title: salmIR IFM 30h APF rep 2

description:
mRNA
salm30h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

data_processing:
Basecalling and demultiplexing by IMP sequencing core facility (Vienna, Austria) using Illumina software.
Quality assessment of the raw data using fastqc v.011.2.
Filtering and trimming of adapter residues and low quality reads with the FASTX toolkit v.0.0.14 and cutadapt v1.4.1.
Sequenced reads were mapped to the Ensembl BDGP6.80 whole genome using STAR v2.4.2a.
Mapped reads were sorted and indexed using samtools v1.2.
Bam files were converted into bigwig for visualisation on the UCSC server.
Counting the mapped reads on the gene and exon level using featureCounts v1.4.6.
Run the differential gene expression analysis using the R package DESeq2 v1.8.2.
Calculate the differential exon usage with the R package DEXSeq.
Genome_build: BDGP6.80 from ENSEMBL
Supplementary_files_format_and_content: Tab-delimited text files including raw counts calculated by featureCount for all libraries

value: indirect flight muscle

value: tubular converted

value: 30h APF

value: Mef2-Gal4, UAS-T3029 (salmIR)

value: grown at 27C, staged 0h white pre-pupae


title: Control at normoxia

status: Public on Jan 21 2020

type: SRA

city: Los Angeles

first: Kailtyn

middle: Yan-Yun

last: Liu

state: CA

address: 10833 Le Conte Ave

department: Medicine

country: USA

institute: UCLA/VA

library_source: transcriptomic

data_processing:
IlluminaHiseq3000 for a single read 50 run.
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited text files

molecule: total RNA

organism: Mus musculus

source_name: Primary cortical neurons

growth_protocol: mouse primary cortiall neuron were growth for 7days. Then cells were subjected to treatment.

extract_protocol:
Cultured primary cortical neurons were exposed to hypoxia (0.2% oxygen) for 7 hours, in either the presence or absence of T3 (5 nM)
RNA libraries were prepared for sequencing using standard Illumina protocols
KAPA Strand RNA-Seq kit

treatment_protocol: Controlat 21% oxgen, hypoxia at 0.2% oxgen

tag: strain

tag: age

value: embryonic day-17 mice

tag: tissue

value: Brain

tag: cell type

value: Primary cortical neurons

tag: treatment

value: control


title: hypoxia/TH [T35]

value: hypoxia+ Thyroid hormone (TH) treatment


title: WT wing disc myoblast rep2 (Myo2)

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

institute: University of Missouri Kansas City

description:
mRNA
IFM_Myoblast_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

organism: Drosophila melanogaster

source_name: wing disc myoblasts

growth_protocol: Flies were grown on standard medium using standard fly husbandry protocol.

extract_protocol:
Total RNA isolated in Tri-Pure reagent (phenol-chloroform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP.
RNA libraries were prepared for sequencing by the IMP sequencing core facility (Vienna, Austria) using standard Illumina protocols.

treatment_protocol: Dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction.

value: wing disc myoblasts

tag: muscle type

value: myoblast

tag: developmental stage

value: 3rd instar

tag: genotype

value: Him-Gal4, UAS-BBM (RFP); salmEGFP

tag: growth protocol

value: grown at 25C, collected crawling 3rd instar larvae


title: TSS whole body NE579 37S rep 2

city: Paris

first: Guilhem

last: Janbon

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Library strategy: TSS-Seq
For TSS analysis we kept only the reads containing both the oligo 3665 (AGATCGGAAGAGCACACGTCTGAAC) and the 11NCGCCGCGNNN tag. These sequenced were removed using cutadapt/1.18 and the trimmed reads were mapped to the Cryptococcus deneoformans JEC21 genome using Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). Wig files were constructed using the 5’ extremities of each reads. Their coverage was normalized using the normalization factor used for spiked in RNA-Seq.

molecule: polyA RNA

organism: Cryptococcus deneoformans

source_name: cells

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: NE579 upf1delta

tag: growth condition

value: exponential phase 30 degrees C

tag: protocol

value: TSS-Seq

tag: sample id

value: Sample 26


title: salmIR IFM 24h APF rep 2

description:
mRNA
salm24h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: indirect flight muscle

value: indirect flight muscle

value: tubular converted

value: 24h APF


title: WT IFM 90h APF rep2

description:
mRNA
IFM90h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: fibrillar

value: 90h APF

value: Mef2-Gal4, UAS-GMA-GFP

value: grown at 27C, staged 0h white pre-pupae


title: DNA NE579 37S rep 2

library_source: genomic

data_processing:
Library strategy: DNA-Seq
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. deneoformans JEC21 and to the S. cerevisiae S288C  genomes with Bowtie2 using default settings. For each sample, total DNA and RNA reads counts aligned to each organism were used to calculate an alpha normalization factor. The file with the alpha noramlization factors is available on the series record: alpha_factor.txt

molecule: genomic DNA

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: DNA-Seq


title: WT IFM 90h APF rep1

description:
mRNA
IFM90h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: RNA_iWAT_RR2

city: Bethesda

first: Paul

middle: M.

last: Hwang

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration:Windows (50), Gaps (50), FDR (1e-10). Signals from the p53 KO cells were filtered out.
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using bowtie2.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include Gene, read count, and RPKM values for each gene.

source_name: Inguinal white adipose tissue

extract_protocol:
For RNA-seq samples, total tissue RNA was purified using the RNeasy kit (Qiagen), and mRNA was isolated using the Dynabead mRNA Purification Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotypes

value: p53178R/R (wild-type)


title: PAS whole body NE579 37S rep 1

data_processing: QuantSeq 3’mRNA-Seq reads containing both the Sequencing and indexing primers (Lexogen) were sorted. The reads were then cleaned using cutadapt/1.18 and trimmed for polyA sequence in their 3’end. PolyA untrimmed and trimmed reads were mapped to the adapted Cryptococcus deneoformans JEC21 genome with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). To eliminate the polyadenylated reads corresponding to genomic polyA stretches, we considered only the reads that aligned to the genomes only after polyA trimming. The 3’end position of these reads were considered as potential PAS. Wig files were constructed using the 3’ extremities of these reads Their coverage was normalized using the normalization alpha factor used for spiked in RNA-Seq.

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: QuantSeq 3-prime RNA-Seq

value: Sample 25


title: WT IFM 48h APF rep3

description:
mRNA
IFM48h_3
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 48h APF


title: WT IFM 48h APF rep2

description:
mRNA
IFM48h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: TSS whole body NE579 37S rep 1


title: PAS whole body NE579 37S rep 2


title: TOF patient 8 after CPB

type: RNA

city: Genova

first: Davide

last: Cangelosi

address: Via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

hyb_protocol: Fragmented cRNA was hybridized on Affymetrix Human Genome U133 Plus PM Array Strips  (Thermo Fisher) containing 54,675 probe sets coding for 47,000 transcripts and variants, including 38,500 unique human genes) on a single array. Chips were stained with streptavidin-phycoerythrin (Invitrogen Life Technologies, Milano).

scan_protocol: GeneChips were scanned using  an Affymetrix GeneChip Scanner 3000.

data_processing: Expression values were quantified, and data were processed by RMA normalization utilizing the ‘Affy’ R package. Statistical analysis using Student’s t-test was performed to identify differentially expressed genes (DEGs). Specifically, unpaired Student’s t-test was used to assess whether there were significant differentially expressed genes between ASD and ToF, whereas paired Student’s t-test was used to identify differences in the gene expression levels between Pre-CPB and Post-CPB in ASD or in ToF. We corrected the p value by Benjamini- Hochberg method for false discovery rate (FDR) control. Only gene differences that passed the test at a confidence level of 95% (P≤0.05) and a FDR ≤ 0.05 were considered significant. Fold-change (FC) was calculated to determine the magnitude of the difference. Genes were considered significantly differentially expressed if they exhibited p value ≤0.05 and FC≥2 or ≤0.5. We filtered out genes having a coefficient of variation (CV) lower than 0.7, because they did not substantially change between the two diseases under consideration, and those having an expression value lower than 100 in at least 20% of the samples because they were not sufficiently expressed in our data set to provide a reliable transcriptional level. Filtering was carried out by ‘GeneFilter’ R package. We converted the Affymetrix probe sets into the corresponding gene symbol by Netaffix tool. When multiple probe sets were associated with the same gene symbol, the probe set with the highest expression signal was considered.

label: biotin

organism: Homo sapiens

source_name: patient with TOF after CPB

extract_protocol: Tissue specimens were mechanically homogenized in lysis reagent from Qiagen (Milano, Italy). The procedure of RNA isolation and cRNA synthesis has been previously described. Briefly, total RNA was purified and DNase treated using the RNeasy MiniKit (Quigen), controlled for integrity by nanoelectrophoresis using an Agilent 2100 Bioanalyzer  (Agilent Technologies Europe, Waldbroon, Germany), quantified by spectrophotometry using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, USA), and reverse-transcribed into double-stranded cDNA on a GeneAmp PCR System 2700 thermal cycler (Applied Biosystems, Milano) using the one-cycle cDNA synthesis kit (Affymetrix, Milano). cDNA was purified, transcribed into cRNA, and biotin labeled using the GeneChip IVT kit (Affymetrix). Labeled cRNA was fragmented according to Affymetrix’s instructions.

