title: Single cell fibroblast CAP26_C64


title: Single cell fibroblast CAP26_C58

status: Public on Oct 08 2019

type: SRA

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

description:
Single cell fibroblast
processed.data.trisomic_diploid.tar.gz

library_source: transcriptomic

data_processing:
[Single cell RNA-seq]  RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 10 million reads and/or cells with <10% of expressed genes (total number of 56680 genes) were excluded from the analyses.
[Allele specific expression]  Cellular Allelic Specific Expression (ASE) of each heterozygous site was calculated in the diploid and trisomic fraction of the genome of each single cell per individual using two different formulas (provided in the manuscript). In both cases, ASE values range from 0 to 1 (Supplementary Figure 5). We consider 0≤ASE≤0.1 as the signature of monoallelic expression of the Alternative allele (euploid) or Single allele (trisomic). Conversely 0.9≤ASE≤1 indicates monoallelic expression of the Reference allele in the case of diploid cells or of the Double allele in the case of (trisomic cells). ASE from 0.1 to 0.9 is an indicator of biallelic expression.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: processed.data.trisomic_diploid.tar.gz, twin1B.10x.processed.csv, twin2A.10x.processed.csv

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described

extract_protocol:
Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer’s procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis.
Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina)
Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 10 million reads and/or cells with <10% of expressed genes (total number of 56680 genes) were excluded from the analyses.

tag: cell type

value: primary skin fibroblast

tag: trisomy type

tag: cell line

value: fibroblast


title: Single cell fibroblast CAP37_C39

treatment_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described


title: Single cell fibroblast CAP37_C35


title: Single cell fibroblast CAP26_C53


title: Single cell fibroblast CAP37_C30


title: Single cell fibroblast CAP37_C45


title: Single cell fibroblast CAP26_C17


title: Single cell fibroblast CAP26_C30


title: Single cell fibroblast CAP26_C07


title: Single cell fibroblast CAP26_C16


title: Single cell fibroblast CAP26_C08


title: Single cell fibroblast CAP37_C96


title: Single cell fibroblast CAP26_C02


title: Single cell fibroblast CAP37_C88


title: Single cell fibroblast CAP37_C95


title: Single cell fibroblast CAP37_C92


title: Single cell fibroblast CAP26_C89


title: Single cell fibroblast CAP37_C84


title: Single cell fibroblast CAP37_C86


title: Single cell fibroblast CAP37_C87


title: Single cell fibroblast CAP37_C83


title: Single cell fibroblast CAP37_C81


title: Single cell fibroblast CAP26_C59


title: Single cell fibroblast CAP37_C80


title: Single cell fibroblast CAP37_C75


title: Single cell fibroblast CAP37_C73


title: Single cell fibroblast CAP37_C70


title: Single cell fibroblast CAP37_C68


title: Single cell fibroblast CAP37_C62


title: Single cell fibroblast CAP37_C67


title: Single cell fibroblast CAP37_C66


title: Single cell fibroblast CAP37_C53


title: Single cell fibroblast CAP37_C54


title: Single cell fibroblast CAP37_C58


title: Single cell fibroblast CAP37_C59


title: Single cell fibroblast CAP37_C48


title: Single cell fibroblast CAP37_C47


title: Single cell fibroblast CAP37_C50


title: Single cell fibroblast CAP37_C52


title: Single cell fibroblast CAP37_C85


title: Single cell fibroblast CAP37_C44


title: Single cell fibroblast CAP37_C41


title: Single cell fibroblast CAP37_C46


title: Single cell fibroblast CAP37_C33


title: Single cell fibroblast CAP37_C32


title: Single cell fibroblast CAP37_C24


title: Single cell fibroblast CAP37_C28


title: Single cell fibroblast CAP37_C26


title: Single cell fibroblast CAP37_C23


title: Single cell fibroblast CAP37_C29


title: Single cell fibroblast CAP37_C21


title: Single cell fibroblast CAP37_C20


title: Single cell fibroblast CAP37_C60


title: Single cell fibroblast CAP37_C15


title: Single cell fibroblast CAP37_C14


title: Single cell fibroblast CAP37_C10


title: Single cell fibroblast CAP37_C34


title: Single cell fibroblast CAP37_C06


title: Single cell fibroblast CAP37_C09


title: Single cell fibroblast CAP37_C31


title: Single cell fibroblast CAP37_C08


title: Single cell fibroblast CAP37_C05


title: Single cell fibroblast CAP37_C12


title: Single cell fibroblast CAP37_C04


title: Single cell fibroblast CAP37_C02


title: Blood_T0_rep2

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
802_1_1
Gene expression T0 (after anesthesia, and before MCA occlusion)
Globin mRNA depleted

hyb_protocol: An equal amount (3.75 µg) of Cy3 cRNA probes were hybridized on 4 x 44k Agilent DNA chip (catalogue number: G2519F, Macacca mulatta). Hybridization was performed for 17 hours, rotating at 10 rpm at 65°C.

scan_protocol: Hybridization images were obtained using Agilent DNA microarray scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Macaca mulatta

source_name: Blood sample T0 before surgery, Monkey S1, replicate 2

label_protocol: RNA from cerebral cortex (30 ng) and from blood sample (30 ng) were labelled using Low Input Quick Amp Labeling kit (Agilent Technologies).

extract_protocol: RNA was isolated from cerebral cortex using the RNeasy Microarray Tissue kit following the manufacturer’s instructions (Qiagen). RNA was isolated from blood samples using PAXgene Blood RNA Kit (PreAnalytix). Globin mRNA were removed from total RNA using the GlobinClear kit (Ambion). RNA integrity was assessed with the Agilent 2100 BioAnalyzer (Agilent Technologies).

tag: gender

value: Male

tag: age

value: 12-13 years old

tag: weight

tag: tissue

value: Peripheral blood


title: Single cell fibroblast CAP26_C95


title: Blood_T4h30_rep1

description:
801_1_4
Gene expression T4H30 after MCA occlusion
Globin mRNA depleted

source_name: Blood sample T4H30 after MCA occlusion, Monkey S2, replicate 1


title: Blood_T3h30_rep1

description:
801_1_3
Gene expression T3H30 after MCA occlusion
Globin mRNA depleted

source_name: Blood sample T3H30 after MCA occlusion, Monkey S2, replicate 1


title: Blood_T2H_rep2

description:
802_1_2
Gene expression T2H after MCA occlusion
Globin mRNA depleted

source_name: Blood sample T2H after MCA occlusion, Monkey S1, replicate 2


title: Blood_T3H30_rep2

description:
802_1_3
Gene expression T3H30 after MCA occlusion
Globin mRNA depleted

source_name: Blood sample T3H30 after MCA occlusion, Monkey S1, replicate 2


title: Blood_T2H_rep1

description:
801_1_2
Gene expression T2H after MCA occlusion
Globin mRNA depleted

source_name: Blood sample T2H after MCA occlusion, Monkey S2, replicate 1


title: Contralateral_S2_rep3

description:
799_1_2
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 2, Monkey S2, replicate 3

value: Brain


title: Blood_T0_rep1

description:
801_1_1
Gene expression T0 (after anesthesia, and before MCA occlusion)
Globin mRNA depleted

source_name: Blood sample T0 before surgery, Monkey S2, replicate 1


title: Ipsilateral_S2_rep4

description:
799_1_3
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 2, Monkey S2, replicate 4


title: Blood_T4H30_rep2

description:
802_1_4
Gene expression T4H30 after MCA occlusion
Globin mRNA depleted

source_name: Blood sample T4H30 after MCA occlusion, Monkey S1, replicate 2


title: Ipsilateral_S2_rep3

description:
799_1_1
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 2, Monkey S2, replicate 3


title: Single cell fibroblast CAP26_C91


title: Single cell fibroblast CAP26_C85


title: Ipsilateral_S2_rep6

description:
798_1_3
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 3, Monkey S2, replicate 6


title: Single cell fibroblast CAP26_C90


title: Contralateral_S2_rep6

description:
798_1_4
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 3, Monkey S2, replicate 6


title: Single cell fibroblast CAP26_C84


title: Contralateral_S2_rep4

description:
799_1_4
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 2, Monkey S2, replicate 4


title: Ipsilateral_S2_rep5

description:
798_1_1
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 2, Monkey S2, replicate 5


title: Contralateral_S2_rep5

description:
798_1_2
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 2, Monkey S2, replicate 5


title: Single cell fibroblast CAP26_C83

description:
Single cell fibroblast
processed.data.trisomic_diploid.tar.gz


title: Contralateral_S2_rep2

description:
797_1_4
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 3, Monkey S2, replicate 2


title: Ipsilateral_S2_rep1

description:
797_1_1
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 3, Monkey S2, replicate 1


title: Contralateral_S2_rep1

description:
797_1_2
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 3, Monkey S2, replicate 1


title: Single cell fibroblast CAP26_C77


title: Single cell fibroblast CAP26_C93


title: Single cell fibroblast CAP26_C78


title: Single cell fibroblast CAP37_C74


title: Ipsilateral_S2_rep2

description:
797_1_3
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 3, Monkey S2, replicate 2


title: Single cell fibroblast CAP26_C76


title: Single cell fibroblast CAP26_C75


title: Single cell fibroblast CAP26_C79


title: Single cell fibroblast CAP26_C74


title: Single cell fibroblast CAP26_C92


title: Single cell fibroblast CAP26_C72


title: Ipsilateral_S1_rep5

description:
796_1_1
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 2, Monkey S1, replicate 5


title: Contralateral_S1_rep6

description:
796_1_4
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 3, Monkey S1, replicate 6


title: Ipsilateral_S1_rep6

description:
796_1_3
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 3, Monkey S1, replicate 6


title: Contralateral_S1_rep5

description:
796_1_2
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 2, Monkey S1, replicate 5


title: Single cell fibroblast CAP26_C67


title: Ipsilateral_S1_rep4

description:
795_1_3
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 2, Monkey S1, replicate 4


title: Contralateral_S1_rep4

description:
795_1_4
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 2, Monkey S1, replicate 4


title: Contralateral_S1_rep3

description:
795_1_2
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 2, Monkey S1, replicate 3


title: Single cell fibroblast CAP26_C63


title: Single cell fibroblast CAP26_C61


title: Contralateral_S1_rep2

description:
794_1_4
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 3, Monkey S1, replicate 2


title: Single cell fibroblast CAP26_C62


title: Ipsilateral_S1_rep3

description:
795_1_1
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 2, Monkey S1, replicate 3


title: AH_LB2

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

country: United Kingdom

institute: Imperial College

description: EMSA-seq assay

library_source: genomic

data_processing:
Library strategy: EMSA-seq
Basecalls performed using CASAVA 1.8.4
Reads were aligned to NC_002578.1  T.acidophilum genome assembly or to E.Coli C600 genome (CP031214) obtained from ncbi, using Bowtie2
Paired-end 100bp reads were first trimmed using BBDuk v37.64 (parameters: ktrim=r, k=21, hdist=1, edist=0, mink=11, qtrim=rl, trimq=30, minlength=10, ordered=t, qin=33) and then merged using BBmerge v37.64 (parameters: mininsert=10, mininsert0=10).
The merged reads were mapped to the T. acidophilum DSM1728 genome (GCA_000195915.1) or to E.Coli C600 genome (CP031214) using Bowtie2 (-U).
Coverage tracks were computed using deeptools bamCoverage (RPGC normalization, effective genome size: 1564906bp), measuring coverage for reads of sizes 40-65bp and 70-100bp separately. Reads from the sonicated DNA control samples were mapped in paired-end mode. Coverage was computed independently of read size and smoothed over 10kbp to avoid introducing noise from the input into the MNase signal. Genome-wide coverage of MNase-digested samples was then divided by its corresponding undigested DNA sample to remove bias in coverage associated with replication. Lastly, coverage was converted into a Z-score using the scale function in R.
Genome_build: T.acidophilum : NC_002578.1 ;  E.coli : CP031214
Supplementary_files_format_and_content: Bigwig

molecule: genomic DNA

organism: synthetic construct

source_name: EMSA on Synthetic oligo nucleotides, Hta-bound fast band

growth_protocol: T. acidophilum strain 122-1B2 was obtained from DSMZ (https://www.dsmz.de/) and cultured using the medium described in (Searcy and Stein 1980), supplemented to a final concentration of 2g/L yeast extract (BD Biosciences). The medium was boiled for five minutes and allowed to cool to 58°C before inoculation. Cultures were incubated at 59°C with shaking (90rpm) in an INFORS Thermotron incubator.

