title: RNAPII rrp6∆

data_processing:
library strategy: CRAC (Crosslinking and analysis of cDNA) experiments
Sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (Webb et al, 2014). Subsequently, the 3' adaptor is clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (Martin M. embnet.journal, 2011) and the resulting insert is quality trimmed from the 3' end using Trimmomatic rolling mean clipping (Bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (Cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (Langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: RPO21::HTP::TRP1 rrp6∆::URA3kl

growth_protocol: For all datasets, 2L of yeast cells expressing HTP-tagged proteins were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) .

extract_protocol:
Defrosted lysates were treated for one hour at 18°C with DNase I to solubilize the chromatin, clarified by centrifugation, followed by stringent, denaturing, two-step affinity purification of the tagged protein as described in the original protocol (Bohnsack et al., 2012) with minor changes. Bound RNA partially degraded with RNase, was ligated to modified 5’ and 3’ linkers adapted to sequence RNA molecules from the 3’ end. Covalent RNA-protein complexes were isolated by Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree). Following Proteinase K digestion of the bound proteins, RNA fragments were amplified by RT-PCR.
Between half to ¾ of the cDNA solution was used to performed multiple PCR reactions in a final volume of 25 µL using the following conditions: 0.4 µM of each primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µL of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per milliliter of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent for sequencing using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were subjected to UV crosslink in a UV lamp system (Megatron) for 80 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume/g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

tag: strain background

value: W303-derived strain

tag: genotype/variation

value: RPO21::HTP::TRP1 rrp6{delta}::URA3kl


title: RNAPII

status: Public on Jul 24 2020

type: SRA

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

library_source: transcriptomic

molecule: total RNA


title: KP_30w_Cis72_m6_PT 10xRNA-seq

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Demultiplexing with cellranger mkfastq v3.1 (bcl2fastq)
UMI expression quantification with cellranger v3.1
R package dropletUtils is used to exclude chimeric reads and identify and exclude empty droplets
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Raw count matrices are in HDF5 Feature Barcode Matrix Format used by 10x, and metadata files are comma-delimited text:
mmLung10x_cis_dZ_annot_annot_smpTable.csv (cvs, annotation)
mmLung10x_cis_dZ_emptyP_emptyP_smpTable.csv (csv, QC empty drop table)
mmLung10x_cis_dZ_mappingStats_mappingStats_smpTable.csv (csv, QC mapping stats table)
mmLung10x_cis_dZ_QCstat_QCstat_smpTable.csv (csv, QC table)
mmLung10x_cis_dZ_saturation_saturation_smpTable.csv (csv, cell sequencing saturation estimates)
mmLung10x_cis_geneTable.csv (csv, gene ids)
mmLung10x_cis_smpTable.csv (csv, sample ids)
mmLung10x_cis_dSp_rawCount.h5 (hdf5, (i,j,v, sparse matrix), Raw counts )
mmLung10x_cis_dSp_normTPM.h5 (hdf5, (i,j,v, sparse matrix), Log2 (transcript/10K+1))

organism: Mus musculus

source_name: Lung tissue, AT2 cells

growth_protocol: We used C57BL/6 x Sv129 mixed background mice from the following previously published strains: KrasLSL-G12D (Jackson et al., 2001), Trp53flox/flox (Marino et al., 2000), Rosa26LSL-tdTomato (Madisen et al., 2010), and Rosa26LSL-Luciferase (Safran et al., 2003).

extract_protocol:
Mice with LUAD tumors were euthanized at 2, 12, 20, or 30 weeks following tumor induction. We chose these time points because they reflect key stages in LUAD progression: atypical adenomatous hyperplasia (AAH) (KT and KPT at 2 weeks), adenoma (KT at 12 and 30 weeks), adenoma-to-LUAD transition (KPT at 12 weeks) and LUAD (KPT at 20 and 30 weeks). We micro-dissected large KPT tumors individually at 20 and 30 weeks, whereas all other samples were harvested by dissociating entire lungs containing mixtures of neoplasias in various stages of tumor progression. Following euthanasia, mice were perfused with S-MEM (Gibco, catalog #11380037) through the right ventricle of the heart. Dissected lungs or microdissected tumors were dissociated either with protease and DNAse solution in the Lung Dissociation Kit (Miltenyi Biotech, catalog #130-095-927) followed by mechanical dissociation using gentleMACS “C” columns (Miltenyi Biotech, catalog #130-093-237) according to the manufacturer’s instructions (Tammela et al., 2017), or by a mixture of Dispase II (Gibco, catalog #17105-041, final concentration 0.6 U/ml), Collagenase Type IV (Thermo Fisher Scientific, catalog #17104019; final concentration 0.083 U/ml), and DNase I (Sigma-Aldrich, catalog #69182-3; final concentration 10 U/ml) in S-MEM solution containing Gentamicin (Gibco, catalog #15750-060, final concentration 20 mg/ml) at 37°C for 30 min (Table S6). The dissociated cells were filtered using a 100 mm strainer and spun at 300 g for 5 min at room temperature. The supernatant was removed by aspiration and red blood cell lysis was performed using ACK (Thermo Fisher Scientific, catalog #A1049201). Cells were then washed with media and pelleted at 300 g for 5 min at 4°C. The supernatant was removed, and the pellet resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (200 mM EDTA with 250 ml heat-inactivated FBS in PBS) before being passed through a 40 mm strainer and counted for use in FACS below.
3' RNAseq (10x V2)
Droplet single-cell RNAseq

treatment_protocol: Tumors were induced in K or KP mice with 0.5-2.5 x 10^8 PFU of AdSPC-Cre (Sutherland et al., 2011) or 2 x 10^8 PFU of AdCMV-FlpO (Iowa).

tag: treatment

value: Cisplatin 72h

tag: genotype

value: KrasMut, Trp53 null

tag: timepoint

value: 30w tumors


title: 6-NTC-HA

city: MINNEAPOLIS

first: Ryan

last: Langlois

state: MN

country: USA

institute: University of Minnesota

description:
A549 cells
Project_018.txt
sample name:
6.NTC.HA_S6

data_processing:
Step 1:  Fastq files were aligned to the reference (mouse mm10 and human hg38) genome with Bowtie2 (refer to method for more details).
Step 2: Mapped reads were assigned to ENSEMBL gene models with featurecounts (refer to method for details)
Step 3: Statistically significant differentially expressed genes were determined using edgeR.
Genome_build: For mouse: Mus_musculus.GRCm38.87; human: Homo_sapiens.GRCh38.87; influenza: A/Puerto Rico/8/34
Supplementary_files_format_and_content: Expression counts files are in tab delimited text format
Project_009.txt: mouse raw gene expression counts; tab-delimited text
Project_015.txt: mouse raw gene expression counts; tab-delimited text
Proj017_flu-forwardreads.txt: Influenza A virus raw gene expression counts - forward reads; tab-delimited text
Proj017_flu-forwardreads.txt: Influenza A virus raw gene expression counts - reverse reads; tab-delimited text
Project_018.txt: human raw gene expression counts; tab-delimited text
Proj024_flu-forwardreads.txt: Influenza A virus raw gene expression counts - forward reads; tab-delimited text
Proj024_flu-reversereads.txt: Influenza A virus raw gene expression counts - reverse reads; tab-delimited text

molecule: polyA RNA

organism: Homo sapiens

source_name: RIG-I KO, MDA5 KO, MAVS KO, or non-targeted wild type control A549 human lung cells were infected with deltaHA-mCherry or deltaPB1-mCherry and harvested at 12 hpi. Uninfected cells used as controls

extract_protocol:
Qiagen RNeasy PLUS Micro kit
Clontech Stranded Total RNA PicoMammalian kit

tag: cell line

value: A549 cells

tag: cell type

value: lung carcinoma

tag: deltaha or deltapb1 infected

value: deltaHA

tag: rig-i ko, mda5 ko, mavs ko, or none (wt)


title: Tigit_neg_pre_1 10xRNA-seq

data_processing:
Demultiplexing with cellranger mkfastq v3.1 (bcl2fastq)
UMI expression quantification with cellranger v3.1
R package dropletUtils is used to exclude chimeric reads and identify and exclude empty droplets
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Raw count matrices are in HDF5 Feature Barcode Matrix Format used by 10x, and metadata files are comma-delimited text:
mmLung10x_Tigit_dZ_annotTigitAll_annotTigitAll_smpTable.csv (csv, annotation post-transplant)
mmLung10x_Tigit_dZ_annotTigitPre_annotTigitPre_smpTable.csv (cvs, annotation pre-transplant)
mmLung10x_Tigit_dZ_emptyP_emptyP_smpTable.csv (csv, QC empty drop table)
mmLung10x_Tigit_dZ_mappingStats_mappingStats_smpTable.csv (csv, QC mapping stats table)
mmLung10x_Tigit_dZ_QCstat_QCstat_smpTable.csv (csv, QC table)
mmLung10x_Tigit_dZ_saturation_saturation_smpTable.csv (csv, cell sequencing saturation estimates)
mmLung10x_Tigit_geneTable.csv (csv, gene ids)
mmLung10x_Tigit_smpTable.csv (csv, sample ids)
mmLung10x_Tigit_dSp_rawCount.h5 (hdf5, (i,j,v, sparse matrix), Raw counts )
mmLung10x_Tigit_dSp_normTPM.h5 (hdf5, (i,j,v, sparse matrix), Log2 (transcript/10K+1))

extract_protocol:
Mice with LUAD tumors were euthanized at 2, 12, 20, or 30 weeks following tumor induction. We chose these time points because they reflect key stages in LUAD progression: atypical adenomatous hyperplasia (AAH) (KT and KPT at 2 weeks), adenoma (KT at 12 and 30 weeks), adenoma-to-LUAD transition (KPT at 12 weeks) and LUAD (KPT at 20 and 30 weeks). We micro-dissected large KPT tumors individually at 20 and 30 weeks, whereas all other samples were harvested by dissociating entire lungs containing mixtures of neoplasias in various stages of tumor progression. Following euthanasia, mice were perfused with S-MEM (Gibco, catalog #11380037) through the right ventricle of the heart. Dissected lungs or microdissected tumors were dissociated either with protease and DNAse solution in the Lung Dissociation Kit (Miltenyi Biotech, catalog #130-095-927) followed by mechanical dissociation using gentleMACS “C” columns (Miltenyi Biotech, catalog #130-093-237) according to the manufacturer’s instructions (Tammela et al., 2017), or by a mixture of Dispase II (Gibco, catalog #17105-041, final concentration 0.6 U/ml), Collagenase Type IV (Thermo Fisher Scientific, catalog #17104019; final concentration 0.083 U/ml), and DNase I (Sigma-Aldrich, catalog #69182-3; final concentration 10 U/ml) in S-MEM solution containing Gentamicin (Gibco, catalog #15750-060, final concentration 20 mg/ml) at 37°C for 30 min (Table S6). The dissociated cells were filtered using a 100 mm strainer and spun at 300 g for 5 min at room temperature. The supernatant was removed by aspiration and red blood cell lysis was performed using ACK (Thermo Fisher Scientific, catalog #A1049201). Cells were then washed with media and pelleted at 300 g for 5 min at 4°C. The supernatant was removed, and the pellet resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (200 mM EDTA with 250 ml heat-inactivated FBS in PBS) before being passed through a 40 mm strainer and counted for use in FACS below.
3' RNAseq (10x V3)
Droplet single-cell RNAseq

tag: time

value: Pre-transplant

tag: tigit

value: Negative

value: Kras mut, Trp53 null


title: LB4b

city: Carson

first: Karin

middle: E.