treatment_protocol: Pre- and post-operative right atrium biopsy specimens were collected at the time of surgical defect correction. The first biopsy was harvested five minutes before AoXC (Pre-CPB), whereas the second biopsy was harvested fifteen minutes after AoXC removal (Post-CPB) (average CPB duration did not exceed 70 minutes). Specimens were harvested with cold sharp dissection, immediately snap-frozen in liquid nitrogen, and stored until use at -80°C in the Integrating Tissueomics Biobank (BIT)–Gaslini, which collects and stores tissue and genomic specimens for diagnostic and research functions under the approval of the Ethical Committee of the Gaslini Institute and the ratification of the Ethical Committee of the Regione Liguria. Atrial sampling was atraumatic, provided full-thickness specimens, and was clinically reproducible.

tag: disease state

value: TOF

tag: individual

value: patient 8

tag: time

value: after CPB

value: Myocardium (right atrium biopsy)


title: HUVEC_2D_starved_rep2

city: Candiolo

last: Cora'

state: TO

department: Dept. of Oncology

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

description:
HUVEC_2D_starved_rep2
Human Umbilical Vein Endothelial Cells cultured in 2D starved in M199 poor with 1% FBS- replicate_2

hyb_protocol: 750 ng of cRNA was hybridized on HumanHT-12_v.4 for 18 h. Array washes were performed using wash buffer

scan_protocol: Hybridized BeadChips were scanned using illumina Array reader

data_processing: Cubic Spline-normalized probe intensity data, togther with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

source_name: Human Umbilical Vein Endothelial Cells cultured in 2D - starved

label_protocol: Bioinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: HUVEC were isolated from umbilical cord veins and maintained in M199, 20% FBS, supplemented with heparin and bovine brain extract.

extract_protocol: RNAs were isolated using RNeasy Mini Kit qiagen( Cat No./ID: 74104)

treatment_protocol: HUVEC were starved in M199 with 1% FBS and 1% BSA for 10 hours and then stimulated with VEGF (20 ng/ml) for 18 hours

tag: cell line

value: HUVEC

tag: culture condition

value: control


title: WT IFM 24h APF rep3

description:
mRNA
IFM24h_3
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: indirect flight muscle


title: RNA whole body NE579 37S rep 2

data_processing: The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. deneoformans JEC21 and to the S. cerevisiae S288C genomes with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). RNA Reads count were evaluated using HTSeq/0.6.1 (intersection-nonempty) normalized using the S. cerevisiae DNA/RNA spike in alpha factor and used to calculate FPKM values.

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

tag: strain

value: NE579 upf1delta

value: exponential phase 30 degrees C

value: RNA-Seq

value: Sample 26


title: WT IFM 24h APF rep2

description:
mRNA
IFM24h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

tag: tissue

value: fibrillar

value: 24h APF

value: Mef2-Gal4, UAS-GMA-GFP

value: grown at 27C, staged 0h white pre-pupae


title: HUVEC_2D_starved_rep1

description:
HUVEC_2D_starved_rep1
Human Umbilical Vein Endothelial Cells cultured in 2D starved in M199 poor with 1% FBS- replicate_1


title: HUVEC_2D_VEGF_rep2

description:
HUVEC_2D_VEGF_rep2
Human Umbilical Vein Endothelial Cells cultured in 2D starved in M199 poor with 1% FBS and then stimulated with VEGF-A for 18 hours- replicate_2

source_name: Human Umbilical Vein Endothelial Cells cultured in 2D - stimulated with VEGF-A

value: stimulated with VEGF-A


title: LG_LCH.CD14_LCH006

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description: CD14+mono-Dcs sorted from LCH lesion

hyb_protocol: Hybridization of cDNA was performed on Illumina Human-HT12 Version 4 chips for 16 hours at 58°C.

scan_protocol: Chips were scanned using the BeadArray Scanner 500GX

data_processing: Probe level expression data were exported from Illlumina GenomeStudio software without background subtraction. These raw data were quantile normalized and log (base 2) transformed and in R (3.1.2) using Bioconductor lumi (version 2.18.0) package.

label: Biotin

source_name: LCH lesion

label_protocol: Biotinylated complementary RNA was prepared according to the protocol by Epicentre TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 using 500pg of total RNA.

extract_protocol: Total RNA was purified from sorted subpopulations from peripheral blood and lesion specimens according to the Qiagen RNeasy Micro kit (Qiagen, Valencia, CA). RNA integrity was determined using Agilent Bioanalyzer and the RNA Integrity Numbers (RIN) was calculated.  All samples had a RIN ≥ 7.1.

value: Lung


title: PAS whole body JEC21 37S rep 3

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: stationnary phase 37 degrees C

value: QuantSeq 3-prime RNA-Seq

value: Sample 24


title: DNA NE579 37S rep 1

value: DNA-Seq

value: Sample 25


title: BN_LCH.CD207_LCH004

description: CD207+cells sorted from LCH lesion

value: Bone


title: LG_LCH.CD207_LCH006

description: CD207+cells sorted from LCH lesion


title: BN_LCH.CD1c_LCH004

description: CD1c+mDCs sorted from LCH lesion


title: TSS whole body JEC21 37S rep 3

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: TSS-Seq


title: WT IFM 16h APF rep3

description:
mRNA
IFM16h_3
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: indirect flight muscle

value: 16h APF


title: BN_LCH.CD207_LCH002

description: CD207+cells sorted from LCH lesion


title: LN_LCH.CD1c_LCH003

description: CD1c+mDCs sorted from LCH lesion

value: Lymph node


title: RNA whole body NE579 37S rep 1

value: NE579 upf1delta

value: exponential phase 30 degrees C

value: RNA-Seq


title: WT IFM 16h APF rep2

description:
mRNA
IFM16h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: fibrillar

value: Mef2-Gal4, UAS-GMA-GFP


title: aretIR IFM 72hAPF rep2poor

description:
mRNA
aret72h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 72h APF

value: Mef2-Gal4, UAS:GMA::GFP, UAS-T41568 (aretIR)

value: grown at 27C, staged 0h white pre-pupae


title: LN_LCH.CD207_LCH003

description: CD207+cells sorted from LCH lesion


title: HUVEC_2D_VEGF_rep1

description:
HUVEC_2D_VEGF_rep1
Human Umbilical Vein Endothelial Cells cultured in 2D starved in M199 poor with 1% FBS and then stimulated with VEGF-A for 18 hours-replicate_1

value: HUVEC

value: stimulated with VEGF-A


title: BN_LCH.CD14_LCH016

description: CD14+mono-Dcs sorted from LCH lesion


title: BN_LCH.CD207_LCH005

description: CD207+cells sorted from LCH lesion


title: BN_LCH.CD207_LCH001

description: CD207+cells sorted from LCH lesion


title: BN_LCH.CD14_LCH001

description: CD14+mono-Dcs sorted from LCH lesion


title: RNA whole body JEC21 37S rep 3

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: stationnary phase 37 degrees C

value: Sample 24


title: BN_LCH.CD1c_LCH001

description: CD1c+mDCs sorted from LCH lesion

value: Bone


title: SP_pDC_3

description: Spleen pDCs from Donor 3

hyb_protocol: Hybridization of cRNA was performed on Illumina Human-HT12 Version 4 chips for 16 hours at 58°C. The arrays were then washed and stained base on Illumina Wash Protocol

scan_protocol: The chips were scanned using BeadArray Scanner 500GX

source_name: spleen

label_protocol: Biotinylated cRNA was prepared according to the protocol by Epicentre TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 using 500pg of total RNA.

extract_protocol: Total RNA was isolated from FACS-sorted skin and spleen DC subsets following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy Micro clean-up procedure according to the manufacturer's protocol. Total RNA integrity was assessed using Agilent Bioanalyzer.

tag: cell type

value: pDC


title: SP_pDC_4

description: Spleen pDCs from Donor 4


title: DNA JEC21 37S rep 3

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: DNA-Seq


title: PAS whole body JEC21 37S rep 2

value: QuantSeq 3-prime RNA-Seq

value: Sample 23


title: TSS whole body JEC21 37S rep 2

value: TSS-Seq


title: RNA whole body JEC21 37S rep 2


title: SK_MAC_11

description: Skin macrophages from donro 11

source_name: skin

value: macrophages


title: SP_pDC_1

description: Spleen pDCs from Donor 1


title: DNA JEC21 37S rep 2


title: Tongue_tissue_10

city: Guangzhou

first: Cheng

last: Wang

address: 56 Lingyuan Road West

country: China

institute: Sun Yat-sen University

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US) at 55℃, 20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) using scan setting for 8x60k array slides (Scan resolution 5um, PMT is set to 100%).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: Tongue, patient 10

label_protocol: MiRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) per the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: patient diagnosis

value: tongue squamous cell carcinoma

value: normal tongue tissue

tag: patient id

tag: gender

value: male

tag: age

tag: tumor stage


title: PAS whole body JEC21 37S rep 1

tag: growth condition

value: Sample 22


title: Tongue_cancer_09

source_name: Tongue, patient 09


title: Tongue_cancer_10


title: Tongue_tissue_09


title: SK_LC_11

description: Skin langerhans cells from donor 11

value: langerhans cells


title: Tongue_tissue_08

source_name: Tongue, patient 08

value: female


title: SK_MAC_10

description: Skin macrophages from donro 10


title: SK_MAC_6

description: Skin macrophages from donro 6


title: TSS whole body JEC21 37S rep 1

tag: protocol


title: RNA whole body JEC21 37S rep 1

value: RNA-Seq

tag: sample id


title: SK_LC_10

description: Skin langerhans cells from donor 10


title: SPHV_shDICER_rep1

description: Human Umbilical Vein Endothelial Cells transduced with a shRNA targeting DICER1 and cultured as spheroids stimulated with VEGF-A - replicate_1

data_processing: Cubic Spline-normalized probe intensity data, togheter with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

extract_protocol: RNA was extracted from SPHC and SPHV collected after collagen digestion using miRNeasy Mini Kit (Qiagen #217004) according to manufacturer's instructions.