extract_protocol: LB Corresponds to HTa bound Faster Samples. For EMSA, fresh HTa aliquots were mixed with a pool of randomized oligos -500ng per reaction- in a mass ratio of 0.2 in a buffer containing a final concentration of 1% glycerol, 20 mM NaCl, 30 mM Tris-Hcl, 0.7 mM EDTA in a final volume of 24µL. 4µL of 6x loading buffer (without SDS, NEB #B7025S) were added just before gel electrophoresis. For each replicate 10 reaction were run on the same gel (12 % polyacrylamide) at 90V for 70 min at 4°C, in a prechilled 10 mM Tris pH8 buffer. DNA was stained with EtBr and gel washed twice before imaging. After imaging, DNA the wo visible bandshifts were separately extracted from the gel following the crush ad soak method, pooling the ten wells for each replicate. DNA concentration was measured by Qbit before library preparation.

treatment_protocol: T. acidophilum cells self-lyse at pH>6 (Robb et al. 1995). Pellets were therefore directly re-suspended in ice-cold MNase digestion buffer (10mM Tris, 5mM Ca2+, pH8) and homogenized by 20 passages through a Dounce homogenizer, on ice. Unfixed crude lysates were digested in the presence of 4U/mL of MNase (Thermo Fisher) at 37°C. Digestion was stopped by addition of EDTA to a final concentration of 20mM. Samples were incubated for an additional 30min at 37°C in the presence of RNAse A to a final concentration of 0.5mg/mL and then overnight at 65°C in the presence of SDS (1%) and proteinase K (125µg/mL). Undigested lysate was incubated as above but without addition of enzyme. Undigested DNA was then sonicated using a Covaris S220 sonicator with the following settings: peak power: 175, duty: 10, cycle/burst: 200 for 430s (target size: 150bp).

tag: strain


title: AH_LB1

description: EMSA-seq assay


title: Ipsilateral_S1_rep2

description:
794_1_3
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 3, Monkey S1, replicate 2


title: Contralateral_S1_rep1

description:
794_1_2
Gene expression after MCA occlusion

source_name: Contralateral hemisphere, Cut 3, Monkey S1, replicate 1


title: Single cell fibroblast CAP26_C54


title: Ipsilateral_S1_rep1

description:
794_1_1
Gene expression after MCA occlusion

source_name: Ipsilateral hemisphere (ischemia), Cut 3, Monkey S1, replicate 1


title: PD101_naive

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Single-cell RNA-seq of unstimulated cells

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 2.0.0).
To identify the CRISPR guide RNAs in each cell, a reference genome was created by extending the human GRCh38 genome with RNA sequences of all used guide RNAs with Cell Ranger mkref.
Sequencing data were aligned to the reference genome with Cell Ranger count and merged with Cell Ranger aggr.
Genome_build: GRCh38/h38
Supplementary_files_format_and_content: raw_gene_bc_matrices_h5.h5; read count matrix with cells / barcodes (columns) and genes (rows)
Supplementary_files_format_and_content: CellAnnotation.tsv; mapping of cells / barcodes to samples

source_name: Jurkat cells

growth_protocol: Jurkat cells stably expressing SpCas9 (after transduction with lentiCas9-Blast, Addgene #52962) were kept in RPMI medium + 10% FCS + penicillin/streptomycin containing 25 μg/ml blasticidin. After transduction with gRNA-encoding lentiviral particles (CROPseq-Guide-Puro), cells were selected with 2 μg/ml puromycin for 10 days, while keeping up the selection for blasticidin, and then used in T cell receptor stimulation experiments followed by CROP-seq (or bulk RNA-seq on single knockout lines for validation). See [Datlinger et al, Nature Methods, 2017].

extract_protocol:
Adherent cells were detached using Trypsin-EDTA (Gibco #25300-054), following standard cell culture practices. Cells were collected by centrifugation at 300 rcf for 5 min, washed once with PBS-0.01% BSA (freshly prepared on the day of the run), and resuspended in 1 ml of PBS-0.01% BSA. Cells were filtered through a 40 µm cell strainer to obtain a suspension of single-cells, which were counted using a CASY device. See [Datlinger et al, Nature Methods, 2017].
Single-cell RNA-seq was performed using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Jurkat cells were serum-starved for 3 hours prior to stimulation. They were stimulated with 1 µg/ml anti-CD3 (eBioscience #16-0037) and 1 µg/ml anti-CD28 antibody (eBioscience #16-0289-81) for 4 hours while under starvation and then subjected to CROP-seq. The unstimulated (naïve) control was subjected to continued starvation. See [Datlinger et al, Nature Methods, 2017].

value: Jurkat cells

tag: condition

value: unstimulated


title: Single cell fibroblast CAP26_C56

description:
Single cell fibroblast
processed.data.trisomic_diploid.tar.gz


title: Single cell fibroblast CAP26_C52


title: Single cell fibroblast CAP26_C49


title: AH_HB2

description: EMSA-seq assay

source_name: EMSA on Synthetic oligo nucleotides, Hta-bound slow band

extract_protocol: HB Corresponds to HTa bound Slower Samples. For EMSA, fresh HTa aliquots were mixed with a pool of randomized oligos -500ng per reaction- in a mass ratio of 0.2 in a buffer containing a final concentration of 1% glycerol, 20 mM NaCl, 30 mM Tris-Hcl, 0.7 mM EDTA in a final volume of 24µL. 4µL of 6x loading buffer (without SDS, NEB #B7025S) were added just before gel electrophoresis. For each replicate 10 reaction were run on the same gel (12 % polyacrylamide) at 90V for 70 min at 4°C, in a prechilled 10 mM Tris pH8 buffer. DNA was stained with EtBr and gel washed twice before imaging. After imaging, DNA the wo visible bandshifts were separately extracted from the gel following the crush ad soak method, pooling the ten wells for each replicate. DNA concentration was measured by Qbit before library preparation.


title: AH_HB1

description: EMSA-seq assay


title: Single cell fibroblast CAP26_C48


title: Single cell fibroblast CAP26_C68


title: Single cell fibroblast CAP26_C45


title: Single cell fibroblast CAP26_C57


title: NCF_WoundClosure_rep6

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

description: WC, donor 6

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCh38.80
Supplementary_files_format_and_content: Raw_counts.txt

source_name: Bronchi

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Kit (Qiagen, Hombrechtikon, Switzerland)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flagelin (1mg/ml) was added for 24h in two conditions: NW and WC

value: Primary culture of regenerated airway epithelium

tag: genotype

value: Wild type

tag: individual

value: donor 6

tag: stage of repair process

value: WoundClosure

tag: disease state

value: NCF


title: NCF_WoundClosure_rep5

description: WC, donor 5

value: donor 5


title: PD101_stim

description: Single-cell RNA-seq of stimulated cells

value: stimulated with anti-CD3 and anti-CD28 antibodies


title: NCF_WoundClosure_rep7

description: WC, donor 7

value: donor 7


title: NCF_WoundClosure_rep2

description: WC, donor 2

value: donor 2


title: NCF_WoundClosure_rep3

description: WC, donor 3

value: donor 3


title: Single cell fibroblast CAP26_C42

value: primary skin fibroblast

value: fibroblast


title: NCF_WoundClosure_rep1

description: WC, donor 1

value: donor 1


title: Single cell fibroblast CAP26_C43


title: Single cell fibroblast CAP26_C38


title: NCF_NotWounded_rep7

description: NW, donor 7

value: NotWounded


title: Single cell fibroblast CAP26_C55


title: Single cell fibroblast CAP26_C37


title: NCF_NotWounded_rep6

description: NW, donor 6


title: Single cell fibroblast CAP26_C35


title: Single cell fibroblast CAP26_C36


title: Single cell fibroblast CAP26_C34


title: NCF_NotWounded_rep5

description: NW, donor 5


title: Single cell fibroblast CAP26_C32


title: Single cell fibroblast CAP26_C26


title: NCF_NotWounded_rep3

description: NW, donor 3


title: NCF_FlagWoundClosure_rep6

description: WC + flagelin 24h, donor 6

tag: treatment

value: flagelin

value: WoundClosure (Flag)


title: NCF_NotWounded_rep2

description: NW, donor 2


title: NCF_FlagWoundClosure_rep7

description: WC + flagelin 24h, donor 7


title: Single cell fibroblast CAP26_C22


title: Single cell fibroblast CAP26_C20


title: NCF_NotWounded_rep1

description: NW, donor 1


title: Single cell fibroblast CAP26_C19


title: Single cell fibroblast CAP26_C18


title: Single cell fibroblast CAP26_C14


title: NCF_FlagWoundClosure_rep5

description: WC + flagelin 24h, donor 5


title: NCF_FlagWoundClosure_rep3

description: WC + flagelin 24h, donor 3


title: NCF_FlagWoundClosure_rep2

description: WC + flagelin 24h, donor 2


title: NCF_FlagWoundClosure_rep1

description: WC + flagelin 24h, donor 1


title: Single cell fibroblast CAP26_C10


title: Single cell fibroblast CAP26_C09


title: NCF_FlagNotWounded_rep6

description: NW + flagelin 24h, donor 6

value: NotWounded (Flag)


title: NCF_FlagNotWounded_rep7

description: NW + flagelin 24h, donor 7

value: Primary culture of regenerated airway epithelium


title: Single cell fibroblast CAP26_C05


title: NCF_FlagNotWounded_rep5

description: NW + flagelin 24h, donor 5

value: Wild type


title: Single cell fibroblast CAP26_C04


title: NCF_FlagNotWounded_rep3

description: NW + flagelin 24h, donor 3


title: SY5Y

city: Kensington

first: Pei

last: Liu

address: C25 Lowy Cancer Research Centre

country: Australia

institute: CCIA

data_processing:
The unique RNA-Seq reads of 6 neuroblastoma cell lines (SKNAS, SY5Y, CHP134, SKNDZ, Kelley, and BE2C) were each aligned to Hg19 using STAR aligner (Dobin:2012). The aligned reads were counted towards Gencode V.18 (Harrow:2012) to quantify gene expression for all genes using the union model. Genes were considered expressed if they had an expression of ≥1 counts per million in at least two samples. The expression of all samples were normalised using the Trimmed Mean of M values model, and differential expression analysis was performed using EdgeR (Robinson:2010), comparing the MYCN-amplified (CHP134, SKNDZ, Kelley, and BE2C) versus the MYCN-non-amplified (SKNAS, SY5Y) cell lines. Genes with an absolute log2 fold change of >1 and a false discovery rate of <0.05 were considered differentially expressed.
Supplementary_files_format_and_content: Excel files include normalized abundance measurements for each Sample.

source_name: SH-SY5Y neuroblastoma cell line

growth_protocol: BE(2)-C, SK-N-AS, SH-SY5Y and SK-N-DZ neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum. CHP134 and Kelly were cultured in Roswell Park Memorial Institute medium (RPMI) supplemented with 10% fetal calf serum.

