title: HiC_teloHAEC_4h_r2

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Rue Bélanger

institute: Montreal Heart Institute

data_processing:
Hi-C reads were processed using the Juicer pipeline (Durand et al. 2016). Hi-C libraries for all biological replicates had reads with the following quality measures: less than 10% below MAPQ threshold of 30 (average of 9.15%), more than 62% intra-chromosomal interactions (average of 68.5%) and less than 26% of inter-chromosomal interactions (average of 20.3%)
Correlation between biological replicates was assessed (Pearson’s r: 10kb resolution > 0.95; 50kb resolution > 0.97; 100kb resolution > 0.98) before merging to increase statistical power. Contacts maps were normalized with Knight-Ruiz (KR) matrix balancing before all downstream analyses
Per chromosome principal component analysis (PCA) was performed by calling the eigenvector function from the Juicer pipeline using 50 kb resolution matrices with KR normalization. Using the R packages TxDb and Sushi, PC1 values were aligned to gene density in 50 kb windows. If needed, the sign of PC1 was adjusted to correlate positive PC1 values with gene-rich regions and negative PC1 with gene-poor regions. Contiguous bins of positive and negative PC1 were labeled as A and B compartments, respectively.
Switching from A-to-B and B-to-A compartments upon TNFα treatment was retrieved from the differences in A/B compartments called between NT and TNFα-treated cells. Genes, ATACseq peaks, BP and CAD SNPs mapping to switching compartments were identified using map and merge functions from BEDTools with default parameters
TAD calling was performed on teloHAEC (0h and 4hrs TNFα). KR normalized sparse matrices of 10 kb resolution were extracted from .hic files by calling the dump function from the Juicer pipeline (Durand et al. 2016). TAD calling was performed using the Crane insulation score algorithm (Crane et al. 2015) Git version eecc2c9, with the default parameters (insulation delta span = 200 kb, insulation square size = 500 kb, insulation mode = "mean", boundary margin of error = 3, noise threshold = 0.1). TADs that overlap with the centromeres, as well as regions at either end of each chromosome, were excluded from analyses.
To determine if a TAD boundary overlapped with a feature (e.g. SNPs, ChIPseq, TSS, enhancer, promoter), we added a 10 kb outward buffer to the boundary coordinates. To determine if TADs were stable or changed following TNFα treatment, we added a 20 kb outward buffer to the boundary coordinates. The physical distance of CAD and BP sentinel SNPs with the closest TAD boundary was compared with the distance of control SNPs matched based on minor allele frequency, gene density, gene proximity and the number of LD proxies using SNPsnap default parameters (Pers et al. 2015). To derive empirical P-values, we considered the median distances to the closest TAD boundary of 100 sets of matched SNPs and compared them to the median distance of the CAD or BP SNPs.
Hi-C reads were processed using the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro). hichipper (https://github.com/aryeelab/hichipper) was used to call loops between promoters and H3K27ac ChIPseq peaks. Gene promoters’ coordinates were downloaded from the EPDnew database (https://epd.vital-it.ch/human/human_database.php). In-house scripts and bedtools (v2.26) were used to combine and integrate the BP and CAD SNPs, the H3K27ac peaks, the ATACseq peaks, the Hi-C loops, the RNAseq data with the GTEx (V6) data.
Genome_build: hg19
Supplementary_files_format_and_content: .hic corresponds to compressed multiple resolution/normalization contact matrices (MAPQ > 30) from Juicer for each biological replicates and merged ; bigWig files are the PC1 values corresponding to A/B compartments in each bin for merged biological replicates of each condition (positive value = A compartment, negative value = B compartment); bed (comp) files are coordinates of the A to B and B to A switching compartments following TNFa treatment (4hrs); bed (TADs) are TADs coordinates called for merged biological replicates of each condition; bedpe corresponds to loop coordinates called with hichipper using promoters and H3k27ac ChIP-seq masterBED as anchors

source_name: Endothelial Cells

growth_protocol: Immortalized human aortic endothelial cells (teloHAEC) were grown in vascular cell basal media supplemented with endothelial cell growth kit-VEGF, 200 U/mL penicillin and 200 μg/mL of streptomycin. TeloHAEC (below 3 passages) were maintained under a 5% CO2 atmosphere at 37°C. Endothelial cells were seeded at 1.4x10^5 cells per 100 mm plates (4 plates per biological replicate), grown to 90-100% confluency (refreshed media every 2-3 days) and subjected to TNF-alpha treatment

extract_protocol:
In situ Hi-C libraries were prepared as previously described (Belaghzal, Decker and Gibcus, 2017) with the following specifications and modifications:  Approximately 8x10^6 cells per sample were crosslinked (PFA 1%), pelleted and washed in ice-cold PBS prior to lysis and chromatin digestion with DpnII. Biotin-14-dATP fill-in and blunt end ligation was performed as described. Reverse crosslinking was performed in two subsequent 16 and 2 hours incubations with 500 μg of proteinase K prepared at 10 mg/mL in 5mM Tris-HCl pH 7.5, 50% glycerol, 1mM CaCl2 for each step. DNA purification was performed using 15mL MaXtract High Density tubes (Qiagen) with subsequent biotin removal from un-ligated ends using T4 DNA polymerase. For NGS preparation, between 20 and 40 μg of purified Hi-C DNA was used as starting material for all subsequent steps. Sonication to 200-300 bp fragments was carried in an S2 Focused-ultrasonicator with no alterations to the suggested parameters. 300-500 bp fragments were purified with AMPure XP beads and end-repaired as described. Biotin pulldown was performed with 200 μg of Dynabeads MyOne Streptavidin C1 (Invitrogen) per sample. A-tailing was performed as described.
Illumina adapters were ligated to 3' d-ATP overhangs using T4 DNA ligase. Production PCR was carried out with 9 cycles of PCR to obtain sufficient quantity for NGS while limiting PCR duplicates. Primers and primer dimers were removed by purification AMPure XP beads.

treatment_protocol: Grown cells were treated with TNF-alpha for 4h. Non treated cells in same culture conditions were used as controls.

value: immortalized Human Aortic Endothelial Cells

tag: passages

value: passages 23 to 25

tag: tnf-alpha treatment


title: PID092

status: Public on Jun 25 2019

type: genomic

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

country: USA

institute: University of Hawaii at Manoa

description:
genomic DNA from monocytes
insulin sensitive monocyte

hyb_protocol: bisulfite DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450K Beadchip following Illumina's standard protocol

scan_protocol: arrays were imaged using iScan SQ instrument (Illumina) following recommended settings

data_processing: RnBeads 0.99.10

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from monocytes using the Qiagen AllPrep DNA/RNA mini kit (ThermoScientific) following manufacturer's recommendations

tag: gender

value: male

tag: sample type

value: monocyte

tag: disease state

value: insulin sensitive

tag: condition

value: HIV


title: PID044


title: HiC_teloHAEC_4h_r1

type: SRA

country: Canada

library_source: genomic

tag: cell type


title: HiC_teloHAEC_0h_r2


title: PID042


title: TLR5 Ctrl 3

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

library_source: transcriptomic

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.5.3 was used to align the raw reads to the reference genome using parameters --ouReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
HTSeq-count version 0.9.1 was used to create raw counts from aligned STAR file using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 was used to normalize the counts and identify differentially expressed genes.
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab delimited Excel file containing raw count values for each gene for each sample

molecule: total RNA

organism: Mus musculus

growth_protocol: FliC of CFT073delta4 or CFT073delta4deltaFliC (for Control) UPEC was prepared in PBS

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
We used the Illumina NextSeq 500 and the latest versions of sequencing reagents and flow cells. Total RNA was subjected to 2 rounds of poly(A)+ selection and converted to cDNA. We used TruSeq library generation kits, as per the manufacturer’s instructions (Illumina, San Diego, California). Library construction consisted of random fragmentation of the poly(A) mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired and A-tailed, and adaptors were ligated for indexing (with up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit (Kapa Biosystems, Woburn, Massachusetts) prior to cluster generation. Clusters were generated to yield approximately 725K–825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed. We ran paired-end 2 × 75–bp sequencing runs to align the cDNA sequences to the reference genome

treatment_protocol: Mice were catheterized using a sterile Teflon catheter and 50 microlitres of PBS containing 30 micrograms of FliC was instilled transurethrally into the bladder (Controls received 50 microlitres of carrier). Whole bladders collected at 2h following challenge

tag: strain/genotype

value: TLR5-deficient B6.129S1-Tlr5tm1Flv/J

tag: treatment

value: control

tag: tissue

value: bladder


title: SACCs Pl_med: SACCs with plain medium

type: RNA

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing: The data were background-subtracted and normalized using the Transcriptome Analysis Console Software (ThermoFisher).

label: biotin

source_name: SACCs

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

growth_protocol: One spleen tissue was divided into 6 pieces and each spleen piece was placed into a single well of 12 (or 24) well dish. Then, each spleen piece was provided with RPMI 1640 medium containing 5% fetal bovine serum (0.5 ml per well) and then placed in regular CO2 incubator. The medium was changed every 2 to 3 days. For isolating SACCs, the medium was replaced by StemMedium®, serum-free medium for mouse ESCs (ES medium; DS Pharma Biomedical, Japan) once initiation of colony formation was evident (approximately 7 to 14 days post initiation of culture).

extract_protocol: Total RNAs were prepared using RNeasy Kit from Qiagen.

tag: strain

value: spleen

tag: cell state

value: compact colony


title: HiC_teloHAEC_0h_r1


title: PID025


title: PID217


title: TLR5 Ctrl 4


title: TLR5 Ctrl 2


title: H3K27ac_teloHAEC_24h_input

data_processing:
H3K27ac ChIPseq library raw reads were filtered for quality (phred33≥30) and length (n≥32) and adapter sequences were removed using Trimmomatic (Bolger et al. 2014)
Filtered reads were aligned to hg19 using BWA and peaks subsequently called using MACS2 (Zhang et al. 2008) with non-IP input DNA as control
Corresponding bedGraphs output of biological replicates and input controls from MACS were merged using UCSC BigWig and BigBed tools (Kent et al. 2010)
To create a “masterBED” peak file across conditions, peak files generated for each condition was merged using the merge function from BEDTools (Quinlan and Hall. 2010)
Genome_build: hg19
Supplementary_files_format_and_content: bigWigs correspond to bedGraphs of narrow peaks output from MACS with a score corresponding to coverage that were merged for all biological replicates; input bigWigs corresponds to MACS2 output for input controls for each condition; bed corresponds to the peaks present at least in one of the merged biological replicates peak list across all conditions; narrowPeak corresponds to MACS2 output of narrowPeaks format for each biological replicates across all conditions

growth_protocol: Immortalized human aortic endothelial cells (teloHAEC) were grown in vascular cell basal media supplemented with endothelial cell growth kit-VEGF, 200 U/mL penicillin and 200  g/mL of streptomycin. TeloHAEC (below 3 passages) were maintained under a 5% CO2 atmosphere at 37 C. Endothelial cells were seeded at 1.4x10^5 cells per 100 mm plates(1 plate per condition, 3 independent biological replicates), grown to 90-100% confluency (refreshed media every 2-3 days) and subjected to TNF-alpha treatment.