last: Kram

state: California

address: 1000 E. Victoria St.

department: Biology

institute: California State University Dominguez Hills

data_processing:
Alighned using TopHat2
SAMTools to generate BAM files
Read counts calculated by HTSeq
Genome_build: E. coli K12 MG1655 from UCSC
Supplementary_files_format_and_content: Comma separated text files for each sample include count files for each gene

organism: Escherichia coli

source_name: LB culture

growth_protocol: Cells inoculated 1:1000 dilution into LB Lenox broth from overnight growth

extract_protocol:
Culture sacrificed, RNAprotect and RNeasy extraction kit used (Qiagen)
Illumina Ribo-zero and RNA library kit

treatment_protocol: Incubated for time specified in sample information

tag: strain

value: PFM2 (MG1655 derivative)

tag: time incubated

value: 4 hours

tag: growth medium

value: LB Lenox


title: KP_30w_ND_m4_PT 10xRNA-seq

value: Control, no-drug


title: KP_30w_Cis72_m5_PT 10xRNA-seq


title: 4-NTC-HA

description:
A549 cells
Project_018.txt
sample name:
4.NTC.HA_S4


title: KP_30w_ND_m3_PT 10xRNA-seq


title: Nrd1 rrp6∆ rep1

source_name: NRD1::HTP::TRP1 rrp6∆::KAN

value: NRD1::HTP::TRP1 rrp6{delta}::KAN


title: Nrd1 rep2


title: Palmera Control 3 [C18]

city: Lisboa

first: Andre

middle: Martinho

last: de Almeida

address: Tapada da Ajuda

department: DCEB

country: Portugal

institute: Instituto Superior de Agronomia / University of Lisbon

data_processing:
Bowtie2 v2.2.3
RSEM v1.2.17
edgeR v3.2.4
DAVID (Database for Annotation, Visualization and Integrated Discovery)  v6.7
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: Raw number of reads and statistical analysis of each gene, with accession number, between Majorera (M), Palmera (P), Control and  Experiemntal as indicated in the file names

organism: Capra hircus

source_name: Palmera control_mammary gland

growth_protocol: Conditions for animal experimentation have been thoroughly described in Lerias et al. (2013). Body live weight and milk production parameters in the Majorera and Palmera goat breeds from the Canary Islands: influence of weight loss. Trop Anim Health Prod. 2013 Nov;45(8):1731-6. doi: 10.1007/s11250-013-0423-2.

extract_protocol:
Total RNA was extracted from the tissue using the E.Z.N.A. Total RNA Kit II (Omega Bio-Tek Inc., Norcross, Georgia, USA). About 30 mg of tissue was finely grinded in liquid nitrogen and used with the kit following manufacturer’s instruction to extract total mRNA. A DNAse digestion step was carried out after extraction to remove contaminating genomic DNA using an Ambion® TURBO™ DNase (Life Technologies, Carlsbad, CA, U.S.A.) following manufacturer´s instructions. A quantitative and qualitative assessment of the isolated RNA was performed using a NanoDrop® 2000c Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, U.S.A.). Purity was also estimated based on the absorbance ratios of the RNA samples at 260/280 nm and 260/230 nm. For pure RNA, ratios should be of about 2.0 and 2.0-2.2, respectively (T042‐Technical Bulletin, Thermo Scientific). RNA integrity was assessed by an electrophoresis in a 2.0% agarose gel. Good quality RNA should present well defined 28S and 18S bands. RNA quality was also analysed using a RNA Nano Kit Chips from the Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA, U.S.A.). Using this approach, a good RNA sample should present well defined peaks corresponding to 28S and 18S bands and a RNA Integrity Number (RIN) above 7. The absence of DNA in RNA treated samples was verified by standard polymerase chain reaction (PCR).
RNA Sequencing was conducted by LC-Sciences (Houston, TX, USA) following the TruSeq® Stranded mRNA  Sample Preparation Guide (Illumina)

treatment_protocol: Samples were excised from the mammary gland, preserved in RNA later following manufacturer's instructions and kept at -80ºC until further analysis

tag: breed

value: Palmera

value: control

tag: tissue

value: Mammary gland

tag: replicate no.

value: Biological Replicate #3


title: 106623_Tigit_Pos_S8 bulk ATACseq

description:
Bulk ATAC of AT2 cells from lung tumors, sorted by FACS for expression of TIGIT
tigit_pos_neg.merged.bed
counts_tigitSamples_featureCounts_filtered_notSubs.tsv.gz

library_source: genomic

data_processing:
Alignment and QC performed using ENCODE ATAC-Seq pipeline, v1.5.4, https://github.com/ENCODE-DCC/atac-seq-pipeline, processed on terra-firecloud
Filter the de-duped .bam files generated by the ENCODE ATAC-Seq pipeline to contain only the main chromosomes (Samtools v1.8)
Subsample the .bam files to the minimum number of reads observed across all replicates and conditions (Samtools v1.8)
Merge the .bam files across replicates from individual condition (Samtools v1.8)
Call peaks (MACS2 v2.2.6)
Filter blacklisted regions (Bedtools v2.26.0)
Merge peak files from Tigit+ and Tigit- conditions (Bedtools v2.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: Peak file in bed format, and featureCounts output

molecule: genomic DNA

extract_protocol: Mice with LUAD tumors were euthanized at 2, 12, 20, or 30 weeks following tumor induction. We chose these time points because they reflect key stages in LUAD progression: atypical adenomatous hyperplasia (AAH) (KT and KPT at 2 weeks), adenoma (KT at 12 and 30 weeks), adenoma-to-LUAD transition (KPT at 12 weeks) and LUAD (KPT at 20 and 30 weeks). We micro-dissected large KPT tumors individually at 20 and 30 weeks, whereas all other samples were harvested by dissociating entire lungs containing mixtures of neoplasias in various stages of tumor progression. Following euthanasia, mice were perfused with S-MEM (Gibco, catalog #11380037) through the right ventricle of the heart. Dissected lungs or microdissected tumors were dissociated either with protease and DNAse solution in the Lung Dissociation Kit (Miltenyi Biotech, catalog #130-095-927) followed by mechanical dissociation using gentleMACS “C” columns (Miltenyi Biotech, catalog #130-093-237) according to the manufacturer’s instructions (Tammela et al., 2017), or by a mixture of Dispase II (Gibco, catalog #17105-041, final concentration 0.6 U/ml), Collagenase Type IV (Thermo Fisher Scientific, catalog #17104019; final concentration 0.083 U/ml), and DNase I (Sigma-Aldrich, catalog #69182-3; final concentration 10 U/ml) in S-MEM solution containing Gentamicin (Gibco, catalog #15750-060, final concentration 20 mg/ml) at 37°C for 30 min (Table S6). The dissociated cells were filtered using a 100 mm strainer and spun at 300 g for 5 min at room temperature. The supernatant was removed by aspiration and red blood cell lysis was performed using ACK (Thermo Fisher Scientific, catalog #A1049201). Cells were then washed with media and pelleted at 300 g for 5 min at 4°C. The supernatant was removed, and the pellet resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (200 mM EDTA with 250 ml heat-inactivated FBS in PBS) before being passed through a 40 mm strainer and counted for use in FACS below.

value: Positive


title: 3-NTC-NAIVE

description:
A549 cells
Project_018.txt
sample name:
3.NTC.NAIVE_S3


title: Palmera Control 2 [C17]

value: Biological Replicate #2


title: Tigit_neg_pre_2 10xRNA-seq


title: 36-MAVS-PB1

description:
A549 cells
Project_018.txt
sample name:
36.MAVS.PB1_S36

value: A549 cells

value: MAVS KO


title: Nrd1 rep1

tag: strain background

value: W303-derived strain


title: Palmera Control 1 [C11]

value: Biological Replicate #1


title: 106621_106642_Tigit_Pos_S6 bulk ATACseq


title: 35-MAVS-PB1

description:
A549 cells
Project_018.txt
sample name:
35.MAVS.PB1_S35

value: lung carcinoma


title: 34-MAVS-PB1

description:
A549 cells
Project_018.txt
sample name:
34.MAVS.PB1_S34


title: Nab3 rrp6∆ rep2

source_name: NAB3::HTP::TRP1 rrp6∆::KAN

tag: genotype/variation

value: NAB3::HTP::TRP1 rrp6{delta}::KAN


title: Nrd1 rrp6∆ rep2


title: 5-NTC-HA

description:
A549 cells
Project_018.txt
sample name:
5.NTC.HA_S5

value: deltaHA


title: YY1916_Tigit_Pos_S4 bulk ATACseq

value: Kras mut, Trp53 null


title: 106621_106642_Tigit_Neg_S5 bulk ATACseq

value: Negative


title: Nab3 rep3


title: 33-MAVS-HA

description:
A549 cells
Project_018.txt
sample name:
33.MAVS.HA_S33


title: Nab3 rrp6∆ rep1


title: Nab3 rep2


title: Majorera Control 3 [C10]

source_name: Majorera control_mammary gland

value: Majorera

tag: treatment


title: YY1916_Tigit_Neg_S3 bulk ATACseq

tag: genotype


title: 31-MAVS-HA

description:
A549 cells
Project_018.txt
sample name:
31.MAVS.HA_S31


title: 32-MAVS-HA

description:
A549 cells
Project_018.txt
sample name:
32.MAVS.HA_S32


title: YY1181_Tigit_Pos_S2 bulk ATACseq


title: Majorera Control 2 [C16]


title: Nab3 rep1


title: YY1181_Tigit_Neg_S1 bulk ATACseq


title: 30-MAVS-NAIVE

description:
A549 cells
Project_018.txt
sample name:
30.MAVS.NAIVE_S30


title: Majorera Control 1 [C13]


title: 106623_Tigit_Neg_S7 bulk ATACseq


title: Leaf, NahG-Rywal_mock3_pool

city: Ljubljana

first: Maja

last: Križnik

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

data_processing:
Reads were trimmed of low-quality bases (phred quality score > 20), ambiguous nucleotides and adapter sequences with the CLC Genomics Workbench 12.0 (Qiagen)).
Merging of overlapping pairs, mapping the reads to the potato genome and read counting were performed using CLC Genomics Workbench 12.0 (read alignment parameters: length fraction: 0.9, similarity fraction: 0.9, maximum number of hits for a read: 1)
Genome_build: merged ITAG and PGSC gene models for S. tuberosum group Phureja DM genome v4.04
Supplementary_files_format_and_content: Tab-delimited text file includes raw and normalized gene counts.  GeneIds can be interpreted at ftp://ftp.solgenomics.net/genomes/Solanum_tuberosum/annotation/ITAG1.0/

organism: Solanum tuberosum

source_name: mock-inoculated potato plants

growth_protocol: Potato (Solanum tuberosum L.) plants cv. Rywal, NahG-Rywal and shRBOHD transgenic lines were grown in stem node tissue culture. Two weeks after node segmentation, they were transferred to soil in a growth chamber and kept under controlled environmental conditions as described elsewhere ((Baebler et al., 2009).