extract_protocol:
RNA was extracted from 6 human neuroblastoma cell lines [BE(2)-C, Kelly, CHP134, SK-N-DZ, SK-N-AS and SY-5Y] using Direct-zol™ RNA kit (Zymo Research, Irvine, CA), purified with RNeasy Plus Mini kit (Qiagen, Valencia, CA), and removed of genomic DNA and ribosomal RNA with Ribo-Zero™ rRNA Removal Magnetic kit (Illumina, San Diego, CA) respectively.
One hundred nanogram of ribosomal-depleted RNA was used as input to the TruSeq mRNA Sample Prep v2 kit (Illumina), without the poly-A pulldown step. Sample preparation was performed according to the manufacturer’s instructions but starting with a 94°C incubation at 2 minutes to elute, fragment and prime the RNA samples. PCR cycles were reduced from 15 to 12 cycles to minimize the duplication rate. The libraries were multiplexed into one lane and sequenced on a HiSeq2000 (Illumina) using TruSeq SBS Kit v3 kit (Illumina) and 100bp paired-end reads.

value: human neuroblastoma cell line


title: SKNDZ

source_name: SK-N-DZ neuroblastoma cell line

value: SKNDZ


title: NCF_FlagNotWounded_rep1

description: NW + flagelin 24h, donor 1

value: NCF


title: NCF_48hPostWoundClosure_rep7

description: pWC, donor 7

value: PostWoundClosure (48h)


title: NCF_FlagNotWounded_rep2

description: NW + flagelin 24h, donor 2


title: SKNAS

source_name: SK-N-AS neuroblastoma cell line

value: SKNAS


title: Kelley

source_name: Kelly neuroblastoma cell line

value: Kelley


title: BE2C

source_name: BE(2)-C neuroblastoma cell line


title: NCF_48hPostWoundClosure_rep6

description: pWC, donor 6

value: donor 6


title: CHP134

source_name: CHP134 neuroblastoma cell line


title: NCF_48hPostWoundClosure_rep2

description: pWC, donor 2

value: donor 2


title: NCF_48hPostWoundClosure_rep1

description: pWC, donor 1


title: NCF_24hPostWound_rep7

description: pW, donor 7

value: donor 7

value: PostWound (24h)


title: fry1_AGO2_IP_2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

country: China

institute: Fudan University

data_processing:
Base-caling was performed by the sequncing company, using Illumina Casava.
Reads with insertion between 18 and 42 nt and the 3' adaptor were retained and then trimmed using cutadapt v1.14
Retained reads were mapped to the reference genome using ShotStack v3.8.5 with mode 'u'.
Mapped reads were separated according to their lengths and normalized using total mapped reads (RPM) manually.
All above processing procedures were integrated into a homemade pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools)
Genome_build: Genome_build: Araport11
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedgraph files showing the 21-nt sRNA coverage normalized in RPM

organism: Arabidopsis thaliana

source_name: seedings

growth_protocol: Arabidopsis seedlings were grown in a growth chamber (Percival) at 23℃ with 16h light

extract_protocol:
AGO1-IP RNA extraction: 0.5g seedlings of Col and fry1-6 were ground in liquid nitrogen, the prowder was suspend with 1.5ml IP buffer containing 50mM Tris-Cl, pH7.5, 150mM NaCl, 0.1% NP40, 4mM MgCl2, 5mM DTT and 1x proteinase inhibitor cocktail (Roche). The slurry was clarified by 12000g centrifugation twice at 4℃. 4ul AGO1 antibody (Agrisera, AS09 527 ) was added into the supernatant and incubate for 2h at 4℃. Then 30ul Protein A Dynabeads (Invitrogen, 10002D) was added for 1h incubation at 4℃. IP products was washed by IP buffer for 4 times. RNAs were isolated from these samples by Tri Reagent (Molecular Research Center).
20ug total RNA was resolved on 15% Ura PAGE, and15-40nt small RNAs were recovered by gel purification. The recovery small RNA products were used for small RNA library construction with NEBNext® Multiplex Small RNA Library kit (NEB, E7300S).

tag: developmental stage

value: two-week

tag: ecotype

tag: antibody


title: fry1rdr6_AGO2_IP_2


title: fry1rdr6_AGO2_IP_1


title: Single cell fibroblast CAP26_C11

tag: cell type

value: primary skin fibroblast

value: fibroblast


title: NCF_24hPostWound_rep5

description: pW, donor 5

value: donor 5


title: WT_AGO2_IP_2


title: WT_AGO2_IP_1


title: fry1rdr6_IP_2


title: fry1rdr6_IP_1


title: NCF_24hPostWound_rep2

description: pW, donor 2


title: fry1rdr6_total_2


title: NCF_24hPostWound_rep1

description: pW, donor 1

value: donor 1


title: CF_WoundClosure_rep5

description: WC, patient 5

value: Primary culture of regenerated airway epithelium

value: patient 5

value: WoundClosure

value: CF


title: NCF_48hPostWoundClosure_rep5

description: pWC, donor 5

value: Wild type

value: NCF


title: fry1rdr6_total_1


title: CF_WoundClosure_rep7

description: WC, patient 7

value: patient 7


title: fry1-6_IP_3

data_processing:
Base-caling was performed by the sequncing company, using Illumina Casava.
Reads with insertion between 18 and 42 nt and the 3' adaptor were retained and then trimmed using cutadapt v1.14
Retained reads were mapped to the reference genome using ShotStack v3.8.5 with mode 'u'.
Mapped reads were separated according to their lengths and normalized using total mapped reads (RPM) manually.
All above processing procedures were integrated into a homemade pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools)
Genome_build: Araport11
Supplementary_files_format_and_content: bedgraph files showing the 21-nt sRNA coverage normalized in RPM

extract_protocol:
AGO1-IP RNA extraction: 0.5g seedlings of Col and fry1-6 were ground in liquid nitrogen, the prowder was suspend with 1.5ml IP buffer containing 50mM Tris-Cl, pH7.5, 150mM NaCl, 0.1% NP40,  4mM MgCl2, 5mM DTT and 1x proteinase inhibitor cocktail (Roche). The slurry was clarified by 12000g centrifugation twice at 4℃. 4ul AGO1 antibody (Agrisera, AS09 527 ) was added into the supernatant  and incubate for 2h  at 4℃. Then 30ul Protein A Dynabeads (Invitrogen, 10002D) was added for 1h incubation at 4℃. IP products was washed by IP buffer for 4 times.  RNAs were isolated from these samples by Tri Reagent (Molecular Research Center).
20ug total RNA was resolved on 15% Ura PAGE, and15-40nt small RNAs were recovered by gel purification. The recovery small RNA products  were used for small RNA  library construction with NEBNext® Multiplex Small RNA Library kit (NEB, E7300S).

value: seedings

value: AS09527 (Agrisera)

tag: molecule subtype

value: sRNA


title: CF_WoundClosure_rep4

description: WC, patient 4

value: patient 4


title: CF_WoundClosure_rep6

description: WC, patient 6

value: patient 6


title: fry1-6_IP_2

value: two-week


title: CF_WoundClosure_rep3

description: WC, patient 3

value: patient 3


title: fry1-6_IP_1


title: CF_WoundClosure_rep1

description: WC, patient 1

value: patient 1


title: WT_IP_2

value: wild type


title: fry1_AGO2_IP_1


title: NCF_24hPostWound_rep6

description: pW, donor 6

value: donor 6

value: PostWound (24h)


title: CF_NotWounded_rep7

description: NW, patient 7

value: Primary culture of regenerated airway epithelium

value: NotWounded


title: CF_WoundClosure_rep2

description: WC, patient 2

value: patient 2

value: WoundClosure

value: CF


title: WT_IP_1


title: fry1-8_total_2

extract_protocol:
Total RNA extraction: 12 day seedlings of Col, fry1-6 and fry1-6 double mutants  were ground in liquid nitrogen, RNAs were extracted by Tri Reagent (Molecular Research Center) following the manufacturer’s instructions.
20ug total RNA was resolved on 15% Ura PAGE, and15-40nt small RNAs were recovered by gel purification. The recovery small RNA products  were used for small RNA  library construction with NEBNext® Multiplex Small RNA Library kit (NEB, E7300S).

value: total sRNA


title: CF_NotWounded_rep6

description: NW, patient 6


title: NCF_24hPostWound_rep3

description: pW, donor 3

value: Wild type

value: donor 3

value: NCF


title: fry1-8_total_1

value: seedings


title: CF_NotWounded_rep4

description: NW, patient 4

value: patient 4


title: fry1-6_total_1

value: two-week


title: fry1-6_total_2


title: CF_NotWounded_rep5

description: NW, patient 5

value: patient 5


title: CF_NotWounded_rep3

description: NW, patient 3

value: patient 3


title: CF_NotWounded_rep2

description: NW, patient 2


title: WT_total_2

value: wild type


title: CF_NotWounded_rep1

description: NW, patient 1

value: patient 1


title: WT_IP_3

value: AS09527 (Agrisera)

value: sRNA


title: WT_total_1


title: CF_FlagWoundClosure_rep7

description: WC + flagelin 24h, patient 7

value: Primary culture of regenerated airway epithelium

value: patient 7

value: flagelin

value: WoundClosure (Flag)


title: CF_FlagWoundClosure_rep6

description: WC + flagelin 24h, patient 6

value: patient 6

value: CF


title: LGK-1

city: New York

first: Kenneth

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology Department

country: USA

institute: New York Univerisity

description: Raw counts of reads in genes were generated with HTSeq-count and normalized via TPM.

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the TAIR10.31 genome assembly using Bowtie 2 with default settings to produce bam files.
Raw transcript abundance values were calculated using HTSeq-count.
Transcript abundance was normalized across samples in Transcripts Per Kilobase Million (TPM).
Genome_build: TAIR 10.31
Supplementary_files_format_and_content: TPM, Matrix in tab delimited text file

source_name: Arabidopsis guard cells

growth_protocol: Seedlings were grown flat on 1/2MS at 22°C under 16 hr-light/8 hr-dark cycles until 12 dpg. Aerial tissue was then harvested and plants were protoplasted. Guard cells were obtained from protoplasts using FACS.

extract_protocol:
Guard cells were sorted directly into RNA extraction buffer. Total RNA was extracted with the Rneasy Micro Kit (Qiagen).
First, cDNA was synthesized using the Ovation RNA-Seq System V2 (NuGEN) and then sequencing libraries were prepared with the Ovation Ultralow Input System V2 (NuGEN).

tag: replicated series

value: fama-1, FAMAp:FAMA-LGK

value: 12 dpg


title: LGKK4-2-input

description:
lgkk4.pool.fc_signal.bw
lgkk4.final.replicated.narrowPeak

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the TAIR10.31 genome assembly using Bowtie 2 with default settings.
ChIP-seq peaks were then called by inputting aligned reads into the ENCODE Histone ChIP-seq pipeline for Replicated Experiments (https://www.encodeproject.org/pages/pipelines/#DNA-binding).
Genome_build: TAIR 10.31
Supplementary_files_format_and_content: bigwig files generated with MACS2 based on pooled replicates. Scores represent fold change over input.