extract_protocol:
Cells were washed with HBSS Gibco and fixed in paraformaldehyde (PFA) 1% for 10 minutes at room temperature (RT). PFA was quenched in 134 mM glycine for 5 minutes at RT. Fixed cells were washed with ice-cold PBS and collected with a cell scraper in ice-cold PBS. Cells were pelleted by centrifugation, washed in ice-cold PBS, and pelleted again before snap freezing in liquid nitrogen. Fixed cells were subject to lysis in 5 mM PIPES-pH 8.5, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and protease inhibitor cocktail. Nuclei were then lysed in 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and protease inhibitor cocktail. Lysed nuclei were sonicated to yield fragments within a 100 to 500 bp range. Chromatin immunoprecipitation was performed using 3.7 µg of H3K27ac antibody (Diagenode) per samples containing 5x10^5 cells (no antibody for input). Samples were purified through silica-membrane-based columns prior to library preparation.
Library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems) for Illumina using with adapters from TruSeq DNA LT Sample Prep Kit (Illumina).

treatment_protocol: Endothelial cells were treated with TNF-alpha prepared in culture media at 10 ng/mL for 4h and 24h periods

tag: chip antibody


title: H3K27ac_teloHAEC_0h_input


title: TLR5 Ctrl 1


title: WT FliC 3

source_name: C57BL/6J mice FliC-treated

value: FliC-treated


title: WT FliC 2


title: PID229

description:
genomic DNA from monocytes
insulin resistant monocyte

value: insulin resistant


title: HCT116

city: Orlando

first: WEI

last: ZHANG

state: FL

address: 4000 central florida blvd

department: Computer Science

institute: UNIVERSITY OF CENTRAL FLORIDA

hyb_protocol: Hybridization of NanoString probes was conducted according to the manufacturer's protocol.

data_processing: The  geometric  mean  of  the  ten  house  keeping  genes  (TAF5L,  HPS6,  DNTTIP2, GNRHR, ZNF407, KCNK7, KIAA1539, RBM12, DGCR14, and KHDRBS1) was applied to normalized the NanoString signal in each cell line. Then, the expressions of isoforms in one gene can be estimated by minimizing the differences between the predicted and observed intensities for all probes in the gene.

label: NanoString labeling

source_name: cancer cell line

label_protocol: NanoString probe labeling was conducted accoding to the manufacturer's protocol.

growth_protocol: Cells were grown in DMEM media supplemented with 10% FBS and antibiotics. Cell were harvested when they were around 70% confluency.

extract_protocol: A standard TriZol RNA extraction method was used for toal RNA extraction from harvested cells.

treatment_protocol: No treatments

value: Colon

value: colon cancer cell line

tag: cell line


title: PID236


title: PID214


title: WT FliC 1


title: H3K27ac_teloHAEC_4h_r3

value: H3K27ac (Diagenode; C15410196)


title: H3K27ac_teloHAEC_24h_r1


title: H3K27ac_teloHAEC_24h_r2


title: WT_sham_61

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Partek Genomics Suite using RMA algorithm.

source_name: heart ventricle

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

extract_protocol: Total RNA was extracted using miRNeasy Mini kits according to manufacturer's protocol. Aftre reperfusion, the ventricles were collected and snap frozen for total RNA extraction.

treatment_protocol: Mice were submitted to ischemia reprfusion protocol in vivo, IR was achieved through ligation of the left anterior descending (LAD) coronary artery for 45 min of ischemia, the heart was  reperfused for 8h. HDL was injected at the onset of reperfuion. Sham operated mice did not have ischemia protocol.

value: heart ventricle

tag: genotype

value: WT

value: sham


title: PID185

value: male


title: WT Ctrl 5

source_name: C57BL/6J Control


title: STAT3_KO_sham_59


title: PID146

value: monocyte


title: WT Ctrl 2


title: PID135

value: insulin sensitive


title: WT Ctrl 1


title: H3K27ac_teloHAEC_4h_r1

value: immortalized Human Aortic Endothelial Cells

value: passages 23 to 25


title: STAT3_KO_sham_58


title: PID209

value: HIV


title: H3K27ac_teloHAEC_0h_r3


title: input_20161219

data_processing:
Basecalls performed using bcl2fastq2 version 2.18.0.12
Data were filtered by using FASTX Toolkit 0.0.1.3 (parameters -Q33 -q 20 -p 75)
ChIP-seq reads were aligned to the mm9 genome assembly using boetie2-2.2.5.
peaks were called using MACS2(q=0.001)
Ensembl Genes were defined using in GREAT (Two nearest genes association rules (within = five Kb) )
Genome_build: mm9
Supplementary_files_format_and_content: Peak file

growth_protocol: ESCs were culture under conventional ESC medium with LIF.

extract_protocol:
Lysates were clarified from sonicated nuclei and Suz12 were isolated with antibody.
Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # E7645S) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335S), according to the manufacturers recommendations. The libraries were indexed and amplified using 8 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution was confirmed by a BioAnalyzer 2100 (Agilent technologies) and quantified by the KAPA Library Quantification Kit (KAPA, Wilmington, MA), respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a NextSeq 500 (Illumina: Single-End 75).

tag: cell-type

value: embryonic stem cells


title: STAT3_KO_sham_56


title: PID122


title: PID181


title: WT Ctrl 4

value: control

value: bladder


title: PID026


title: H3K27ac_teloHAEC_0h_r2


title: Suz12_Mbd3KO_deltaCC

source_name: Mbd3 Knock-out ESCs

value: Suz12 (Millipore, 04-046)


title: WT_IR+HDL_50

value: IR + HDL


title: H3K27ac_teloHAEC_24h_r3


title: STAT3_KO_IR_48

value: IR


title: H3K27ac_teloHAEC_0h_r1


title: Suz12_Mbd3KO_deltaMBD


title: WT_ME_3 (Sample 257)

city: Houston

first: Paul

last: Bernard

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description:
Isogenics.xlsx
wild-type strain

data_processing:
Reads were mapped to the genome of serotype M28 GAS reference strain MGAS6180 using EDGEpro and differentional transcript analysis was performed with DESeq2 (version 1.14.1) using the default settings.
Genome_build: ASM1216v2 (serotype M28 GAS reference strain MGAS6180)
Supplementary_files_format_and_content: xlsx; contains RPKMs for each sample at the corresponding time point

organism: Streptococcus pyogenes

source_name: serotype M28 group A streptococcus strain

growth_protocol: Strains were grown in Todd-Hewitt broth with 0.2% yeast extract until ME (OD600 = 0.5) and ES (OD600 = 1.65) and RNAprotect was added (2:1)

extract_protocol:
Strains were lysed by ballistic disintegration and RNA extracted using Rneasy Mini Kit (Qiagen)
Libraries were prepared using standard Illumina protocols for Gram (+) organisms (clinical isolates) and standard MicrobExpress and NEB protocols for Gram (+) organisms (isogenics)

value: clinical isolate

tag: time point

value: ME


title: WT_ME_2 (Sample 256)

description:
Isogenics.xlsx
wild-type strain


title: Suz12_Mbd3KO_WT


title: PID043

value: insulin resistant


title: Suz12_Mbd3KO_GFP


title: PID069


title: STAT3_KO_IR+HDL_41

value: heart ventricle


title: PID005


title: PID081


title: HCC1937_BRCA1

value: Breast

value: breast cancer cell line


title: WT_IR_40

value: WT


title: VNTR_H60Y_ME_3 (Sample 254)

description:
Isogenics.xlsx
isogenic RocA VNTR + H60Y strain

value: isogenic


title: VNTR_H60Y_ME_2 (Sample 253)


title: VNTR_H60Y_ME_1 (Sample 252)


title: WT_sham_37

value: sham


title: F2-combined

city: Tampa

first: Steven

last: Eschrich

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

data_processing:
Reads were aligned using tophat 2.0.13
Genes/transcipts were assembled using Cufflinks 2.2.1
Read counts from BAM files were calculated using HT-Seq (htseq-count, vHTSeq-0.6.1)
Read counts were normalized in DESeq2 using estimated library size (median ratio method).
Genome_build: hs37d5
Supplementary_files_format_and_content: comma-separated, normalized abundance measurements of gene-level quantification

source_name: H1155 cells

growth_protocol: Cells were cultivated in RPMI-1640 media with 10% FBS (complete RPMI) and maintained in the incubator with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted following manufacturer instructions (RNeasy Mini Kit – Qiagen, #74104), with the addition of an extra DNase digestion step to increase the quality of the RNA. This digestion was performed following the method in appendix E: DNase digestion of RNA before RNA cleanup from the RNase-Free DNase Set (Qiagen, #79254). To 87.5 µl of RNA sample was added 10 µl Buffer RDD and 2.5 µl DNase I stock solution (provided by the Moffitt’s Molecular Genomics Core). The sample volumes were brought up to 100 µl with RNase-free water and incubated at room temperature for 10 minutes before proceeding with the cleanup protocol of the RNeasy Mini Kit (Qiagen). Also, we performed an ethanol precipitation after RNA extraction. The volume of each sample was brought up to 200 µl and 1/10 volume (20 µl) of 5 M NaCl plus 2.5 volumes (500 µl) of absolute ethanol were added prior to thorough vortex. Samples were centrifuged at 1,000 xg for 10 minutes; the supernatant was discarded, and pellets were washed with 500 µl of freshly diluted 75% ethanol in RNase-free water. Samples were centrifuged again at 1,000 xg for 10 minutes, supernatant was discarded, and samples were left to air-dry. Samples were resuspended in RNase-free water and analyzed by Nanodrop to verify the 260/280 and 260/230 ratio > 1.8 and ~2.0.
RNA-Seq library generation was performed following the Encore Complete RNA-Seq Library System protocol (Nugen). The KAPA library amplification kit for Illumina platform (KAPABiosystem) was used as described in the technical data sheet.  Beads were resuspended in 20 µl of elution buffer.

treatment_protocol: H1155 cells were plated at a density of 0.5 x 106 cells in a 35 mm dish/treatment. After 24 hours, cells were treated with 1 µM of foretinib or cabozantinib for 4 hours and then collected, pelleted and kept on -80°C until all biological triplicates were harvested.

