title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S153


title: KP_30w_ND_m3_T7_170907Amo_D17-180069 scDNA

status: Public on Jul 24 2020

type: SRA

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

description: DNA sequencing of tumor cells

library_source: genomic

data_processing:
Library strategy: WGS
Alignment with BWA (v.0.7.17)
Duplicate marking with SAMBLASTER (v. 0.1.24)
CNVkit (v 0.9.6) was used to calculate read abudance in 200kb windows normalized for GC content and accessibility.
Genome_build: GRCm38.p
Supplementary_files_format_and_content: mmLungKP_KP_30w_ND_m3_depth.tsv.gz, mmLungKP_KP_30w_ND_m3_weight.tsv.gz, mmLungKP_KP_30w_ND_m3_log2ratio.tsv.gz

molecule: genomic DNA

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.
Single tumor cells were isolated by microaspiration after tumor dissociation, and genomic DNA was amplified with the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma, catalog #254-457-8). Amplified DNA was purified,

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: timepoint

tag: animal

tag: tumor


title: UCSD-AML1_H3K27ac_rep2

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

country: USA

institute: Children's Hospital of philadelphia

data_processing:
BWA Alignment
MACS2 peak calling
samtools convert files
IGV 2.8.0
Genome_build: GRCh37
Supplementary_files_format_and_content: bigwig file

organism: Homo sapiens

source_name: UCSD-AML1 cell line

growth_protocol: UCSD-AML1 were grown in RPMI 1640 medium supplemented with 10% heat inactivated FBS, 1% Penicillin/Streptomycin, and human GM-CSF (10ng/mL). Molm13 and Monomac6 were grown in RPMI 1640 medium supplemented with 10% heat inactivated FBS, and 1% Penicillin/Streptomycin.

extract_protocol:
Briefly, samples were crosslinked, lysed, sonicated and immunoprecipated with the indicated antibody overnight. After a series of washes they were reverse crosslinked overnight and DNA extracted.
Library prep was performed at Genewiz, Illumina HiSeq, 2x150bp paired-end reads, multiplexed

tag: cell line

tag: cell type

value: AML

tag: genome variation

tag: chip antibody

value: H3K27ac (abcam ab4729)


title: KP_30w_ND_m3_T7_170907Amo_D17-180067 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S152

library_source: transcriptomic

data_processing:
bcl2fastq was used to extract invidual cell read files
Transcript/gene counts estimated using RSEM, using STAR for alignment
Picard-Tools CollectRNASeqMetrics is applied to each bam
QC filtering
Sequencing depth normalization
log2(transcripts/100K + 1)
Genome_build: Gencode GRCm38.p5 (M15)
Supplementary_files_format_and_content: Raw count matrices are in HDF5 Feature Barcode Matrix Format, and metadata files are comma-delimited text:
mmLungPlate_fQC_dSp_normTPM.h5 (hdf5, (i,j,v, sparse matrix), Log2 (transcript/100K+1))
mmLungPlate_fQC_dSp_rawCount.h5 (hdf5, (i,j,v, sparse matrix), Raw counts, after depth normalization.)
mmLungPlate_fQC_dSp_rawCountOrig.h5 (hdf5, (i,j,v, sparse matrix), Raw counts )
mmLungPlate_fQC_dZ_QCstat_smpTable.csv (csv, QC table)
mmLungPlate_fQC_dZ_annot_smpTable.csv (csv, sample annotations)
mmLungPlate_fQC_geneTable.csv (csv, gene ids)
mmLungPlate_fQC_smpTable.csv (csv, sample ids)

molecule: total RNA

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.
Cells were dissociated as above, stained with DAPI and live cells were sorted as described above into 96 well plates containing 5 ml of TCL Buffer (Qiagen, catalog #1031576) with 1% beta-mercaptoethanol. Plates were processed by a modified SMART-Seq2 protocol (Picelli et al., 2013), with the following modifications: RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter, catalog #A63881) using Bravo Automated Liquid Handling Platform prior to oligo-dT primed reverse transcription with Maxima reverse transcriptase (Thermo Fischer, catalog #EP0752) and locked TSO oligonucleotide (Exiqon, custom made), which was followed by a 21 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, catalog #KK2601). The WTA product was purified using Agencourt AMPure XP beads (Beckman-Coulter, catalog #A63881) and a Bravo Automated Liquid Handling Platform. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina, catalog #FC-131-1096) with custom barcode adapters. Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina, catalog #FC-404-2005) at the Broad Genomics Platform.
SmartSeq2