source_name: Arabidopsis Guard Cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Ovation Ultralow System V2 (NuGEN)

tag: sample type

value: Input

tag: sample group

tag: chip input pair

tag: chip antibody


title: LGKK4-1-input

tag: age


title: CF_FlagWoundClosure_rep5

description: WC + flagelin 24h, patient 5


title: CF_FlagWoundClosure_rep2

description: WC + flagelin 24h, patient 2

value: patient 2


title: LGKK4-2

value: ChIP


title: WT-1

value: Wild Type


title: CF_FlagWoundClosure_rep3

description: WC + flagelin 24h, patient 3

value: patient 3


title: LGK-2


title: CF_FlagWoundClosure_rep1

description: WC + flagelin 24h, patient 1


title: CF_FlagWoundClosure_rep4

description: WC + flagelin 24h, patient 4

value: patient 4


title: LGKK4-1


title: CF_FlagNotWounded_rep6

description: NW + flagelin 24h, patient 6

value: NotWounded (Flag)


title: CF_FlagNotWounded_rep4

description: NW + flagelin 24h, patient 4


title: LGKK27-2-input

description:
lgkk27.pool.fc_signal.bw
lgkk27.final.replicated.narrowPeak


title: CF_FlagNotWounded_rep7

description: NW + flagelin 24h, patient 7


title: LGKK27-1


title: LGKK27-2


title: CF_FlagNotWounded_rep3

description: NW + flagelin 24h, patient 3


title: CF_FlagNotWounded_rep5

description: NW + flagelin 24h, patient 5

value: patient 5


title: WTK4-1-input

description:
wtk4.pool.fc_signal.bw
wtk4.final.replicated.narrowPeak


title: CF_FlagNotWounded_rep1

description: NW + flagelin 24h, patient 1

value: patient 1


title: WTK4-2


title: CF_48hPostWoundClosure_rep7

description: pWC, patient 7

value: Primary culture of regenerated airway epithelium

value: PostWoundClosure (48h)


title: WTK4-2-input


title: WTK4-1


title: WT-2


title: NCF_48hPostWoundClosure_rep3

description: pWC, donor 3

value: Wild type

value: donor 3

value: NCF


title: CF_48hPostWoundClosure_rep6

description: pWC, patient 6

value: patient 6

value: CF


title: WTK27-1-input

description:
wtk27.pool.fc_signal.bw
wtk27.final.replicated.narrowPeak

value: 12 dpg


title: CF_48hPostWoundClosure_rep3

description: pWC, patient 3


title: CF_48hPostWoundClosure_rep1

description: pWC, patient 1


title: LGKK27-1-input

value: Input

value: fama-1, FAMAp:FAMA-LGK


title: WTK27-1

value: ChIP


title: CF_48hPostWoundClosure_rep5

description: pWC, patient 5


title: PSC 3

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

data_processing:
Paired-end 150nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to Homo sapiens sequence GRCh38.p12 Nov-'18, with CLCGenomicsServer 10.0.1 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 10.0.1 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: Homo sapiens sequence GRCh38.p12
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples.

source_name: Human perivascular stem cells

growth_protocol: Human perivascular stem cells (PSCs) were isolated from human adipose tissue and cultured in culture medium (DMEM medium plus 15% FBS)

extract_protocol:
We isolated extracellular vesicle from human perivascular stem cells. Total RNA was extract from PSCs by Trizol (Life technologies corporation, Gaitherburg, MD, USA). PSC-EV-derived RNA was isolated using exoRNeasy Serum Plasma Kits (Qiagen, Hilden, Germany). In this dataset, we isolated paired PSC-EVs with their parent PSCs and detected the expression data by RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA protocols for 2x150bp.

treatment_protocol: PSC-EVs were collected by serial centrifugation at 300 × g for 10 min, 2 000 × g for 30 min, 10 000 × g for 30 min, and 120 000 × g for 4 h at 4°C. The supernatant was discarded and the pellets were resuspended in 1X phosphate-buffered saline (PBS).

tag: tissue

value: adipose

tag: psc-ev isolation method

tag: cell passage

value: Passage 4-9

tag: cell compartment

value: whole cell


title: CF_48hPostWoundClosure_rep4

description: pWC, patient 4

tag: genotype

tag: individual

value: patient 4

tag: stage of repair process

tag: disease state


title: CF_24hPostWound_rep7

description: pW, patient 7

value: patient 7

value: PostWound (24h)


title: PSC 2


title: CF_FlagNotWounded_rep2

description: NW + flagelin 24h, patient 2

value: Primary culture of regenerated airway epithelium

value: patient 2

tag: treatment

value: flagelin

value: NotWounded (Flag)


title: PSC 1


title: CF_48hPostWoundClosure_rep2

description: pWC, patient 2

tag: cell type

value: PostWoundClosure (48h)


title: PSC-EV 2

description: Isolated from PSC 2

source_name: Human perivascular stem cell-derived extracellular vesicles

value: Serial centrifugation

value: Extracellular Vesicles


title: CF_24hPostWound_rep6

description: pW, patient 6

value: patient 6

value: CF


title: CF_24hPostWound_rep4

description: pW, patient 4


title: PSC-EV 3

description: Isolated from PSC 3


title: CF_24hPostWound_rep3

description: pW, patient 3

value: patient 3


title: CF_24hPostWound_rep2

description: pW, patient 2


title: BMDCs Control

city: seoul

first: seongmin

last: cho

country: South Korea

institute: Seoul national university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mus musculus

source_name: BMDC

growth_protocol: BMDC were obtained from female C57BL/6 mice and cultured in RPMI media containing 10% FBS, 1% streptomycin, and 20 ng/ml GM-CSF (R&D). On day 3, GM-CSF was added with fresh RPMI media and immature DCs were harvested from non-adherent and loosely attached cells on day 6.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: 100 nM of UNE-C1 was treated for 24 h

tag: strain

value: Bone marrow

value: bone marrow-derived dendritic cells (BMDCs)


title: BMDCs UNE-C1


title: CF_24hPostWound_rep1

description: pW, patient 1

value: patient 1


title: WTK27-2-input

value: Input

value: Wild Type

value: 12 dpg


title: WTK27-2

value: ChIP


title: Donor B resting blood

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Read 1 contains barcode; read 2 contains transcript.
16-nt cell barcodes (CBs) and 10-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 15-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0. Only reads with unique, strand-specific alignments to exons were kept for further analysis.
Index swapping between sample indices was corrected using the algorithm reported by Griffiths et al, Nature Communications, 2018.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cellsusing the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the estimated molecular counts associated with each gene in each cell. Rows correspond to genes. The first two columns contain the Ensembl ID and gene symbol for each gene. Each of the other columns contains the molecular counts for an individual cell. There is a simple header.

molecule: polyA RNA

source_name: human blood

extract_protocol:
mRNA molecues were captured using barcoded oligo(dT) primers from hydrogel beads in the 10x Chromium v2 Single Cell 3'-Solution.
3'-end pooled single-cell RNA-seq library construction was done using the 10x Chromium v2 Single Cell 3'-Solution kit according to the manufacturer's instructions.

treatment_protocol: T cells were enriched from single-cell suspensions of each tissue by negative selection using the MojoSort Human CD3+ T cell isolation kit (BioLegend). To eliminate dead cells prior to stimuation, we used the Dead Cell Removal kit (Miltenyi). For each sample, we cultured 0.5-1x10^6 CD3+ enriched cells for 16 hours at 37C in complete medium with or without T cell receptor stimulation using Human CD3/CD28 T cell Activator (STEMCELL Technologies).

value: Donor B

tag: gender

value: male

value: blood

value: media control

value: enriched for T cells by CD3 negative selection


title: Donor B activated blood

value: anti-CD3/anti-CD28 stimulation


title: BMmono_Dll4TgfbDes_rep1

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

description: Bmmono.rawTPM.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of TPM values, the parameters -condenseGenes -count exons  -tpm were used which extract only one transcript (most aboundace) for a gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: Table of TPM values for RNA-Seq

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research). FACS purified cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer (100mM Tris-HCl pH7.5, 500mM LiCl, 10mM EDTA pH8.0, 1% LiDS, 5mM DTT) and stored at –80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S).
Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Thermo Fisher Scientific), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primers (3 µg/µL) (Thermo Fisher Scientific), 0.5 µL of Oligo dT primer (50 µM) (Thermo Fisher Scientific), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.5 µL of Superscript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer's instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 2.5 hours. The resulting dUTP-marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 16 cycles, size selected by gel extraction.

value: in vitro

value: 2 day cultured bone marrow monocytes

value: DLL4 48h

value: TGF-β 48h

value: desmosterol 48h


title: Donor 2 activated lymph node

source_name: human lymph node

value: Donor 2

value: lymph node


title: BMmono_Dll4Tgfb_rep2

description: Bmmono.rawTPM.txt


title: Donor A activated blood

value: Donor A


title: CF_24hPostWound_rep5

description: pW, patient 5

value: Primary culture of regenerated airway epithelium

value: patient 5

value: PostWound (24h)

value: CF


title: BMmono_Dll4_rep2

description: Bmmono.rawTPM.txt


title: BMmono_Des_rep1

description: Bmmono.rawTPM.txt


title: BMmono_Dll4TgfbDes_rep2

description: Bmmono.rawTPM.txt


title: Donor 2 resting lymph node

value: male


title: Donor 2 activated bone marrow

source_name: human bone marrow

value: bone marrow


title: BMmono_Dll4_rep1

description: Bmmono.rawTPM.txt


title: PSC-EV 1

description: Isolated from PSC 1

value: adipose

value: Serial centrifugation

value: Extracellular Vesicles


title: BMmono_Des_rep2

description: Bmmono.rawTPM.txt

value: in vitro


title: Donor 2 resting lung

source_name: human lung tissue

value: lung

value: media control

value: enriched for T cells by CD3 negative selection


title: Donor 2 activated lung

value: anti-CD3/anti-CD28 stimulation


title: Donor 2 resting bone marrow

value: Donor 2


title: BMmono_NoTx_rep1

description: Bmmono.rawTPM.txt

value: 2 day cultured bone marrow monocytes

value: No treatment 48h


title: Dll1Ab_Tx_rep4

description:
Dll1Ab_Tx_rep4
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Male_RLM_RNA_polyA_DLL1AbDLL4AbDT24h_Fasted_rep5_MS_l20190630_CCGTCC TPM

value: Diphtheria toxin 24h

value: DLL1Ab and DLL4Ab


title: Donor 1 activated lymph node

value: Donor 1

value: lymph node


title: BMmono_NoTx_rep2

description: Bmmono.rawTPM.txt


title: Dll1Ab_Tx_rep2

description:
Dll1Ab_Tx_rep2
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Male_RLM_RNA_polyA_DLL1AbDLL4AbDT24h_Fasted_rep3_MS_l20190630_AGTTCC TPM


title: Dll1Ab_Tx_rep1

description:
Dll1Ab_Tx_rep1
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Male_RLM_RNA_polyA_DLL1AbDLL4AbDT24h_Fasted_rep2_MS_l20190630_AGTCAA TPM


title: Donor 1 activated bone marrow

value: male


title: Donor 1 resting bone marrow

value: bone marrow


title: BMmono_Dll4Tgfb_rep1

description: Bmmono.rawTPM.txt

value: DLL4 48h

value: TGF-β 48h


title: Donor A resting blood

value: Donor A

value: blood


title: Dll1Ab_Ctrl_rep2

description:
Dll1Ab_Ctrl_rep2
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Male_RLM_RNA_polyA_CtrlDT24h_Fasted_rep3_MS_l20190630_TAGCTT TPM


title: Donor 1 resting lung

value: lung


title: LY411575_Tx_rep2

description:
LY411575_Tx_rep2
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Female_RLM_RNA_polyA_LY411575DT24h_Fasted_rep2_MS_l20190630_CAGATC TPM


title: Aortic_Valve_Sclerosis_2

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

data_processing:
The RNA-seq raw paired-end fastq files were aligned in Gencode v19 by STAR with default options. The mapped SAM files were converted to BAM files and sorted by SAMTOOLs.
Transcripts were assembled using Cufflinks version 2.2.1 with template Gencode v19.
For each protein-encoding gene we compared the estimated expression level measured as Fragments Per Kilobase of transcript per Million (FPKM).
This procedure was carried out for all tissues together and then repeated separately for each of the different tissue types: AVSc and AVS.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Sclerotic Aortic Valve Tissue

extract_protocol:
Patients undergoing surgical aortic valve (AV) surgery or orthotopic heart transplant (OHT) between 2010 and 2017 were enrolled in the study in accordance with approved Institutional Review Board (IRB) protocols from the University of Pennsylvania Perelman School of Medicine (protocol #809349), the Columbia University Irving Medical Center (protocol #809349) and the Valley Hospital (Institutional Tracking #NRBUTS1109). Informed consent was obtained from all patients for study enrollment, and clinical information was obtained by patient interview and chart review. Exclusion criteria included bicuspid AV patients, genetic disease associated with thoracic aortic aneurysm, connective tissue disease, previous myocardial infarction, severe heart failure (NYHAIII+, IV), endocarditis, and active cancer. Control and aortic valve sclerosis (AVSc) specimens were obtained from patients undergoing OHT.
RNA libraries were prepared for sequencing using Nugen Ovation RNA-Seq library preparation kit.