value: foretinib


title: F4-combined


title: F1-combined


title: WT_ME_1 (Sample 255)

description:
Isogenics.xlsx
wild-type strain


title: WT_IR+HDL_32


title: WT_sham_36


title: WT_IR_33


title: T442P_ME_3 (Sample 251)

description:
Isogenics.xlsx
isogenic RocA T442P strain


title: D4-combined

value: DMSO


title: WT_IR_27


title: PID020

value: male

value: monocyte

value: HIV


title: T442P_ME_2 (Sample 250)


title: D2-combined


title: C5-combined

value: cabozantinib


title: R258K_ME_3 (Sample 248)

description:
Isogenics.xlsx
isogenic RocA R258K strain


title: C4-combined


title: T442P_ME_1 (Sample 249)


title: C3-combined


title: PID004


title: R258K_ME_1 (Sample 246)


title: D5-combined


title: STAT3_KO_IR_25


title: STAT3_KO_IR+HDL_24

value: IR + HDL


title: WT_IR+HDL_26


title: ADGFP2399

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq analysis:
RNA-seq data were analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/), as follows: RNA-seq reads were aligned to the mouse genome (NCBI37/mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing two mismatches and twenty multihits. Differential expression tests were done with DESeq2, using the mouse NCBI37/mm9 genome annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Normalized counts calculated with DESeq2

molecule: polyA RNA

source_name: PDAC cell lines

extract_protocol:
RNA extraction protocol from Quiagen
1ug of total RNA from the samples was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA LT Sample Prep Kit" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced in paired-end format (Illumina NovaSeq 6000), leading to 101bp paired-end reads.
Strand-specific RNA-Seq (dUTP)

treatment_protocol: 25 MOI of AdGFP

value: PDAC

tag: genotype/variation

tag: infected with

value: 25 MOI of AdGFP


title: P97L_ME_3 (Sample 245)

description:
Isogenics.xlsx
isogenic RocA P97L strain

value: ME


title: P97L_ME_2 (Sample 244)


title: ADGFP2365


title: ADGFP2257


title: P97L_ME_1 (Sample 243)


title: STAT3_KO_IR_22

value: IR


title: ADGFP1803


title: G184W_ME_3 (Sample 242)

description:
Isogenics.xlsx
isogenic RocA G184W strain


title: ADGFP1439


title: G184W_ME_1 (Sample 240)


title: ADGFP1078


title: G184W_ME_2 (Sample 241)


title: R258K_ME_2 (Sample 247)


title: STAT3_KO_IR+HDL_23

value: heart ventricle


title: delta_rocA_ME_1 (Sample 237)

description:
Isogenics.xlsx
isogenic rocA gene deletion strain


title: delta_rocA_ME_3 (Sample 239)


title: WT_ES_2 (Sample 235)

description:
Isogenics.xlsx
wild-type strain

value: clinical isolate

value: ES


title: WT_ES_3 (Sample 236)

description:
Isogenics.xlsx
wild-type strain


title: WT_ES_1 (Sample 234)

description:
Isogenics.xlsx
wild-type strain


title: VNTR_H60Y_ES_3 (Sample 233)


title: VNTR_H60Y_ES_2 (Sample 232)


title: VNTR_H60Y_ES_1 (Sample 231)


title: T442P_ES_3 (Sample 230)


title: T442P_ES_2 (Sample 229)


title: H3K27ac_teloHAEC_4h_r2

value: immortalized Human Aortic Endothelial Cells

tag: passages

value: passages 23 to 25

value: H3K27ac (Diagenode; C15410196)

tag: tnf-alpha treatment


title: delta_rocA_ME_2 (Sample 238)

tag: sample type

value: isogenic


title: T442P_ES_1 (Sample 228)


title: donorC_RNase-treated EC-12_rep2

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

institute: Kyoto Prefectural University

hyb_protocol: Slide was hybridized with 600 ng Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.

scan_protocol: After 17 h of hybridization at 65 °C, the slide was washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. Slides were scanned  after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The intensity signals was imported to CLC Main workbench 6.0 and normalized by the quartile normalization method and log2 transformed.

source_name: PBMC, healthy adult, replicate 3

label_protocol: Complementary RNA amplification and Cy3 labelling was carried out from 25 ng of total RNA using Low Input Quick Amp Labeling kit (Agilent).

growth_protocol: PBMC was isolated by density gradient centrifugation on Percoll (d = 1.077) .

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified by RNeasy MinElute Cleanup kit.

treatment_protocol: PBMC was cultured in medium (medium) or co-cultured with RNase-treated EC-12 or Untreated-EC-12 for 6h.

tag: individual

value: donorC

tag: disease state

value: healthy

value: whole blood

value: PBMC

value: RNase-treated EC-12


title: donorB_RNase-treated EC-12_rep2

source_name: PBMC, healthy adult, replicate 2

value: donorB

tag: cell type


title: donorB_RNase-treated EC-12_rep1

tag: treatment


title: donorC_RNase-treated EC-12_rep3

tag: tissue


title: donorA_RNase-treated EC-12_rep2

source_name: PBMC, healthy adult, replicate 1

value: donorA


title: donorA_RNase-treated EC-12_rep3


title: donorA_RNase-treated EC-12_rep1


title: donorC_RNase-treated EC-12_rep1


title: donorC_untreated EC-12_rep3

value: untreated EC-12


title: R258K_ES_2 (Sample 226)

tag: strain


title: P97L_ES_2 (Sample 223)


title: donorB_untreated EC-12_rep3


title: P97L_ES_3 (Sample 224)


title: donorB_RNase-treated EC-12_rep3


title: donorC_untreated EC-12_rep2


title: donorB_untreated EC-12_rep2


title: donorC_untreated EC-12_rep1


title: H3K27ac_teloHAEC_4h_input


title: P97L_ES_1 (Sample 222)


title: R258K_ES_3 (Sample 227)


title: G184W_ES_2 (Sample 220)


title: R258K_ES_1 (Sample 225)


title: delta_rocA_ES_3 (Sample 218)


title: donorA_untreated EC-12_rep3


title: donorB_untreated EC-12_rep1


title: G184W_ES_1 (Sample 219)


title: G184W_ES_3 (Sample 221)


title: donorA_untreated EC-12_rep1


title: donorA_untreated EC-12_rep2


title: eaf3 deletion, RNA Pol II S2P ChIP

city: Los Angeles

first: Stephen

last: Douglass

state: CA

address: 5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
eaf3delta.bw
genomic DNA

data_processing:
The processed data file is RPKM measurements for each gene in each sample
Illumina CASAVA used for basecalling
Reads demultiplexed requiring 2 or fewer mismatches
Replicates were merged, where applicable
Unfiltered reads aligned using Bowtie v0.12.8 allowing up to 2 mismatches
Peak calling versus input was calculated using MACS2 with a bandwidth of 300, model fold of 5 to 50, and q-value cutoff of 0.05.
The processed data is bigWig files of measurements of each sample versus input
Genome_build: saccer3

organism: Saccharomyces cerevisiae

growth_protocol: Cell were grown to mid-log phase in YPD at 30 degrees C

extract_protocol:
DNA was extracted using AMPure XP beads
Library was constructed using Ovation Ultralow DR kit (NuGEN)

value: MATa his3-leu2-met15-ura3-

tag: ploidy

value: Haploid


title: delta_rocA_ES_1 (Sample 214)

description:
Clinical_isolates_ES_v2.xlsx
isogenic rocA gene deletion strain


title: MGAS32014_ES_1 (Sample 210)

description:
Clinical_isolates_ES_v2.xlsx
clinical isolate


title: Wildtype, H3K36me3 ChIP, Replicate 2

description:
H3K36me3.bw
genomic DNA


title: H3K36A, RNA Pol II S2P ChIP

description:
H3K36A.bw
genomic DNA


title: donorB_medium_rep2

value: medium


title: donorC_medium_rep1


title: MGAS32014_ES_2 (Sample 211)

value: clinical isolate


title: Wildtype, H3K36me3 ChIP, Replicate 1

description:
H3K36me3.bw
genomic DNA


title: donorC_medium_rep2


title: eaf3 deletion, input

description:
eaf3delta.bw
genomic DNA


title: MGAS7967_ES_2 (Sample 213)

value: ES


title: MGAS29562_ES_2 (Sample 209)


title: delta_rocA_ES_2 (Sample 215)


title: donorB_medium_rep1


title: H3K36A, input

description:
H3K36A.bw
genomic DNA


title: Wildtype, RNA Pol II S2P ChIP, Replicate 1

description:
WT.bw
genomic DNA


title: MGAS7967_ES_1 (Sample 212)


title: delta_rocA_ES_2 (Sample 217)


title: Wildtype, input

description:
WT.bw
H3K36me3.bw
genomic DNA


title: delta_rocA_ES_1 (Sample 216)


title: eaf3 deletion, replicate 2

description:
RPKMs.xlsx
rRNA-depleted RNA

data_processing:
Illumina CASAVA used for basecalling
Reads demultiplexed requiring exact barcode match
Unfiltered reads aligned using TopHat v2.0.14
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, the number of reads falling in the exons of each transcript were counted and normalized by the size of the transcript and library.
Mean of replicates taken
Genes with less than 1 RPKM removed
The processed data file is RPKM measurements for each gene in each sample
Genome_build: saccer3

extract_protocol:
RNA was extracted by hot phenol:chloroform:isoamyl alcohol extraction. 20 ug of total RNA was then treated with DNase I (Roche)
Library was constructed using TruSeq Stranded Total RNA Kit (Illumina)


title: donorA_medium_rep2


title: MGAS29454_ES_4 (Sample 207)


title: MGAS29454_ES_3 (Sample 206)


title: MGAS28689_ES_2 (Sample 205)


title: MGAS29562_ES_1 (Sample 208)


title: Wildtype, RNA Pol II S2P ChIP, Replicate 2

description:
WT.bw
genomic DNA


title: H3K36A, replicate 2

description:
RPKMs.xlsx
rRNA-depleted RNA


title: MGAS28689_ES_1 (Sample 204)


title: eaf3 deletion, replicate 1

description:
RPKMs.xlsx
rRNA-depleted RNA


title: MGAS28050_ES_2 (Sample 203)


title: H3K36A, replicate 1

description:
RPKMs.xlsx
rRNA-depleted RNA


title: MGAS28050_ES_1 (Sample 202)


title: MGAS8020_ES_2 (Sample 201)


title: Wildtype, replicate 1

description:
RPKMs.xlsx
rRNA-depleted RNA


title: set2 deletion, replicate 2

description:
RPKMs.xlsx
rRNA-depleted RNA


title: Wildtype, replicate 2

description:
RPKMs.xlsx
rRNA-depleted RNA


title: MGAS8020_ES_1 (Sample 200)


title: Whole, E7, replicate 3

city: Edinburgh

first: Joe

last: Rainger

state: Midlothian

address: Easter Bush

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads psuedoaligned using Kallisto v0.43.1 to transcriptome index derived from ensembl 81 reference transcripts
Genome_build: Galgal4
Supplementary_files_format_and_content: Tab separated Kallisto output containing TPM expression estimates

organism: Gallus gallus

source_name: Whole eye, including lens

growth_protocol: Eggs at 37oC for 5+ days

extract_protocol:
Trizol, Dynabeads mRNA DIRECT Micro Kit
Ion Total RNA-Seq Kit v2 with Ion Xpress RNA-Seq Barcodes.