treatment_protocol: HUVEC aggregates (spheroids) were generated by culturing cells in hanging drops for 10 hours, then embedded in a collagen matrix. VEGF-A 20 ng/ml was used to trigger sprouting. Sprouted spheroids were collected after 15 hours VEGF-A treatment.

tag: shRNA

value: shRNA targeting DICER1

tag: growth

value: HUVEC


title: Tongue_cancer_08


title: Tongue_cancer_07

source_name: Tongue, patient 07


title: SPHV_shDICER_rep2

description: Human Umbilical Vein Endothelial Cells transduced with a shRNA targeting DICER1 and cultured as spheroids stimulated with VEGF-A - replicate_2


title: Tongue_tissue_07


title: SPHV_pLKO_rep1

description: Human Umbilical Vein Endothelial Cells transduced with non-targeting shRNA and cultured as spheroids stimulated with VEGF-A - replicate_1

value: non-targeting shRNA


title: SPHC_shDICER_rep2

description: Human Umbilical Vein Endothelial Cells transduced with a shRNA targeting DICER1 and cultured as spheroids - replicate_2

value: cultured as spheroids


title: SPHV_pLKO_rep2

description: Human Umbilical Vein Endothelial Cells transduced with non-targeting shRNA and cultured as spheroids stimulated with VEGF-A - replicate_2


title: SK_LC_3

description: Skin langerhans cells from donor 3


title: SPHC_shDICER_rep1

description: Human Umbilical Vein Endothelial Cells transduced with a shRNA targeting DICER1 and cultured as spheroids - replicate_1


title: SPHC_pLKO_rep1

description: Human Umbilical Vein Endothelial Cells transduced with non-targeting shRNA and cultured as spheroids - replicate_1


title: SPHC_pLKO_rep2

description: Human Umbilical Vein Endothelial Cells transduced with non-targeting shRNA and cultured as spheroids - replicate_2


title: DNA JEC21 37S rep 1

value: stationnary phase 37 degrees C


title: Tongue_tissue_06

source_name: Tongue, patient 06


title: PAS whole body JEC21 30S  rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: stationnary phase 30 degrees C

value: Sample 21


title: naïve-BM 2 (bm260_2b)

city: Leeds

first: Mihaela

last: Lorger

address: Beckett street

department: Leeds Institute of Cancer and Pathology

country: United Kingdom

institute: University of Leeds

hyb_protocol: According to the manufacturer protocol (Illumina)

data_processing: Raw data were processed using GenomeStudio version 2011.1. Data processing and visualization were performed using R/Bioconductor. Microarray raw data pre-processing was performed using LIMMA. Background correction was performed using the normexp algorithm and normalization between arrays was performed using A-value quantile normalization.

source_name: Bone marrow

extract_protocol: RNA was isolated using RNAqueous Micro Total RNA Isolation Kit (Ambion).

value: 14 weeks

value: Bone marrow


title: TSS whole body JEC21 30S rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: TSS-Seq


title: naïve-S 2 (s261_2)

scan_protocol: According to the manufacturer protocol (Illumina)

source_name: Spleen

value: Spleen


title: naïve-S 1 (s260_2)

label_protocol: According to the manufacturer protocol (Illumina)


title: naïve-BM 1 (bm260_2)


title: RNA whole body JEC21 30S rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: Tongue_cancer_06

value: tongue squamous cell carcinoma


title: DNA JEC21 30S rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: DNA-Seq


title: UMSCC1_NC_rep3

data_processing:
Hisat2 for mapping
StringTie assembles transcripts from the alignments produced by Hisat2, including quantitates those transcripts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HNSCC cell line, control mimics

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Mini Kit (QIAGEN, Duesseldorf, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HNSCC cell line

value: UM-SCC1 cells

tag: transfection

value: control mimics


title: Tongue_tissue_05

source_name: Tongue, patient 05

value: normal tongue tissue

value: male


title: PAS whole body JEC21 3S rep 2

source_name: cells

value: QuantSeq 3-prime RNA-Seq

value: Sample 20


title: Tongue_cancer_05


title: EO771-Br 2 (b114/118)

source_name: Intracranial tumor

value: Intracranial tumor


title: UMSCC1_NC_rep1


title: TSS whole body JEC21 3S rep 2


title: Tongue_cancer_04

source_name: Tongue, patient 04


title: Tongue_tissue_04


title: UMSCC1_NC_rep2


title: Tongue_tissue_03

source_name: Tongue, patient 03

value: female


title: EO771-Br 1 (b120)


title: UMSCC1_miR204_rep3

source_name: HNSCC cell line, miR-204-5p mimics

value: miR-204-5p mimics


title: RNA whole body JEC21 30S rep 2

value: stationnary phase 30 degrees C

value: RNA-Seq


title: PyMT-BM 1 (P1-BM)

value: 14 weeks

value: Bone marrow


title: PyMT-Br 1 (PM2-B)


title: PyMT-S 2 (P2-S)

value: Spleen


title: PyMT-S 1 (P1-S)


title: PyMT-Br 3 (P1-B)


title: UMSCC1_miR204_rep2


title: UMSCC1_miR204_rep1


title: Tongue_cancer_03

value: tongue squamous cell carcinoma


title: PyMT-S 3 (PM1-S)


title: DNA JEC21 30S rep 2

value: DNA-Seq


title: Tongue_tissue_02

source_name: Tongue, patient 02


title: PyMT-Br 2 (P2-B)


title: miRNA SS5

city: Beijing

first: lulu

last: wang

address: Malianwa

institute: China Agricultural University

data_processing:
Reads containing adapter, poly-N, and low-quality bases at high proportion were removed to obtain clean reads
Short reads were aligned to reference genome using Burrows-Wheeler Aligner (BWA) with ¡®aln¡¯ and ¡®samse¡¯ options and default parameters
Annotated chicken miRNAs file was downloaded from miRbase (http://www.mirbase.org/index.shtml)
Reads counts that assigned to genome were computed by FeatureCounts (0.18.1)
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Tab-delimited text files include readcount of each Sample

organism: Gallus gallus

source_name: spleen

extract_protocol:
The total RNA was extracted from spleen tissues by Trizol (Invitrogen, CA) according to the manufacturer¡¯s instruction.
A total of 3 ¦Ìg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext? Multiplex Small RNA Library Prep Set for Illumina? (NEB, USA.) following the manufacturer¡¯s recommendations and index codes were added to attribute sequences to each sample.

tag: Sex

tag: treatment

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain

value: survivor


title: miRNA SS3


title: miRNA SS4


title: PyMT-Br 4 (PM1-B)


title: miRNA SS2


title: miRNA SS1


title: miRNA NS3

value: the same volume of diluent (0.2 mL)


title: TSS whole body JEC21 30S rep 1

value: TSS-Seq

value: Sample 19


title: miRNA NS4


title: Tongue_cancer_02


title: RNA whole body JEC21 30S rep 1


title: miRNA NS2

value: male


title: PC9_LeptoM_AD_2

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

description: 09014B_HTseq_PC9_LeptoM_rawcountmatrix.txt

data_processing:
Reads from generated FASTQ files were quality checked and mapped to the mouse reference genome (hg19) using STAR2.5.0.a. The expression count matrix of uniquely mapped reads was computed with HTseq v0.5.3.
Genome_build: hg19
Supplementary_files_format_and_content: RNA STAR-aligned reads are submitted as BAM. The expression count matrix of uniquely mapped reads is submitted as TXT and was computed with HTseq.

source_name: Leptomeningeal metastatic cells

growth_protocol: PC9 LeptoM cells were cultured as described previously (Boire 2017). For collection of floating and adherent fractions, 1.5x10^6 cells were seeded into 100 mm dish. Two days later, cells were fractionated using trypsin/EDTA-based protocol and lysed in RNA lysis buffer (RLT).

extract_protocol:
RNA was extracted from lysates using Rneasy Mini columns (Qiagen).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, #RS-122-2102), with 8 cycles of PCR.