value: Aortic Valve Tissue

tag: condition

value: sclerotic


title: Dll1Ab_Ctrl_rep1

description:
Dll1Ab_Ctrl_rep1
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Male_RLM_RNA_polyA_CtrlDT24h_Fasted_rep1_MS_l20190630_ACTTGA TPM


title: LY411575_Ctrl_rep1

description:
LY411575_Ctrl_rep1
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Female_RLM_RNA_polyA_CtrlDT24h_Fasted_rep1_MS_l20190630_CGATGT TPM


title: Aortic_Valve_Sclerosis_3


title: LY411575_Ctrl_rep2

description:
LY411575_Ctrl_rep2
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Female_RLM_RNA_polyA_CtrlDT24h_Fasted_rep2_MS_l20190630_TGACCA TPM


title: Aortic_Valve_Sclerosis_1


title: Dll1Ab_Tx_rep3

description:
Dll1Ab_Tx_rep3
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Male_RLM_RNA_polyA_DLL1AbDLL4AbDT24h_Fasted_rep4_MS_l20190630_ATGTCA TPM


title: Invitro_Tpt6H_IL7_IL33_B1

city: Cambridge

first: Samantha

last: Riesenfeld

state: MA

address: 415 Main St

institute: Broad Institute

description:
Bulk_all.matrix.counts.txt
Bulk_all.matrix.abundance_TPM.txt

data_processing:
For bulk RNA-seq (in vitro samples) data, the raw data was converted to fastq files using bcl2fastq 2.17.1.14 with options “--minimum-trimmed-read-length 10 --mask-short-adapter-reads 10”. Transcript quantification was done using Kallisto 0.42.3 (Bray et al., 2016) with the mm10 mouse genome annotation, and transcript counts were then converted to gene counts and normalized TPM values using the R package tximport (Soneson et al., 2015).
For scRNA-seq data data, gene counts were obtained by aligning reads to the mm10 genome using CellRanger software (v1.3) (10x Genomics). To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in their sample or condition of origin in terms of number of genes or number of unique molecular identifiers (UMIs), which left 83.1% and 84.2% of cells from CGRP and PBS, respectively, and 90.3% and 93% of cells from IL-33 and IL-33+CGRP conditions. Sample-specific minimum and maxium cut-offs per cell were 900–5,000 genes for IL-33 and IL-33+CGRP conditions and 900–3,900 genes for CGRP and PBS. Another 2.1% of the remaining cells were excluded for having greather than 10% of mitochondrial gene counts.
For scRNA-seq data, normalization of gene counts was performed using regularized negative binomial regression via the SCTransform() function from Seurat v3, with the “batch_var” parameter set to the replicate indicator variable and the “vars_to_regress” parameter set to the variable capturing the percentage of mitochondrial gene counts in each cell (Butler et al., 2018; Hafemeister and Satija, 2019). This step takes the place of the typical steps of log-normalization, variable gene selection, and scaling. We used log1p of the corrected counts to compute principle components analysis (PCA).
ATAC-seq: Read alignment, filtering, visualization of signal tracks, and measurement of quality control metrics was performed using a publicly available ATAC-seq pipeline (Lee et al., 2016). Briefly, reads were aligned to the mm10 genome using Bowtie2 and filtered to remove duplicates and mitochondrial reads. Alignment files were merged for biological replicates for peak-calling using MACS2 (Zhang et al., 2008). Read counts per peak were compiled using the bedtools multicov tool. Counts were normalized and processed for differential peak accessibility between conditions using DESeq2 (Love et al., 2014). Gene annotation with putative regulatory elements was performed using GREAT with default parameters (McLean et al., 2010).
Genome_build: mm10

source_name: Lung Innate lymphoid cells

extract_protocol:
Lungs were digested with the lung dissociation kit (Miltenyi Biotec) and subsequently enriched for CD90.2+ cells using CD90.2 MicroBeads (Miltenyi Biotec). Lung ILCs were isolated by fluorescence-activated cell sorting as 7AAD- CD45+ CD90.2+ CD127+ Lineage (CD3, CD4, CD8, CD11b, CD11c, CD19, NK1.1, TCRβ, TCRγδ)- cells.
Two replicates from each batch of distinct experiments were sequenced. RNA was quantified using a Qubit RNA HS Assay kit (Invitrogen), and 2ng of RNA were used as input for a modified SMART-Seq2 protocol (Picelli et al., 2014) entailing RNA secondary structure denaturation (72˚C for three minutes), reverse transcription with Maxima Reverse Transcriptase (Life Technologies), and whole transcriptome amplification (WTA) with KAPA HiFi HotStart ReadyMix 2X (Kapa Biosystems) for 12 cycles. WTA products were purified with Ampure XP beads (Beckman Coulter), quantified with a Qubit dsDNA HS Assay Kit (Invitrogen), and quality accessed with a High Sensitivity DNA Chip run on a Bioanalyzer 2100 system (Agilent). 0.2 ng of purified WTA product was used as input for Nextera XT DNA Library Preparation Kit (Illumina). Uniquely barcoded libraries were pooled and sequenced with a NextSeq 500 sequencer using a high output V2 75 cycle kit (Illumina) and 2x38 paired end reads.

treatment_protocol: Sort-purified lung ILC2s were cultured overnight with IL-7 and for additional 6 hours with IL-7, IL-7+CGRP, IL-7+IL-33 or IL-7+IL-33+CGRP.

value: Innate lymphoid cells

tag: batch

value: B

tag: cgrp-treated

value: No

value: Yes

tag: timepoint

value: 6 hours

tag: in vitro vs. in vivo

value: In vitro

tag: protocol

value: Bulk RNA-seq (Smart-Seq2)


title: Replicative-1

city: Minato-ku

first: Yoshikazu

last: Johmura

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

data_processing:
The libraries were paired-end sequenced on a Hiseq2500 platform
The sequeincing data were aligned to huan genome using TopHot
Genome_build: hg19
Supplementary_files_format_and_content: diff file includes RPKM values for each Sample

source_name: HCA2 (MJ90)

growth_protocol: Cells were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Rneasy mini kit (Qiagen)  according to the manufacturer’s instructions.
NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs)  according to the manufacturer’s instructions.

treatment_protocol: Doxorubicin (100 nM) for 24 hrs, turt-butyl hydroperoxide (100 uM) for 24 hrs, or RO3306 (9 uM) + Nutlin3a (10 uM) for 48 hrs

value: skin fibroblast

value: high passage


title: Invitro_Tpt6H_IL7_IL33_CGRP_B2

tag: tissue


title: RON-1

value: 21 days after RO3306+nutlin3a treatment


title: Aortic_Valve_Stenosis_2

source_name: Stenotic Aortic Valve Tissue

value: stenotic


title: Donor 1 resting lymph node

value: Donor 1

tag: age

value: male

value: lymph node

value: media control

value: enriched for T cells by CD3 negative selection


title: Aortic_Valve_Stenosis_1

value: Aortic Valve Tissue


title: Invitro_Tpt6H_IL7_IL33_CGRP_B1

value: lung

value: Innate lymphoid cells


title: BHT-1

value: 21 days after turt-butyl hydroperoxide treatment


title: Invitro_Tpt6H_IL7_IL33_B2

value: B

value: No

value: Yes


title: young-1

value: low passage


title: LY411575_Tx_rep3

description:
LY411575_Tx_rep3
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Female_RLM_RNA_polyA_LY411575DT24h_Fasted_rep3_MS_l20190630_CTTGTA TPM

value: Diphtheria toxin 24h


title: Doxo-1

value: skin fibroblast

value: 21 days after doxorubicin treatment


title: Invitro_Tpt6H_IL7_CGRP_B1

value: 6 hours

value: In vitro

value: Bulk RNA-seq (Smart-Seq2)


title: Invitro_Tpt6H_IL7_B2


title: Invitro_Tpt6H_IL7_B1


title: Invitro_Tpt6H_IL7_IL33_CGRP_A2

value: A


title: Invitro_Tpt6H_IL7_CGRP_B2


title: Invitro_Tpt6H_IL7_IL33_CGRP_A1


title: Invitro_Tpt6H_IL7_IL33_A2


title: Aortic_Valve_Stenosis_3

value: stenotic


title: LY411575_Tx_rep1

description:
LY411575_Tx_rep1
Dll1AB_LY411575.rawTPM.txt
mouse_C57B6J_Female_RLM_RNA_polyA_LY411575DT24h_Fasted_rep1_MS_l20190630_ACAGTG TPM


title: Invitro_Tpt3D_IL7_IL33_CGRP_B2

treatment_protocol: Sort-purified lung ILCs were cultured for 3 days with IL-7, IL-7+CGRP, IL-7+IL-33 or IL-7+IL-33+CGRP.

value: 3 days


title: Invitro_Tpt6H_IL7_A2


title: Invitro_Tpt3D_IL7_IL33_CGRP_B1


title: Donor 1 activated lung

value: Donor 1

value: male

value: anti-CD3/anti-CD28 stimulation

value: enriched for T cells by CD3 negative selection


title: Invitro_Tpt3D_IL7_IL33_B1

value: lung

value: Innate lymphoid cells

value: B


title: Invitro_Tpt6H_IL7_IL33_A1

value: No

value: Yes


title: Invitro_Tpt6H_IL7_CGRP_A1


title: Invitro_Tpt6H_IL7_CGRP_A2


title: Invitro_Tpt6H_IL7_A1


title: Invitro_Tpt3D_IL7_IL33_B2


title: Invitro_Tpt3D_IL7_CGRP_B2


title: Invitro_Tpt3D_IL7_CGRP_A1


title: Invitro_Tpt3D_IL7_IL33_CGRP_A1


title: ChIP_H3K27ac_BMDM_notx_rep2

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
H3K27ac single was quantified at corresponding ATAC peaks by HOMER (Heinz et al., 2010). Other ChIP peak files were generated by HOMER ‘findPeaks’ by providing the corresponding input with default  parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated Homer  annotation files /HOMER Peak files

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For LXR, SMAD4, and RBPJ ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for LXR, SMAD4, and RBPJ ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Nuclei were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 2-3 million cells or nuclei (for LXR, SMAD4, or RBPJ ChIP), 30 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for LXR ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), LXR (2 µg each of the indicated LXR specific antibodies, Santa Cruz Biotechnology: sc-1000X, sc-133221X, sc-271064X)), SMAD4 (1 μg each of Cell Signaling technology 46535 and 38454) or RBPJ (2 μg, Abcam, ab25949) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For LXR, SMAD4, or RBPJ ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA).
Libraries were prepared with NEBNext Ultra II DNA library prep kit (NEB) reagents according to the manufacturer’s protocol on the beads suspended in 25 µL TT (10mM Tris/HCl pH7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 µl 10% SDS, 4.5 µl 5 M NaCl, 3 µl EDTA, 1 µl proteinase K (20 mg/ml), 20 µl water, incubating for 1 h at 55°C , then 30 minutes to overnight at 65°C . DNA was purified using 2 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 1.5M NaCl to final of 12% PEG, eluted with 25 µl TT. DNA contained in the eluate was then amplified for 12 cycles in 50 µl PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. ChIP input material (1 percent of sheared DNA) was treated with RNase for 15 minutes at 37°C in EB buffer (10 mM Tris pH 8, 0.5% SDS, 5 mM EDTA, 280 mM NaCl), then digested with Proteinase K for 1 h at 55°C and crosslinks reversed at 65°C for 30 minutes to overnight. DNA was purified using 2 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 1.5M NaCl to final of 12% PEG, eluted with 25 µl TT and library prep and amplification were performed as described for ChIP samples. Resulting libraries were size selected by gel excision to 225-325 bp and purified.