treatment_protocol: Dissect into PBS

tag: developmental stage

value: Whole eye, including lens


title: set2 deletion, replicate 1

description:
RPKMs.xlsx
rRNA-depleted RNA


title: MGAS7966_ES_1 (Sample 196)


title: Ventral, E7, replicate 3

source_name: Ventral eye (neural retina, RPE, and optic fissure margin)


title: MGAS7966_ES_2 (Sample 197)


title: Whole, E7, replicate 2


title: MGAS7909_ES_2 (Sample 195)


title: Fissure, E7, replicate 3

source_name: Optic fissure margin environment (neural retina, RPE, peri-ocualr mesenchyme)


title: MGAS7909_ES_1 (Sample 194)


title: MGAS7904_ES_2 (Sample 193)


title: MGAS7904_ES_1 (Sample 192)


title: Whole, E7, replicate 1


title: Ventral, E7, replicate 1

value: Ventral eye (neural retina, RPE, and optic fissure margin)


title: MGAS7895_ES_2 (Sample 191)


title: Ventral, E7, replicate 2


title: donorA_medium_rep1


title: Fissure, E7, replicate 1

value: Optic fissure margin environment (neural retina, RPE, peri-ocualr mesenchyme)


title: Whole, E6, replicate 3


title: MGAS7995_ES_1 (Sample 198)


title: MGAS7995_ES_2 (Sample 199)


title: MGAS32031_ES_2 (Sample 187)


title: MGAS7893_ES_2 (Sample 189)


title: Fissure, E6, replicate 3


title: Ventral, E6, replicate 3


title: Whole, E6, replicate 2


title: Ventral, E6, replicate 2


title: Fissure, E6, replicate 2


title: MGAS32031_ES_1 (Sample 186)


title: Fissure, E7, replicate 2


title: Whole, E6, replicate 1


title: Ventral, E6, replicate 1


title: MGAS32013_ES_2 (Sample 185)


title: MGAS32013_ES_1 (Sample 184)


title: MGAS31997_ES_1 (Sample 182)


title: Fissure, E6, replicate 1


title: MGAS31997_ES_2 (Sample 183)


title: MGAS31971_ES_2 (Sample 181)


title: MGAS31971_ES_1 (Sample 180)


title: MGAS31968_ES_2 (Sample 179)


title: MGAS7895_ES_1 (Sample 190)


title: Fissure, E5, replicate 3


title: Whole, E5, replicate 3


title: MGAS31968_ES_1 (Sample 178)


title: Ventral, E5, replicate 3


title: Dorsal, E5, replicate 3

source_name: Dorsal eye (neural retina, RPE)

value: Dorsal eye (neural retina, RPE)


title: Whole, E5, replicate 2


title: MGAS31960_ES_2 (Sample 177)


title: MGAS7893_ES_1 (Sample 188)


title: Ventral, E5, replicate 2


title: MGAS29475_ES_2 (Sample 175)


title: MGAS31960_ES_1 (Sample 176)


title: Fissure, E5, replicate 2


title: Dorsal, E5, replicate 2


title: MGAS29146_ES_2 (Sample 173)


title: MGAS29475_ES_1 (Sample 174)


title: Whole, E5, replicate 1


title: MGAS29146_ES_1 (Sample 172)


title: Dorsal, E5, replicate 1


title: MGAS28941_ES_2 (Sample 171)


title: MGAS28941_ES_1 (Sample 170)


title: MGAS28742_ES_2 (Sample 167)


title: MGAS28912_ES_1 (Sample 168)


title: MGAS28912_ES_2 (Sample 169)


title: MGAS28742_ES_1 (Sample 166)


title: MGAS28706_ES_1 (Sample 164)


title: Ventral, E5, replicate 1


title: MGAS28652_ES_2 (Sample 163)


title: MGAS28652_ES_1 (Sample 162)


title: MGAS28706_ES_2 (Sample 165)


title: MGAS28426_ES_1 (Sample 160)

description:
Clinical_isolates_ES_v2.xlsx
wild-type strain

value: wild-type strain


title: MGAS28330_ES_2 (Sample 159)


title: MGAS28426_ES_2 (Sample 161)


title: MGAS28330_ES_1 (Sample 158)


title: MGAS28101_ES_2 (Sample 157)


title: MGAS27961_ES_2 (Sample 155)


title: MGAS28101_ES_1 (Sample 156)


title: MGAS27961_ES_1 (Sample 154)


title: Fissure, E5, replicate 1


title: TB 300

type: protein

city: Guangzhou

first: Huihua

last: Zhang

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

country: China

institute: Jinan University

description: A combination of 16 non-overlapping arrays to quantitatively measure 640 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

hyb_protocol: 2-fold diluted culture supernatant was added to each well. After overnight incubation at 4°C and extensive washing, the biotin-labeled detection antibody was added for 2 hours and then washed away. AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 300 scanner (Innopsys, Carbonne, France).

data_processing: Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls. For protein quantification, standard curves were generated using purified proteins representing the proteins-of-interest.

label: AlexaFluor 555

molecule: protein

source_name: Culture supernatant from Mtb-stimulated whole blood

treatment_protocol: Whole blood (250 µl) collected from participants using an EDTA anticoagulation tube was cultured in serum-free medium (DKW34-EHK0100, DAKEWE) in absence or presence of 2.5 µg/ml phytohemagglutinin (PHA, L8754, Sigma) or 10 µg/ml Mtb-antigen peptide pool for 24 h at 37°C, 5% CO2, and then the supernatant was collected.

value: Whole blood

tag: histology

value: Pulmonary tuberculosis


title: TB 302

label_protocol: AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

extract_protocol: Culture supernatant from Mtb-stimulated whole blood


title: MGAS11107_ES_2 (Sample 151)


title: MGAS11107_ES_1 (Sample 150)


title: TB 298


title: TB 286


title: TB 288


title: TB 304


title: TB 284


title: TB 220


title: MGAS29596_ES_1 (Sample 146)


title: TB 222


title: MGAS29555_ES_2 (Sample 145)


title: MGAS12250_ES_1 (Sample 152)


title: TB 208


title: MGAS10816_ES_1 (Sample 148)


title: TB 218


title: TB 204


title: TB 202


title: TB 224


title: TB 206


title: MGAS29555_ES_1 (Sample 144)


title: MGAS12250_ES_2 (Sample 153)


title: MGAS10816_ES_2 (Sample 149)


title: TB 282


title: TB 190


title: TB 192


title: MGAS29596_ES_2 (Sample 147)


title: MGAS29454_ES_1 (Sample 140)


title: MGAS29395_ES_2 (Sample 139)


title: MGAS29454_ES_2 (Sample 141)


title: MGAS29460_ES_1 (Sample 142)


title: TB 188


title: TB 186


title: MGAS29336_ES_2 (Sample 137)


title: MGAS29395_ES_1 (Sample 138)


title: MGAS29336_ES_1 (Sample 136)


title: TB 142


title: TB 140


title: TB 138


title: MGAS29298_ES_2 (Sample 135)


title: MGAS29251_ES_2 (Sample 133)


title: TB 128


title: TB 122


title: MGAS29251_ES_1 (Sample 132)


title: MGAS29460_ES_2 (Sample 143)


title: TB 126


title: MGAS29250_ES_2 (Sample 131)


title: MGAS29298_ES_1 (Sample 134)


title: TB 124


title: MGAS29250_ES_1 (Sample 130)


title: TB 94


title: TB 96


title: TB 144


title: TB 90


title: TB 92


title: MGAS29160_ES_2 (Sample 129)


title: MGAS29160_ES_1 (Sample 128)


title: MGAS28632_ES_2 (Sample 125)


title: MGAS28632_ES_1 (Sample 124)


title: TB 38


title: TB 40


title: MGAS28677_ES_1 (Sample 126)


title: TB 34


title: TB 16


title: MGAS28411_ES_2 (Sample 121)


title: MGAS28553_ES_1 (Sample 122)


title: MGAS28553_ES_2 (Sample 123)


title: MGAS28299_ES_2 (Sample 119)


title: MGAS28253_ES_2 (Sample 117)


title: MGAS28411_ES_1 (Sample 120)


title: MGAS28299_ES_1 (Sample 118)


title: MGAS28253_ES_1 (Sample 116)


title: MGAS28245_ES_1 (Sample 114)


title: TB 12


title: PN 308

value: Non-TB pulmonary inflammations


title: MGAS28245_ES_2 (Sample 115)


title: TB 10


title: MGAS28677_ES_2 (Sample 127)


title: MGAS28204_ES_2 (Sample 113)


title: PN 312


title: PN 310


title: TB 14


title: ATACseq_HCAEC_24h_r2

data_processing:
ATAC library reads were processed through the ATACseq pipeline (https://github.com/kundajelab/atac_dnase_pipelines). Adapters were removed using Cut-adapt.
Reads were then mapped to hg19 using Bowtie2. Peak calling from BAM files was performed using MACS2 (Zhang et al. 2008).
To create a “masterBED” peak file across conditions, peak files generated for each condition was merged using the merge function from BEDTools (Quinlan and Hall. 2010)
Mean scores from bedGraphs for each individual biological replicate were assigned to masterBED peak files using intersect (default parameters) and merge (-o mean) and used as input for differential analysis using DESeq2 (Love et al. 2014)
All comparisons for NT, TNFα 4 hours and 24 hours treatments were performed using the analysis of deviance function with default parameters in DEseq2. ATACseq peaks with FDR ≤0.001 and fold-change ≥2 or ≤-2 were considered differentially opened or closed
Corresponding biological replicates bedGraphs output from MACS were merged using UCSC BigWig and BigBed tools (Kent et al. 2010)
Genome_build: hg19
Supplementary_files_format_and_content: bigWigs correspond to bedGraphs of narrow peaks output from MACS with a score corresponding to coverage that were merged for all biological replicates;  bed corresponds to the peaks present at least in one of the merged biological replicates peak list across all conditions for teloHAEC; narrowPeak corresponds to pooled pseudo replicates and 0.1 IDR thresholded narrowPeaks file for each cell lines across all conditions using the Kundaje lab ATAC-seq pipeline (ENCODE)

source_name: Endothelial Cells

growth_protocol: Immortalized human aortic endothelial cells (teloHAEC) were grown in vascular cell basal media supplemented with endothelial cell growth kit-VEGF, 200 U/mL penicillin and 200 μg/mL of streptomycin. Primary human coronary artery endothelial cells (HCAEC) from a single male donor were grown in EGM-2MV supplemented with 200 U/mL penicillin and 200 μg/mL of streptomycin. TeloHAEC and HCAEC (below 3 passages) were maintained under a 5% CO2 atmosphere at 37°C. Endothelial cells were seeded at 2x10^5 cells per well in 6-well plates, grown for 3 days (refreshed media at day 2) until reaching 95-100% confluency and subjected to TNF-alpha treatment.

extract_protocol:
5x10^4 cells were spun down at 500g for 5 minutes at 4°C. Whole cell pellets were subjected to a first round of cell membrane lysis using 50 μL of ice-cold hypotonic buffer (0.1% Sodium citrate tribasic dehydrate; 0.1% Triton X-100) and incubating on ice for 30 minutes. The hypotonic buffer was removed by centrifugation at 500g for 5 minutes at 4°C and we subsequently discarded the supernatant. Crude nuclei lysates were prepared by resuspending cells in lysis buffer (10mM Tris-HCl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% Igepal CA-630 and incubating for 30 minutes on ice. Following the removal of lysis buffer by centrifugation at 500g for 5 minutes at °4C, transposition reaction of open chromatin was achieved by resuspending free nuclei in tagmentation mix (22.5 μL Tagment DNA Buffer; 2.5 μL Tagment DNA enzyme; 25 μL H2O) (Illumina) and incubating at 37°C for 30 minutes. Purification of DNA was performed with MinElute (Qiagen) according to the manufacturer’s protocol.
Barcoding and amplification was prepared using Nextera Index Kit (Illumina, FC-121-1011) with the following thermal profile: 30 seconds at 98°C and a three-step cycle of 10 seconds at 98°C, 30 seconds at 63°C and 1 minute at 72°C repeated 12 times followed by 5 minutes at 72°C. Amplified ATACseq libraries were purified using GeneRead Size Selection Kit (Qiagen).