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and Direct-zol RNA MicroPrep Kit, DNAse treated and purified with RNA Clean & Concentrator kit (both Zymo Research).
Libraries were generated using TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMART-Seq_v4 Ultra Low Input RNA Kit (TaKaRa Bio) and Nextera XT kit (Illumina). RNA-seq was performed on the HiSeq platform (Illumina) using 150-bp paired-end reads.

treatment_protocol: After three to four weeks of growth in soil, the potato plants were inoculated with PVYN-Wilga (PVYN–Wi; EF558545) or mock-inoculated as described by Baebler et al., 2009.

tag: cultivar

value: Rywal

tag: transgenic line

value: NahG-Rywal

value: leaf-tissue between veins

value: mock-inoculated (4 dpi)

tag: pool

value: mock pool


title: Nab3 rrp6∆ rep3


title: 29-MAVS-NAIVE

description:
A549 cells
Project_018.txt
sample name:
29.MAVS.NAIVE_S29

tag: cell line

tag: cell type

tag: deltaha or deltapb1 infected


title: Leaf, NahG-Rywal_mock2_pool


title: 9-HA-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATII_S8

source_name: Mice were infected with deltaPB1_cre or deltaHA-Cre and lung cells were sorted into tdTomato+ and negative populations at 24 hpi. Uninfected used as controls. AT-I, AT-II and ciliated cells sorted.

value: lung

tag: iav deltapb1_cre or deltaha_cre

tag: positive or negative for iav deltapb1_cre or deltaha_cre

value: positive

tag: ciliated cells, ati cells, or atii cells

value: atii cells


title: 2-NTC-NAIVE

description:
A549 cells
Project_018.txt
sample name:
2.NTC.NAIVE_S2

value: A549 cells

tag: rig-i ko, mda5 ko, mavs ko, or none (wt)


title: Leaf, NahG-Rywal_mock1_pool


title: 7-HA-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.CC_S7

tag: strain

value: ciliated cells


title: Tigit_pos, Single cell ATACseq

data_processing:
cellranger-atac count (1.2.0)
Genome_build: mm10 (refdata-cellranger-atac-mm10-1.2.0)
Supplementary_files_format_and_content: 10x peark barcode index, fragment interval files

extract_protocol:
Mice with LUAD tumors were euthanized at 2, 12, 20, or 30 weeks following tumor induction. We chose these time points because they reflect key stages in LUAD progression: atypical adenomatous hyperplasia (AAH) (KT and KPT at 2 weeks), adenoma (KT at 12 and 30 weeks), adenoma-to-LUAD transition (KPT at 12 weeks) and LUAD (KPT at 20 and 30 weeks). We micro-dissected large KPT tumors individually at 20 and 30 weeks, whereas all other samples were harvested by dissociating entire lungs containing mixtures of neoplasias in various stages of tumor progression. Following euthanasia, mice were perfused with S-MEM (Gibco, catalog #11380037) through the right ventricle of the heart. Dissected lungs or microdissected tumors were dissociated either with protease and DNAse solution in the Lung Dissociation Kit (Miltenyi Biotech, catalog #130-095-927) followed by mechanical dissociation using gentleMACS “C” columns (Miltenyi Biotech, catalog #130-093-237) according to the manufacturer’s instructions (Tammela et al., 2017), or by a mixture of Dispase II (Gibco, catalog #17105-041, final concentration 0.6 U/ml), Collagenase Type IV (Thermo Fisher Scientific, catalog #17104019; final concentration 0.083 U/ml), and DNase I (Sigma-Aldrich, catalog #69182-3; final concentration 10 U/ml) in S-MEM solution containing Gentamicin (Gibco, catalog #15750-060, final concentration 20 mg/ml) at 37°C for 30 min (Table S6). The dissociated cells were filtered using a 100 mm strainer and spun at 300 g for 5 min at room temperature. The supernatant was removed by aspiration and red blood cell lysis was performed using ACK (Thermo Fisher Scientific, catalog #A1049201). Cells were then washed with media and pelleted at 300 g for 5 min at 4°C. The supernatant was removed, and the pellet resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (200 mM EDTA with 250 ml heat-inactivated FBS in PBS) before being passed through a 40 mm strainer and counted for use in FACS below.
10x single cell ATACseq
Droplet single-cell ATACseq

tag: tigit

value: Positive


title: 28-MAVS-NAIVE

description:
A549 cells
Project_018.txt
sample name:
28.MAVS.NAIVE_S28

value: lung carcinoma

value: MAVS KO


title: 6-HA-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATII_S6

value: negative


title: Leaf, NahG-Rywal_wilga_3_poolB

source_name: PVYN-Wilga-infected potato plants

tag: tissue

value: leaf-immediate surrounding

value: PVYN-Wilga-inoculated (4 dpi)

value: poolB


title: 61-NAIVE-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.ATII_S56


title: 27-MDA5-PB1

description:
A549 cells
Project_018.txt
sample name:
27.MDA5.PB1_S27

value: MDA5 KO


title: Leaf, NahG-Rywal_wilga_3_poolA

value: Rywal

value: NahG-Rywal

value: leaf-cell death cone

value: poolA


title: Leaf, NahG-Rywal_wilga_2_poolB


title: 26-MDA5-PB1

description:
A549 cells
Project_018.txt
sample name:
26.MDA5.PB1_S26


title: 60-NAIVE-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.ATI_S55

value: lung

value: ati cells


title: 5-HA-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATI_S5


title: 25-MDA5-PB1

description:
A549 cells
Project_018.txt
sample name:
25.MDA5.PB1_S25


title: 59-NAIVE-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.CC_S54


title: Leaf, NahG-Rywal_wilga_2_poolA


title: Leaf, NahG-Rywal_wilga_1_poolB


title: 23-MDA5-HA

description:
A549 cells
Project_018.txt
sample name:
23.MDA5.HA_S23

value: deltaHA


title: 24-MDA5-HA

description:
A549 cells
Project_018.txt
sample name:
24.MDA5.HA_S24

value: A549 cells


title: 58-NAIVE-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.ATII_S53

value: atii cells


title: 21-MDA5-NAIVE

description:
A549 cells
Project_018.txt
sample name:
21.MDA5.NAIVE_S21


title: Leaf, shRBOHD_mock3_pool

value: shRBOHD

value: leaf-tissue between veins

value: mock-inoculated (4 dpi)

value: mock pool


title: 22-MDA5-HA

description:
A549 cells
Project_018.txt
sample name:
22.MDA5.HA_S22

value: lung carcinoma


title: Tigit_neg, Single cell ATACseq

value: Negative

value: Kras mut, Trp53 null


title: 57-NAIVE-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.ATI_S52

value: negative


title: Leaf, shRBOHD_mock2_pool

value: Rywal


title: 20-MDA5-NAIVE

description:
A549 cells
Project_018.txt
sample name:
20.MDA5.NAIVE_S20

value: MDA5 KO


title: 56-NAIVE-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.CC_S51

value: ciliated cells


title: Leaf, shRBOHD_mock1_pool


title: 54-PB1-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.ATI_S49


title: 1-NTC-NAIVE

description:
A549 cells
Project_018.txt
sample name:
1.NTC.NAIVE_S1


title: 19-MDA5-NAIVE

description:
A549 cells
Project_018.txt
sample name:
19.MDA5.NAIVE_S19


title: 55-PB1-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.ATII_S50


title: Leaf, shRBOHD_wilga_3_poolB

value: leaf-immediate surrounding

value: PVYN-Wilga-inoculated (4 dpi)

value: poolB


title: Leaf, shRBOHD_wilga_3_poolA

value: leaf-cell death cone

value: poolA


title: 52-PB1-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.ATII_S47

value: lung

value: positive

value: atii cells


title: 17-RIGI-PB1

description:
A549 cells
Project_018.txt
sample name:
17.RIGI.PB1_S17

value: A549 cells

value: RIG-I KO


title: Leaf, shRBOHD_wilga_2_poolB

value: shRBOHD


title: 16-RIGI-PB1

description:
A549 cells
Project_018.txt
sample name:
16.RIGI.PB1_S16

value: lung carcinoma


title: 50-PB1-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.CC_S46


title: Leaf, shRBOHD_wilga_2_poolA


title: noTD_CTRL

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
Kallisto
DEseq2
R, EnhancedVolcano, GSEA
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: Transduced HSPC

growth_protocol: Cells were grown in IMDM medium supplemented with 15% heat inactivated FBS, 1% Penicillin/Streptomycin, 1% L-Glutamine, murine IL-3, murine IL-6 (10ng/mL), and murine SCF (20ng/mL).

extract_protocol:
HSPCs were isolated and transduced with the respective plasmid, then sorted. After 7-9 days in culture RNA was purified using Qiagen Rneasy nini or micro kits according to manufacturer's instructions
Library prep was performed at Genewiz on PolyA selected mRNA species (eukaryotic), Illumina HiSeq, 2x150bp paired-end reads, multiplexed

value: HSPCs

tag: overexpression


title: 4-HA-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.CC_S4

value: negative


title: Leaf, shRBOHD_wilga_1_poolB

value: Rywal


title: MN1pQdel_rep3


title: 15-RIGI-HA

description:
A549 cells
Project_018.txt
sample name:
15.RIGI.HA_S15

value: deltaHA


title: Leaf, shRBOHD_wilga_1_poolA


title: 48-HA-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATI_S45

value: ati cells


title: MN1pQdel_rep2


title: 53-PB1-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.CC_S48

value: ciliated cells


title: 18-RIGI-PB1

description:
A549 cells
Project_018.txt
sample name:
18.RIGI.PB1_S18


title: MN1pQdel_rep1


title: 13-RIGI-HA

description:
A549 cells
Project_018.txt
sample name:
13.RIGI.HA_S13


title: Leaf, Rywal_mock3_pool

value: leaf-tissue between veins

value: mock-inoculated (4 dpi)

value: mock pool


title: Leaf, Rywal_mock2_pool


title: liver_nonT

type: RNA

city: Minami Uonuma

first: Takeshi

last: Suda

state: Niigata

address: 4132 Urasa

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Uonuma Institute of Community Medicine, Niigata University Medical and Dental Hospital

description: Gene expression data from surrounding non-cancerous liver tissues suffering from chronic hepatitis C (F3)

hyb_protocol: GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, USA) was incubated in GeneChip® Hybridization Oven 645 for 16 hours at 45°C under rotation at the speed of 60 rpm with 5.2 g of the fragmented and biotin-labeled sense stranded -cDNA in hybridization mixture followed by washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G. Raw data were obtained using GeneChip® Command Console® followed by a background adjustment, quantile normalization, and final summarization based on a robust multichip average algorithm using Affymetrix Expression Console.