tag: breed

tag: strain

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: plate

tag: sack_timepoint (weeks)

tag: age (weeks)

tag: Sex

value: male


title: KP_30w_ND_m3_T7_170907Amo_D17-180066 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S151


title: KP_30w_ND_m3_T7_170907Amo_D17-180065 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180064 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S149


title: KP_30w_ND_m3_T7_170907Amo_D17-180063 scDNA

description: DNA sequencing of tumor cells


title: A549_siTAZ replicate3

city: Rehovot

first: Moshe

last: Oren

address: 234 Herzl

institute: Weizmann Institute of Science

description: IZ-siTAZ

data_processing:
RNA-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). In short, reads were trimmed using cutadapt and mapped to genome GRCh38 (Gencode) using STAR v2.4.2a with default parameters. Genes having minimum five reads in at least one sample were considered. For A549 RNA-seq, batch correction was done using the sva (3.26.0) R package.Normalization of the counts and detection of differential expression was performed using DESeq2 with the betaPrior, cooksCutoff and independent filtering parameters set to False. Raw P values were adjusted for multiple testing, using the procedure of Benjamini and Hochberg. For A549 RNA-seq, batch correction was done using the sva (3.26.0) R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: text files include read counts and differential gene expression analysis

source_name: A549 cells

growth_protocol: H1299 were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Biological Industries, Israel) and 1% penicillin-streptomycin antibiotics solution. A549 cells were grown in DMEM (Biological Industries) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone, USA) and 1% penicillin-streptomycin antibiotics solution (Biological Industries). Cells were maintained at 37˚C with 5% CO2.

extract_protocol:
Total RNA was isolated using a NucleoSpin RNA kit (Macherey Nagel, Germany).
The polyA fraction was purified from 500ng of total RNA, followed by fragmentation and generation of double-stranded cDNA, Agencourt Ampure XP beads cleanup (Beckman Coulter, USA), end repair, A base addition, adapter ligation and PCR amplification. Libraries were quantified by Qubit (Thermo fisher scientific, USA) and TapeStation (Agilent, USA).

treatment_protocol: Either H1299 or A549 cells were transfected with 30nM siControl, siYAP or siTAZ SMARTpool oligonucleotides for 48 hours and serum-starved for the last 18 hours.

value: non-small cell lung cancer

tag: knockdown

value: siTAZ


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S148


title: A549_siYAP replicate3

description: IZ-siYAP

value: siYAP


title: A549_siTAZ replicate2

description: IY-siTAZ


title: A549_siTAZ replicate1

description: IQ-siTAZ


title: A549_siYAP replicate2

description: IY-siYAP


title: A549_siYAP replicate1

description: IQ-siYAP


title: A549_siControl replicate3

description: IZ-siC

value: siControl


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S150


title: KP_30w_ND_m3_T7_170907Amo_D17-180062 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S147


title: A549_siControl replicate2

description: IY-siC


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S146


title: KP_30w_ND_m3_T7_170907Amo_D17-180061 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S145


title: A549_siControl replicate1

description: IQ-siC


title: KP_30w_ND_m3_T7_170907Amo_D17-180060 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180059 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S144


title: H1299_siTAZ replicate2

source_name: H1299 cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180058 scDNA

description: DNA sequencing of tumor cells


title: H1299_siTAZ replicate3


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S143


title: KP_30w_ND_m3_T7_170907Amo_D17-180056 scDNA

description: DNA sequencing of tumor cells


title: H1299_siYAP replicate3


title: H1299_siTAZ replicate1


title: KP_30w_ND_m3_T7_170907Amo_D17-180055 scDNA

description: DNA sequencing of tumor cells


title: H1299_siYAP replicate2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S141


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S140


title: human adult dermal fibroblasts_biological rep4 [hADF_meth_4]

type: genomic

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.

