IL4_1


title: Genomic DNA from FF breast tumor tissue_9960

description: Tumor


title: calcified bicuspid aortic valve + DMSO [TN-2955_28_S36_L003]


title: Genomic DNA from FF breast tumor tissue_13240

description: Tumor


title: Genomic DNA from FF breast tumor tissue_17411

description: Tumor


title: GRO-Seq WT_LPS_3

value: WT


title: calcified bicuspid aortic valve + DMSO [TN-2955_24_S32_L003]


title: GRO-Seq WT_LPS_2


title: calcified bicuspid aortic valve + DMSO [TN-2955_21_S29_L003]


title: Frog1 Progeny Mid Neurula


title: GRO-Seq WT_LPS_1


title: Frog3 Progeny Early Neurula

value: Stage 14

value: 16 hours


title: GRO-Seq WT_IL4_3


title: Genomic DNA from FF breast tumor tissue_14097

description: Tumor


title: calcified bicuspid aortic valve + DMSO [TN-2955_17_S25_L003]


title: Frog2 Progeny Early Neurula


title: calcified bicuspid aortic valve + DMSO [TN-2955_15_S23_L003]


title: Frog2 Progeny Mid Neurula


title: Frog1 Progeny Early Neurula


title: Genomic DNA from FF breast tumor tissue_14128

description: Tumor


title: GRO-Seq WT_IL4_2


title: Genomic DNA from FF breast tumor tissue_10711

description: Tumor


title: calcified bicuspid aortic valve + DMSO [TN-2955_10_S18_L003]


title: Genomic DNA from FF breast tumor tissue_15362

description: Tumor


title: calcified bicuspid aortic valve + DMSO [TN-2955_07_S15_L003]


title: Genomic DNA from FF breast tumor tissue_18751

description: Tumor


title: GRO-Seq 3CBEsD_nonsti_3

value: without stimulation


title: calcified bicuspid aortic valve + DMSO [TN-2955_02_S10_L003]


title: GRO-Seq WT_nonsti_3


title: Frog1 Progeny Gastrula

value: Stage 11

value: 11 hours


title: calcified tricuspid aortic valve + XCT790 [TN-2955_43_S51_L003]

value: tricuspid


title: Frog3 Progeny Blastula

value: Stage 8

value: 5 hours


title: GRO-Seq WT_IL4_1

value: AID-deficient splenic mature B cells

value: Run-on RNA


title: Frog3 Progeny Gastrula


title: calcified tricuspid aortic valve + XCT790 [TN-2955_41_S49_L003]

value: calcified


title: Genomic DNA from FF breast tumor tissue_18268

description: Tumor

value: Female


title: GRO-Seq WT_nonsti_2


title: GRO-Seq 3CBEsD_nonsti_2


title: Frog2 Progeny Gastrula


title: Genomic DNA from FF breast tumor tissue_16665

description: Tumor

value: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_17453

description: Tumor


title: Frog2 Progeny Blastula


title: calcified tricuspid aortic valve + XCT790 [TN-2955_37_S45_L003]


title: GRO-Seq 3CBEsD_nonsti_1


title: Frog1 Progeny Blastula


title: Genomic DNA from FF breast tumor tissue_14129

description: Tumor


title: calcified tricuspid aortic valve + XCT790 [TN-2955_33_S41_L003]


title: Genomic DNA from FF breast tumor tissue_11513

description: Tumor


title: calcified tricuspid aortic valve + XCT790 [TN-2955_31_S39_L003]


title: Frog3 Progeny 32Cell

value: Stage 6

value: 3 hours


title: Genomic DNA from FF breast tumor tissue_14994

description: Tumor


title: Frog2 Progeny 32Cell

value: Fluorescent Descendant


title: calcified tricuspid aortic valve + XCT790 [TN-2955_27_S35_L003]


title: Frog1 Progeny 32Cell


title: calcified tricuspid aortic valve + XCT790 [TN-2955_20_S28_L003]


title: Genomic DNA from FF breast tumor tissue_17959

description: Tumor


title: Genomic DNA from FF breast tumor tissue_9745

description: Tumor


title: 3C-HTGTS 3CBEsD_LPS_iEm_3

library_source: genomic

data_processing:
Library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated for displaying (Jane et al., 2018)