value: Adherent


title: miRNA NS1


title: Tongue_tissue_01

source_name: Tongue, patient 01

value: normal tongue tissue


title: DNA JEC21 30S rep 1


title: miRNA TS5

value: female

value: tumorous


title: PC9_LeptoM_FL_2

value: Floating


title: Tongue_cancer_01


title: PC9_LeptoM_AD_1


title: TSS whole body JEC21 37E rep 3

extract_protocol: Cells were grown on YPD at 37°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: exponential phase 37 degrees C

value: Sample 18


title: PAS whole body JEC21 37E rep 3

extract_protocol: Cells were grown on YPD at 37°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: QuantSeq 3-prime RNA-Seq


title: PC9_LeptoM_FL_1


title: PAS whole body JEC21 30Srep 1

value: stationnary phase 30 degrees C


title: miRNA TS3


title: miRNA TS2


title: miRNA TS1


title: RNA whole body JEC21 37E rep 3

extract_protocol: Cells were grown on YPD at 37°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: RNA-Seq


title: DNA JEC21 37E rep 3

extract_protocol: Cells were grown on YPD at 37°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: DNA-Seq


title: TSS whole body KN99alpha 37S rep 3

data_processing:
Library strategy: TSS-Seq
For TSS analysis we kept only the reads containing both the oligo 3665 (AGATCGGAAGAGCACACGTCTGAAC) and the 11NCGCCGCGNNN tag. These sequenced were removed using cutadapt/1.18 and the trimmed reads were mapped to the Cryptococcus neoformans H99 genome using Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). Wig files were constructed using the 5’ extremities of each reads. Their coverage was normalized using the normalization factor used for spiked in RNA-Seq.

organism: Cryptococcus neoformans

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: stationnary phase 37 degrees C

value: Sample 12


title: PAS whole body KN99alpha 37S rep 3

data_processing: QuantSeq 3’mRNA-Seq reads containing both the Sequencing and indexing primers (Lexogen) were sorted. The reads were then cleaned using cutadapt/1.18 and trimmed for polyA sequence in their 3’end. PolyA untrimmed and trimmed reads were mapped to the adapted Cryptococcus neoformans H99 genome with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). To eliminate the polyadenylated reads corresponding to genomic polyA stretches, we considered only the reads that aligned to the genomes only after polyA trimming. The 3’end position of these reads were considered as potential PAS. Wig files were constructed using the 3’ extremities of these reads Their coverage was normalized using the normalization alpha factor used for spiked in RNA-Seq.

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).


title: PAS whole body JEC21 37E rep 2

value: Sample 17


title: RNA whole body JEC21 37E rep 2


title: RNA whole body KN99alpha 37S rep 3

data_processing: The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. neoformans H99 and to the S. cerevisiae S288C genomes with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). RNA Reads count were evaluated using HTSeq/0.6.1 (intersection-nonempty) normalized using the S. cerevisiae DNA/RNA spike in alpha factor and used to calculate FPKM values.

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: DNA JEC21 37E rep 2


title: miRNA TS4

value: 2,000 plaque-forming units (PFU) of the MDV-GA strain


title: TSS whole body KN99alpha 37S rep 2

value: TSS-Seq

value: Sample 11


title: DNA KN99alpha 37S rep 3

data_processing:
Library strategy: DNA-Seq
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. neoformans H99 and to the S. cerevisiae S288C  genomes with Bowtie2 using default settings. For each sample, total DNA and RNA reads counts aligned to each organism were used to calculate an alpha normalization factor. The file with the alpha noramlization factors is available on the series record: alpha_factor.txt

extract_protocol: Cells were grown on YPD at 37°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: PAS whole body KN99alpha 37S rep 1

value: Sample 10


title: TSS whole body JEC21 37E rep 1

data_processing:
Library strategy: TSS-Seq
For TSS analysis we kept only the reads containing both the oligo 3665 (AGATCGGAAGAGCACACGTCTGAAC) and the 11NCGCCGCGNNN tag. These sequenced were removed using cutadapt/1.18 and the trimmed reads were mapped to the Cryptococcus deneoformans JEC21 genome using Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). Wig files were constructed using the 5’ extremities of each reads. Their coverage was normalized using the normalization factor used for spiked in RNA-Seq.

value: Sample 16


title: PAS whole body JEC21 37E rep 1


title: RNA whole body KN99alpha 37S rep 2


title: RNA whole body JEC21 37E rep 1


title: TSS whole body KN99alpha 37S rep 1


title: PAS whole body JEC21 30E rep 3

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: exponential phase 30 degrees C

value: Sample 15


title: DNA KN99alpha 37S rep 1


title: RNA whole body JEC21 30E rep 3

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: TSS whole body JEC21 30E rep 3

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: PAS whole body KN99alpha 30S  rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: Sample 9


title: DNA JEC21 30E rep 3

data_processing:
Library strategy: DNA-Seq
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. deneoformans JEC21 and to the S. cerevisiae S288C  genomes with Bowtie2 using default settings. For each sample, total DNA and RNA reads counts aligned to each organism were used to calculate an alpha normalization factor. The file with the alpha noramlization factors is available on the series record: alpha_factor.txt

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: TSS whole body KN99alpha 30S rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: PAS whole body JEC21 30E rep 2

data_processing: QuantSeq 3’mRNA-Seq reads containing both the Sequencing and indexing primers (Lexogen) were sorted. The reads were then cleaned using cutadapt/1.18 and trimmed for polyA sequence in their 3’end. PolyA untrimmed and trimmed reads were mapped to the adapted Cryptococcus deneoformans JEC21 genome with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). To eliminate the polyadenylated reads corresponding to genomic polyA stretches, we considered only the reads that aligned to the genomes only after polyA trimming. The 3’end position of these reads were considered as potential PAS. Wig files were constructed using the 3’ extremities of these reads Their coverage was normalized using the normalization alpha factor used for spiked in RNA-Seq.

value: Sample 14


title: TSS whole body JEC21 37E rep 2

value: exponential phase 37 degrees C


title: TSS whole body JEC21 30E rep 2


title: RNA whole body JEC21 30E rep 2


title: PAS whole body KN99alpha 37S rep 2

value: QuantSeq 3-prime RNA-Seq


title: RNA whole body KN99alpha 30S rep 3

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: stationnary phase 30 degrees C


title: PAS whole body KN99alpha 3S rep 2

value: Sample 8


title: DNA JEC21 30E rep 2

value: DNA-Seq


title: DNA KN99alpha 37S rep 2

value: stationnary phase 37 degrees C


title: TSS whole body KN99alpha 3S rep 2


title: PAS whole body JEC21 30E rep 1

value: Sample 13


title: DNA JEC21 37E rep 1


title: RNA whole body KN99alpha 30S rep 2

value: RNA-Seq


title: DNA KN99alpha 30S rep 2

extract_protocol: Cells were grown on YPD at 30°C in stationary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).


title: RNA whole body JEC21 30E rep 1


title: RNA whole body KN99alpha 37S rep 1


title: PAS whole body KN99alpha 30Srep 1

value: Sample 7


title: DNA JEC21 30E rep 1


title: RNA whole body KN99alpha 30S rep 1


title: PAS whole body KN99alpha 37E rep 3

value: Sample 6


title: TSS whole body KN99alpha 30S rep 1

value: TSS-Seq


title: TSS whole body KN99alpha 37E rep 3


title: DNA KN99alpha 30S rep 1


title: RNA whole body KN99alpha 37E rep 3


title: RNA whole body KN99alpha 37E rep 2

value: Sample 5


title: DNA KN99alpha 30S rep 3


title: PAS whole body KN99alpha 37E rep 2


title: DNA KN99alpha 37E rep 3


title: DNA KN99alpha 37E rep 2


title: TSS whole body KN99alpha 37E rep 2


title: PAS whole body KN99alpha 37E rep 1

value: Sample 4


title: TSS whole body KN99alpha 37E rep 1


title: DNA KN99alpha 37E rep 1


title: RNA whole body KN99alpha 37E rep 1


title: PAS whole body KN99alpha 30E rep 3

value: exponential phase 30 degrees C

value: Sample 3


title: TSS whole body JEC21 30E rep 1


title: TSS whole body KN99alpha 30E rep 3


title: DNA KN99alpha 30E rep 3


title: RNA whole body KN99alpha 30E rep 3


title: PAS whole body KN99alpha 30E rep 2

value: Sample 2


title: RNA whole body KN99alpha 30E rep 2


title: DNA KN99alpha 30E rep 2


title: TSS whole body KN99alpha 30E rep 1

value: Sample 1


title: PAS whole body KN99alpha 30E rep 1


title: RNA whole body KN99alpha 30E rep 1


title: DNA KN99alpha 30E rep 1


title: MS6_Sample_97

city: Odense M

first: Tobias

last: Frisch

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description: processed data file: countMatrix.txt

data_processing:
Sequenced reads were trimmed with trimmomatic: (TRIM:2:30:10 LEADING:20 TRAILING:20 SLIDING:4:20 TRAILING:20 MIN:17)
Mapping with STAR Aligner (version 2.5.3a).
Read counting with HTSeq-count (strict).
EdgeR was used to train generalized linear models to find differentially expressed genes while correcting for age, sex and sample distribution.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: countMatrix.txt contains read counts for every gene (row) and every sample (column).
Supplementary_files_format_and_content: Tab-separated text files with the results from EdgeR.

extract_protocol:
miRNeasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA library prep kit (Illumina).
Total RNA seq (deletion of ribosomal RNA).

tag: diagnosis

value: Multiple sclerosis

value: Brain

tag: lesion type

value: Remyelinating (RL)

tag: individual


title: MS9_Sample_93

description: processed data file: countMatrix.txt

tag: tissue

value: Inactive (IL)


title: MS9_Sample_96

description: processed data file: countMatrix.txt


title: MS6_Sample_95

description: processed data file: countMatrix.txt


title: MS5_Sample_94

description: processed data file: countMatrix.txt

value: Normal appearing white matter (NAWM)


title: MS9_Sample_98

description: processed data file: countMatrix.txt


title: F-WT2

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

institute: IBDM / CNRS

description:
C-LTMR Female WT
all_mm10_exon_counts.txt
DGE_female_FDR5_logFC_ordered.txt