label: Cy5 and Cy3

source_name: human adult dermal fibroblasts_donor-04

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

tag: gender

value: female

tag: status

value: healthy

value: primary cell line

tag: passage

value: passage 2-4


title: KP_30w_ND_m3_T7_170907Amo_D17-180054 scDNA

description: DNA sequencing of tumor cells

tag: timepoint

tag: animal


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S139

tag: tumor


title: H1299_siYAP replicate1

tag: cell type

tag: cell line


title: human adult bone marrow mesenchymal stem cells_biological rep3 [BM_MSC_meth_3]

source_name: human adult bone marrow mesenchymal stem cells_donor03


title: human adult bone marrow mesenchymal stem cells_biological rep2 [BM_MSC_meth_2]

source_name: human adult bone marrow mesenchymal stem cells_donor02


title: human adult menstrual derived stromal cells_biological rep4 [MnSC_meth_4]

source_name: human adult menstrual derived stromal cells_donor04


title: human adult bone marrow mesenchymal stem cells_biological rep1 [BM_MSC_meth_1]

source_name: human adult bone marrow mesenchymal stem cells_donor01


title: human adult dermal fibroblasts_biological rep1 [hADF_meth_1]

source_name: human adult dermal fibroblasts_donor-01


title: human adult menstrual derived stromal cells_biological rep1 [MnSC_meth_1]

source_name: human adult menstrual derived stromal cells_donor01


title: H1299_siControl replicate3


title: KP_30w_ND_m3_T7_170907Amo_D17-180053 scDNA

description: DNA sequencing of tumor cells


title: H1299_siControl replicate2


title: human adult menstrual derived stromal cells_biological rep3 [MnSC_meth_3]

source_name: human adult menstrual derived stromal cells_donor03


title: human adult dermal fibroblasts_biological rep3 [hADF_meth_3]

source_name: human adult dermal fibroblasts_donor-03


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S137


title: KP_30w_ND_m3_T7_170907Amo_D17-180052 scDNA

description: DNA sequencing of tumor cells


title: H1299_siControl replicate1


title: human Embryonic Stem Cells-WA09 [hESC_meth_1]

source_name: hESC-H9 p33

value: hESC

value: passage 33


title: human Embryonic Stem Cells-WA09 [hESC_meth_2]

source_name: hESC-H9 p67

value: passage 67


title: human Embryonic Stem Cells-WA01 [hESC_meth_3]

value: passage 57


title: KP_30w_ND_m3_T7_170907Amo_D17-180057 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S136


title: iPS_AOX5_biological rep1 [iPS-AOX5_meth_1]

source_name: MnSC-donor-01 reprogrammed with AOX5

value: iPSC reprogrammed from primary MnSC cell lines

value: Passage 10-20 of iPSC


title: human adult menstrual derived stromal cells_biological rep2 [MnSC_meth_2]

source_name: human adult menstrual derived stromal cells_donor02


title: human adult dermal fibroblasts_biological rep2 [hADF_meth_2]

source_name: human adult dermal fibroblasts_donor-02


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S142

source_name: Lung tissue, AT2 cells


title: iPS_AOX5_biological rep3 [iPS-AOX5_meth_3]

source_name: MnSC-donor-03 reprogrammed with AOX5


title: KP_30w_ND_m3_T7_170907Amo_D17-180051 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180050 scDNA

description: DNA sequencing of tumor cells


title: iPS_AOX5_biological rep2 [iPS-AOX5_meth_2]

source_name: MnSC-donor-02 reprogrammed with AOX5


title: input replicate2

data_processing:
Raw fastq files were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 20 -m 25). Reads were mapped to human genome (hg19) using bowtie2 (parameters: –local). Aligned duplicated reads were removed using samtools view (parameters: -h -F 4 for all reads and -f 0x2 for paired end reads). Remaining unique reads were indexed and sorted using samtools. Broad peaks were called using MACS2 against the input samples (parameters: --bw 300 -B -f --SPMR -keep-dup auto -q 0.01).
Genome_build: hg19

source_name: H1299 cells

growth_protocol: H1299 were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Biological Industries, Israel) and 1% penicillin-streptomycin antibiotics solution. Cells were maintained at 37˚C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei. The chromatin solution was immunoprecipitated with either YAP antibody or TAZ antibody. The immunoprecipitations were performed using Pierce ChIP-grade Protein G magnetic beads (Thermo Fisher Scientific). Reverse cross-linking and DNA purification was performed by ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
Libraries were prepared as described in Blecher-Gonen et al., Nat Protoc, 2013. 8(3): p. 539-54.

treatment_protocol: H1299 cells were seeded on 150mm plates and serum starved for 18 hours.