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

value: Splenic mature B cells

value: LPS/alphaIgD-dextran

tag: treatment protocol

value: cytokine stimulation

tag: target locus

tag: growth conditions


title: Frog2 Progeny 16Cell

value: Stage 5

tag: tissue

value: 2 hours 45 mins


title: calcified tricuspid aortic valve + XCT790 [TN-2955_14_S22_L003]


title: Frog1 Progeny 16Cell


title: Frog3 Progeny 16Cell


title: calcified tricuspid aortic valve + XCT790 [TN-2955_06_S14_L003]


title: 3C-HTGTS 3CBEsD_IL4_iEm_3


title: 3C-HTGTS 3CBEsD_LPS_iEm_2


title: 3C-HTGTS 3CBEsD_LPS_iEm_1


title: calcified tricuspid aortic valve + DMSO [TN-2955_42_S50_L003]

value: DMSO


title: 3C-HTGTS 3CBEsD_IL4_iEm_1


title: Genomic DNA from FF breast tumor tissue_12866

description: Tumor

tag: gender


title: GRO-Seq WT_nonsti_1

value: without stimulation

value: WT


title: calcified tricuspid aortic valve + DMSO [TN-2955_40_S48_L003]

value: tricuspid


title: Frog2 Progeny 8Cell

value: Stage 4

value: 2 hours 15 mins


title: calcified tricuspid aortic valve + DMSO [TN-2955_36_S44_L003]

value: calcified


title: 3C-HTGTS WT_LPS_iEm_2


title: 15612X12_DHR39

city: Salt Lake City

first: Carl

middle: S

last: Thummel

state: UTAH

address: 15 North 2030 East, Room 5200, University of Utah, Department of Human Genetics

department: Human Genetics

institute: University of Utah

description: 15612X12_181109_A00421_0024_BHGNYWDMXX_S12_L001

data_processing:
The Drosophila BDGP6 genome and gene feature files were downloaded from Ensembl release 94 and the reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads (Dobin et al 2013). Reads were trimmed of adapters using cutadapt 1.16 and then aligned to the reference database using STAR in two pass mode with alignIntronMax 100000 to output a BAM file sorted by coordinates. Mapped reads were assigned to annotated genes using featureCounts version 1.6.3 and differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.20.0.
Genome_build: dm6
Supplementary_files_format_and_content: excel file, has raw counts, normalized counts, vsd log counts (DESeq2 version 1.22.2), fpkm values, and sample IDs.

organism: Drosophila melanogaster

source_name: DHR39_whole fly

growth_protocol: Animals were staged as freshly eclosed adults and aged to 8 days of adulthood

extract_protocol:
Zymo Direct-zol RNA miniprep kit (with DNase treatment)
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10) with UDI. Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664).  Following transfer of the flowcell to an Illumina NovaSeq instrument, a 2 x 51 cycle paired end sequence run was performed using a NovaSeq S1 reagent Kit (20027465).

treatment_protocol: All animals were reared on a control diet of 8% Yeast 9% Sugar and transferred every 2-4 days to fresh food.

tag: genotype/variation

tag: timepoint

value: whole fly


title: Genomic DNA from FF breast tumor tissue_17469

description: Tumor

data_processing:
The raw intensity IDAT files were extracted using GenomeStudio,and processed by the minfi R package. Only loci with a median detection p value <0.05 were retained for analysis, and only samples with detection p values < 1.0E-05 at more than 75% of CpG lici passed the performance criteria for inclusion. Probes containing SNPs and/or those that were ambiguously mapped were excluded from the analysis. The final dataset contained 276,108 CpG loci across 138 samples.
The signal_intensities.txt contains unmethylated and methylated signal intensities

value: Female

value: Flash frozen breast tumor tissue


title: calcified tricuspid aortic valve + DMSO [TN-2955_30_S38_L003]


title: 15612X10_control [re-used]

description: 15612X10_181109_A00421_0024_BHGNYWDMXX_S10_L001

source_name: control_whole fly

value: control


title: Frog3 Progeny 8Cell

tag: developmental stage

value: Fluorescent Descendant


title: calcified tricuspid aortic valve + DMSO [TN-2955_26_S34_L003]