data_processing: The output files were imported in Transcriptome Analysis Console 4.0 Software (Affymetrix, Santa Clara, USA) to identify differentially expressed genes and carry out clustering and principal component analyses. Genes defining principal components were visualized in a three-dimensional space using R 3.5.1 (R project, http://www.r-project.org) with pca3d package.

label: biotin

source_name: surrounding nontumorous liver tissues

label_protocol: cDNA was generated through the extension from T7 promotor from 100 ng of total RNA followed by cRNA production using T7 RNA polymerase. A sense strand cDNA was synthetized by reverse transcription and purified by hydrolyzing cRNA using RNase H. The sense cDNA was fragmented into 40 to 70 nucleotides using Uracil-DNA glycosylase and covalently linked to biotin by terminal deoxynucleotidyl transferase. All reactions were performed using GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, USA).

extract_protocol: The liver tissues obtained by ultrasound-guided needle biopsy were immersed in RNAlater™ Storage Solution (Ambion, Austin, USA) and disrupted into emulsion using Micro Smash™ (Tomy Digital Biolog, Tokyo, Japan). Total RNA was extracted using RNeasy® Plus Micro Kit (Qiagen, Hilden, Germany) according to the instruction. The quality of RNA was confirmed by measuring its amount and concentration (NanoDrop 1000 Spectrophotometer, Thermo Fisher Scientific, Wilmington, USA), and RNA integrity number (Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit, Waldbronn, Germany) of higher than 100 ng/L, 1000 ng, and 8.0, respectively.

tag: mri arterial phase

value: iso

tag: mri portal phase


title: liver_DN

description: Gene expression data from dysplastic nodule

source_name: dysplastic nodule

value: high


title: 12-RIGI-NAIVE

description:
A549 cells
Project_018.txt
sample name:
12.RIGI.NAIVE_S12


title: 46-HA-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATII_S43

value: lung

value: positive


title: liver_mod

description: Gene expression data from moderately differentiated hepatocellular carcinoma

source_name: moderately differentiated HCC

value: low


title: liver_wel

description: Gene expression data from well differentiated hepatocellular carcinoma

source_name: well differentiated HCC


title: MN1_rep3


title: 45-HA-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATI_S58


title: Leaf, Rywal_mock1_pool

tag: treatment

tag: genotype


title: MN1_rep2


title: 11-RIGI-NAIVE

description:
A549 cells
Project_018.txt
sample name:
11.RIGI.NAIVE_S11

value: A549 cells

value: RIG-I KO


title: 47-HA-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.CC_S44


title: 43-HA-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATI_S41


title: 44-HA-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATII_S42

value: atii cells


title: 14-RIGI-HA

description:
A549 cells
Project_018.txt
sample name:
14.RIGI.HA_S14

value: lung carcinoma


title: 10-RIGI-NAIVE

description:
A549 cells
Project_018.txt
sample name:
10.RIGI.NAIVE_S10


title: Leaf, Rywal_wilga_3_poolA

tag: cultivar

value: leaf-cell death cone

value: PVYN-Wilga-inoculated (4 dpi)

value: poolA


title: MN1_rep1

value: HSPCs


title: 6-3_single_high

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_high_S12

source_name: Mice were infected with mCherry IAV and lung cells were sorted into mCherry high, low, and negative populations at 12 hpi. High mCherry cells have high levels of IAV replication.

tag: iav mcherry status


title: 42-HA-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.CC_S40

value: negative

value: ciliated cells


title: 9-naive-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
9-naive-0

source_name: A549 human lung cells were infected with deltaHA-mCherry or deltaPB1-mCherry at MOI=1 and harvested at 0, 3, 6, 9, and 12 hpi. Uninfected cells used as controls.

extract_protocol:
TRIzol RNA extraction + clonetech total stranded RNA
Clontech Stranded Total RNA PicoMammalian kit

tag: cell line

tag: hours post deltaha or deltapb1 infection (hpi)


title: Leaf, Rywal_wilga_2_poolB

value: Rywal

value: leaf-immediate surrounding

tag: pool

value: poolB


title: 6-2_single_low

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_low_S11

source_name: Mice were infected with mCherry IAV and lung cells were sorted into mCherry high, low, and negative populations at 12 hpi. Low mCherry cells have low levels of IAV replication.

tag: cell type


title: 8-naive-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
8-naive-0

tag: deltaha or deltapb1 infected


title: Leaf, Rywal_wilga_2_poolA


title: 6-1_single_neg

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_neg_S10

source_name: Mice were infected with mCherry IAV and lung cells were sorted into mCherry high, low, and negative populations at 12 hpi. Negative cells do not contain virus.


title: 6-PB1-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
6-PB1-0


title: 41-HA-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATII_S39

tag: iav deltapb1_cre or deltaha_cre

tag: positive or negative for iav deltapb1_cre or deltaha_cre

tag: ciliated cells, ati cells, or atii cells


title: 3-HA-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATII_S3

tag: strain


title: 40-HA-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATI_S38

value: ati cells


title: Leaf, Rywal_wilga_3_poolB

tag: tissue


title: 5-3_single_high

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_high_S9

value: lung

value: high


title: 5-PB1-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
5-PB1-0


title: 7-naive-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
7-naive-0


title: 39-HA-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATII_S37


title: 37-HA-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.CC_S35


title: 45-naive-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
45-naive-12


title: 5-2_single_low

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_low_S8

value: low


title: 4-3_single_high

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_high_S6


title: 4-2_single_low

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_low_S5


title: 44-naive-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
44-naive-12

value: A549 cells


title: 36-HA-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATII_S34

value: positive


title: 4-PB1-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
4-PB1-0


title: 38-HA-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATI_S36


title: 43-naive-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
43-naive-12


title: Leaf, Rywal_wilga_1_poolB


title: 4-1_single_neg

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_neg_S4


title: 35-HA-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATI_S33


title: Leaf, Rywal_wilga_1_poolA


title: 34-HA-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.CC_S57


title: 3-1_naive

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
naive_S3

source_name: Uninfected mouse lung cells


title: 33-NAIVE-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.ATII_S32

value: atii cells


title: 41-PB1-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
41-PB1-12

value: lung carcinoma


title: 42-PB1-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
42-PB1-12


title: 2-1_naive

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
naive_S2


title: 5-1_single_neg

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
single_neg_S7


title: HL-60 control, replicate 2

city: Bologna

first: Annalisa

last: Lonetti

address: Via Massarenti, 11

department: “Giorgio Prodi” Interdepartmental Cancer Research Centre

country: Italy

institute: University of Bologna

description: Gene expression data from AML cell line treated with vehicle (DMSO 0.01%) as control

hyb_protocol: According to Affymetrix GeneChip® Expression Wash, Stain and Scan UserGuide (P/N 702731 Rev. 4)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with R version 3.6.1(Bioconductor), using RMA algorithm for normalization

source_name: non MLL-r AML cell line (control sample)

label_protocol: According to Affymetrix GeneChip® WT PLUS Reagent Kit UserGuide (P/N 703174 Rev. 5)

extract_protocol: Total RNA was isolated by RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

value: MLL wild type

value: 8 days vehicle (DMSO 0.01%)


title: HL-60 treated, replicate 2

description: Gene expression data from AML cell line treated with 1 µM Pinometostat

source_name: non MLL-r AML cell line (Pinometostat treated sample)

value: 8 days Pinometostat (1 uM)


title: 40-PB1-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
40-PB1-12


title: HL-60 treated, replicate 1


title: 31-NAIVE-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.CC_S30


title: 3-HA-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
3-HA-0

value: deltaHA


title: 32-NAIVE-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
NAIVE.ATI_S31

value: negative


title: 1-1_naive

description:
FACS-sorted cells from mouse lung
Project_009.txt
sample name:
naive_S1


title: U-937 treated, replicate 2


title: mHipp_Rep2_Input

city: Portland

first: James

middle: Christopher

last: McGann

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Vollum Institute

institute: Oregon Health and Science University

data_processing:
Sequenced reads were processed and analyzed by the ENCODE ChIP-seq analysis pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters using the GRCh38 (hg38) version of the human genome and the mm10 version of the mouse genome.
Peaks for each replicate were called and then the final peak list was based on the optimal set calculated using the SPP peak caller and the irreproducible discovery rate (IDR), which incorporates all the replicates into the analysis.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bed files contain macs-called peaks for each replicate. Bigwig files contain genome wide signal (fold enrichment ChIP/Input)

extract_protocol:
~100-200 mg tissue from mouse hippocampus/ human hippocampus was cross-linked in Cross-linking buffer (10 mM HEPES, pH 7.2, 100 mM NaCl, 1 mM EDTA and 1 mM EGTA) containing 1% formaldehyde (Thermo; methanol free) for 10 minutes at room temperature. Excess formaldehyde was quenched by glycine for 5 minutes at room temperature. Tissue was resuspended in homogenization buffer (250 mM Sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH; pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and protease inhibitors) after a wash with ice-cold PBS. Tissue was homogenized using Dounce homogenizer with loose (A) and tight (B) pestle (5 strokes each), followed by additional 5 strokes of tight pestle with 0.3% NP-40, and then the homogenate was passed through a 40 um strainer. Nuclei were isolated at 4000g/ 4°C for 5 minutes and resuspended in ~0.5 ml sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 mM EGTA). Fragmented chromatin was prepared from ~10 million nuclei in Covaris S220 (200 cycle per burst, 5% duty cycle at power level 4 for 12 minutes at 4°C) in presence of 0.3% SDS. For ChIP, Protein G Dynabeads (Invitrogen; 30 ul/reaction) were equilibrated in TBSTBp (TBS with 1% BSA, 1% Triton-X-100, and protease inhibitors). 10 ul Protein G beads were used for preclearing the chromatin in ChIP buffer (10 mM Tris-HCl pH 8.0, 1% Triton-X-100, 150 mM NaCl and 1 mM EDTA, and protease inhibitors) for 4 hours at 4°C. 20 ul Protein G beads were used to make the bead-Ab complex with 20 ug anti-REST-C antibodies (Ballas et al., 2005) for 2 hours at room temperature in 0.5 ml TBSTBp. After washing bead-Ab complex three times with TBSTBp, ChIP was carried out overnight at 4°C with precleared chromatin. Beads were washed twice with low salt, high salt and LiCl buffers at 4°C, followed by two washes with TE at room temperature. DNA was eluted and crosslinks were reversed overnight at 65°C. Contaminants were removed from DNA by RNaseA and Proteinase K treatment followed by purification with PCR purification kit (QIAGEN)
Ten nanograms of fragmented DNA was used as input for a modified TruSeq Nano DNA library preparation protocol (Illumina). Briefly, input DNA was treated with 3’ to 5’ exonuclease activity and 5’ to 3’ polymerase activity to blunt the ends. There was no size selection of the fragments. A single “A” nucleotide was added to the 3’ ends to enhance ligation to the adapters. RNA adapters (Illumina) were ligated to the fragmented DNA followed by cleanup using sample purification beads (SPB) provided with the kit. The ligation product was enriched using 14 cycles of polymerase chain reaction. The amplification product was cleaned using SPB. Libraries were profiled using the TapeStation D1000 DNA tape. Library concentrations were determined using the Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems) on a StepOnePlus Real Time PCR Workstation (ThermoFisher).  Libraries were mixed for multiplexing and the concentration of the mix was determined by real time PCR.