tag: antibodies


title: iPS_AOX5_biological rep4 [iPS-AOX5_meth_4]

source_name: MnSC-donor-04 reprogrammed with AOX5


title: iPS_OSK_biological rep5 [iPS_OSK_meth_5]

source_name: MnSC-donor-04 reprogrammed with OSK


title: iPS_AOX5_biological rep5 [iPS-AOX5_meth_5]


title: input replicate1


title: KP_30w_ND_m3_T1_170907Amo_D17-180049 scDNA

description: DNA sequencing of tumor cells


title: WM.1366_No_S3_L007 [WM.1366.Ctrl]

city: Los Angeles

first: Antoni

last: Ribas

state: CA

address: 9-954 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

data_processing:
RNAseq reads were mapped using HISAT2 version 2.0.4  and aligned to the hg19 genome using default parameters.
Reads were quantified by HTSeq version 0.6.1 with the intersection-non-empty mode and counting ambiguous reads if fully overlapping.
Raw counts were then normalized to fragments per kilobase of exon per million fragments mapped (FPKM) expression values.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Melanoma_wild type_IFNG Control

growth_protocol: Melanoma cells were seeded on 10 cm tissue culture plates in RPMI media with 10% FBS and 1% PSA.

extract_protocol:
Cells were collected, cell pellets were frozen immediately and stored at -80oC. RNA was extracted with miRNeasy Mini Kit (Qiagen, Cat No. 217004).
RNA library was generated to be 1X50 poly-A selected
RNA sequencing was performed on Illumina HiSeq 3000, with a 1x50 run and with data quality check done on Illumina SAV and demultiplexing performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: After allowing 2-3 passages during exponential growth phase at 70% confluence cells were exposed to interferon-gamma at concentration 5 ng/ml (Recombinant Human IFN-gamma, 0.1-2.0x10^8 units/mg, BD Biosciences, Cat No. 554617). Culture media without interferon-gamma was added simultaneously to the controls.

tag: tissue/cell type

value: Melanoma

tag: genotypes

value: wild type

tag: treatment

value: IFNG Control

tag: molecule subtype

value: poly-A selected


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S138

tag: breed

tag: strain

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: plate

tag: sack_timepoint (weeks)

tag: age (weeks)

value: male


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S134

tag: Sex


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S133


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S135


title: T640a_No_S43_L007 [T640a.Ctrl]


title: Anti-TAZ replicate2

value: non-small cell lung cancer

value: Anti-TAZ


title: Anti-TAZ replicate1

value: Anti-TAZ (Proteintech Cat:23306-1-AP, RRID:AB_2721185)


title: iPS_OSK_biological rep4 [iPS_OSK_meth_4]

tag: donor id

tag: gender

value: female

tag: status

value: healthy

tag: passage


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S131

tag: timepoint

tag: tumor


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S132


title: iPS_OSK_biological rep3 [iPS_OSK_meth_3]

source_name: MnSC-donor-03 reprogrammed with OSK

tag: cell type


title: T640a_Yes_S8_L005 [T640a.Expt]

source_name: Melanoma_wild type_IFNG 6hr

tag: cell line

tag: tissue/cell type

value: IFNG 6hr


title: KP_30w_ND_m3_T1_170907Amo_D17-180048 scDNA

description: DNA sequencing of tumor cells

tag: animal


title: iPS_OSK_biological rep2 [iPS_OSK_meth_2]

source_name: MnSC-donor-02 reprogrammed with OSK


title: KP_30w_ND_m3_T1_170907Amo_D17-180047 scDNA

description: DNA sequencing of tumor cells


title: T618a_Yes_S15_L005 [T618a.Expt]

tag: genotypes

tag: treatment

tag: molecule subtype


title: KP_30w_ND_m3_T1_170907Amo_D17-180044 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180046 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180045 scDNA

description: DNA sequencing of tumor cells


title: Anti-YAP replicate1

tag: antibodies

value: Anti-YAP (Thermo Fisher Scientific Cat:PA1-46189, RRID:AB_2219137)


title: T618a_No_S50_L007 [T618a.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S130

tag: breed

tag: strain

tag: plate

tag: sack_timepoint (weeks)


title: WM.1366_Yes_S2_L007 [WM.1366.Expt]


title: T311b_Yes_S14_L005 [T311b.Expt]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S128

tag: age (weeks)