title: 3C-HTGTS 3CBEsD_IL4_iEm_2

value: Splenic mature B cells


title: Genomic DNA from FF breast tumor tissue_17982

description: Tumor


title: Frog1 Progeny 8Cell

tag: age


title: 15612X9_DHR39

description: 15612X9_181109_A00421_0024_BHGNYWDMXX_S9_L001


title: calcified tricuspid aortic valve + DMSO [TN-2955_19_S27_L003]


title: 15612X7_control [re-used]

description: 15612X7_181109_A00421_0024_BHGNYWDMXX_S7_L001


title: calcified tricuspid aortic valve + DMSO [TN-2955_13_S21_L003]


title: 3C-HTGTS WT_IL4_iEm_2

tag: cell type


title: 3C-HTGTS WT_IL4_iEm_3


title: 3C-HTGTS WT_LPS_iEm_1

value: LPS/alphaIgD-dextran


title: 3C-HTGTS WT_IL4_iEm_1

value: cytokine stimulation


title: calcified tricuspid aortic valve + DMSO [TN-2955_05_S13_L003]

tag: agent


title: healthy tricuspid aortic valve + DMSO [TN-2955_23_S31_L003]

tag: aortic valve anatomy

value: healthy


title: Genomic DNA from FF breast tumor tissue_10820

description: Tumor


title: healthy tricuspid aortic valve + DMSO [TN-2955_12_S20_L003]

tag: disease


title: healthy tricuspid aortic valve + DMSO [TN-2955_09_S17_L003]


title: Genomic DNA from FF breast tumor tissue_12694

description: Tumor


title: Genomic DNA from FF breast tumor tissue_18367

description: Tumor


title: 15612X1_control [re-used]

description: 15612X1_181109_A00421_0024_BHGNYWDMXX_S1_L001


title: 15612X5_control [re-used]

description: 15612X5_181109_A00421_0024_BHGNYWDMXX_S5_L001


title: 15612X6_DHR39

description: 15612X6_181109_A00421_0024_BHGNYWDMXX_S6_L001


title: 15612X3_control [re-used]

description: 15612X3_181109_A00421_0024_BHGNYWDMXX_S3_L001


title: Genomic DNA from FF breast tumor tissue_10428

description: Tumor


title: Genomic DNA from FF breast tumor tissue_16172

description: Tumor


title: Genomic DNA from FF breast tumor tissue_9390

description: Tumor


title: CSR-HTGTS-Seq 3CBEsD_LPS_2

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

extract_protocol:
DNA was extracted overnight at 56 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using CSR-HTGTS-Seq (Dong et al., 2015)
CSR-HTGTS-Seq

treatment_protocol: Primary splenic B cells  were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4 or LPS +anti-IgD-dextran for 96 hrs.

tag: activation

value: LPS/aIgD-dextran


title: CSR-HTGTS-Seq 3CBEsD_IL4_3

tag: genotype


title: healthy tricuspid aortic valve + DMSO [TN-2955_04_S12_L003]

value: DMSO


title: CSR-HTGTS-Seq 3CBEsD_LPS_3


title: 15612X11: E78A mutant

source_name: whole fly


title: CSR-HTGTS-Seq 3CBEsD_IL4_1


title: CSR-HTGTS-Seq 3CBEsD_IL4_2


title: healthy tricuspid aortic valve + DMSO [TN-2955_01_S9_L003]


title: 15612X10: control

value: E78A mutant


title: 15612X8: E78A mutant


title: A375_wt_NT_3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo Sapiens, Ensembl, GRCh38.p10
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: RNA-Seq_A375_parental cells_withoutDox

growth_protocol: A375 and A549 cells were grown in DMEM supplementet with 10% FBS and 1% Penicillin-Streptomycin at 37°C in a humified atmosphere with 5% of CO2

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (#74104 Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dox-inducible shMCM7 or parental A549 and A375 cells, each arrested in G1 by double thymidine block, were treated for 72 hours with/without 1μg/ml Dox.

tag: cell line

value: human melanoma cell line

tag: knockdown

tag: transduced with

tag: cell synchronization

value: Double thymidine synchronized

tag: dox treatment

value: No Dox treatment


title: CSR-HTGTS-Seq 3CBEsD_LPS_1

tag: treatment protocol

tag: target locus

tag: growth conditions


title: Genomic DNA from FF breast tumor tissue_17058

description: Tumor

extract_protocol: DNA was extracted using a MasterPure DNA purification kit (Epicentre).