value: Human Coronary Artery Endothelial Cells

value: passages 7 to 9


title: PN 262


title: PN 232


title: TB 36


title: ATACseq_HCAEC_24h_r1


title: MGAS28166_ES_2 (Sample 111)


title: MGAS28204_ES_1 (Sample 112)


title: PN 258


title: PN 230


title: ATACseq_HCAEC_4h_r2


title: MGAS28166_ES_1 (Sample 110)


title: MGAS12241_ES_2 (Sample 109)


title: ATACseq_HCAEC_4h_r1


title: PN 264


title: PN 306


title: PN 228


title: delta_rocA_ME_2 (Sample 107)

description:
Clinical_isolates_ME_v2.xlsx
isogenic rocA gene deletion strain

value: isogenic

value: ME


title: ATACseq_HCAEC_0h_r1


title: MGAS12241_ES_1 (Sample 108)


title: PN 216


title: delta_rocA_ME_1 (Sample 106)


title: PN 260


title: ATACseq_teloHAEC_24h_r1

value: immortalized Human Aortic Endothelial Cells

value: passages 23 to 25


title: MGAS7967_ME_2 (Sample 105)

description:
Clinical_isolates_ME_v2.xlsx
clinical isolate


title: ATACseq_teloHAEC_24h_r2


title: MGAS7967_ME_1 (Sample 104)


title: MGAS32014_ME_2 (Sample 103)


title: ATACseq_teloHAEC_4h_r2


title: PN 212


title: ATACseq_teloHAEC_4h_r1


title: PN 214


title: PN 210


title: PN 168


title: ATACseq_teloHAEC_0h_r2


title: MGAS32014_ME_1 (Sample 102)


title: PN 164


title: ATACseq_teloHAEC_0h_r1


title: MGAS29562_ME_2 (Sample 101)


title: PN 166


title: MGAS29562_ME_1 (Sample 100)


title: PN 162


title: Day40 HPS8-mutant lung epithelial cells replicate 3

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 W. 168th Street, BB816

department: Medicine

institute: Columbia University Medical Center

description:
HPS8-Rep3
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to a reference genome (Human: NCBI/build37.2) using STAR (2.5.2b) and featureCounts (v1.5.0-p3).
We test for differentially expressed genes under various mutants using DESeq2.
Genome_build: NCBI/build37.2 (GRCh37)
Supplementary_files_format_and_content: Counts_Table.txt: Tab-delimited text file includes gene symbols and raw count values for each sample.
Supplementary_files_format_and_content: Keygenes_Table.txt: Tab-delimited text file includes Ensembl gene IDs and raw count values for each sample.

source_name: RUES2 Human Embryonic Stem Cells

growth_protocol: Human pluripotent stem cells (hPSCs)–derived lung epithelial cells were generated by directed differentiation of RUES2 Embryonic Stem Cell line first to definitive endoderm, then anterior foregut endoderm, followed by specification for the lung field according to established protocols (Huang, SX. et al. Nature Protocols (2015), Chen YC. et al. Nature Cell Biology (2017)). 3-dimensional maturation of the lung bud organoids was achieved after embedding in Matrigel in the presence of CHIR9921, FGF10, KGF, BMP4 and all-trans Retinoic Acid.

extract_protocol:
TRIzol Reagent and Direct-zol RNA-MiniPrep Plus kit (Zymo Research, Irvine CA).
Libraries were generated using Illumina TruSeq RNA prep kit after poly-A pull-down to enrich mRNAs from total RNA samples.

treatment_protocol: 3D organoids from wild-type hPSCs or hPSCs harboring Hermansky-Pudlak Syndrome-associated mutations introduced by CRISPR/Cas9 genome-editing were differentiated to Day40 3D lung organoids and EPCAM+ epithelial cells were sorted.

value: HPS8 mutant

value: Lung epithelial cells


title: MGAS29454_ME_4 (Sample 99)

value: clinical isolate


title: PN 152


title: Day40 HPS8-mutant lung epithelial cells replicate 1

description:
HPS8-Rep1
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: PN 150


title: MGAS28689_ME_2 (Sample 97)


title: Day40 HPS2-mutant lung epithelial cells replicate 3

description:
HPS2-Rep3
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt

value: HPS2 mutant


title: MGAS29454_ME_3 (Sample 98)


title: MGAS28050_ME_2 (Sample 95)


title: Day40 HPS1-mutant lung epithelial cells replicate 3

description:
HPS1-Rep3
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt

value: HPS1 mutant


title: Day40 HPS8-mutant lung epithelial cells replicate 2

description:
HPS8-Rep2
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: Day40 HPS2-mutant lung epithelial cells replicate 1

description:
HPS2-Rep1
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: PN 146


title: PN 104


title: PN 226


title: MGAS8020_ME_2 (Sample 93)


title: PN 102


title: Day40 HPS1-mutant lung epithelial cells replicate 2

description:
HPS1-Rep2
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: Day40 HPS1-mutant lung epithelial cells replicate 1

description:
HPS1-Rep1
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: PN 148


title: MGAS8020_ME_1 (Sample 92)


title: MGAS7995_ME_2 (Sample 91)


title: PN 98


title: PN 72


title: PN 70


title: MGAS7995_ME_1 (Sample 90)


title: Day40 wild-type lung epithelial cells replicate 2

description:
WT-Rep2
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt

value: Wild-type


title: PN 68


title: MGAS7966_ME_2 (Sample 89)


title: PN 66


title: Day40 HPS2-mutant lung epithelial cells replicate 2

description:
HPS2-Rep2
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: MGAS28689_ME_1 (Sample 96)


title: MGAS7966_ME_1 (Sample 88)


title: PN 48


title: PN 100


title: PN 46


title: MGAS7909_ME_1 (Sample 86)


title: PN 44


title: MGAS7909_ME_2 (Sample 87)


title: MGAS7904_ME_2 (Sample 85)


title: MGAS7904_ME_1 (Sample 84)


title: Day40 wild-type lung epithelial cells replicate 3

description:
WT-Rep3
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: PN 42


title: MGAS7895_ME_2 (Sample 83)


title: MGAS7895_ME_1 (Sample 82)


title: MGAS7893_ME_2 (Sample 81)


title: PN 24


title: PN 22


title: Day40 wild-type lung epithelial cells replicate 1

description:
WT-Rep1
processed data file: Counts_Table.txt
processed data file: Keygenes_Table.txt


title: MGAS32031_ME_2 (Sample 79)


title: MGAS32031_ME_1 (Sample 78)


title: ATACseq_HCAEC_0h_r2


title: MGAS32013_ME_2 (Sample 77)


title: PN 20


title: LTBI 320

value: Latent tuberculosis infection


title: PN 18


title: LTBI 316


title: MGAS7893_ME_1 (Sample 80)


title: LTBI 314


title: LTBI 272


title: MGAS32013_ME_1 (Sample 76)


title: MGAS31997_ME_2 (Sample 75)


title: LTBI 270


title: MGAS31997_ME_1 (Sample 74)


title: R128-H-005

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis*.
Gene level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the GENCODE GRCh38.p10 gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files containing: ensemble gene ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

source_name: bone marrow

extract_protocol:
Cells were resuspended in RLT Plus buffer (Qiagen) and stored at -80 degrees. RNA extraction was carried out using a RNAeasy Plus micro kit (Qiagen) following the manufacturers instructions. Total RNA quality and quantity was assessed using Agilent 2100 Bioanalyser and a RNA Nano 6000 kit (Agilent Technologies). 30-260ng of Total RNA with a RIN value >8 was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), (New England BioLabs, NEB)
Total RNA samples underwent library construction using the NEBNext® Single Cell/ Low input RNA Library Prep Kit for Illumina® (E6420, New England Biolabs®).  One ng of total RNA in 7µL was annealed with cDNA primer to initiate first strand synthesis. Reverse transcription and template switching of the primed samples were followed by amplification of the cDNA by PCR (11 cycles). Amplified cDNA samples were then cleaned using a 1.8x Agencourt AMPure® Beads (Beckman Coulter®). Fragmentation of the cDNA and end repair with 5’phosphorylation and dA-tailing were followed by NEBNext adaptor ligation, U excision, size selection using Agencourt AMPure® XP beads (Beckman Coulter®) and PCR enrichment (8 cycles) of the adaptor-ligated DNA using NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs)(E6440) followed by a clean up of the PCR product using Agencourt AMPure® XP beads (Beckman Coulter®). The libraries were validated using the Agilent 4200 TapStation and kit  (Agilent Technologies) to ascertain the insert size. The Qubit® (Life Technologies) was used to perform the fluorometric quantitation. Following validation, the libraries were normalized to 4nM, pooled together and clustered on the cBot™2 following the manufacturer’s recommendations. The pool was then sequenced using a 75-base paired-end (2x75bp PE) dual index read format on the Illumina® HiSeq4000 according to the manufacturer’s instructions.

tag: immunophenotype

value: LSK CD48- CD150+ (HSC)

tag: genotype

value: Gata2 KO


title: R128-H-007


title: R128-H-006


title: LTBI 268

value: Whole blood


title: R128-H-004

value: Gata2 WT


title: MGAS31971_ME_1 (Sample 72)

tag: time point


title: R128-H-003


title: LTBI 266


title: MGAS31968_ME_2 (Sample 71)


title: LTBI 256


title: MGAS31971_ME_2 (Sample 73)


title: R128-H-002


title: R128-H-001


title: MGAS31960_ME_2 (Sample 69)


title: MGAS31968_ME_1 (Sample 70)


title: LTBI 318


title: LTBI 240


title: MGAS31960_ME_1 (Sample 68)


title: LTBI 250


title: LTBI 252


title: LTBI 254


title: R098-H-012

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis*.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the GENCODE GRCh38.p10 gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

extract_protocol:
Cells were resuspended in RLT Plus buffer (Qiagen) and stored at -80 degrees. RNA extraction was carried out using a RNAeasy Plus micro kit (Qiagen) following the manufacturers instructions. Total RNA quality and quantity was assessed using Agilent 2100 Bioanalyser and a RNA Nano 6000 kit (Agilent Technologies). 30-260ng of Total RNA with a RIN value >8 was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), (New England BioLabs, NEB)
Sequencing libraries were prepared using the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB). The steps included RNA fragmentation and priming, 1st strand cDNA synthesis, 2nd strand cDNA synthesis, adenylation of 3’ ends, adapter ligation, PCR amplification (11-cycles) and validation. The manufacturer’s instructions were followed. The libraries were validated using the Agilent 2100 Bioanalyser and a high-sensitivity kit (Agilent Technologies) to ascertain the insert size, and the Qubit® (Life Technologies) was used to perform the fluorometric quantitation. Following validation, the libraries were normalized to 10nM, pooled together and clustered on the cBot™2 following the manufacturer’s recommendations. The pool was then sequenced using a 75-base paired-end (2x75bp PE) dual index read format on the Illumina® HiSeq4000 according to the manufacturer’s instructions.