tag: age

value: 5 weeks

value: Hippocampus


title: U-937 control, replicate 2


title: mHipp_Rep2_REST_ChIP

tag: chip antibody

value: anti-REST-C antibody


title: U-937 treated, replicate 1


title: 30-PB1-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.ATII_S29


title: 38-HA-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
38-HA-12


title: HL-60 control, replicate 1


title: 2-HA-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATI_S2


title: mHipp_Rep1_Input


title: U-937 control, replicate 1


title: OCI-AML3 treated, replicate 2


title: mHipp_Rep1_REST_ChIP


title: 29-PB1-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.ATI_S28


title: 36-naive-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
36-naive-9


title: OCI-AML3 control, replicate 2


title: 39-HA-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
39-HA-12


title: 28-PB1-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.CC_S27

value: ciliated cells


title: MI_3dMI_2 []

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

description:
microRNA_count_3d_MI.txt
DESeq2_result_3d_MI.txt
6047

data_processing:
FASTQ files were explored using FASTQC prior to cleaning
Reads were trimmed for the adapter and quality score less than 20 from both ends, and removed if length is less than 15 nucleotides
Cleaned reads were aligned to genome mm10 using Bowtie incorporated in Partek Flow
Aligned read were quantified against the mm10 mirbase precursor 21 v2  in Partek Flow
DESeq2 Bioconductor package was used for differential expression in sham vs MI
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing counts and DESeq results

source_name: heart tissue

extract_protocol:
RNA was extracted using a Qiagen miRNeasy mini kit according to manufacturer’s instructions.
Total RNA samples were sent to Genewiz (South Plainfield, NJ) for small RNA library preparation and 1 x 50bp single read sequencing on an Illumina HiSeq2500.

value: heart left ventricle (free wall)

tag: gender

value: male

value: 8-12 weeks

tag: surgery

value: LAD ligation


title: 34-naive-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
34-naive-9

value: A549 cells


title: 35-naive-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
35-naive-9


title: 26-PB1-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.ATI_S25

value: lung

value: positive

value: ati cells


title: 27-PB1-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.ATII_S26

value: atii cells


title: sham_3dMI_2 [6046]

description:
microRNA_count_3d_MI.txt
DESeq2_result_3d_MI.txt
6247

value: sham


title: MI_3dMI_1 [6047]

description:
microRNA_count_3d_MI.txt
DESeq2_result_3d_MI.txt
6046


title: 25-PB1-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.CC_S24


title: 33-PB1-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
33-PB1-9

value: lung carcinoma


title: 37-HA-12

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
37-HA-12

value: deltaHA


title: sham_3dMI_1 [6247]

description:
microRNA_count_3d_MI.txt
DESeq2_result_3d_MI.txt
6246


title: MI_1dMI_2 [6246]

description:
microRNA_count_1d_MI.txt
DESeq2_result_1d_MI.txt
3995


title: 32-PB1-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
32-PB1-9


title: 24-PB1-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.ATII_S23

value: negative


title: MI_1dMI_1 [3995]

description:
microRNA_count_1d_MI.txt
DESeq2_result_1d_MI.txt
3991


title: 31-PB1-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
31-PB1-9


title: 23-PB1-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.ATI_S22


title: OCI-AML3 control, replicate 1

description: Gene expression data from AML cell line treated with vehicle (DMSO 0.01%) as control

tag: genotype

value: MLL wild type

tag: treatment

value: 8 days vehicle (DMSO 0.01%)


title: OCI-AML3 treated, replicate 1

description: Gene expression data from AML cell line treated with 1 µM Pinometostat

value: 8 days Pinometostat (1 uM)


title: 30-HA-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
30-HA-9


title: 22-PB1-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.CC_S21

value: ciliated cells


title: 2-HA-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
2-HA-0


title: sham_1dMI_2 [3991]

description:
microRNA_count_1d_MI.txt
DESeq2_result_1d_MI.txt
6103

value: heart left ventricle (free wall)


title: 21-PB1-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.ATII_S20


title: THP-1 treated, replicate 2

source_name: MLL-r AML cell line (Pinometostat treated sample)

value: MLL rearranged


title: THP-1 control, replicate 1

source_name: MLL-r AML cell line (control sample)


title: sham_1dMI_1 [6103]

description:
microRNA_count_1d_MI.txt
DESeq2_result_1d_MI.txt
6102

value: male

value: 8-12 weeks


title: THP-1 control, replicate 2


title: THP-1 treated, replicate 1


title: 20-PB1-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.ATI_S19

source_name: Mice were infected with deltaPB1_cre or deltaHA-Cre and lung cells were sorted into tdTomato+ and negative populations at 24 hpi. Uninfected used as controls. AT-I, AT-II and ciliated cells sorted.


title: 28-HA-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
28-HA-9

value: A549 cells


title: 29-HA-9

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
29-HA-9


title: 1-HA-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.CC_S1

value: lung


title: Leaf, NahG-Rywal_wilga_1_poolA

source_name: PVYN-Wilga-infected potato plants

tag: cultivar

value: Rywal

tag: transgenic line

value: NahG-Rywal

value: leaf-cell death cone

value: PVYN-Wilga-inoculated (4 dpi)

value: poolA


title: 27-naive-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
27-naive-6

tag: cell line

value: lung carcinoma

tag: hours post deltaha or deltapb1 infection (hpi)


title: 18-HA-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATII_S17

tag: cell type

value: negative

value: atii cells


title: 25-naive-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
25-naive-6

tag: deltaha or deltapb1 infected


title: 17-HA-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATI_S16

tag: iav deltapb1_cre or deltaha_cre

value: ati cells


title: 24-PB1-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
24-PB1-6


title: 16-HA-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.CC_S15

tag: positive or negative for iav deltapb1_cre or deltaha_cre


title: 23-PB1-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
23-PB1-6


title: 19-PB1-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
PB1.IAV.CC_S18

value: positive

tag: ciliated cells, ati cells, or atii cells


title: 15-HA-IAV-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATII_S14

tag: strain


title: 26-naive-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
26-naive-6


title: 22-PB1-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
22-PB1-6


title: NOMO-1 treated, replicate 2

description: Gene expression data from AML cell line treated with 1 µM Pinometostat

value: 8 days Pinometostat (1 uM)


title: CD4+ TEM cells from P2rx7-/- mice, biological rep1

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description: Gene expression profile of CD4+ TEM cells from P2rx7-/- mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on MG-430 PM array strips.  GeneChip strip was washed and stained in the Affymetrix GeneAtlas Platform according to the manufacturer's instructions

scan_protocol: GeneChip strip images were acquired using the GeneAtlas Imaging Station and the GeneAtlas Instrument Control (GAIC) software according to the standard Affymetrix protocol

data_processing: RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF HTMG430PM_Mm_ENTREZG_22.0.0. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization. Batch correction using the ComBat function of the sva package was applied to remove some batch effect affecting replicate 2 samples of TEM cells from WT and P2rx7-/- mice (batch 1), as compared to all other samples (batch 2).

source_name: CD4+ TEM cells from P2rx7-/- mice

label_protocol: Biotinylated cRNA were prepared using GeneChip™ 3' IVT PLUS Reagent Kit (Thermo Fisher Scientific Santa Clara, California, United States) according to the manufacturer's instructions

growth_protocol: CD4+ T naïve and TEM cells were sorted at FACSAria (BD Biosciences) from pooled cell suspensions of spleen, inguinal, axillary, brachial, cervical and mesenteric lymph nodes collected from C57BL/6J and P2rx7-/- mice

extract_protocol: Total RNA was extracted using Qiagen Rneasy (Qiagen, Hilden, Germany) accordingly to the manufacturer's instructions

treatment_protocol: T naïve cells were sorted as CD4+ or CD8+, CD62L+, CD44- and CD25- cells, while TEM cells were sorted as CD4+ or CD8+, CD62L-, CD44+ and CD25- cells

value: CD4+ TEM cells

tag: genotype/variation

tag: experimental condition

value: ex vivo isolated


title: CD4+ TEM cells from WT mice, biological rep2

description: Gene expression profile of CD4+ TEM cells from WT mice

source_name: CD4+ TEM cells from WT mice

value: WT


title: CD4+ TEM cells from WT mice, biological rep1


title: 14-HA-IAV-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.ATI_S13


title: MOLM-13 control, replicate 2

description: Gene expression data from AML cell line treated with vehicle (DMSO 0.01%) as control

value: MLL rearranged

value: 8 days vehicle (DMSO 0.01%)


title: CD4+ TEM cells from WT mice, biological rep3


title: CD4+ TEM cells from P2rx7-/- mice, biological rep3


title: CD4+ TEM cells from P2rx7-/- mice, biological rep2


title: NOMO-1 control, replicate 2


title: NOMO-1 treated, replicate 1


title: 21-HA-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
21-HA-6

value: A549 cells

value: deltaHA


title: MV4-11 control, replicate 2


title: MOLM-13 treated, replicate 2


title: NOMO-1 control, replicate 1


title: 13-HA-IAV-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.IAV.CC_S12

value: lung

value: ciliated cells


title: MV4-11 treated, replicate 2


title: MOLM-13 control, replicate 1


title: MV4-11 treated, replicate 1


title: CD4+ naïve cells from P2rx7-/- mice, biological rep2

description: Gene expression profile of CD4+ naïve cells from P2rx7-/- mice

source_name: CD4+ naïve cells from P2rx7-/- mice

value: CD4+ naïve cells


title: 20-HA-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
20-HA-6


title: MOLM-13 treated, replicate 1


title: 12-HA-ATII

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATII_S11


title: 1-HA-0

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
1-HA-0


title: 11-HA-ATI

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.ATI_S10


title: T-J22

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

country: China

institute: Northeast Forestry University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: text file with abundance measurements.

organism: Populus ussuriensis

source_name: 1μM MeJA treated basal ends of stem cuttings  1h after cutting  rep2

growth_protocol: Approximately 3 cm stem segments were excised from 4-week-old in vitro plants and cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Media used in experiments were adjusted to pH 5.8 before adding 3 g l-1 Gelrite (Duchefa). MeJA were filter sterilized and added to the medium after autoclaving. Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

extract_protocol:
Basal ends of in vitro stem cuttings (0.5 cm) were harvested, flash frozen on dry ice, and RNA was isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: two week-old seedlings were cutting and subsequently transfer to 1/2 MS medium with or without 1 μM MeJA

tag: tissue

value: basal ends of stem cuttings

tag: age

value: 1h after cutting


title: 19-HA-6

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
19-HA-6

value: lung carcinoma


title: 10-HA-CC

description:
FACS-sorted cells from mouse lung
Project_015.txt
sample name:
HA.CC_S9

value: negative


title: 18-naive-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
18-naive-3


title: transgenic line8 rep3

city: Haikou

first: Pingjuan

last: Zhao

address: XueYuan Road 4

department: Institute of Tropical Bioscience and Biotechnology

institute: Chinese Academy of Tropical Agricultural Sciences

data_processing:
Seqtk used for filter data
Hisat2 version:2.0.4 used for mapping genome
Stringtie version:1.3.0 used for Standardization of gene expression
Genome_build: Mesculenta_305_v6
Supplementary_files_format_and_content: excel files include FPKM and count values for each Gene

organism: Manihot esculenta

source_name: leaf

growth_protocol: 2-month-old WT and transgenic cassava seedlings were cultured by stem segment cuttings  in MS medium and sterile bottle for two months.