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Mapping to mm10 genome using subread-align 1.6.4 using default paired end parameters
Read counts mapping to exons performed using featureCounts of the Subread package 1.6.4
Differential gene expression analyses performed using DESeq2 1.14.1
Genome_build: mm10
Supplementary_files_format_and_content: tab separated values of mm10 exon counts and differentially expressed genes of KO vs WT

source_name: C-LTMR RNA from female wild type mice

extract_protocol:
RNA was extracted from FACS-sorted C-LTMRs (GFP+) using RNeasy Micro Kit (Quiagen) following the manufactures protocol.RNA quality was assessed using the RNA Agilent 2100 Bioanalyzer system (RNA Pico chips).
Full length cDNA were generated from 500 pg of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 13 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: Female

tag: genotype

value: Wild Type


title: MS9_Sample_92

description: processed data file: countMatrix.txt


title: F-WT1


title: F-KO2

description:
C-LTMR Female bhlha9 KO
all_mm10_exon_counts.txt
DGE_female_FDR5_logFC_ordered.txt

source_name: C-LTMR RNA from female bhlha9 KO mice

value: bhlha9 KO


title: M-WT2

description:
C-LTMR Male WT
all_mm10_exon_counts.txt
DGE_male_FDR5_logFC_ordered.txt

source_name: C-LTMR RNA from male wild type mice

value: Male


title: TSS whole body KN99alpha 30E rep 2

tag: strain


title: MS6_Sample_89

description: processed data file: countMatrix.txt

value: Active (AL)


title: MS2_Sample_88

description: processed data file: countMatrix.txt


title: MS4_Sample_90

description: processed data file: countMatrix.txt


title: M-KO1

description:
C-LTMR Male bhlha9 KO
all_mm10_exon_counts.txt
DGE_male_FDR5_logFC_ordered.txt

source_name: C-LTMR RNA from male bhlha9 KO mice


title: F-KO1


title: MS9_Sample_87

description: processed data file: countMatrix.txt


title: M-KO2


title: left ventricular_Control rats_rep1

city: Shanghai

first: Jun

last: Zhang

address: No.100 of Guilin Road

institute: Shanghai Normal University

description:
physiological left ventricular hypertrophy
Experimental animals in control group were female and commercially-available Wistar rats (SLAC, Shanghai, China).

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change.

organism: Rattus norvegicus

source_name: left ventricular_Control rats

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: All rats (200 ± 20 g, n = 32) were fed a standard diet, exposed to a 12-h light–12-h dark cycle, and maintained in a constant room temperature (22 ± 2°C) and humidity (50 ± 10%) .

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: For 10 weeks, from Monday to Friday, the rats in the EX group completed a 1-h swimming exercise schedule. The exercise training was performed by placing the rats in a swimming pool (150 cm × 60 cm × 70 cm) filled with warm water to a depth of 60 cm. The pool was divided by plastic barriers into eight lanes. The water temperature was maintained at 31 ± 1°C.

value: Wistar

value: female

value: control

value: left ventricular


title: 3T3_H3K27ac_control input rep 2

city: Austin

first: Steven

last: Vokes

state: Texas

address: 2500 Speedway, Stop A4800

department: Department of Molecular Biosciences, Institute for Cellular & Molecular Biology

institute: The University of Texas at Austin

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using Cisgenome with default parameters.  When available, Input data was incorporated in the peak calling.
For differential H3K27ac and H3K4me2 peak analysis and peak classifications, Cisgenome was used to call peaks for Wild Type and Shh-/- (or control and Purmorphamine treated NIH3T3 cells) respectively.  For the union of peaks from Wild Type and Shh-/-, we calculated the number of H3K27ac reads for WT H3K27ac, WT input, Shh-/- H3K27ac and Shh-/- input samples that overlap with each of the union peaks. The read counts are then divided by library size and log2 transformed after adding a pseudo count of 1 to generate the normalized read counts. We use Limma [2] to perform differential analysis in order to independently compare WT H3K27ac vs WT input, Shh-/- H3K27ac vs Shh-/- input, and WT H3K27ac vs Shh-/- H3K27ac to obtain adjusted p-values.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files: aligned sequencing reads to mm10 genome using Bowtie2 and converted to bedgraph
Supplementary_files_format_and_content: txt files: peaks called by Cisgenome

source_name: NIH3T3 cell culture

extract_protocol:
Cells were fixed for 15 minutes at room temperature with 1% formaldehyde then lysed.  After cell lysis, chromatin was sheared in shearing buffer containing 0.25% SDS using a Covaris S2 focused ultrasonicator.   Sheared chromatin was incubated with antibody coated dynabead preparations (1ug antibody with 20ul beads) overnight.  Beads were washed 5 times with RIPA buffer (1% NP40, 0.7% Sodium Deoxycholate, 1mM EDTA pH8, 50mM Hepes-KOH pH7.5, 2% w/v Lithium Chloride) and then eluted at 70°C for 15 minutes in elution buffer (50mM TRIS pH 8, 10mM EDTA  pH 8, 1% SDS).  Crosslinks were reversed overnight at 70°C and chromatin was purified and concentrated by phenol chloroform extraction and EtOH precipitation.
One third of each ChIP sample was used for library preparation.  Library preparation was done according to the Broad Pond method, (PMCID: PMC3091298) using the NEBNext library preparation kit (NEB E6040L) using non-standard 15 cycles of PCR amplification.

treatment_protocol: NIH3T3 cells were grown in 60 mm plates at 37°C and 5% CO2 in DMEM (ATCC 30-2002) supplemented with 10% Calf Serum (ATCC 30-2030), 1x L-Glutamine (Gibco 25030-08), 100 uM non-essential amino acids (NEAA from Gibco 11140-050), and 50 ug/mL Pen/Strep (Gibco 15140-122).  For Hedgehog pathway stimulation, cells were switched to low serum media (0.5% calf serum) 24 hours prior to treatment with 400nM Purmorphamine (Stemgent cat # 04-0009).  Cells were incubated in the presence of Purmorphamine for 48 hours then collected for ChIP.

tag: strain background

tag: tissue/chip rxn

value: 1x10^6 cells/ChIP

tag: chip antibody

tag: genotype or treatment

value: 48 hours LIF + DMSO control


title: left ventricular_Control rats_rep2


title: MS7_Sample_86

description: processed data file: countMatrix.txt


title: 3T3_H3K27ac_control input rep 1

tag: age


title: MS4_Sample_85

description: processed data file: countMatrix.txt


title: left ventricular_Exercise rats_rep2

description:
physiological left ventricular hypertrophy
Experimental animals in Ex group were female and commercially-available Wistar rats (SLAC, Shanghai, China). For 10 weeks, from Monday to Friday, the rats in the EX group completed a 1-h swimming exercise schedule.

source_name: left ventricular_Exercise rats

value: Exercise


title: left ventricular_Exercise rats_rep1


title: MS9_Sample_84

description: processed data file: countMatrix.txt

value: Multiple sclerosis


title: MS7_Sample_91

description: processed data file: countMatrix.txt

value: Brain


title: MS9_Sample_83

description: processed data file: countMatrix.txt


title: 3T3_H3K27ac_control rep 1

description: NIH3T3_H3K27ac_control_peaks.narrowPeak.gz

value: H3K27ac (abcam ab4729)


title: 3T3_H3K27ac_pur input rep 2

value: 48 hours LIF + 400 nm purmorphamine


title: 3T3_H3K27ac_pur input rep 1


title: MS2_Sample_80

description: processed data file: countMatrix.txt

value: Inactive (IL)


title: M-WT1


title: 3T3_H3K27ac_control rep 2


title: 3T3_H3K27ac_pur rep 1


title: MS10_Sample_79

description: processed data file: countMatrix.txt


title: 3T3_H3K27ac_pur rep 2


title: MS2_Sample_78

description: processed data file: countMatrix.txt


title: MS1_Sample_76

description: processed data file: countMatrix.txt


title: MS2_Sample_75

description: processed data file: countMatrix.txt


title: MS2_Sample_77

description: processed data file: countMatrix.txt


title: Shh-/-_H3K4me2 input

source_name: forelimb bud

treatment_protocol: limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.

value: Swiss Webster

value: ~400,000 cells/ChIP

value: Shh-/-


title: Shh-/-_H3K4me2 rep 2

value: H3K4me2 (millipore 07-030)


title: Shh-/-_H3K4me2 rep 1


title: WT_H3K4me2 input

value: wild type


title: MS1_Sample_74

description: processed data file: countMatrix.txt

value: Active (AL)


title: WT_H3K4me2 rep 2


title: WT_H3K4me2 rep 1


title: MS10_Sample_73

description: processed data file: countMatrix.txt


title: MS6_Sample_72

description: processed data file: countMatrix.txt


title: MS7_Sample_82

description: processed data file: countMatrix.txt

value: Remyelinating (RL)


title: MS3_Sample_81

description: processed data file: countMatrix.txt


title: MS6_Sample_70

description: processed data file: countMatrix.txt


title: MS2_Sample_69

description: processed data file: countMatrix.txt


title: MS1_Sample_71

description: processed data file: countMatrix.txt


title: MS5_Sample_68

description: processed data file: countMatrix.txt


title: MS6_Sample_67

description: processed data file: countMatrix.txt


title: NC_ISN2_Bioreplicate_3

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: sensory neurons induced by short term NGN2-BRN3A expression in iPSC-derived nueral crest (NC_iSN2)