tag: oncogene


title: R098-H-008


title: R098-H-002


title: MGAS29475_ME_1 (Sample 66)


title: MGAS29146_ME_2 (Sample 65)


title: MGAS29146_ME_1 (Sample 64)


title: LTBI 236


title: R098-H-011


title: MGAS28941_ME_2 (Sample 63)


title: LTBI 234


title: MGAS28941_ME_1 (Sample 62)


title: R098-H-006


title: MGAS29475_ME_2 (Sample 67)


title: LTBI 174


title: MGAS28912_ME_1 (Sample 60)


title: LTBI 170


title: MGAS28742_ME_2 (Sample 59)


title: LTBI 172


title: R098-H-005


title: LTBI 160


title: R098-H-001


title: MGAS28742_ME_1 (Sample 58)


title: LTBI 238


title: LTBI 158


title: LTBI 156


title: LTBI 176


title: LTBI 154


title: MGAS28706_ME_2 (Sample 57)


title: MGAS28706_ME_1 (Sample 56)


title: R128-H-008


title: R098-H-013


title: MGAS28912_ME_2 (Sample 61)


title: 20-Mbd3-KO-Mbd3a(deltaMBD&C.C.-LIF_minus

description: cultured  under conventional ESCs medium without LIF for 12days.

hyb_protocol: Affymetrix Standard WT Plus Protocol.

scan_protocol: AGCC Standard Protocol.

data_processing: The data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al.  Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.

label_protocol: Affymetrix WT Plus Kit.

extract_protocol: Total RNAs were prepared using RNeasy Kit from Qiagen.

treatment_protocol: Differentiation of ESCs were induced  by withdrawal LIF for 12days.

tag: gender

value: male

tag: cell-type

value: embryonic stem cells


title: MGAS28652_ME_2 (Sample 55)


title: LTBI 110


title: LTBI 108


title: MGAS28652_ME_1 (Sample 54)


title: MGAS28426_ME_1 (Sample 52)

description:
Clinical_isolates_ME_v2.xlsx
wild-type strain


title: MHV68_3T12_18h [Iso-Seq]

city: Gainesville

first: Scott

last: Tibbetts

department: Molecular Genetics & Microbiology

institute: University of Florida

description: poly(A)-selected RNA

data_processing:
Library strategy: Iso-Seq
SMRTportal RS_IsoSeq v.1 with ICE to obtain full-length consensus isoforms
Alignment to the MHV68.ORF73bla genome using GMAP 2014-07-21 with the parameter -n 1
TRIMD end validator and TRIMD start validator to produce bedgraph files of read 5' and 3' ends
Genome_build: The MHV68.ORF73bla genome is a modified version of GCF_000845665.1 genome assembly, with a b-lactamase insert.
Supplementary_files_format_and_content: BedGraph files of read 5' and 3' ends

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) with L-glutamine, 4.5g/L glucose and sodium pyruvate supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared for sequencing using Pacific Biosciences Iso-Seq protocols

treatment_protocol: Cells were plated at a density of 2 x 10^5 cells/well in a flat-bottom 6-well TC-treated cell culture plate. Twenty four hours later, cells were infected at MOI 5 with a floxed, BAC-derived wild-type MHV68 which carries a β-lactamase marker fused to ORF73 (MHV68.ORF73bla). RNA was harvested after 18 hours.

value: NIH 3T12

tag: hpi

tag: virus strain


title: MGAS28330_ME_2 (Sample 51)

tag: sample type

value: ME


title: LTBI 80

description: A combination of 16 non-overlapping arrays to quantitatively measure 640 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: MGAS28330_ME_1 (Sample 50)


title: LTBI 76


title: LTBI 78


title: MGAS28101_ME_1 (Sample 48)


title: LTBI 112


title: 15-Mbd3-KO-Mbd3a(deltaMBD)-LIF_plus

description: cultured  under conventional ESCs medium with LIF.

source_name: 15-Mbd3-KO-Mbd3a(deltaMBD)-LIF plus


title: 16-Mbd3-KO-Mbd3a(deltaCC)-LIF_plus

source_name: 16-Mbd3-KO-Mbd3a(deltaCC)-LIF plus


title: 19-Mbd3-KO-Mbd3a(deltaC.C.)-LIF_minus

source_name: 19-Mbd3-KO-Mbd3a(deltaC.C.)-LIF minus


title: LTBI 56


title: 18-Mbd3-KO-Mbd3a(deltaMBD)-LIF_minus

source_name: 18-Mbd3-KO-Mbd3a(deltaMBD)-LIF minus


title: LTBI 54


title: 17-Mbd3-KO-Mbd3a(delataMBD&C.C.)-LIF_plus


title: 10-Mbd3KO-Empty-LIF_minus

source_name: 10-Mbd3KO-Empty-LIF minus


title: 09-Mbd3KO-Mbd3c-LIF_minus

source_name: 09-Mbd3KO-Mbd3c-LIF minus


title: LTBI 106


title: MGAS28101_ME_2 (Sample 49)

description:
Clinical_isolates_ME_v2.xlsx
clinical isolate

source_name: serotype M28 group A streptococcus strain


title: 07-Mbd3KO-Mbd3a-LIF_minus

source_name: 07-Mbd3KO-Mbd3a-LIF minus


title: 05-Mbd3KO-Empty-LIF_plus

source_name: 05-Mbd3KO-Empty-LIF plus


title: 06-EBRTcH3-LIF_minus

source_name: 06-EBRTcH3-LIF minus


title: MGAS28426_ME_2 (Sample 53)


title: MGAS27961_ME_1 (Sample 46)


title: 04-Mbd3KO-Mbd3c-LIF_plus

source_name: 04-Mbd3KO-Mbd3c-LIF plus


title: LTBI 52


title: 08-Mbd3KO-Mbd3b-LIF_minus

source_name: 08-Mbd3KO-Mbd3b-LIF minus


title: LTBI 50


title: MGAS27961_ME_2 (Sample 47)


title: MGAS28050_ME_1 (Sample 94)


title: MGAS12250_ME_1 (Sample 44)


title: LTBI 32


title: MGAS11107_ME_2 (Sample 43)


title: LTBI 30


title: MGAS11107_ME_1 (Sample 42)


title: LTBI 74


title: 02-Mbd3KO-Mbd3a-LIF_plus

source_name: 02-Mbd3KO-Mbd3a-LIF plus


title: MGAS12250_ME_2 (Sample 45)


title: MGAS10816_ME_2 (Sample 41)


title: LTBI 28

source_name: Culture supernatant from Mtb-stimulated whole blood


title: MGAS29596_ME_1 (Sample 38)


title: MGAS10816_ME_1 (Sample 40)


title: HC 296

value: Healthy


title: LTBI 26


title: HC 292


title: MGAS29555_ME_1 (Sample 36)


title: MGAS29555_ME_2 (Sample 37)


title: HC 294


title: MGAS29596_ME_2 (Sample 39)


title: HC 290


title: MGAS29460_ME_2 (Sample 35)


title: MGAS29454_ME_1 (Sample 33)


title: HC 280


title: MGAS29460_ME_1 (Sample 34)


title: HC 278


title: HC 276


title: MGAS29336_ME_2 (Sample 30)


title: HC 274


title: HC 244


title: HC 242


title: MGAS29298_ME_1 (Sample 27)


title: MGAS29298_ME_2 (Sample 28)


title: HC 200


title: MGAS29251_ME_2 (Sample 26)


title: HC 198


title: MGAS29251_ME_1 (Sample 25)


title: MGAS29250_ME_2 (Sample 24)


title: HC 196


title: MGAS29395_ME_2 (Sample 32)


title: HC 194


title: HC 184


title: MGAS29160_ME_2 (Sample 22)


title: MGAS29160_ME_1 (Sample 21)


title: Human normal lung

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads on containing ploy- N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http:// ) directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
In order to search for novel promoter-associated lncRNA of tumor related  genes, we opened BAM files with IGV and searched promoter region of each  tumor related gene by manually. As a result, we founded a novel transcript  expressed from the promoter region of a tumor suppressor gene. Expression  of the novel RNA was confirmed by RACE and Real-time PCR analysis. Although  there are a normal lung and a lung cancer sample, comparison of expression  level is not performed. Therefore, there is no more advanced analysis data  than BAM.
Genome_build: hg38

source_name: Normal lung

extract_protocol:
Total RNA was prepared from lung cancer specimens using miRNeasy RNA isolation kit (Qiagen, Inc.). Firstly, ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation.
Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C be fore PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Normal lung


title: HC 248


title: HC 246


title: Human lung cancer

source_name: Lung cancer

value: Lung cancer


title: MGAS29336_ME_1 (Sample 29)


title: HC 136


title: HC 178


title: HC 182


title: MGAS29395_ME_1 (Sample 31)


title: HC 180


title: HC 134


title: MGAS28677_ME_2 (Sample 20)


title: RNAseq_HCAEC_24h_r1

city: Montreal

first: Guillaume

last: Lettre

institute: Montreal Heart Institute

data_processing:
Reads were mapped to hg19 using hisat2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
Samtools was used to sort the reads and convert to the BAM format.
Transcripts were first identified for each sample, and then pooled together using stringtie (http://ccb.jhu.edu/software/stringtie/index.shtml)
Transcript abundance was estimated by stringtie and a fragments per kilobase of transcript per million (FPKM) count table was generated
Differential analysis of gene expression was performed using DESeq2 (Love et al. 2014). All possible comparisons for NT, TNFα 4 hours and 24 hours treatments were performed using the analysis of deviance function with default parameters. Genes with a false discovery rate (FDR, Benjamini & Hochberg correction) ≤0.001 and fold-change ≥2 or ≤-2 were considered differentially expressed.
Corresponding biological replicates output were merged using UCSC BigWig and BigBed tools (Kent et al. 2010)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to coverage per bp for merged biological replicates for each condition; abundance measurements corresponds to transcripts FPKM table for each cell line

source_name: Endothelial Cells

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen)
NEBNext mRNA Library Prep Reagent Set for Illumina

value: Human Coronary Artery Endothelial Cells

tag: passages

value: passages 7 to 9

tag: tnf-alpha treatment


title: MGAS28677_ME_1 (Sample 19)

value: clinical isolate


title: MGAS28632_ME_2 (Sample 18)


title: 03-Mbd3KO-Mbd3b-LIF_plus

source_name: 03-Mbd3KO-Mbd3b-LIF plus


title: HC 132


title: MGAS29250_ME_1 (Sample 23)


title: MGAS28632_ME_1 (Sample 17)


title: RNAseq_HCAEC_4h_r1

tag: cell type


title: HC 130

tag: tissue


title: MGAS28553_ME_2 (Sample 16)

tag: strain


title: RNAseq_HCAEC_0h_r2


title: MGAS28411_ME_2 (Sample 14)


title: MGAS28553_ME_1 (Sample 15)


title: MGAS28411_ME_1 (Sample 13)


title: RNAseq_teloHAEC_24h_r2

description:
RNAseq_teloHAEC_24h_merged.bw
RNAseq_teloHAEC_abundance.txt

value: immortalized Human Aortic Endothelial Cells

value: passages 23 to 25


title: HC 114


title: HC 118


title: HC 116


title: RNAseq_teloHAEC_4h_r2

description:
RNAseq_teloHAEC_4h_merged.bw
RNAseq_teloHAEC_abundance.txt


title: HC 88


title: a/α cell with MATa1 deleted [y351b]

city: San Franisco

first: Candace

middle: Sarah

last: Britton

address: N372 Genentech Hall, 600 16th Street, Box 2200

department: Microbiology and Immunology

institute: University of California, San Francisco

description:
MATa/MATα mata1Δ::Nat
y351b

data_processing:
Pseudo-alignment to W. anomalus transcriptome, using kallisto software.
Quantification of gene expression, using sleuth R package.
Genome_build: Wican1_GeneCatalog_CDS_20110222.fasta, downloaded from Joint Genome Institute
Supplementary_files_format_and_content: csv file with transcripts per million for each coding sequenec in the genome in each sample.