extract_protocol: leaves were removed, flash frozen on dry ice, and RNA was harvested using  RNAplant Plus Reagent (Tiangen, DP441) .

treatment_protocol: no treatment

tag: developmental stage

value: 2-month-old seedlings

value: transgenic line2 (HOE8)


title: T-J21

source_name: 1μM MeJA treated basal ends of stem cuttings  1h after cutting  rep1


title: 17-naive-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
17-naive-3

source_name: A549 human lung cells were infected with deltaHA-mCherry or deltaPB1-mCherry at MOI=1 and harvested at 0, 3, 6, 9, and 12 hpi. Uninfected cells used as controls.


title: T-J12

source_name: 1μM MeJA treated basal ends of stem cuttings  0.5h after cutting  rep2

value: 0.5h after cutting


title: transgenic line8 rep1


title: T-J11

source_name: 1μM MeJA treated basal ends of stem cuttings  0.5h after cutting  rep1


title: 16-naive-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
16-naive-3


title: CD4+ naïve cells from P2rx7-/- mice, biological rep1


title: Heart_Sham_4weeks_rep1

city: Qingdao

first: Kun

last: Wang

state: Shandong

address: 308 Ningxia Road

institute: Qingdao University

description: Arraystar Custom Mouse MM9 piRNA Microarray

hyb_protocol: Sample labeling was performed using a RNA ligase method. Hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, piRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: left ventricle, Sham 4 weeks, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from sham and TAC-operated mice hearts and piRNA microarray analysis was performed by Kangcheng Bio-tech Inc., (Shanghai, China). RNA were quantified using a NanoDrop instrument (ND-1000, Thermo Scientific) and integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Left ventricle hypertrophy was induced in 8 weeks old C57BL/6 mice by transverse aortic constriction (TAC). 4 weeks later,  Left ventricle tissue of  TAC mouse and  sham operration mouse were used for piRNA microarray analysis.

value: heart

value: Sham


title: transgenic line1 rep3

value: transgenic line1 (HOE1)


title: transgenic line8 rep2


title: Heart_TAC_4weeks_rep1

source_name: left ventricle, TAC 4 weeks, replicate 1

value: TAC


title: MnSC-day5 after AO9 transduction_biological rep2

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

hyb_protocol: For Affymetrix samples, 100 ng of total RNA was hybridized with 2.5 ug of labeled ss-DNA following the Affymetrix protocol. Illumina expression samples hybridization was performed following Whole-Genome Gene Expression Direct Hybridization Assay Guide, Illumina (BD-901-1002 Part # 11322355 Rev. A) protocol. For methylation samples, Infinium® HD Assay Methylation Protocol Guide, Illumina Material # 20002138, Document # 15019519 v01, November 2015 protocol was used.

scan_protocol: Affymetrix arrays were scanned with Affymetrix 3000 7G Scanner. Illumina BeadChips were scanned with an Illumina iScan software.

data_processing: For Affymetrix expression samples, CEL files were generated with Affymetrix® GeneChip® Command Console® 2.0 software. Normalized CHP files were obtained applying SST (Signal Space Transformation)-RMA (Robust Microarray Analysis; Irizarry et al. 2003) method with Thermofisher TAC 4.0 (Transcriptome Analysis Console) software. For Illumina expression samples, raw data was obtained with Illumina GenomeStudio software. To generate the processed expression matrix, limma package (Ritchie et al., 2015) was used to correct the background with the NormExp method (McGee and Chen, 2016) and to apply quantile normalization. Methylation raw data was obtained reading war idat files with minfi R package. Processed methylation signals were obtained filtering sexual chromosomes and probes with Detection P-value > 0.01 in > 10 % of samples. Cross.hybrydizing probes and probes proximal to SNPs were removed too. Noob and BMIQ normalizations were applied to get the final methylation matrix.

source_name: MnSC-day5 after AO9 transduction_donor_02

label_protocol: Affymetrix samples were biotin-labeled following the manufacturer protocol (Affymetrix, WT PLUS). Illumina expression samples were labeled following Illumina Total PrepTMRNA Amplification Kit protocol, Ambion by Life technologies protocol. For methylation samples, Zymo EZ – 96 - DNA methylation kit protocol, Zymo Research protocol was used.

growth_protocol: All cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 with appropriate cell culture media

extract_protocol: DNA was purified (QIAGEN Gentra Puregene Cell Kit) and RNA was isolated using RNeasy kit (Qiagen) according to manufacturer´s protocol

treatment_protocol: For methylation samples, DNA (500 ng) was bisulfite-converted with EZ DNA Methylation Kit (Zymo Research, Orange, CA) according to Illumina’s protocol for methylation profiling

tag: donor id

value: donor 02

tag: gender

value: female

tag: status

value: healthy

value: primary MnS

tag: passage

value: passage 2-4

value: AO9 transduction


title: MnSC-day5 after AO9 transduction_biological rep3

source_name: MnSC-day5 after AO9 transduction_donor_03

value: donor 03


title: MV4-11 control, replicate 1

tag: genotype

value: MLL rearranged

tag: treatment

value: 8 days vehicle (DMSO 0.01%)


title: 14-PB1-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
14-PB1-3

data_processing:
Step 1:  Fastq files were aligned to the reference (mouse mm10 and human hg38) genome with Bowtie2 (refer to method for more details).
Step 2: Mapped reads were assigned to ENSEMBL gene models with featurecounts (refer to method for details)
Step 3: Statistically significant differentially expressed genes were determined using edgeR.
Genome_build: For mouse: Mus_musculus.GRCm38.87; human: Homo_sapiens.GRCh38.87; influenza: A/Puerto Rico/8/34
Supplementary_files_format_and_content: Expression counts files are in tab delimited text format
Project_009.txt: mouse raw gene expression counts; tab-delimited text
Project_015.txt: mouse raw gene expression counts; tab-delimited text
Proj017_flu-forwardreads.txt: Influenza A virus raw gene expression counts - forward reads; tab-delimited text
Proj017_flu-forwardreads.txt: Influenza A virus raw gene expression counts - reverse reads; tab-delimited text
Project_018.txt: human raw gene expression counts; tab-delimited text
Proj024_flu-forwardreads.txt: Influenza A virus raw gene expression counts - forward reads; tab-delimited text
Proj024_flu-reversereads.txt: Influenza A virus raw gene expression counts - reverse reads; tab-delimited text

tag: cell line

value: A549 cells

tag: cell type

value: lung carcinoma

tag: hours post deltaha or deltapb1 infection (hpi)


title: 15-PB1-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
15-PB1-3

tag: deltaha or deltapb1 infected


title: C-22

source_name: nontreated basal ends of stem cuttings  1h after cutting rep2

value: basal ends of stem cuttings

value: 1h after cutting


title: transgenic line1 rep2

value: 2-month-old seedlings


title: transgenic line1 rep1


title: 13-PB1-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
13-PB1-3


title: C-21

source_name: nontreated basal ends of stem cuttings  1h after cutting rep1


title: CD4+ naïve cells from WT mice, biological rep2

description: Gene expression profile of CD4+ naïve cells from WT mice

source_name: CD4+ naïve cells from WT mice

value: CD4+ naïve cells

value: WT

value: ex vivo isolated


title: MnSC-day5 after AO9 transduction_biological rep1

source_name: MnSC-day5 after AO9 transduction_donor_01

value: donor 01


title: 12-HA-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
12-HA-3

value: deltaHA


title: WT rep2

value: wild type


title: CD4+ naïve cells from WT mice, biological rep1


title: 11-HA-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
11-HA-3


title: MnSC-day5 after AOX5 transduction_biological rep1

source_name: MnSC-day5 after AOX5 transduction_donor_01

value: female

value: healthy

value: primary MnS

value: AOX5 transduction


title: MnSC-day5 after AOX5 transduction_biological rep3

source_name: MnSC-day5 after AOX5 transduction_donor_03

value: donor 03

value: passage 2-4


title: 10-HA-3

description:
A549 cells
Proj017_flu-forwardreads.txt
Proj017_flu-reversereads.txt
sample name:
10-HA-3

value: A549 cells


title: C-11

source_name: nontreated basal ends of stem cuttings  0.5h after cutting rep1

value: 0.5h after cutting


title: MnSC-day5 after OSK transduction_biological rep3

source_name: MnSC-day5 after OSK transduction_donor_03

value: OSK transduction


title: WT rep1

source_name: leaf


title: MnSC-day5 after GFP transduction_biological rep2

source_name: MnSC-day5 after GFP transduction_donor_02

value: donor 02

value: GFP transduction


title: MnSC-day5 after AOX5 transduction_biological rep2

source_name: MnSC-day5 after AOX5 transduction_donor_02


title: MnSC-day5 after OSK transduction_biological rep1

source_name: MnSC-day5 after OSK transduction_donor_01


title: MnSC-day5 after OSK transduction_biological rep2

source_name: MnSC-day5 after OSK transduction_donor_02


title: MnSC-day5 after GFP transduction_biological rep3

source_name: MnSC-day5 after GFP transduction_donor_03


title: WT_D15 P10253_231

status: Public on Jul 23 2020

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
Clustering was done by 'onboard clustering' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq Rapid SBS Kit v2' chemistry. The Bcl to FastQ conversion was performed using None from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
The Bcl to FastQ conversion was performed using bcl2fastq from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm8 whole genome using STAR in the scilifelab NGI-RNAseq nextlow pipeline
https://github.com/SciLifeLab/NGI-RNAseq
Genome_build: GRCm38
Supplementary_files_format_and_content: ; seperated csv file include Dseq2 normalized counts for every sample

extract_protocol:
The singe cell suspension was labeled with magnetic anti-CD11b (130-049-601) and anti-Glast (130-095-825) beads at dilution suggested by manufacturer and incubated and separated using LS columns also according to manufacturer´s exact instructions. The negative fraction was stained with anti-O4 beads (130-094-543) and isolated using MS columns. Beads, reagents and columns were provided by Milteny Biotec, Bergisch Gladbach, Germany. RNA was isolated using RNeasy Micro Kit (Qiagen, Venlo, Netherlands) according to manufacturer´s instructions with minor modifications to the protocol. In brief, isolated cells were lyzed in 500mL Qiazol following sorting, 100mL chloroform was added and samples spun at 2500 x g for 15min at +4°C in a MaXtract column (Qiagen, Venlo, Netherlands). Mixed with 500mL 70% EtOH and spun at 3000 x g for 30s at +4°C in a MiniElute column, washed with 350mL RW1, on-column digestion for 15 min at room temperature, washed with 350mL RW1, 500mL RLT, followed by 500mL 80% EtOH and spun for 2min. RNA was eluted using 10mM Tris pH7.5. Buffer.
RNA libraries were prepared for sequencing using the SMARTer Stranded Total RNA-seq Kit - Pico Input Mammalian (Clontech).