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Raw sequence files generated per library were quality inspected using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:15) and low quality calls (TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:15) using the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic). Surviving intact pairs of reads per library were then reference mapped against the current instance of the human genome (GRCh38.82) using the RNA-Seq tool supported in v11 of the CLCbio Genomics Workbench (www.qiagenbioinformatics.com). After, expression per known annotated gene (Homo_sapiens.GRCh38.82.chr.gtf) were enumerated and exported in Transcripts Per Kilobase Million (TPM) units.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: One tab-delimited text file per sequenced library are provided describing the observed gene expression in Transcript Per Kilobase Million (TPM) units.

growth_protocol: The hDRG was purchased as a pooled RNA sample (Clontech, 636150). The iPSC, iSN, NC-iSN1, and NC-iSN2 samples were all derived from the WTC11 control iPSCs, an iPSC line generated previously (Miyaoka et al., 2014). iPSCs were maintained on tissue culture-treated polystyrene plates with Matrigel (Corning, 354277) in E8 medium (Thermo Fisher, A1517001). The medium was changed daily and the iPSCs were split every 4 – 6 days using Accutase (Invitrogen, A1110501). The rho kinase (ROCK) inhibitor 10 µM Y-27632 (Tocris, 1254) was included in the medium on the day of passaging. To generate iSN samples, on day 0 iPSCs were dissociated with Accutase, and 20,000 cells/cm2 were plated on Matrigel-coated dishes in neural differentiation medium (NDM) supplemented with 10 µM Y-27632 and 2µg/mL doxycycline (Clontech, 631311). NDM (all from Invitrogen) consisted of equal parts DMEM/F12 (11330032) and Neurobasal medium (21103049), containing GlutaMAX (35050061), B27 (17504044), and N2 (17502048). The medium could be optionally changed on day 1 to remove Y-27632, but is otherwise the same composition. On day 2, the cells were dissociated with Accutase, and 50,000 cells/cm2 were seeded on plates coated with 0.1% polyethylenimine (Sigma, P3143) and 15 µg/mL laminin (Invitrogen, 23017015) in NDM with doxycycline. The medium was changed every other day through day 8, after which only half volume medium changes were made. If undifferentiated cells persist, 20 µM BrdU could be optionally added on day 4 to eliminate dividing cells and achieve a pure neuronal culture. Starting on day 8 onward, neurotrophic factors (NTFs) (all R&D Systems) were added to the NDM, consisting of BDNF (248BD025), GDNF (212GD010), β-NGF (256GF100), and NT-3 (267N3025), each at 10 ng/mL. Doxycycline was discontinued starting on day 14. Cells were collected for analysis on day 21. To generate NC-iSN1 and NC-iSN2 samples, the neural crest differentiation was a modified form of previous protocols (Bajpai et al., 2010; Schrenk-Siemens et al., 2015). On day -1 iPSCs were dissociated with Accutase and seeded in an Aggrewell 400 plate for spheroid formation (STEMCELL Technologies, 34411) according to manufacturer’s instructions in E8 medium with 10 µM Y-27632. On day 0, spheroids were transferred to uncoated tissue culture-treated dishes in NDM with 20 µg/mL bFGF (R&D Systems, 233FB025), 20 µg/mL EGF (R&D Systems, 236EG200), and 10 µM of the TGF-β receptor ALK4/5/7 inhibitor SB431542 (Tocris, 1614). This medium was changed every other day. SB431542 was discontinued starting on day 6. After 1-2 weeks, spheroids spontaneously attached to the culture surface and neural crest cells migrated outward. All spheroids were manually removed, and the neural crest cells were re-plated at 40,000 cells/cm2 on polyethylenimine and laminin-coated dishes in NDM – this is denoted as day 0 of neural induction. For NC-iSN1s, doxycycline was added from day 0 until day 14, and NTFs were supplemented beginning on day 8. For NC-iSN2s, doxycycline was added on day 0 for 24 hours. NTFs and 50 nM retinoic acid (Sigma, R2625) were supplemented from day 0 onwards. On day 2, the neural crest cells were re-plated for the final time onto polyethylenimine and laminin-coated dishes at 50,000 cells/cm2. Medium was changed every other day, and half medium changes were made after day 8. Cells were collected for analysis on day 21.

extract_protocol:
RNA was extracted from iPSCs and iSNs using TRIzol (Thermo Fisher, 15596018) and chloroform and purified with an miRNeasy kit (Qiagen, 217004) following manufacturer’s instructions. Total RNA quantity and integrity were assessed on a Bioanalyzer (Agilent).
For the iSN samples, 500 ng total RNA was used in conjunction with the TruSeq Stranded Total RNA Library Prep kit (Illumina) to prepare libraries. The library quality was checked via Bioanalyzer and quantitated by Qubit (Thermo Fisher). Equimolar quantities from each library were pooled and run on a NextSeq 500/550 High Output kit v2.5 (150 cycles) (Illumina, 20024907) at approximately 40 million paired-end reads per sample. For the hDRG (Clontech 636150) and iPSCs, sequencing libraries were constructed from 100 ng – 500 ng of total RNA using the TruSeq Stranded Total RNA kit (Illumina) with Ribo-Zero following the manufacturer’s instructions. The fragment size of the libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentrations were determined using Qubit instrument (Thermo Fisher). The libraries were loaded onto the Illumina HiSeq 3000 for 2 x 75 base pair paired-end read sequencing at approximately 40 million reads per sample.

tag: biological replicate

tag: sample group

tag: donor

value: X

tag: gender

value: Male

tag: race

value: Japanese


title: Vaginal mucosa 1

city: Copenhagen

first: Lauge Hjorth

last: Mikkelsen

address: Frederik V's Vej 11, 1st Floor

department: Pathology

institute: Copenhagen University Hospital

description: FFPE tissue

hyb_protocol: NanoString Standard protocol. 100 ng RNA greater than 200 nt length.

scan_protocol: NanoString nCounter SPRINT profiler

data_processing: NanoString nsolver ver. 4, Standard normalization

label: NanoString

source_name: Vaginal mucosa 1

label_protocol: NanoString Standard protocol

extract_protocol: miRNeasy FFPE Kit, Qiagen, Standard protocol

tag: disease

value: normal tissue


title: Vaginal melanoma 9

description: FFPE tissue

source_name: Vaginal melanoma 9

value: Vaginal melanoma


title: Vaginal mucosa 2

description: FFPE tissue

source_name: Vaginal mucosa 2


title: Vaginal melanoma 10

description: FFPE tissue

source_name: Vaginal melanoma 10


title: Vaginal melanoma 7

description: FFPE tissue

source_name: Vaginal melanoma 7


title: NC_ISN2_Bioreplicate_2

source_name: sensory neurons induced by short term NGN2-BRN3A expression in iPSC-derived nueral crest (NC_iSN2)


title: C3_Sample_63

description: processed data file: countMatrix.txt

tag: diagnosis

value: Control

value: White matter (WM)


title: MS5_Sample_64

description: processed data file: countMatrix.txt

value: Multiple sclerosis

value: Brain

tag: lesion type


title: MS4_Sample_65

description: processed data file: countMatrix.txt

tag: individual


title: Vaginal melanoma 6

description: FFPE tissue

source_name: Vaginal melanoma 6


title: Vaginal melanoma 8

description: FFPE tissue

source_name: Vaginal melanoma 8


title: NC_ISN2_Bioreplicate_1


title: NC_iSN1_Bioreplicate_3

description: sensory neurons induced by long term NGN2-BRN3A expression in iPSC-derived neural crest (NC_iSN1)


title: Vaginal melanoma 5

description: FFPE tissue

source_name: Vaginal melanoma 5


title: Vaginal melanoma 4

description: FFPE tissue

source_name: Vaginal melanoma 4


title: C2_Sample_62

description: processed data file: countMatrix.txt

tag: tissue


title: NC_iSN1_Bioreplicate_2

source_name: sensory neurons induced by long term NGN2-BRN3A expression in iPSC-derived neural crest (NC_iSN1)


title: NC_iSN1_Bioreplicate_1


title: C2_Sample_61

description: processed data file: countMatrix.txt


title: C1_Sample_60

description: processed data file: countMatrix.txt


title: Vaginal melanoma 2

description: FFPE tissue

source_name: Vaginal melanoma 2


title: MS6_Sample_66

description: processed data file: countMatrix.txt


title: Vaginal melanoma 1

description: FFPE tissue

source_name: Vaginal melanoma 1


title: Rectal mucosa 2

description: FFPE tissue

source_name: Rectal mucosa 2


title: C2_Sample_58

description: processed data file: countMatrix.txt


title: C1_Sample_59

description: processed data file: countMatrix.txt


title: C3_Sample_55

description: processed data file: countMatrix.txt


title: Vaginal melanoma 3

description: FFPE tissue

source_name: Vaginal melanoma 3


title: C1_Sample_57

description: processed data file: countMatrix.txt


title: iSN_Bioreplicate_1

description: sensory neurons induced by NGN2-BRN3A expression in iPSCs (iSN)