organism: Wickerhamomyces anomalus

source_name: a/α cell

growth_protocol: Yeast strains were struck out on YEPD plates from glycerol stocks and grown on YEPD plates for 3-4 days at 30C, single colonies were grown overnight in liquid YEPD at 30C, then diluted back to OD600 = 0.15 in fresh YEPD, grown for about 4 hours at 30C, harvested by centrifugation, and flash frozen in liquid nitrogen.

extract_protocol:
RNA was isolated using a phenol chloroform extraction. mRNA was selected by polyA selection.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MATa/MATalpha mata1delta::Nat

tag: growth conditions

value: YEPD, 30C

tag: strain name

value: yCSB 351


title: RNAseq_HCAEC_4h_r2

address: 5000 Rue Bélanger


title: MGAS28299_ME_2 (Sample 12)

data_processing:
Reads were mapped to the genome of serotype M28 GAS reference strain MGAS6180 using EDGEpro and differentional transcript analysis was performed with DESeq2 (version 1.14.1) using the default settings.
Genome_build: ASM1216v2 (serotype M28 GAS reference strain MGAS6180)
Supplementary_files_format_and_content: xlsx; contains RPKMs for each sample at the corresponding time point

extract_protocol:
Strains were lysed by ballistic disintegration and RNA extracted using Rneasy Mini Kit (Qiagen)
Libraries were prepared using standard Illumina protocols for Gram (+) organisms (clinical isolates) and standard MicrobExpress and NEB protocols for Gram (+) organisms (isogenics)


title: a/α cell with MATa1 deleted [y351a]

description:
MATa/MATα mata1Δ::Nat
y351a


title: HC 86

value: Whole blood

tag: histology


title: RNAseq_HCAEC_24h_r2


title: MGAS28299_ME_1 (Sample 11)


title: MGAS28253_ME_2 (Sample 10)


title: a/α cell with MATα2 deleted [y340a]

description:
MATa/MATα matα2Δ-3::Nat
y340a

value: MATa/MATalpha matalpha2delta-3::Nat

value: yCSB 340


title: HC 84


title: wildtype a/α cell [y8iii]

description:
MATa/MATα
y8iii

value: MATa/MATalpha

value: yCSB 8


title: a/α cell with MATα2 deleted [y340b]

description:
MATa/MATα matα2Δ-3::Nat
y340b


title: HC 120


title: MGAS28245_ME_2 (Sample 8)

value: ME


title: HC 64

value: Healthy


title: HC 82


title: RNAseq_HCAEC_0h_r1


title: RNAseq_teloHAEC_0h_r1

description:
RNAseq_teloHAEC_0h_merged.bw
RNAseq_teloHAEC_abundance.txt


title: RNAseq_teloHAEC_4h_r1


title: wildtype a/α cell [y8ii]

description:
MATa/MATα
y8ii


title: α cell with MATα2 deleted (independently derived deletion) [y339b]

description:
MATα matα2Δ-2::Nat
y339b

source_name: α cell

value: MATalpha matalpha2delta-2::Nat

value: yCSB 339


title: Patient1_Nonmalignant after the patient progressed on the therapy

city: Iowa City

first: Ali

last: Jabbari

state: Iowa

address: 200 Hawkins Drive

department: Dermatology

institute: University of Iowa

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division
10x data was processed with the Cell Ranger pipeline, version 2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix

source_name: PBMC

extract_protocol:
Malignant (CD3+CD4+CD5brightSSChi) and nonmalignant CD4 (CD3+CD4+CD5intSSCint) T cell populations were flow sorted in parallel. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Normal PBMC T Cells


title: MGAS28245_ME_1 (Sample 7)


title: RNAseq_teloHAEC_24h_r1


title: Patient1_Malignant after the patient progressed on the therapy

value: Sezary Syndrome T Cells


title: MGAS28204_ME_2 (Sample 6)

value: clinical isolate


title: MGAS28204_ME_1 (Sample 5)


title: α cell with MATα2 deleted (independently derived deletion) [y339a]

description:
MATα matα2Δ-2::Nat
y339a

tag: genotype


title: RNAseq_teloHAEC_0h_r2

value: immortalized Human Aortic Endothelial Cells


title: WT_DMSO_control_5

city: Haifa

first: Benny

last: Horwitz

address: Faculty of Biology

country: Israel

institute: Technion

data_processing:
Library quality control
FASTQC version 0.11.5
Quality and adapter trimming
trim_galore (uses cutadapt version 1.10)
Mapping
Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting
HTseq-count version 0.6.1
Normalization and differential expression analysis
DESeq2 R package version 1.14.1
Genome_build: GCF_000354255.1_CocheC4_1
Supplementary_files_format_and_content: Normalized counts were created using DESeq2 software.

organism: Bipolaris maydis

source_name: mycelia

growth_protocol: The wild-type C4 (MAT1-2 Tox1+) and the chap1 deletion mutant (∆chap1) strains of C. heterostrophus were grown at 22ºC on complete xylose medium (CMX)  in 16 h white light, 8 h dark cycles

extract_protocol:
Mycelia were harvested, ground in liquid nitrogen and extracted with TriReagent following the manufacturer's instructions.
Illumina TruSeq RNA Library Preparation Kit v2

treatment_protocol: Spores were transferred to liquid CMX medium and incubated with shaking (200 rpm) at 22ºC for 3 days; the cultures were then treated with 0 (DMSO controls) and 0.5, 1, 2 mM ferulic acid acid were incubated for 30 min at 22ºC with shaking (200 rpm).

value: wild type C4

tag: treatment

value: DMSO control


title: α cell with MATα2 deleted [y338b]

description:
MATα matα2Δ-1::Nat
y338b

value: MATalpha matalpha2delta-1::Nat

value: YEPD, 30C

value: yCSB 338


title: α cell with MATα2 deleted [y338a]

description:
MATα matα2Δ-1::Nat
y338a


title: MGAS28166_ME_2 (Sample 4)

tag: time point


title: WT_2mM_5

value: 2 mM FA


title: WT_0_5mM_5

value: 0.5 mM FA


title: MGAS28166_ME_1 (Sample 3)


title: HC 58

value: Whole blood


title: wildtype α cell [y342ii]

description:
MATα
y342ii

value: MATalpha

value: yCSB 342


title: WT_1mM_5

value: 1 mM FA


title: MGAS12241_ME_2 (Sample 2)

value: ME


title: wildtype α cell [y342i]

description:
MATα
y342i


title: HC 8

value: Healthy


title: HC 6


title: Chap_2mM_2

value: chap1 deletion


title: HC 60


title: MGAS12241_ME_1 (Sample 1)


title: HC 4


title: HC 62


title: HC 2


title: CASC9_1

status: Public on Jun 24 2019

city: Wenzhou

first: jingwen

last: geng

address: 270  Xueyuan Road

institute: Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: colon cancer cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon cancer cells

value: colon

tag: cell line

tag: transfection

value: CASC9 GapmeR (GapC9)


title: NC_3

value: control GapmeR (GapNC)


title: control rep3

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

data_processing:
Sequencer Software HiSeq Control Software 2.2.58 was used for base calling of samples processed on Illumina HiSeq 2000. Base calling of samples processed in NextSeq Sequencer was performed with the Real-Time Analysis (RTA) v2.
Sequence reads were trimmed for adapter sequence, and  masked for low-complexityy or low-quality sequence (bbduk v35.92). Read quality was checked for each sample using FastqC v0.11.5. High-quality reads were mapped to CRCh38 whole genome using STAR v2.5.2a aligner.
Counting reads mapped to each gene was performed with HTSeq-count v0.6.0 software. RseqC v2.6.4 was used to distribute reads mapping to annotated genes (CDS_Exons, 5'UTR_Exons, 3'UTR_Exons, Introns)
Genome_build: Human (GRCh38) Lexogen QuantSeq 2.2.3 FWD (genome version GRCh38.77)
Supplementary_files_format_and_content: Non-normalized read counts (tab-delimited text files including features (genes) and the number of reads mapped to each of them)

source_name: control

growth_protocol: 2D culture condition - Cells were seeded onto Matrigel coated 12-well tissue culture plates at a cell density of 4x10^5 cells/well in mTeSR1. Culture medium was changed daily until a confluence of around 90-95%. 3D culture condition- For 3D aggregates formation, cell were incubated with Accutase at 37ºC for 7 min. Cells were then resuspended in mTeSR1 supplemented with ROCKi followed by seeding onto AggrewellTM 800 plate with a cell density of 1.5x10^6 cells/well for a final volume of 1.5 mL/well. After the first 24h of culture medium was changed without ROCKi. Aggregates were maintained in the microwell plate until day 7 of differentiation, when they were transferred to a 6 Well Ultra-Low Attachment Multiple Well plate.

extract_protocol:
Samples from 2D monolayer and 3D aggregates at different stages of cardiac differentiation were singularized with 0.25% trypsin-EDTA at 37ºC for (7-15) min. For enzymatic digestion neutralization, RPMI+10% FBS was added. After centrifugation and washing the cells one time with PBS, the cell pellet was frozen at -80ºC. Total RNA from the samples was extracted using High Pure RNA Isolation Kit (Roche, Cat. 11828665001), according to manufacturer´s instructions. Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina (Cat. No. 015.96) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Lexogen and Illumina standard protocols. Briefly, 500 ng of total RNA were primed with the oligo dT primer containing Illumina-compatible linker sequences. After first strand synthesis, the RNA is removed and second strand is synthesized with Illumina-compatible random primers. After magnetic bead-based purification the libraries were PCR amplified introducing the sequences required for cluster generation. Sequencing was performed using HiSeq (50 cycles protocol) or NextSeq (75 cycles protocol) platforms.

treatment_protocol: In both culture conditions, a temporal modulation of WNT signalling protocol was used. From day 0 to day 6, cells were cultured in RPMI 1640 medium supplemented with B27 minus insulin. At day 0 cells were supplemented with GSK3 inhibitor CHIR at a final concentration of 5 µM in 2D and 11 µM in 3D culture condition. After 24 hours, medium was changed to remove CHIR. At day 3, cells were supplemented with Wnt inhibitor IWP-4 at a final concentration of 5 µM. At day 5, medium was changed. From day 7 until the end of differentiation, cells were cultured in RPMI 1640 supplemented with B27, with medium changed every 3 days until cell harvest.