treatment_protocol: Adult DAWt/DAGsta4 animals were sacrificed and perfused 3, 10 or 15 days post administration of LPC. In addition also naive animals were used. Corpus callosum was dissected and prepared as samples for flow cytometry

tag: genetics

tag: day


title: Tg_D3 P10253_128

tag: strain

value: Tg


title: WT_D15 P10253_233

value: WT


title: Tg_D15 P10253_235


title: Tg_D3 P10253_126


title: Tg_D15 P10253_234


title: WT_D3 P10253_129


title: WT_D3 P10253_130


title: Tg_D3 P10253_125


title: C-12

source_name: nontreated basal ends of stem cuttings  0.5h after cutting rep2

value: basal ends of stem cuttings


title: Tg_D15 P10253_236


title: MnSC-day5 after GFP transduction_biological rep1

source_name: MnSC-day5 after GFP transduction_donor_01

value: donor 01

tag: genotype/variation


title: WT_D3 P10253_127


title: WT_D3 P10253_124


title: Tg_D0 P10253_119


title: Tg_D3 P10253_123


title: WT_D0 P10253_118


title: WT_D0 P10253_114


title: Tg_D0 P10253_115


title: Tg_D0 P10253_117


title: WT_D0 P10253_116


title: Tg_D0 P10253_113


title: WT_D15 P10253_232


title: WT_D0 P10253_120


title: WT_D10 P10253_103


title: WT_D10 P10253_104


title: Tg_D10 P10253_107


title: Tg_D10 P10253_102


title: WT_D10 P10253_108


title: Tg_D0 P9560_104

description:
Tg_D0
`D704-D504 (GAGATTCC-GGCTCTGA)`


title: UBX mice rep1 (TGi)

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the mouse reference genome (mm10) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
Tophat alignments were then processed by Cuffdiff to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

source_name: quadriceps muscles

extract_protocol:
Total RNA was prepared from quadriceps muscles of 4-6 h fasted UBX and WT mice (N=3 each). A NucleoSpin RNA preparation kit (Macherey-Nagel) was used with tissues that had been flash frozen and stored at -80° C. 100 mg of each sample was defrosted on ice and lysed using 10 strokes in a 2 ml glass dounce-type tissue grinder in the buffers provided
Ribo-zero, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: Transgenic mice with constitutive, insulin-independent TUG cleavage (UBX mice) and wildtype mice

tag: tissue

value: muscle

value: 12 weeks

value: mTUGUBX-Cter


title: Tg_D10 P10253_101


title: Tg_D10 P10253_105


title: UBX mice rep3  (TGi)

tag: age


title: WT mice rep1 (WTi)


title: WT mice rep2 (WTi)


title: UBX mice rep2  (TGi)


title: WT mice rep3 (WTi)


title: Flox 1 Tfh

city: Boston

first: Erin

last: Janssen

state: Massachusetts

address: 1 Blackfan St, Karp 10

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
TopHat was used to align reads to mouse genome [Mm9, National Center for Biotechnology Information (NCBI)],
HTSeq was used to estimate read counts
Genome_build: Mm9
Supplementary_files_format_and_content: excel file that contains gene ID, baseMean, log2Fold change, pvalue and padj

source_name: Inguinal and popliteal LNs

extract_protocol:
Tfh cells were isolated by fluorescent  sorting for CD4+CD19-CD25-CXCR5+ICOS+ cells from the draining LNs of mice immunized  in the hock with TNP-KLH. RNA was isolated using an RNAeasy Plus micro kit (Qiagen)  according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cd4-CreTgDock8flox/flox and  Cd4-CreTg control mice were immunized in the hock with TNP-KLH in alhydrogel

value: T follicular helper cells

tag: immunization

value: in the bilateral hocks with 10 μg  of TNP-KLH


title: WT2 Tfh


title: Flox2 Tfh


title: WT1 Tfh


title: WT3 Tfh Old


title: WT_D10 P10253_106


title: Flox 3 Tfh Old


title: CG18: D4C9-sgFbxw7#12 + Ifng

first: Rizwan

last: Haq

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Bcl2fastq v2.18
Raw reads were mapped or aligned to the reference organism using STAR software.
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks v2.2.1
Differential gene expression analysis was performed using both limma and DESeq2.
Genome_build: KEGG analysis was performed using BioJupies software
Supplementary_files_format_and_content: Matrix table with normalized RPKM counts for every gene and every sample

source_name: Ifng (10ng/mL) for 24h

growth_protocol: D4M3A cells were grown in DMEM supplemented with 5%FBS and penicillin–streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol.
Libraries were prepared using Kapa mRNA Hyper Prep reagent kits from 100ng of purified total RNA according to manufacturer's protocol

treatment_protocol: Cells were treated with Ifng (10ng/mL) or vehicle for 24h

value: Murine melanoma cells

value: D4M3A-Cas9 melanoma

tag: cell passage


title: CG16: D4C9-sgFbxw7#12 + Ifng


title: CG17: D4C9-sgFbxw7#12 + vehicle

source_name: PBS 0.1% BSA 24h


title: CG13: D4C9-sgFbxw7#12 + vehicle


title: CG11: D4C9-sgFbxw7#9 + vehicle


title: CG10: D4C9-sgFbxw7#9 + Ifng


title: CG9: D4C9-sgFbxw7#9 + vehicle


title: CG6: D4C9-sgCtrl + Ifng


title: CG5: D4C9-sgCtrl + vehicle


title: CG4: D4C9-sgCtrl + Ifng


title: CG1: D4C9-sgCtrl + vehicle


title: CG3: D4C9-sgCtrl + vehicle


title: CG2: D4C9-sgCtrl + Ifng


title: 853T2_Runx3_OE_sg1_rep1

city: Cambridge

first: Lindsay

middle: M

last: LaFave

address: 77 Massachusetts Avenue; 76-453

institute: MIT

data_processing:
Base calls were converted to fastq format using bcl2fastq. Raw sequencing reads were trimmed using custom python scripts to remove adapter sequences. The reads were aligned to hg19 or mm10 genome using Bowtie2 (Langmead et  al. 2012) with maximum fragment length set to 2 kb, and all other default settings (bowtie2 -X2000 --rg-id). The data were demultiplexed tolerating one mismatched base within barcodes. Mitochondrial, discordant and low quality reads were removed using SAMtools (Li et al. 2009) (samtools view -b -q 30 -f 0x2). Duplicate sequences were removed using the picard toolkit (http:// broadinstitute.github.io/picard/). Profiles for all cells were first merged into a single alignment (.bam) file and used as input for peak calling with MACS v2.1.2 (MACS2) (Zhang et al., 2008). All default options were used, with the following flags explicitly set: --nomodel, --nolambda, --keep-dup all, --call-summits. This returned a list of single base pair peak summits with associated significance scores (corresponding to log FDR q-value from MACS2). Only peak summits with FDR < 0.01 were retained. Next, a previously described iterative filtering approach was implemented to obtain a list of significant, non-overlapping fixed-width peak windows (Lareau et al., 2019). Briefly, the called peak summits were first padded with 150 base pairs (bp) at either end to generate evenly sized 301 bp window peak regions. Peaks were then sorted in decreasing order of their significance scores. Keeping the most significant peak, overlapping peak windows that had lower significance scores were identified and then removed. This was repeated for the next most significant peak window. Through this iterative process, lower significance overlapping peak regions were filtered out, resulting in 285,956 disjoint 301 bp peak windows.
Genome_build: mm10
Supplementary_files_format_and_content: count files are tab-delimited .txt files of reads in peaks across samples in sparse matrix format. Row names for peaks can be pulled from .bed peak file.
Supplementary_files_format_and_content: bam files for each individual sample are provided following peak calling and data processing
Supplementary_files_format_and_content: .bed peak file, can be used to find peaks for CRISPR data

source_name: 853T2; tumor-derived lung cell line

extract_protocol:
Individual tumors were dissected, digested in an enzymatic buffer (1X HBSS, 5mM HEPES, DNaseI, Collagenase IV), and incubated with rotation at 37°C for 30 minutes. The enzymatic buffer was quenched with DMEM and spun at 1000 rpm. Cell pellets were resuspended in DMEM and plated in 6-well plates to allow for attachment. Cell lines were genotyped for Kras, p53, and tomato after 5 passages in culture. The cell lines used in this study were established from mouse LUAD over the course of the study. All lines were grown in DMEM, 10% FBS, and 1% pen-strep. KP cell lines have not been authenticated because the cell lines are not found in established databases. The KP cell lines were tested for mycoplasma and found to be negative. GM12878 cells were grown in DMEM, 10% FBS, and 1% pen-strep and 3T3 cells were grown in RPMI 1640, 10% FBS, and 1% pen-strep. GM12878 cells were authenticated by STR Profiling Service from ATCC.
For CRISPR knockout experiments, guides were cloned into the lentiCRISPR-V2 lentiviral vector (Joung et al., 2017). The lentiCRISPR-V2 vector was digested with Fast Digest EspI and ligated with EspI-compatible annealed oligonucleotides for sgRNAs. KP cell lines were infected with constructs containing guides and selected with puromycin after 48 hours. After puromycin selection, guide performance was tested by western blotting. For CRISPR activation (CRISPRa) experiments, the Lenti-Sam-puro construct was used (developed in the Jacks lab), an adaption of the previously published Lenti-Sam activation construct (Pentinmikko et al., 2019). EspI-compatible cloning was completed and cells were infected with constructs containing guides based on CRISPRa prediction software. Truncated guides of 15 bp were cloned into a lentiviral based expression construct which also encodes for a transcriptional activation complex (MS2-P65-HSF1) and a puromycin selection cassette. Non-metastatic and metastatic cell lines were engineered to express Cas9 following stable selection of a Cas9-Blast construct.

treatment_protocol: Tumor were induced at age 6-10 weeks. Mice were provided Adeno-SPC-Cre virus intratracheally resulting in recombination of Kras G12D, p53, and tdTomato in alveolar type II cells. Cell lines were generated followed by CRISPR perturbation.