value: iSN


title: iSN_Bioreplicate_2

source_name: sensory neurons induced by NGN2-BRN3A expression in iPSCs (iSN)


title: C1_Sample_56

description: processed data file: countMatrix.txt


title: iSN_Bioreplicate_3


title: Rectal melanoma 7

description: FFPE tissue

source_name: Rectal melanoma 7

value: Rectal melanoma


title: Rectal melanoma 8

description: FFPE tissue

source_name: Rectal melanoma 8


title: Rectal melanoma 6

description: FFPE tissue

source_name: Rectal melanoma 6


title: iPSC_Bioreplicate_2

description: undifferentiated induced pluripotent stem cells (iPSC)

value: iPSC


title: iPSC_Bioreplicate_3

source_name: undifferentiated induced pluripotent stem cells (iPSC)


title: Rectal melanoma 5

description: FFPE tissue

source_name: Rectal melanoma 5


title: hDRG_Bioreplicate_1

description: human Dorsal Root Ganglia (hDRG)

source_name: human Dorsal Root Ganglia (hDRG)

value: hDRG

value: Pool (Clontech, catalog # 636150)

value: pooled male and female

value: Caucasian


title: Rectal melanoma 4

description: FFPE tissue

source_name: Rectal melanoma 4


title: Rectal mucosa 1

description: FFPE tissue

source_name: Rectal mucosa 1


title: iPSC_Bioreplicate_1


title: C3_Sample_53

description: processed data file: countMatrix.txt


title: BkF_72_hpf

city: Corvallis

first: Robyn

last: Tanguay

state: OR

address: 28645 East Highway 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

data_processing:
Base-calling was performed using the Illumina HiSeq 2500 system.
Sequences were filtered according to Phred scores and analyzed for quality using FastQC.
Sequences were trimmed using Trimmomatic.
Reads were aligned with Salmon using its quasi-mapping alignment method.
Transcript abundances were aggregated to gene level counts using tximport.
Normalized counts were generated using DESeq2.
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files contain mean normalized counts respective to the indicated condition.

organism: Danio rerio

source_name: Distal trunk tissue

growth_protocol: Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf, they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure, wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.

extract_protocol:
Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct-zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol.
Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Static chemical exposures (1% DMSO or 12 μM BkF final concentrations) started at 6-8 hpf and were performed using a Hewlett-Packard D500e chemical dispenser. After covering with parafilm and foil, plates were placed on an automated shaker overnight at 28.5˚C.

value: 72 hpf

tag: treatment

value: 12 μM Benzo[k]fluoranthene


title: MS4_Sample_52

description: processed data file: countMatrix.txt

value: Normal appearing white matter (NAWM)


title: C4_Sample_54

description: processed data file: countMatrix.txt


title: Rectal melanoma 2

description: FFPE tissue

source_name: Rectal melanoma 2


title: MS6_Sample_51

description: processed data file: countMatrix.txt


title: BkF_48_hpf

value: 48 hpf


title: MS5_Sample_50

description: processed data file: countMatrix.txt


title: Control_96_hpf

value: 96 hpf

value: 1% DMSO


title: BkF_96_hpf


title: BkF_60_hpf

value: 60 hpf


title: Control_72_hpf


title: Rectal melanoma 3

description: FFPE tissue

source_name: Rectal melanoma 3


title: MS8_Sample_49

description: processed data file: countMatrix.txt


title: MS9_Sample_48

description: processed data file: countMatrix.txt


title: MS6_Sample_47

description: processed data file: countMatrix.txt


title: Control_48_hpf


title: MS8_Sample_46

description: processed data file: countMatrix.txt


title: Control_60_hpf


title: MS1_Sample_45

description: processed data file: countMatrix.txt


title: LTH_24h_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: Biological repeat 2 for LTH at 24 hpi with M.oryzae infection

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  and Qvalue <= 0.05
Reads were mapped using BWA
SAM files were then used to identify circRNAs with CIRI2
Reads were mapped to circRNAs using NovoAlign for calculating back-spliced reads
Genome_build: IRGSP v5.0
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Oryza sativa

source_name: leaves of three-week-old seedlings

growth_protocol: All rice plants were grown at 26 ± 2 ℃ and 70% relative humidity under 12 h light : 12 darkness. M. oryzae strains (NC-24, NC-34, B9, Zhong8-10-14, 97-95-1, F1, NC-14, B13 and E37) were cultured in complete media at 28 ℃ under 12 h light : 12 darkness for two weeks

extract_protocol:
Total RNA of each sample was isolated using TRIzol (Ambion) according to the manufacturer’s instructions.
For each sample, 25 µg of total RNA was used for circRNA-seq library preparation. Total RNA was depleted for ribosomal RNAs using the RiboMinus kit. The remaining RNAs were iron fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and subjected to PCR amplification. PCR products corresponding to 300-500 bp were purified and quantified, and then stored at -80 ℃ until used for sequencing

treatment_protocol: Spores of each strain were mixed as the inoculum, and sprayed onto three-week-old seedlings of LTH and IR25. Leaves were collected at 0, 12, 24 hour post inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80 ℃ until use

tag: cultivar

value: LTH

tag: genotype/variation

value: blast-susceptible

tag: developmental stage

value: three-week-old seedlings

value: leaf tissue


title: FBXL19fl_RA_TAM_rep2_NatInput

city: Oxford

first: Angelika

last: Feldmann

state: England

address: South Parks Road

institute: University of Oxford, Department of Biochemistry

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
To internally calibrated cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells) to each experimental sample. For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample. To account for any variation in spike-in cell mixing in different biological replicates, the downsampling factors were additionally corrected using the ratio of dm6/mm10 total read counts in corresponding Input samples.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
Metaprofile visualization was carried out using the Deeptools (Ramirez et al., 2016) software and the commands i) computeMatrix reference-point with the option --referencePoint center and ii) plotHeatmap.
ChIP-seq enrichments were quantified from bedgraph files using the annotatePeaks.pl script from HOMER (Heinz et al., 2010). Log2 fold changes between samples were calculated following the addition of a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq profiles

organism:
Drosophila melanogaster
Mus musculus

source_name: mESCs_tamoxifen-treated (96hr OHT),  retinoic-acid treated (72hr RA)_input

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For native cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following tamoxifen treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitors (Sigma)). Each sample was then incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform in biological duplicate.

treatment_protocol: To induce conditional removal of FBXL19 CxxC domain, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 96 hours. To induce RA-differentiation mouse ES cells were treated with 1uM retinoic acid (RA) for 72 hours.

tag: cell type

value: Mouse embryonic stem cells (mESCs)

tag: genotype/vairation

value: Fbxl19fl; inducible conditional removal of FBXL19 CxxC domain

tag: replicate

tag: treatment agent

value: tamoxifen (OHT), retinoic acid (RA)

tag: treatment time point

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: chip antibody

tag: chip antibody info.


title: FBXL19fl_RA_TAM_rep1_NatInput


title: LTH_24h_1

description: Biological repeat 1 for LTH at 24 hpi with M.oryzae infection


title: MS3_Sample_44

description: processed data file: countMatrix.txt

tag: diagnosis

value: Multiple sclerosis

value: Brain


title: LTH_12h_2

description: Biological repeat 2 for LTH at 12 hpi with M.oryzae infection


title: MS1_Sample_43

description: processed data file: countMatrix.txt

tag: lesion type


title: Sinonasal normal mucosa 2

description: FFPE tissue

source_name: Sinonasal normal mucosa 2

tag: disease

value: normal tissue


title: Sinonasal melanoma 9

description: FFPE tissue

source_name: Sinonasal melanoma 9

value: Sinonasal melanoma


title: Rectal melanoma 1

description: FFPE tissue

source_name: Rectal melanoma 1

value: Rectal melanoma


title: Sinonasal normal mucosa 1

description: FFPE tissue

source_name: Sinonasal normal mucosa 1


title: Sinonasal melanoma 10

description: FFPE tissue

source_name: Sinonasal melanoma 10


title: Sinonasal melanoma 6

description: FFPE tissue

source_name: Sinonasal melanoma 6


title: Sinonasal melanoma 8

description: FFPE tissue

source_name: Sinonasal melanoma 8


title: Sinonasal melanoma 7

description: FFPE tissue

source_name: Sinonasal melanoma 7


title: FBXL19fl_RA_UNT_rep2_NatInput

source_name: mESCs_control, retinoic-acid treated (72hr RA)_input

value: retinoic acid (RA)

value: 72 hr


title: FBXL19fl_RA_UNT_rep1_NatInput


title: LTH_12h_1

description: Biological repeat 1 for LTH at 12 hpi with M.oryzae infection

tag: tissue


title: MS4_Sample_42

description: processed data file: countMatrix.txt

value: Normal appearing white matter (NAWM)

tag: individual


title: Sinonasal melanoma 5

description: FFPE tissue

source_name: Sinonasal melanoma 5


title: LTH_0h_2

description: Biological repeat 2 for LTH without M.oryzae infection

tag: cultivar


title: MS3_Sample_41

description: processed data file: countMatrix.txt


title: FBXL19fl_ES_TAM_rep1_NatInput

value: tamoxifen (OHT)