tag: antibody

value: H3K27ac (2 ug, Active Motif, 39133)

value: in vitro

value: 4 day cultured BMDMs

value: No treatment


title: Invitro_Tpt3D_IL7_B1

value: In vitro

value: Bulk RNA-seq (Smart-Seq2)


title: ChIP_H3K27ac_BMDM_DLL4_rep1

value: DLL4 24h


title: Invitro_Tpt3D_IL7_B2

value: 3 days


title: ChIP_H3K27ac_BMDM_DLL4_rep2


title: Invitro_Tpt3D_IL7_IL33_A1

value: A


title: Invitro_Tpt3D_IL7_CGRP_B1


title: Invitro_Tpt3D_IL7_IL33_A2


title: Invitro_Tpt3D_IL7_IL33_CGRP_A2


title: ChIP_H3K27ac_BMDM_notx_rep1


title: Invitro_Tpt3D_IL7_CGRP_A2


title: ChIP_input_RBPJ_BMDM_notx_rep1

value: input


title: Invitro_Tpt3D_IL7_A2


title: Invitro_Tpt3D_IL7_A1


title: ChIP_RBPJ_BMDM_notx_rep1

value: RBPJ (2 ug, Abcam, ab25949)


title: ChIP_input_SMAD4_BMDM_notx_rep1


title: ChIP_SMAD4_BMDM_notx_rep2

value: SMAD4 (1 ug each of Cell Signaling technology 46535 and 38454)


title: ChIP_input_RBPJ_BMDM_notx_rep2


title: ChIP_RBPJ_BMDM_notx_rep2


title: ChIP_input_SMAD4_BMDM_notx_rep2


title: ChIP_input_SMAD4_KcNuclei_notx_rep2


title: ChIP_SMAD4_KcNuclei_notx_rep2


title: ChIP_SMAD4_BMDM_notx_rep1


title: ChIP_input_LXR_BMDM_GW3965_rep2

value: 7 day cultured BMDMs


title: ChIP_input_LXR_BMDM_GW3965_rep1


title: ChIP_LXR_BMDM_GW3965_rep1

value: LXR (2 ug each of  LXR specific antibodies, Santa Cruz Biotechnology:sc-1000X, sc-133221X, sc-271064X)


title: ChIP_LXR_BMDM_GW3965_rep2


title: ChIP_input_LXR_KC_notx_rep2


title: ChIP_LXR_KC_notx_rep2


title: ChIP_input_LXR_KC_notx_rep1


title: ChIP_H3K27ac_KC_notx_rep2


title: BMDMdll4Tgfb72h_rep1

value: 6 day cultured BMDMs

value: TGF-beta 24h


title: BMDMdll4Tgfb72h_rep2


title: BMDMdll4TgfbDmhca72h_rep2

value: DMHCA 24h


title: ChIP_LXR_KC_notx_rep1


title: BMDMdll472h_rep2


title: BMDMdll472h_rep1


title: BMDMnotx72h_rep2

value: No treatment 72h


title: PG_8C_R2_C2

city: Changsha

first: leng

last: lizhi

address: xiangya road

institute: Central South University

data_processing:
quality control using Trimmomatic version 0.35
clean reads were mapped to the human reference genome of GRCh38 using STAR version v 2.5.2b aligne
uniquely mapped read counts of each annotated Ensemble gene were calculated by HTSeq (v0.9.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: Embryo

extract_protocol:
Single-cell poly-A(+) RNA was reverse transcribed and amplified by Smart-seq2 protocol
Single-cell libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina Cat#FC-131-1096)

tag: embryo type

value: PG embryo

tag: developmental stage


title: PG_8C_R1_C1


title: PG_4C_R2_C4


title: PG_8C_R2_C7


title: PG_8C_R2_C4


title: PG_4C_R2_C2


title: PG_8C_R1_C5


title: PG_8C_R2_C5


title: PG_4C_R1_C2


title: PG_4C_R1_C1


title: PG_2C_R2_C2


title: BMDMdll4TgfbDmhca72h_rep1

value: in vitro


title: BMDMdll4TgfbDmhca24h_rep1

value: 4 day cultured BMDMs


title: PG_8C_R1_C6


title: BMDMdll4TgfbDmhca24h_rep2


title: PG_2C_R1_C2


title: PG_2C_R2_C1


title: BMDMdll4Tgfb24h_rep2


title: BMDMdll4Tgfb24h_rep1


title: PG_2C_R1_C1


title: PG_1C_R2


title: BMDMdll424h_rep1


title: BMDMdll424h_rep2


title: PG_1C_R1


title: BMDMnotx24h_rep2

value: No treatment 24h


title: BMDMnotx72h_rep1


title: BMDMnotx24h_rep1


title: US-3: Canine prostate fine-needle aspirate

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

institute: Graz University of Technology

data_processing:
Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
Adaptors and low-quality bases were trimmed using Trimmomatic (v0.32) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were then mapped to the CanFam3.1 assembly of the dog genome using TopHat2 with default parameters and supplying the Ensembl GTF annotation (Ensembl release 85) through the -G option.
Read counts for each protein-coding gene were calculated for each sample using the htseq-count tool of the Python package HTSeq with default parameters.
Genome_build: CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text files that include counts for each Ensembl gene.

organism: Canis lupus familiaris

source_name: Canine prostate fine-needle aspirate

extract_protocol:
Canine prostate tissue samples were collected post mortem from macroscopically representative areas after prostatectomy. The samples were immediately snap frozen in liquid nitrogen and stored at -80°C. Prostate tissue samples were disrupted using Buffer RLT Plus and 5mm stainless steel beads by tissueLyser II (Qiagen). Total RNA from prostate tissue samples was isolated using AllPrep® DNA/RNA/miRNA Universal Kit (Qiagen)  according to the manufacturer’s instructions.
Ultrasound-guided fine-needle aspirates were collected intra vitam, snap frozen in liquid nitrogen and stored at -80°C. Total RNA from aspirates were isolated using Qiazol Lysis Reagent with Qiagen miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: canine prostate carcinoma

tag: diagnosed by

value: Diagnosed by cytology as canine prostate carcinoma

tag: sample type

value: FNA

tag: diagnosis

value: malignant

tag: reproductive status

value: male neutered

tag: breed

value: Mixed breed

value: 10 years


title: US-40: Canine prostate fine-needle aspirate

value: Diagnosed by cytology as normal to hyperplastic canine prostate tissue

value: non-malignant

value: male intact

value: 8 years


title: US-32: Canine prostate fine-needle aspirate

value: normal to hyperplastic canine prostate tissue

value: Dobermann

value: 4 years


title: US-4: Canine prostate fine-needle aspirate

value: Miniature Pinscher

value: 9 years


title: US-15: Canine prostate fine-needle aspirate

value: Long-Haired Collie

value: 7 years


title: AG_8C_R1_C3

value: AG embryo


title: AG_8C_R2_C1


title: AG_8C_R2_C3


title: AG_8C_R2_C2


title: AG_8C_R1_C6


title: AG_8C_R2_C4


title: AG_8C_R1_C2


title: AG_4C_R1_C3


title: AG_8C_R1_C1


title: PT-16: Canine prostate tissue

source_name: Canine prostate tissue

value: normal to hyperplastic prostate tissue

value: Diagnosed by histopathology as normal to hyperplastic prostate tissue

value: tissue

value: Old German Shepherd Dog


title: US-13: Canine prostate fine-needle aspirate

value: FNA

value: Mixed breed

value: 10 years


title: AG_4C_R2_C1


title: AG_2C_R1_C2


title: PT-13: Canine prostate tissue

value: non-malignant

value: male intact

value: Labrador Retriever

value: 5 years


title: AG_4C_R2_C2


title: PT-14: Canine prostate tissue

value: Cocker Spaniel

value: 13 years


title: PT-18: Canine prostate tissue

value: Pyrenean Shepherd

value: 1 year


title: AG_2C_R2_C2


title: PT-15: Canine prostate tissue

value: Rottweiler

value: 6 years


title: PT-17: Canine prostate tissue

value: normal to hyperplastic prostate tissue

value: Pug


title: PT-12: Canine prostate tissue

value: Diagnosed by histopathology as normal to hyperplastic prostate tissue

value: tissue

value: 9 years


title: AG_4C_R1_C2

value: AG embryo


title: US-7: Canine prostate fine-needle aspirate

value: Diagnosed by cytology as normal to hyperplastic canine prostate tissue

value: FNA

value: Mixed breed


title: AG_2C_R2_C1


title: PT-11: Canine prostate tissue

value: non-malignant

value: male intact

value: Great Dane


title: PT-6: Canine prostate tissue

value: canine prostate carcinoma

value: Diagnosed by histopathology as canine prostate carcinoma

value: malignant

value: male neutered

value: 10 years


title: PT-8: Canine prostate tissue

value: English Bulldog

value: 8 years


title: PT-9: Canine prostate tissue

value: Beagle


title: PT-7: Canine prostate tissue

value: tissue

value: 12 years


title: AG_1C_R1

value: AG embryo


title: AG_1C_R2


title: PT-10: Canine prostate tissue

value: normal to hyperplastic prostate tissue

value: Diagnosed by histopathology as normal to hyperplastic prostate tissue

value: 16 years


title: BI_8C_R5_C4

value: BI embryo


title: BI_8C_R5_C3


title: BI_8C_R5_C2


title: BI_8C_R5_C1


title: PT-5: Canine prostate tissue

value: Tyrolean Hound


title: BI_8C_R4_C6


title: PT-4: Canine prostate tissue

value: male intact

value: West Highland White Terrier

value: 9 years


title: PT-3: Canine prostate tissue

value: canine prostate carcinoma

value: Diagnosed by histopathology as canine prostate carcinoma

value: malignant

value: Dachshound

value: 11 years


title: AG_2C_R1_C1


title: BI_8C_R4_C5


title: PT-2: Canine prostate tissue

value: male neutered

value: Beagle

value: 10 years


title: BI_8C_R4_C4


title: BI_8C_R4_C2


title: PT-1: Canine prostate tissue

value: tissue

value: Briard


title: BI_8C_R3_C4


title: BI_8C_R3_C2


title: BI_8C_R3_C3


title: Backfat_castrated pigs

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

data_processing:
The clean data was obtained by removing the poor-quality bases and adapter sequences from the raw sequencing data.
The TopHat2 software (Kim et al., 2013) was used to map the clean data to the porcine reference genome (Sscrofa10.2, ftp://ftp.ncbi.nlm.nih.gov/ genomes/Sus_scrofa/).
Then Cufflinks (Trapnell et al., 2010) was used to perform the transcript assembly and abundance estimation. The Findcirc software was used to predict the circRNAs (Memczak et al., 2013).The lncRNA was identified by the following steps: (1) Transcripts were removed that were detected in fewer than two experiments. (2) Transcripts with single exon and with the length less than 200 bp were removed. (3) Transcripts with coverage of less than 3 were removed; (4) Transcripts similar to or the same as known porcine small RNAs were removed. (5) Transcripts that did not pass any analyses of Coding Potential Calculator (CPC), Coding-Non-Coding-Index (CNCI), and Pfam software were removed.
The expression profile of circRNAs, mRNAs and lncRNAs were reflected by the fragments per kilo base per million reads (FPKMs), and the expression profile of circRNAs were reflected by the transcripts per million (TPM).
Genome_build: Sscrofa10.2, ftp://ftp.ncbi.nlm.nih.gov/ genomes/Sus_scrofa/

organism: Sus scrofa

source_name: subcutaneous adipose tissue

growth_protocol: Three HN intact male pigs and three HN castrated male pigs aged 300 days were obtained from the Henan Xing Rui Agricultural and Animal Husbandry Technology Co., LTD in the Henan province of China. All of the pigs were fed on a standard diet and watered ad libitum under normal condition.