value: mixed; C57/BL/6J; 129/SV

tag: tumor stage

value: normal; 25 weeks post-initiation


title: 853T2_Runx2_OE_sg1_rep2


title: T-M6T2, T-M7Pool, T-M7T1, T-M7T2, T-M7T3, T-M7T4, M-M13N1, M-M12N1, M-M12N2, M-M13N1, M-M12N1, M-M12N2

description:
sciATAC whole tumor burdened lung, plucked tumor, and metastasis
scATACseq_colData_new.txt
scATACseq_mouse_lung_counts.txt
scATACseq_mouse_lung_peaks.bed

data_processing:
Base calls were converted to fastq format using bcl2fastq. Raw sequencing reads were trimmed with custom python scripts to remove adapter sequences. The reads were aligned to hg19 or mm10 genome using Bowtie2 with default settings (bowtie2 -X2000 --rg-id). The data were demultiplexed tolerating one mismatched base in barcodes. Mitochondrial and low quality reads were removed using SAMtools (samtools view -b -q 30 -f 0x2). Duplicates were removed using picardTools (http:// broadinstitute.github.io/picard/).
sciATAC-seq profiles for all cells were first merged into a single alignment file and used as input for peak calling with MACS v2.1.2 (MACS2). All default options were used, with the following flags explicitly set: --nomodel, --nolabmda, --keep-dup all, --call-summits. This returned a list of single base pair peak summits with associated significance scores (corresponding to -log10(FDR q-value)). Only peak summits with FDR < 0.01 were retained. To obtain a list of significant, non-overlapping fixed-width peak windows, these summits were first padded with + 150 base pairs to generate evenly sized 301 bp window peak regions. Peaks were then sorted in decreasing order of their significance scores. Keeping the most significant peak, we asked if there were any overlapping peak windows that had lower significance scores, which were then removed. We then did the same for the next most significant peak window. Through this iterative process we filtered out lower significance overlapping peak regions, resulting in 285,956 disjoint 300 bp peak windows.
Genome_build: mm10
Genome_build: hg19
Supplementary_files_format_and_content: Bed files include coordinates for fixed-width peaks (301 base pairs for mouse lung data, and 501 base pairs for species mixing cell line data) determined using MACS2 from merged scATACseq data used for all analyses (counts, annotation etc)
Supplementary_files_format_and_content: Reads in peaks count files are three-column tab-delimited .txt files in sparse matrix format. First and second columns correspond to the peak and cell barcode ID number, respectively, and the third column having the corresponding count value. Matrix can be read directly using the readMM function as part of the Matrix package in R.
Supplementary_files_format_and_content: Excel spreadsheet containing cell and sample-specific barcodes to demultiplex pooled sequence read files in .txt format. Columns include Cell ID, Barcode ID, TissueSource, TissueType, Annotation, Index 1, and Index 2.

source_name: Whole Tumor-Burdened Lung, Plucked Tumor, Metastasis

growth_protocol: 3T3 cells were grown in DMEM + 10% FBS + 1% pen/strep; GM12878 cells were grown in RPMI + 10% FBS + 1% pen/strep

extract_protocol:
Lungs were dissociated with fine scissors and then proteolytic digestion was performed using the Lung Dissociation kit (Miltenyi Biotech) following the manufacturer’s instructions. Dissociated cells were then incubated at 37 degrees C for 20 minutes with rotation, then filtered using a 100-μm strainer. Red blood cells were lysed using ACK buffer (Thermo Scientific) and stained with APC-conjugated CD45 (BD, 559864), CD11b (eBioscience 17-0112-82), CD31 (Biolegend, 102510), Ter119 (BD, 557909), and DAPI (Sigma-Aldrich). Fluorescence-activated cell sorting (FACS) of immuno-stained primary cells was performed using a FACSAria sorter (BD) to isolate tdTomato+; DAPI-; APC- tumor cells for sciATAC-seq. Cells were then processed for sciATAC-Seq profiling following 0.1% fixation.
The PCR reaction was carried out at the following conditions: 72 °C for 5 minutes (extension), 98 °C for 5 min, and then thermocycling at 98 °C for 10 s, 70 °C for 30 s and 72 °C for 1 min. After thermocycling for 5 cycles, we took 5 µl sample from a few randomly selected wells and added 10 µl of PCR cocktail with 0.6x SYBRgreen. The 15 µl reactions were amplified to saturation to determine the number of cycles required for the remaining samples on the plate. Libraries were amplified for 13-14 cycles in total. Libraries were pooled and purified using Qiagen MinElute PCR purification column. The libraries were quantified using KAPA library quantification kit. Libraries were sequenced on the Next-seq platform (Illumina) using a 150-cycle kit (Read 1: 47 cycles, Index 1: 36 cycles, Index 2: 36 cycles, Read 2: 47 cycles).

treatment_protocol: Mice with tumors were induced at age 6-10 weeks. Mice were provided Adeno-SPC-Cre virus intratracheally resulting in recombination of Kras G12D, p53, and tdTomato in alveolar type II cells.

value: late-stage tumor and metastasis


title: M-M11N2, M-M8N1, M-M10N1, M-M11N1, M-M12, M-M10N3, M-M11N3, M-M9N1, M-M9N2, M-M9N3, M-M10N2, M-M10N4, M-M10N5

description:
sciATAC metastases
scATACseq_colData_new.txt
scATACseq_mouse_lung_counts.txt
scATACseq_mouse_lung_peaks.bed

source_name: Lymph node, Thymic and Liver Metastases

value: metastasis


title: CG15: D4C9-sgFbxw7#12 + vehicle


title: 853T2_Runx2_OE_sg1_rep1


title: 853T2_Runx3_OE_sg1_rep2


title: 860T3_Control_sgCON_rep2

source_name: 860T3; tumor-derived lung cell line


title: CG12: D4C9-sgFbxw7#9 + Ifng


title: 860T3_Control_sgCON_rep1


title: 860T3_Runx3_KO_sg4_rep2


title: 1183T3_Runx3_KO_sg3_rep1

source_name: 1183T3; tumor-derived lung cell line


title: 860T3_Runx2_KO_sg4_rep5


title: 860T3_Control_sgCON_rep5


title: CG7: D4C9-sgFbxw7#9 + vehicle


title: 860T3_Control_sgCON_rep4


title: 860T3_Control_sgCON_rep3


title: CG8: D4C9-sgFbxw7#9 + Ifng


title: 860T3_Runx3_KO_sg3_rep2


title: 1183T3_Runx3_KO_sg3_rep2


title: 860T3_Runx2_KO_sg3_rep6


title: 860T3_Runx2_KO_sg4_rep3


title: 860T3_Runx2_KO_sg4_rep4


title: 860T3_Runx2_KO_sg3_rep4


title: 860T3_Runx2_KO_sg3_rep5


title: 860T3_Runx2_KO_sg3_rep3


title: 860T3_Runx2_KO_sg4_rep1


title: 860T3_Runx2_KO_sg4_rep6


title: 1183T3_Runx2_KO_sg4_rep1


title: 860T3_Runx1_KO_sg4_rep2


title: 1183T3_Runx2_KO_sg3_rep1


title: 860T3_Runx1_KO_sg5_rep2


title: 860T3_Runx1_KO_sg3_rep1


title: 860T3_Runx1_KO_sg4_rep1


title: 860T3_Runx1_KO_sg2_rep1


title: 860T3_Runx1_KO_sg1_rep2


title: 860T3_Runx1_KO_sg1_rep1


title: ATAC-Seq_SU-DHL-4-2

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
we obtained on average 13 ± 7 million paired-end reads
Adaptor sequences were trimmed using cutadapt in paired-end mode (non-default parameters: -q 15 -O 5 -m 30)
Reads were aligned to hg19 using bowtie (version 0.12.8; non-default parameters: -X 2000, -m 1) after which duplicate reads were removed using Picard MarkDuplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: B lymphocyte; metastatic to peritoneal effusion

growth_protocol: All cell lines were cultured following the manufacturer’s recommendations

extract_protocol: ATAC-seq was carried out as previously described (Buenrostro 2013) and sequenced on an Illumina HiSeq 4000 with 2x100 paired end sequencing.

tag: disease

value: large cell lymphoma

tag: germ layer

value: Mesoderm


title: 860T3_Cas9_Control_rep3


title: ATAC-Seq_SU-DHL-4-1


title: ATAC-Seq_NP-2

source_name: Neural progenitor

value: normal

value: Ectoderm


title: 860T3_Runx1_KO_sg2_rep2


title: 860T3_Cas9_Control_rep2


title: ATAC-Seq_SU-DHL-2-2

source_name: Lymph node; metastatic to peritoneal effusion

value: large cell lymphoma; histiocytic


title: 860T3_Cas9_Control_rep1


title: ATAC-Seq_SU-DHL-2-1


title: 860T3_Cas9_Control_rep4


title: ATAC-Seq_H1437-2

source_name: lung; metastatic site to pleural effusion

value: adenocarcinoma; non-small cell lung cancer

value: Endoderm


title: 853T2_Cas9_Control_rep5


title: ATAC-Seq_H1437-1


title: 860T3_Runx1_KO_sg3_rep2


title: ATAC-Seq_NP-1


title: 853T2_Runx2_OE_sg1_rep3


title: 853T2_Runx3_OE_sg1_rep3


title: ATAC-Seq_MSLCL-1

source_name: B cell; lymphoblastoid

value: Immortalized with EBV


title: ATAC-Seq_MSIPS-2

source_name: iPS Line

value: Primitive


title: ATAC-Seq_MSIPS-1


title: 853T2_Runx2_OE_sg1_rep4


title: 853T2_Runx3_OE_sg1_rep4


title: 853T2_Cas9_Control_rep4


title: ATAC-Seq_MSFIB-1

source_name: skin; fibroblast


title: ATAC-Seq_MCF7-2

source_name: mammary gland; metastatic to pleural effusion

value: adenocarcinoma


title: 853T2_Cas9_Control_rep3


title: 1183T3_Control_sgCON_rep5


title: 853T2_Cas9_Control_rep2


title: 1183T3_Control_sgCON_rep1


title: ATAC-Seq_LX-1

source_name: Liver cell


title: ATAC-Seq_MCF7-1


title: 860T3_Runx1_KO_sg5_rep1


title: ATAC-Seq_LNCAP-2

source_name: prostate; metastatic site to lymph node

value: carcinoma


title: ATAC-Seq_LX-2


title: 1183T3_Control_sgCON_rep3


title: 853T2_Cas9_Control_rep1


title: ATAC-Seq_LNCAP-1


title: 1183T3_Control_sgCON_rep4


title: ATAC-Seq_KU19-2

source_name: urinary bladder transitional cell


title: ATAC-Seq_KU19-1


title: ATAC-Seq_MSLCL-2


title: 1183T3_Runx2_KO_sg4_rep5


title: 1183T3_Runx2_KO_sg4_rep6


title: 1183T3_Control_sgCON_rep2


title: 1183T3_Runx2_KO_sg4_rep4


title: ATAC-Seq_K562-2

source_name: bone marrow

value: chronic myelogenous leukemia


title: ATAC-Seq_K1-1

source_name: Thryoid

value: papillary thyroid carcinoma


title: 1183T3_Runx2_KO_sg3_rep5

value: mixed; C57/BL/6J; 129/SV


title: ATAC-Seq_Jurkat-1

source_name: T lymphocyte

value: acute T cell leukemia


title: 1183T3_Runx2_KO_sg3_rep4

value: normal; 25 weeks post-initiation