value: induced pluripotent stem cells

tag: source

value: foreskin fibroblasts

tag: mode of growth

value: seeding

tag: time

value: control


title: CASC9_3


title: NC_1


title: control rep1


title: control rep2


title: 2D_t20 rep3

value: 2D monolayer

value: 20 days


title: 2D_t18 rep3

value: 18 days


title: 2D_t12 rep3

value: 12 days


title: 2D_t15 rep3

value: 15 days


title: 2D_t9 rep3

value: 9 days


title: 2D_t1 rep3

value: 1 day


title: 2D_t5 rep3

value: 5 days


title: 2D_t7 rep3

value: 7 days


title: 2D_t20 rep2


title: 2D_t0 rep3

value: 0 days


title: 2D_t18 rep2


title: 2D_t3 rep3

value: 3 days


title: CASC9_2

value: colon cancer cells

value: colon

value: CASC9 GapmeR (GapC9)


title: 2D_t15 rep2

value: induced pluripotent stem cells

value: foreskin fibroblasts


title: 2D_t5 rep2


title: 01-EBRTcH3-LIF_plus

city: Hidaka

first: Akihiko

last: Okuda

address: 1397-1 Yamane

institute: Saitama Medical University

source_name: 01-EBRTcH3-LIF plus

tag: gender

value: male

tag: cell-type

value: embryonic stem cells


title: 2D_t7 rep2

tag: cell type

value: 2D monolayer


title: 2D_t12 rep2


title: NC_2

tag: tissue

value: control GapmeR (GapNC)


title: 2D_t3 rep2


title: 2D_t1 rep2


title: 2D_t9 rep2


title: 2D_t0 rep2


title: 2D_t20 rep1

value: 20 days


title: 2D_t18 rep1

value: 18 days


title: 2D_t15 rep1

value: 15 days


title: 2D_t7 rep1


title: 2D_t5 rep1


title: 2D_t0 rep1


title: 2D_t1 rep1

value: 1 day


title: ChIPseq_Input

city: Boston

first: Li

last: Jia

state: MA

address: 20 Shattuck Street

department: Surgery

institute: Brigham and Women's Hospital

data_processing:
bcl2fastq v2.18 used for base calling with default parameters
ChIP-seq data was mapped to human genome (hg19) using Bowtie2 (v2.3.0) with default settings.
Reads that did not map uniquely were removed.
Genomic coverage of each factor was generated with the deepTools2 program (v2.4.0) with the following configurations --binSize 10 --normalizeTo1x 2451960000 --ignoreForNormalization chrX --ignoreDuplicates
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files that contain the genomic coverage of each factor

source_name: prostate cancer cell line

growth_protocol: LNCaP cells were maintaned in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
Protein-DNA complexes were isolated from sonicated LNCaP cell lysates with indicated antibodies, and the ChIP DNA was extracted using phenol chloroform extraction method. Purified ChIP DNA was dissolved in TE buffer and re-sheared using Covaris sonicator to enable enrichment of fragments with an average size of 300 bp. The re-sheared DNA samples were purified for library preparation using the minElute PCR purification kit (Qiagen).
The ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics; R400427) according to the manufacturer’s instructions.

treatment_protocol: LNCaP cells were treated with vehicle control or 10 uM of UPF-1069 for 16 hours.

value: prostate cancer cell line

value: LNCaP

value: DMSO

tag: chip-antibody


title: ChIPseq_FOXA1_DMSO_rep2

value: FOXA1 (Abcam, ab23738)


title: ChIPseq_H3K27Ac_DMSO_rep2

value: H3K27Ac (Abcam, ab4729)


title: ChIPseq_FOXA1_UPF1069_rep1


title: ChIPseq_FOXA1_UPF_1069_rep2


title: ChIPseq_H3K27Ac_UPF1069_rep1


title: ChIPseq_H3K27Ac_DMSO_rep1


title: ChIPseq_H3K27Ac_UPF_1069_rep2


title: MGAS28253_ME_1 (Sample 9)

city: Houston

first: Paul

last: Bernard

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

source_name: serotype M28 group A streptococcus strain

tag: strain

tag: sample type

value: clinical isolate

value: ME


title: ChIPseq_AR_DMSO_rep2

value: AR (Abcam, ab74272)


title: ChIPseq_AR_UPF_1069_rep2


title: ChIPseq_AR_DMSO_rep1


title: ChIPseq_AR_UPF1069_rep1


title: siPARP2-A-rep1

description: processed data file: PARP_KO.csv

data_processing:
bcl2fastq v2.18 used for base calling with default parameters
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat2 (v2.1.0) with default setting.
Raw counts (counts per million, cpm) were generated by HTseq (v0.6.1) using the union method with default parameters. Genes that had at least 1 read per million in at least half of the samples were kept for further analysis.
The number of reads were normalized using the EdgeR package (3.12.0) for R.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited csv files include normalized counts per million for each Sample

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA-Seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit (New England BioLabs; E7530) according to the manufacturer’s instructions

treatment_protocol: LNCaP cells were treated with vehicle control or 10 uM of each PARP inhibitors for 24 hours. And for gene knockdown experiments, LNCaP cells were transfected with indicated siRNA for 72 hours.

value: siPARP2 #A


title: siPARP2-B-rep2

description: processed data file: PARP_KO.csv

value: siPARP2 #B


title: siPARP2-B-rep1

description: processed data file: PARP_KO.csv


title: siPARP1-B-rep2

description: processed data file: PARP_KO.csv

value: siPARP1 #B


title: 2D_t9 rep1

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 2D monolayer

value: 9 days


title: 2D_t3 rep1

value: 3 days


title: siPARP2-A-rep2

description: processed data file: PARP_KO.csv


title: siPARP1-A-rep2

description: processed data file: PARP_KO.csv

value: siPARP1 #A


title: siNC-rep2

description: processed data file: PARP_KO.csv

value: prostate cancer cell line

value: siNC


title: RiboMethSeq shCtrl rep2

city: Riverside

first: LIN

last: LI

state: California

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

description:
ribosome RNA
RiboMethScore.xlsx

data_processing:
Library strategy: Ribometh-seq
The sequencing results were first trimmed using Trimmomatic-0.35 and then aligned to the reference rRNA sequence using Bowtie2 (2.3.4.2). After 5’-end counting, the RiboMethScore were calculated.
RiboMethScore=1- ni/(0.5*((SUM(nj*Wj))/(SUM(Wj))+(SUM(nk*Wk))/(SUM(Wk)))).In the formula, ni is the 5’-end count for a given position. j and k denotes the position i-6 to i-1 and position i+1 to i+6, respectively. The weight parameters (W) were defined as Wj = 1–0.1*(j−1) or Wk = 1–0.1*(k−1).
Genome_build: reference rRNA sequence U13369.1
Supplementary_files_format_and_content: For RiboMethSeq, the csv files include the 5'-end count of every given position. The xlsx file includes the calculated RiboMethScore for given positions for each replicates.

growth_protocol: Cells were cultured at 37 oC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted with Omega Total RNA Kit I (Omega) and quantified.Generally, 200 ng RNA was fragmented in a bicarbonate buffer (50 mM Sodium bicarbonate, pH 9.2) at 95 °C for 6 min. After purification, the RNA samples were 3'-end dephosphorylated using 5 U of Antarctic phosphatase (NEB) for 30 min at 37 °C. The 5'-end phosphorylation was subsequently performed using T4 PNK (NEB) at 37 °C for 1 hr. The RNA samples were purified with RNeasy MinElute Cleanup kit (Qiagen).
The library construction was conducted using NEBNext Small RNA Library kit (NEB) following the manufacturer’s instructions. Multiplexed libraries were sequenced with Illumina Hiseq4000 instrument in a 50 bp single-end read mode (Illumina).

treatment_protocol: Cells were transfected with shCtrl or shSLIRP for 48 hours before harvest.

value: Human embryonic kidney cells

value: control


title: RiboMethSeq shCtrl rep3

description:
ribosome RNA
RiboMethScore.xlsx


title: RiboMethSeq shSLIRP rep2

description:
ribosome RNA
RiboMethScore.xlsx

value: SLIRP knockdown


title: RiboMethSeq shSLIRP rep3

description:
ribosome RNA
RiboMethScore.xlsx


title: ChIPseq_FOXA1_DMSO_rep1

value: LNCaP

value: DMSO

value: FOXA1 (Abcam, ab23738)


title: siPARP1-A-rep1

description: processed data file: PARP_KO.csv


title: siPARP1-B-rep1

description: processed data file: PARP_KO.csv


title: RiboMethSeq shCtrl rep1

description:
ribosome RNA
RiboMethScore.xlsx


title: siNC-rep1

description: processed data file: PARP_KO.csv


title: RiboMethSeq shSLIRP rep1

description:
ribosome RNA
RiboMethScore.xlsx


title: veliparib-rep1

description: processed data file: PARPi.csv

value: veliparib


title: Treated replicate 2

city: Seattle

first: Amit

last: Sharma

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to Mnem 1.0 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1p1.
Genome_build: Mnem 1.0
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq v0.6.1p1

organism: Macaca nemestrina

source_name: CD4+ T-cells

growth_protocol: Immortalized pig-tailed macaque (Ptm) CD4+ lymphocytes were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% FBS, 2 mM L-glutamine, 1x Anti-anti, and 100 U/ml of interleukin-2 (Roche).

extract_protocol:
RNA was extracted and purified from the Ptm lymphocytes using the RNeasy Mini kit (Qiagen) following manufacturer's protocol. Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences).
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) and a Sciclone NGSx Workstation (PerkinElmer).  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies). Additional  library QC, blending of pooled indexed libraries, and cluster optimization were performed using Life Technologies’ Invitrogen Qubit 2.0 Fluorometer (Life Technologies-Invitrogen). RNA-seq libraries were pooled (6-plex) onto a flow cell lane. Sequencing was performed using an Illumina HiSeq 2500 in rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy.

treatment_protocol: Triplicate cultures of immortalized pig-tailed macaque lymphocytes were left untreated or treated with IFNα at a concentration similar to that observed in natural SIV and HIV-1 infection (1000 U/ml) for 24 hours.

value: Immortalized CD4+ T-cells

value: Blood

tag: ifna treatment (1000 u/ml; 24 hours)

value: Treated


title: Treated replicate 1


title: Treated replicate 3


title: Untreated replicate 3

value: Untreated


title: olaparib-rep2

description: processed data file: PARPi.csv

value: olaparib


title: Untreated replicate 2


title: UPF1069-rep2

description: processed data file: PARPi.csv


title: UPF1069-rep1

description: processed data file: PARPi.csv


title: DMSO-rep2

description: processed data file: PARPi.csv


title: Untreated replicate 1


title: DMSO-rep1

description: processed data file: PARPi.csv


title: cisLiver10D2

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: replicate 2

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: mm10
Supplementary_files_format_and_content: no

source_name: Liver

extract_protocol: Briefly, the excised oligomers are immunopricipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with anti-cisplatin antibodies.  This is followed by PCR amplification with index primers and NGS sequencing on HiSeq 4000 platform.

value: cisplatin

value: wild type

tag: age

value: post natal day 6 months


title: cisLiver36h2

description: replicate 2

tag: genotype


title: veliparib-rep2

description: processed data file: PARPi.csv

value: prostate cancer cell line

tag: treatment


title: cisLiver4D2

description: replicate 2