extract_protocol:
Backfat were removed from intact and castrated pigs, frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The ribosomal RNA (rRNA) was removed using Ribo-ZeroTM kit (Epicentre, Madison, WY, USA) from the DNA-free RNA. Then, the DNA and rRNA-free RNA was used to prepare the library using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs lnc., Beverly, MA), and then sequenced by HiSeq 2500 (Illumina, San Diego, CA, USA).

value: 300 days

value: Huainan

tag: Sex

value: male

tag: stress

value: castrated


title: Backfat_intact pigs

value: intact


title: BI_8C_R2_C5

value: BI embryo


title: PG_8C_M5 [methylation]

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean reads were aligned to the human reference genome (hg19) by BSMAP (v2.74) with the parameter “-u -v 5 -z 33 -p 6 -n 1 -w 20 -s 16 -r 0 -f 10 -L 126” .
Genome_build: hg19
Supplementary_files_format_and_content: The cout.gz file for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, coordinate, strand, cytosine type, cytosine context, methylated cytosines reads and unmethylated cytosines reads.

source_name: PG embryo_8-cell

extract_protocol: Single embryo was isolated by lysis buffer and bisulfite conversion was done using EZ DNA Methylation-Direct Kit (Zymo Research, D5020). Bisulfite treated DNA was purified and recovered using PureLink PCR Micro Kit (Thermo Fisher, K310050). Sequencing libraries were constructed using EpiGnome Methyl-Seq kit (Epicenter, EGMK81312).

value: PG embryo


title: PG_8C_M3 [methylation]


title: PG_8C_M4 [methylation]


title: BI_8C_R2_C1


title: BI_8C_R3_C1


title: PG_8C_M1 [methylation]


title: PG_4C_M5 [methylation]

source_name: PG embryo_4-cell


title: BI_8C_R1_C3


title: PG_4C_M6 [methylation]


title: PG_8C_M2 [methylation]


title: BI_8C_R2_C2


title: PG_4C_M4 [methylation]


title: BI_8C_R1_C2


title: PG_4C_M3 [methylation]


title: BI_8C_R1_C4


title: PG_4C_M2 [methylation]


title: PG_4C_M1 [methylation]


title: BI_4C_R8_C3


title: BI_4C_R8_C2


title: PG_2C_M3 [methylation]

source_name: PG embryo_2-cell


title: BI_4C_R8_C1


title: BI_4C_R3_C2


title: PG_2C_M2 [methylation]


title: BI_4C_R3_C1


title: BI_4C_R2_C2


title: BI_8C_R1_C1


title: PG_2C_M1 [methylation]


title: AG_4C_M3 [methylation]

source_name: AG embryo_4-cell

value: AG embryo


title: BI_4C_R1_C1


title: BI_2C_R4


title: AG_8C_M2 [methylation]

source_name: AG embryo_8-cell


title: AG_2C_M4 [methylation]

source_name: AG embryo_2-cell


title: BI_2C_R5


title: AG_8C_M1 [methylation]


title: BI_4C_R2_C1


title: AG_2C_M3 [methylation]


title: BI_4C_R8_C4


title: BI_2C_R1


title: BI_2C_R3


title: AG_4C_M2 [methylation]


title: AG_4C_M1 [methylation]


title: BI_1C_R5


title: AG_2C_M2 [methylation]


title: PG_2C_M4 [methylation]


title: BI_1C_R3


title: BI_8C_M3 [methylation]

source_name: BI embryo_8-cell


title: BI_1C_R4


title: BI_8C_M2 [methylation]


title: BI_8C_M1 [methylation]


title: BI_1C_R1


title: Oocyte_R9

source_name: Oocyte

value: Oocyte


title: BI_4C_M2 [methylation]

source_name: BI embryo_4-cell


title: BI_4C_M1 [methylation]


title: Oocyte_R7


title: BI_2C_M2 [methylation]

source_name: BI embryo_2-cell


title: AG_2C_M1 [methylation]


title: Oocyte_R5


title: PG_Mor_R4_C9

value: morula


title: BI_2C_M1 [methylation]


title: BI_1C_R2


title: Oocyte_R6


title: PG_Mor_R4_C5


title: DLBCL_8813_05

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned using STAR and annotated to SIRT3 RefSeq annotation using Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: DLBCL

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).  Library was prepared as described in manuscript.

value: Diffuse large B-cell lymphomas


title: Oocyte_R1


title: Oocyte_R4


title: PG_Mor_R4_C4


title: Oocyte_R3


title: PG_Mor_R4_C6


title: PG_Mor_R4_C8


title: PG_Mor_R4_C3


title: Oocyte_R2


title: PG_Mor_R4_C7


title: DLBCL_8432_07


title: DLBCL_8595_06


title: PG_Mor_R4_C2


title: PG_Mor_R4_C15


title: DLBCL_7416_08


title: DLBCL_7284_08


title: DLBCL_8222_07


title: PG_Mor_R4_C16


title: DLBCL_7013_08


title: PG_Mor_R4_C13


title: PG_Mor_R4_C14


title: Oocyte_R8


title: DLBCL_7135_08


title: PG_Mor_R4_C12


title: PG_Mor_R4_C11


title: DLBCL_5283_08


title: DLBCL_491_08


title: PG_Mor_R4_C10


title: DLBCL_4943_10


title: PG_Mor_R3_C7


title: PG_Mor_R4_C1


title: DLBCL_5121_08


title: DLBCL_3919_08


title: PG_Mor_R3_C8


title: PG_Mor_R3_C5


title: PG_Mor_R3_C9


title: DLBCL_1937_09


title: DLBCL_2125_11


title: DLBCL_1321_07


title: PG_Mor_R3_C4


title: PG_Mor_R3_C6


title: DLBCL_1085_08


title: PG_Mor_R3_C2


title: DLBCL_6859_07


title: DLBCL_950_10


title: DLBCL_9682_12


title: DLBCL_6362_07


title: PG_Mor_R3_C13


title: PG_Mor_R3_C12


title: DLBCL_8671_08


title: DLBCL_9379_11


title: DLBCL_856_T2


title: PG_Mor_R3_C10


title: PG_Mor_R3_C11


title: PG_8C_R4_C8


title: DLBCL_8513_07


title: DLBCL_8279_11


title: PG_Mor_R3_C1


title: DLBCL_8270_09


title: DLBCL_8485_05


title: PG_8C_R4_C6


title: DLBCL_7798_11


title: PG_Mor_R3_C3


title: DLBCL_7591_10


title: PG_8C_R4_C3


title: PG_8C_R4_C4


title: DLBCL_6070_12


title: DLBCL_6385_11


title: PG_Mor_R3_C14


title: PG_8C_R4_C2


title: PG_8C_R4_C1


title: DLBCL_5944_07


title: DLBCL_5656_03


title: PG_8C_R3_C7


title: DLBCL_5283


title: DLBCL_5102_09


title: PG_8C_R3_C4


title: DLBCL_5075_11


title: PG_8C_R3_C2


title: DLBCL_5060_11


title: PG_8C_R4_C5


title: PG_4C_R5_C3


title: DLBCL_4049_06


title: PG_8C_R3_C1


title: DLBCL_3854_99


title: PG_4C_R5_C2


title: DLBCL_36_06


title: PG_4C_R4_C3


title: PG_4C_R4_C4


title: DLBCL_3334_12


title: PG_4C_R5_C1


title: DLBCL_3449_12


title: PG_4C_R4_C2


title: PG_4C_R4_C1


title: PG_8C_R3_C5


title: DLBCL_2802_T2


title: DLBCL_2943_08


title: DLBCL_2711_08


title: PG_2C_R5_C2


title: PG_2C_R5_C1


title: PG_8C_R3_C3


title: DLBCL_3876_08


title: PG_2C_R4_C2


title: DLBCL_2180_T2


title: DLBCL_2107_T2


title: DLBCL_2084_T2


title: DLBCL_3666_08


title: PG_2C_R4_C1


title: PG_1C_R4


title: DLBCL_1819_06


title: PG_2C_R3_C1


title: AG_Mor_R5_C9


title: PG_1C_R3


title: AG_Mor_R5_C8


title: DLBCL_2623_12


title: DLBCL_2598_T2


title: DLBCL_13078_11


title: AG_Mor_R5_C6


title: DLBCL_12163_10


title: AG_Mor_R5_C5


title: AG_Mor_R5_C3


title: DLBCL_11717_12


title: DLBCL_1072_08


title: PG_8C_R4_C7


title: AG_Mor_R5_C2


title: AG_Mor_R5_C12


title: DLBCL_10640_11


title: DLBCL_10561_12


title: PG_2C_R3_C2


title: AG_Mor_R5_C11


title: VKVC320SC-3_002

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

data_processing:
Illumina HiSeq2500 was used for basecalling. Real Time Analysis (RTA) software
Primary analysis sample de-multiplexing and  alignment to the human genome was performed using Illumina's CASAVA 1.8.2 software suite.
Reads were trimmed for quality and aligned with the hg19 reference genome using TopHat2
Transcripts were assembled using Cufflinks
Assembled transcripts were used to estimate transcript abundance and differential gene-expression using Cuffdiff
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: normalized fpkm

source_name: COLO320 cells

growth_protocol: COLO320 cells (American Type Culture Collection; ATCC, VA, USA) were cultured in RPMI 1640 (Life Technologies, Carlsbad, CA) medium supplemented with an antibiotic-antimycotic cocktail (100 U/mL penicillin and 100 μg/mL streptomycin; Life Technologies, Carlsbad, CA) and 10% heatinactivated fetal bovine serum (FBS; Life Technologies, Carlsbad, CA) under a humidified atmosphere of 5% CO2 in air at 37°C. Cells (∼0.5-1.0×106 ) were seeded into 25 cm2 culture flasks (Eppendorf AG, Hamburg, Germany) and passaged at 70-80% confluency. To assess the effect of puromycin on cell viability, 0.02-0.1 × 105 cells were seeded in RPMI containing 10% FBS (100 µL/well) in a 96-well cell culture plate (Eppendorf AG, Hamburg, Germany)

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cellular ALDH1A1 expression was suppressed using MISSION shRNA lentiviral transduction particles  containing validated ALDH1A1 shRNA in a pLKO plasmid vector. Scramble control shRNA in pLKO  plasmid vector was used to generate control cells

value: colon neoplasm

tag: genotype

value: wild type


title: VKVC320SC-6_004


title: VKVC320KO-6_007

value: ALDH1A1 knockdown


title: AG_Mor_R5_C1


title: DLBCL_1697_11


title: DLBCL_1747_12


title: AG_Mor_R5_C7


title: DLBCL_2410_11


title: AG_Mor_R4_C9


title: VKVC320KO-5_006


title: AG_Mor_R5_C4


title: AG_Mor_R4_C8


title: AG_Mor_R4_C7


title: VKVC320KO-1_005


title: AG_Mor_R4_C6


title: ATAC_IL33_CGRP_3

description:
ATAC_all.rawcounts.tab.gz
ATAC_all.normalized_counts.txt

source_name: Lung Innate lymphoid cells

extract_protocol:
Lungs were digested with the lung dissociation kit (Miltenyi Biotec) and subsequently enriched for CD90.2+ cells using CD90.2 MicroBeads (Miltenyi Biotec). Lung ILCs were isolated by fluorescence-activated cell sorting as 7AAD- CD45+ CD90.2+ CD127+ Lineage (CD3, CD4, CD8, CD11b, CD11c, CD19, NK1.1, TCRβ, TCRγδ)- cells.
6,000 viable ILC2s were sorted into DPBS supplemented with 2% FCS. Cells were pelleted by centrifugation and stored in BambankerTM cell freezing media (LYMPHOTEC Inc.) at -80 °C. For ATAC-seq library preparation, cells were thawed at 37 °C, washed once with PBS, and lysed and tagmented in 1X TD Buffer, 0.2ul TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS in 40ul reaction volume following the protocol described in Corces at al. (Corces et al., 2016). Transposition was performed at 37 °C for 30 min at 300 rpm. The DNA was purified immediately with the MinElute PCR purification kit (Qiagen). The complete eluate was then amplified with PCR, as follows. First, 5 cycles of pre-amplification were performed using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB). The number of additional cycles was assessed by SYBR Green quantitative PCR. After purifying the final library with the MinElute PCR purification kit (Qiagen), the library was quantified with the Kapa Library Quantification Kit (Kapa Biosystems) and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

treatment_protocol: Sort-purified lung ILC2s were cultured overnight with IL-7 and for additional 6 hours with IL-7+IL-33 or IL-7+IL-33+CGRP.