value: 96 hr


title: LTH_0h_1

description: Biological repeat 1 for LTH without M.oryzae infection

value: LTH

tag: genotype/variation

value: blast-susceptible


title: MS8_Sample_40

description: processed data file: countMatrix.txt

value: Chronic active (CA)


title: FBXL19fl_ES_TAM_rep2_NatInput

value: Mouse embryonic stem cells (mESCs)


title: FBXL19fl_ES_UNT_rep2_NatInput

source_name: mESCs_untreated control_input

value: Fbxl19fl; inducible conditional removal of FBXL19 CxxC domain

value: 0 hr


title: Sinonasal melanoma 3

description: FFPE tissue

source_name: Sinonasal melanoma 3


title: Sinonasal melanoma 4

description: FFPE tissue

source_name: Sinonasal melanoma 4


title: IR25_24h_2

description: Biological repeat 2 for IR25 at 24 hpi with M.oryzae infection

value: blast-resistant

tag: developmental stage

value: three-week-old seedlings

value: leaf tissue


title: FBXL19fl_ES_UNT_rep1_NatInput

tag: cell type

value: Drosophila melanogaster


title: MS10_Sample_39

description: processed data file: countMatrix.txt

value: Multiple sclerosis

value: Brain


title: Sinonasal melanoma 2

description: FFPE tissue

source_name: Sinonasal melanoma 2

value: Sinonasal melanoma


title: IR25_12h_2

description: Biological repeat 2 for IR25 at 12 hpi with M.oryzae infection


title: Sinonasal melanoma 1

description: FFPE tissue

source_name: Sinonasal melanoma 1


title: MS8_Sample_37

description: processed data file: countMatrix.txt


title: MS6_Sample_38

description: processed data file: countMatrix.txt


title: FBXL19fl_RA_TAM_rep2_ChIP_H3K27ac

source_name: mESCs_tamoxifen-treated (96hr OHT),  retinoic-acid treated (72hr RA), H3K27ac ChIP-Seq

tag: genotype/vairation

value: tamoxifen (OHT), retinoic acid (RA)

value: Cell Signaling Technology(#8173 )


title: Conjunctival normal 2

description: FFPE tissue

source_name: Conjunctival normal 2

value: normal tissue


title: IR25_24h_1

description: Biological repeat 1 for IR25 at 24 hpi with M.oryzae infection

source_name: leaves of three-week-old seedlings


title: FBXL19fl_RA_TAM_rep1_ChIP_H3K27ac

tag: replicate


title: IR25_12h_1

description: Biological repeat 1 for IR25 at 12 hpi with M.oryzae infection


title: MS3_Sample_36

description: processed data file: countMatrix.txt


title: FBXL19fl_RA_UNT_rep2_ChIP_H3K27ac

source_name: mESCs_control, retinoic-acid treated (72hr RA), H3K27ac ChIP-Seq

tag: treatment agent

value: retinoic acid (RA)

value: 72 hr


title: IR25_0h_2

description: Biological repeat 2 for IR25 without M.oryzae infection


title: Conj. Mel 12

description: FFPE tissue

source_name: Conj. Mel 12

value: conjunctival melanomas


title: FBXL19fl_RA_UNT_rep1_ChIP_H3K27ac

tag: treatment time point


title: C4_Sample_34

description: processed data file: countMatrix.txt

value: Control

value: White matter (WM)


title: Conj. Mel 11

description: FFPE tissue

source_name: Conj. Mel 11


title: FBXL19fl_ES_TAM_rep2_ChIP_H3K27ac

source_name: mESCs_tamoxifen-treated (96hr OHT), H3K27ac ChIP-Seq

value: Mouse embryonic stem cells (mESCs)

value: Fbxl19fl; inducible conditional removal of FBXL19 CxxC domain

value: tamoxifen (OHT)

value: 96 hr

tag: spike-in reference organism


title: IR25_0h_1

description: Biological repeat 1 for IR25 without M.oryzae infection

value: blast-resistant

value: three-week-old seedlings

value: leaf tissue


title: Low Responder_Exposed to E. coli_3 hrs [JFM_93F]

city: Guelph

first: Mehdi

last: Emam

state: ON

address: 419 Gordon St

department: Pathobiology

country: Canada

institute: University of Guelph

data_processing:
Sequencing reads were filtered for quality and removing the index (universal illumina index) using Trimmomatic in the pair-end mode. Nucleotides with quality of less than 30 (in Phred score) at the beginning or the end of the reads were removed. In addition, reads shorter than 100 bp or with quality of less than 20 (in Phred score) in 5 adjacent base pair were removed from the analysis. The quality of the reads was checked by FastQC (v. 0.11.5) before and after trimming.
Clean reads were mapped to the bovine reference genome (UMD 3.1, Release 94) by using Spliced Transcripts Alignment to a Reference (STAR) v. 2.7.0a
The quantity of expression per annotated genes was calculated by using RNA-Seq by Expectation Maximization (RSEM) package (v. 1.3)
The raw count data were imported by R’ Bioconductor package “tximport” (v 1.10.1) and analyzed by DESeq2 (v. 1.22.2) by employing negative binomial GLM fitting approach. Every sample was numbered within a phenotype and consisted of two reads files, treated and control. The model term in DESeq2 was designed to calculate the differential expression in fold change (FC) between the phenotypes in the treated group after accounting for the expression level of the respective control sample
Genome_build: UMD 3.1, Release 94
Supplementary_files_format_and_content: RSEM aboundance; Gene_ID,external_gene_name,baseMean,log2 FoldChange,lfcSE,stat,pvalue,padj

organism: Bos taurus

source_name: Low Responder_Exposed to E. coli_3 hrs

growth_protocol: Blood Mononuclear Cells (BMCs) were purified based on the gradient centrifuge separation method and cultured for 2 hours in Monocyte Attachment Medium at 37 °C. Non-adherent cells were removed and the medium was replaced with AIM V® Medium in the presence of 5 ng/ml recombinant bovine Granulocyte-macrophage colony-stimulating factor and 5% CO2 for 6 days.

extract_protocol:
Briefly, 1 ml of Trizol Reagent was used to extract total RNA from 0.4E6 MDMs based on company’s recommendation.
Library construction was performed using the TruSeq Stranded mRNA Libraries Prep kit (Illumina Inc. San Diego, CA). Adapters were ligated to the ends of double-stranded cDNA and PCR amplified to create libraries.

treatment_protocol: One well of each sample was assigned as the control and the other well was exposed to PFA inactivated E. coli (MOI: 5)

tag: breed

value: Holstein

tag: Sex

value: Female

tag: lactating status

value: Lactating

tag: response to e.coli

value: Low Responder

tag: treatment

value: Exposed to E. coli

tag: time point

value: 3 hrs

value: monocyte-derived macrophages


title: C5_Sample_33

description: processed data file: countMatrix.txt

tag: diagnosis

tag: tissue

value: Brain

tag: lesion type


title: FBXL19fl_ES_TAM_rep1_ChIP_H3K27ac

value: Drosophila melanogaster

tag: spike-in cell line

tag: chip antibody

tag: chip antibody info.

value: Cell Signaling Technology(#8173 )


title: Conj. Mel 10

description: FFPE tissue

source_name: Conj. Mel 10

tag: disease

value: conjunctival melanomas


title: Conj. Mel 9

description: FFPE tissue

source_name: Conj. Mel 9


title: Conjunctival normal 1

description: FFPE tissue

source_name: Conjunctival normal 1

value: normal tissue


title: Person 7 VeinEndothelialCells Treated

type: genomic

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

scan_protocol: GenomeStudio

data_processing: R function preprocessQuantile in the minfi R package.

label: Cy3, Cy5

source_name: Person 7 VeinEndothelialCells Treated

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research).

extract_protocol: Genomic DNA of whole blood samples

treatment_protocol: Transient on-integrative reprogramming protocol optimized based on a cocktail of mRNAs expressing OCT4, SOX2, KLF4, c-MYC, LIN28 and NANOG (OSKMLN). This protocol consistently produces induced pluripotent stem cell (iPSC) colonies, regardless of age of the donors, after 12-15 daily transfections. Here we adopted a transient reprogramming protocol where OSKMLN were daily transfected for only four consecutive days.

tag: individual

tag: age

tag: cell type

value: vein endothelial cells

tag: treatmentstatus

value: Treated

tag: dnamage

tag: dnamageskinbloodclock


title: MS3_Sample_31

description: processed data file: countMatrix.txt

value: Multiple sclerosis

value: Normal appearing white matter (NAWM)


title: FBXL19fl_ES_UNT_rep2_ChIP_H3K27ac

source_name: mESCs_untreated control, H3K27ac ChIP-Seq

value: Mouse embryonic stem cells (mESCs)

tag: genotype/vairation

value: Fbxl19fl; inducible conditional removal of FBXL19 CxxC domain

tag: replicate

tag: treatment agent

tag: treatment time point

value: 0 hr

tag: spike-in reference organism


title: Conj. Mel 8

description: FFPE tissue

source_name: Conj. Mel 8


title: Person 8 VeinEndothelialCells Treated

source_name: Person 8 VeinEndothelialCells Treated

tag: Sex

value: Female