tag: gender

tag: tissue


title: Genomic DNA from FF breast tumor tissue_18612

description: Tumor


title: 15612X7: control

tag: genotype/variation

tag: timepoint


title: CSR-HTGTS-Seq WT_LPS_3

value: WT


title: CSR-HTGTS-Seq WT_LPS_2


title: A375_wt_NT_2

tag: cell type


title: CSR-HTGTS-Seq WT_IL4_3


title: CSR-HTGTS-Seq WT_LPS_1


title: 15612X5: control


title: A375_wt_NT_1


title: 15612X3: control


title: CSR-HTGTS-Seq WT_IL4_1


title: A375_wt_Dox_2

source_name: RNA-Seq_A375_parental cells_withDox

value: 1 microgram/ml Dox 72h


title: 15612X4: E78A mutant

value: whole fly


title: Genomic DNA from FF breast tumor tissue_11942

description: Tumor

value: Female


title: CSR-HTGTS-Seq WT_IL4_2


title: A375_wt_Dox_3


title: calcified tricuspid aortic valve + DMSO [TN-2955_32_S40_L003]

tag: agent

tag: aortic valve anatomy

value: tricuspid

value: calcified


title: Genomic DNA from FF breast tumor tissue_15599

description: Tumor

value: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_12266

description: Tumor


title: 3C-HTGTS WT_LPS_iEm_3

value: Splenic mature B cells

tag: activation


title: Genomic DNA from FF breast tumor tissue_14308

description: Tumor


title: Genomic DNA from FF breast tumor tissue_12154

description: Tumor


title: Genomic DNA from FF breast tumor tissue_19282

description: Tumor


title: Genomic DNA from FF breast tumor tissue_9048

description: Tumor


title: Genomic DNA from FF breast tumor tissue_18035

description: Tumor


title: Genomic DNA from FF breast tumor tissue_12599

description: Tumor


title: 15612X2: E78A mutant


title: Genomic DNA from FF breast tumor tissue_17812

description: Tumor


title: Genomic DNA from FF breast tumor tissue_10124

description: Tumor


title: Genomic DNA from FF breast tumor tissue_11772

description: Tumor


title: Genomic DNA from FF breast tumor tissue_13336

description: Tumor


title: IRI_mouse

city: Edinburgh

first: Eoin

middle: D

last: O'Sullivan

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequencing was performed on a NextSeq 550 High Output Kit v2 (Illumina) for 150 cycles at 400M PE reads comprising of 2x75bp and 8bp index reads.
Using the Cell Ranger Single Cell software suite 2.1.0 by 10x Genomics the cellranger mkfastq wrapper demultiplexed the illumina output BCL files to library specific FASTQ files.  Subsequently, alignment was performed using the cellranger count function using STAR aligner 2.5.1b.1 The GRCm38 mouse reference genome, mm10 (Ensembl 93) was used.
Genome_build: mm10
Supplementary_files_format_and_content: genecounts are found in matrix.mtx files, cell  barcodes in barcodes.tsv and genes names in genes.tsv

source_name: injured mouse kidney harvested 2 weeks post-injury

extract_protocol:
kidneys were removed , digested on ice and FACS sorted using DAPI as a live/dead gate. Libraries were constructed using the standard 10x single cell 3' V2 workflow
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Unilateral renal artery ligation for 15 minutes performed under general anaesthesia to arrest renal blood flow. Mouse kidney was harvested 2 weeks following injury.

tag: strain

value: Kidney

tag: age

value: 8 week


title: A375_sh_NT_3

tag: cell line

tag: knockdown

value: CAG AGG AGG ATT TCT ACG AAA in pRSIT17 MOI=1.4


title: WT golden hamster small intestine

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description: WT golden hamster

data_processing:
Cell Ranger (v3.0.2) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to MesAur1.0 reference genome
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT hamster organs' single cell data

organism: Mesocricetus auratus

source_name: golden hamster small intestine

extract_protocol:
After tissue preparation and cell digestion, single-cell suspensions were processed on the 10X chromium system following the manufacturer's protocols.
cDNA libraries were constructed using Chromium Single cell 3' v3 Reagent Kit (10X genomics)

tag: developmental stage

value: Adult

value: small intestine


title: WT golden hamster kidney

description: WT golden hamster

source_name: golden hamster kidney

value: kidney