tag: strain

value: lung

tag: cell type

value: Innate lymphoid cells

tag: cgrp-treated

value: Yes

value: 6 hours

value: In vitro

value: ATAC-seq


title: ATAC_IL33_CGRP_2

tag: timepoint

tag: in vitro vs. in vivo

tag: protocol


title: ATAC_IL33_CGRP_1

tag: tissue


title: AG_Mor_R4_C5

source_name: Embryo

tag: embryo type


title: ATAC_IL33_3

value: No


title: ATAC_IL33_2


title: AG_Mor_R4_C4

tag: developmental stage


title: AG_Mor_R4_C3


title: ATAC_IL33_1


title: AG_Mor_R5_C10


title: AG_Mor_R4_C23


title: AG_Mor_R4_C22


title: VKVC320SC-2_001


title: AG_Mor_R4_C24


title: BMDM_ATAC_DLL4_24h_rep1

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome.  Bowtie2 with default parameters was used to map ATAC-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Peaks were called with HOMER for each tag directory with parameters -minDist 200 - size 200.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated HOMER peak files

extract_protocol:
Approximately 50,000 cells were washed once with PBS and once with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Cells were then suspended in 50 µl 1X reaction buffer (25μl Tagment DNA Buffer, 2.5μl Tagment DNA enzyme I, and 22.5μl water) (Nextera DNA Library Preparation Kit, Illumina). Transposase reactions were carried out at 37°C for 30 minutes and immediately DNA was purified using ChIP DNA Clean & Concentrator kits (Zymo Research).
DNA was amplified using the Nextera primer Ad1 and a unique Ad2.n barcoding primer using NEBNext High-Fidelity 2XPCR Master Mix (NEB) for 14 cycles. Resulting libraries were size selected by gel excision to 175-225 bp and purified.

value: in vitro

value: 4 day cultured BMDMs

value: DLL4 24h


title: BMDM_ATAC_DLL4_24h_rep2


title: AG_Mor_R4_C21

value: AG embryo


title: BMDM_ATAC_NoTx_24h_rep2

value: No treatment


title: AG_Mor_R4_C19

value: morula


title: BMDM_ATAC_NoTx_24h_rep1


title: AG_Mor_R4_C20


title: AG_Mor_R4_C2


title: Smad4KO_KC_ATAC_NoTx_382

source_name: Smad4 flox/flox

value: Smad4 flox/flox


title: Control_KC_ATAC_NoTx_383

source_name: Smad4 flox/flox Clec4f-cre +/-

value: Smad4 flox/flox Clec4f-cre +/-


title: Control_KC_ATAC_NoTx_381


title: AG_Mor_R4_C17


title: AG_Mor_R4_C18


title: AG_Mor_R4_C15


title: KcClecPosTim4Pos_ATAC_NoTx_KO_rep1

source_name: Nr1h3 flox/flox Clec4f-cre +/-

value: Nr1h3 flox/flox Clec4f-cre +/-


title: AG_Mor_R4_C16


title: AG_Mor_R4_C14


title: KcClecPosTim4Neg_ATAC_NoTx_KO_rep1


title: AG_Mor_R4_C12


title: KcClecNegTim4Pos_ATAC_NoTx_Control_rep2

source_name: Nr1h3 flox/flox

value: Nr1h3 flox/flox


title: AG_Mor_R4_C11


title: KcClecNegTim4Pos_ATAC_NoTx_Control_rep1


title: KcClecPosTim4Neg_ATAC_NoTx_KO_rep2


title: RLM_mouse195_ATAC_DT48h

value: Diphtheria toxin 48h


title: KC_mouse60_ATAC_PBS

value: PBS


title: AG_Mor_R4_C10


title: AG_Mor_R3_C8


title: AG_Mor_R3_C9


title: KC_mouse216_ATAC_PBS


title: AG_Mor_R4_C1


title: RLM_mouse212_ATAC_DT48h


title: Smad4KO_KC_ATAC_NoTx_366


title: KcClecPosTim4Pos_ATAC_NoTx_KO_rep2


title: AG_Mor_R3_C7


title: RLM_mouse215_ATAC_DT24h

value: Diphtheria toxin 24h


title: RLM_mouse106_ATAC_DT24h


title: AG_Mor_R3_C6


title: AG_Mor_R3_C5


title: AG_Mor_R3_C4


title: RLM_mouse58_ATAC_DT24h


title: AG_Mor_R3_C3


title: BloodLy6cHi_mouse3_ATAC_notx


title: BloodLy6cHi_mouse8_ATAC_notx


title: AG_Mor_R4_C13


title: AG_Mor_R3_C2


title: ChIP_input_RBPJ_KcNuclei_notx_rep2

tag: antibody

value: input


title: AG_Mor_R3_C1


title: AG_Mor_R3_C10


title: ChIP_RBPJ_KcNuclei_notx_rep2

value: RBPJ (2 ug, Abcam, ab25949)


title: ChIP_input_RBPJ_KcNuclei_notx_rep1


title: AG_8C_R4_C8


title: ChIP_H3K27ac_KC_notx_rep1

value: H3K27ac (2 ug, Active Motif, 39133)


title: AG_8C_R4_C3


title: ChIP_RBPJ_KcNuclei_notx_rep1


title: ChIP_SMAD4_KcNuclei_notx_rep1

value: SMAD4 (1 ug each of Cell Signaling technology 46535 and 38454)


title: ChIP_input_SMAD4_KcNuclei_notx_rep1


title: AG_8C_R4_C7


title: ChIP_H3K27ac_RLM_DT24h_rep1


title: AG_8C_R4_C5


title: ChIP_H3K27ac_RLM_DT24h_rep2


title: AG_8C_R4_C2


title: ChIP_H3K27ac_BloodLy6cHi_notx_rep1


title: AG_8C_R4_C4


title: ChIP_H3K27ac_BloodLy6cHi_notx_rep2


title: AG_8C_R3_C6


title: AG_8C_R3_C8


title: AG_8C_R4_C6


title: AG_8C_R3_C7


title: BMDMdmhca_24h_rep2

value: in vitro

value: DMHCA 24h


title: AG_8C_R3_C1


title: BMDMdmhca_24h_rep1

value: 4 day cultured BMDMs


title: BMDMsmad4KODll4Tgfb_rep2

value: DLL4 24h

value: TGF-beta 24h


title: BMDMsmad4KODll4Tgfb_rep1


title: BMDMsmad4KODll4_rep2


title: AG_8C_R3_C3

value: AG embryo


title: BMDMsmad4KODll4Dapt_rep2

value: DAPT 24h


title: BMDMsmad4KONotx_rep2

value: Smad4 flox/flox Clec4f-cre +/-

value: No treatment


title: BMDMctrDll4Tgfb_rep1

value: Smad4 flox/flox


title: AG_8C_R3_C2


title: BMDMsmad4KODll4Dapt_rep1


title: AG_4C_R4_C4


title: BMDMsmad4KODll4_rep1


title: BMDMsmad4KOTgfb_rep2


title: AG_4C_R4_C2


title: AG_4C_R3_C2


title: AG_4C_R4_C3


title: BMDMsmad4KOTgfb_rep1


title: AG_8C_R3_C5


title: AG_4C_R3_C3


title: BMDMsmad4KONotx_rep1


title: AG_2C_R3_C1


title: AG_4C_R3_C1


title: AG_1C_R3


title: AG_2C_R4_C2


title: BMDMctrTgfb_rep2


title: BMDMctrDll4Tgfb_rep2


title: AG_2C_R4_C1


title: BMDMctrDll4Dapt_rep2


title: AG_2C_R3_C2


title: AG_8C_R3_C4


title: BI_Mor_R7_C8

value: BI embryo

value: morula


title: BMDMctrDll4_rep2


title: BMDMctrDll4_rep1


title: BMDMctrDll4Dapt_rep1


title: BI_Mor_R7_C7


title: BMDMctrNotx_rep2


title: AG_1C_R4


title: BMDMctrTgfb_rep1


title: BI_Mor_R7_C6


title: smadKOt4n_TT


title: BI_Mor_R7_C9


title: BMDMctrNotx_rep1


title: BI_Mor_R7_C5


title: smadKOt4p_CG


title: smadKOt4p_GC


title: smadKOt4n_716


title: BI_Mor_R7_C3


title: BI_Mor_R7_C22


title: smadCTRt4_CA


title: BI_Mor_R7_C2


title: Stab2Hig_317


title: smadCTRt4_AT


title: BI_Mor_R7_C20


title: BI_Mor_R7_C21


title: smadKOt4p_716


title: BI_Mor_R7_C4


title: Stab2Int_210


title: BI_Mor_R7_C15


title: BI_Mor_R7_C14


title: BI_Mor_R7_C13


title: Stab2Hig_210


title: Stab2Int_317


title: BI_Mor_R7_C18


title: Stab2Low_317


title: BI_Mor_R7_C17


title: lxrKO_BMDM_rep2

source_name: Nr1h3 KO

value: Nr1h3 KO

value: 7 day cultured BMDMs


title: Stab2Low_210


title: lxrKO_BMDM_rep1


title: BI_Mor_R6_C9


title: BI_Mor_R7_C11


title: BI_Mor_R7_C12


title: BI_Mor_R7_C16


title: BI_Mor_R7_C19


title: BI_Mor_R6_C5


title: BI_Mor_R6_C8


title: lxrCTR_BMDM_rep1

source_name: Nr1h3 WT

value: Nr1h3 WT


title: BI_Mor_R6_C7


title: lxrKO_clePtimP_rep2

value: Nr1h3 flox/flox Clec4f-cre +/-


title: lxrCTR_BMDM_rep2


title: BI_Mor_R6_C4


title: BI_Mor_R6_C6


title: lxrCTR_cleNtimP_rep2

value: Nr1h3 flox/flox


title: lxrKO_clePtimP_rep1


title: lxrCTR_cleNtimP_rep1


title: BI_Mor_R7_C1


title: KCctr_166

value: PBS 72h


title: BI_Mor_R6_C3


title: lxrKO_clePtimN_rep2


title: KCctr_31


title: KCctr_164


title: RLM336h_565

value: Diphtheria toxin 336h


title: BI_Mor_R6_C26


title: lxrKO_clePtimN_rep1


title: BI_Mor_R7_C10


title: BI_Mor_R6_C24


title: RLM336h_567


title: RLM336h_566


title: RLM168h_568

value: Diphtheria toxin 168h


title: BI_Mor_R6_C25


title: BI_Mor_R6_C23


title: BI_Mor_R6_C22


title: RLM168h_571


title: RLM168h_570


title: BI_Mor_R6_C20


title: RLM072h_41

value: Diphtheria toxin 72h


title: RLM072h_32


title: BI_Mor_R6_C21


title: BI_Mor_R6_C19


title: BI_Mor_R6_C2