tag: Sex


title: hHipp_Rep3_REST_ChIP

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

tag: postmortem interval (pmi)

tag: tissue

value: Hippocampus

tag: chip antibody

value: anti-REST-C antibody


title: T311b_No_S49_L007 [T311b.Ctrl]

tag: cell line


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S129

tag: timepoint

tag: tumor


title: hHipp_Rep2_Input

value: 14 hrs


title: iPS_OSK_biological rep1 [iPS_OSK_meth_1]

source_name: MnSC-donor-01 reprogrammed with OSK

tag: donor id

tag: gender

tag: status

tag: cell type

value: iPSC reprogrammed from primary MnSC cell lines

tag: passage

value: Passage 10-20 of iPSC


title: KP_30w_ND_m3_T1_170907Amo_D17-180042 scDNA

description: DNA sequencing of tumor cells

tag: animal


title: T1349a_Yes_S13_L005 [T1349a.Expt]

tag: tissue/cell type

value: Melanoma

tag: genotypes

value: wild type

tag: treatment

tag: molecule subtype


title: KP_30w_ND_m3_T1_170907Amo_D17-180043 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S126

tag: breed

tag: strain

tag: plate

tag: sack_timepoint (weeks)

tag: age (weeks)

tag: Sex


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S127

tag: timepoint

tag: tumor


title: KP_30w_ND_m3_T1_170907Amo_D17-180040 scDNA

description: DNA sequencing of tumor cells


title: T1349a_No_S48_L007 [T1349a.Ctrl]

tag: cell line

value: IFNG Control

value: poly-A selected


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S125

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: hHipp_Rep3_Input

tag: age

tag: postmortem interval (pmi)

tag: tissue


title: hHipp_Rep1_Input

value: 24 hrs


title: KP_30w_ND_m3_T1_170907Amo_D17-180041 scDNA

description: DNA sequencing of tumor cells

tag: animal


title: SK.MEL.176_No_S23_L008 [SK.MEL.176.Ctrl]

tag: tissue/cell type


title: SK.MEL.176_Yes_S22_L008 [SK.MEL.176.Expt]

tag: genotypes


title: KP_30w_ND_m3_T1_170907Amo_D17-180039 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S124


title: hHipp_Rep2_REST_ChIP

tag: chip antibody


title: hHipp_Rep1_REST_ChIP


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S123


title: SBcl2_Yes_S12_L005 [SBcl2.Expt]

tag: treatment

tag: molecule subtype


title: PT37

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

country: Germany

institute: Heidelberg University

description: Single tumor cell isolated from a disgregated primary tumor of a Highly metastatic pancreatic ductal adenocarcinoma Patient-Derived Xenograft model

data_processing:
Any remaining putative murine cell was discarded by FastQ Screen software (v. 0.4.4), which is able to detect mRNA sample reads that belongs to the human or to the mouse transcriptomes.
mRNA reads were aligned on the human genome reference (hg19 assembly, UCSC) using the TopHat2 algorithm (v. 2.0.10), retrieving the best hit with the default parameters, but allowing a maximum of five multi-hits with the same alignment score.
The gene-level expressions was quantified as the sum of all reads mapping on the exons for each gene towards the gene annotation for the human genome (hg19, UCSC) using HTSeq-count (v. 0.5.4p5).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample (output of htseq-count)

source_name: Primary Tumor Cell (Pancreas)

growth_protocol: Freshly collected xenograft grown tumors were cut with a sterile scalpel into small pieces of 1–2 mm3 and embedded in matrigel solution. Six-eight week-old NSG mice (purchased from Charles River or reproduced in the CNIO animal facility) were anesthetized using Isoflurane gas anesthesia and treated with buprenorphine dosed at 0.2 mg/kg. The left abdominal flank was shaved and the skin was sterilized with 70% ethanol. Using a sterile surgical microscissors, small incision was made in the upper left abdomen, and the pancreas was exposed. Small tumor pieces from each xenograft model were implanted into the splenic lobe of the pancreas using 6-0mm absorbable sutures (B. Braun).

extract_protocol:
All solid tissues, including primary tumor and liver were dissociated using a human tumor dissociation kit (Miltenyi Biotec) and a gentleMACS dissociator (Miltenyi Biotec) according to the manufacturer's instructions. The dissociated  single-cell suspension was then passed through a 40-μm cell strainer (BD Biosciences) and suspended in MACS cell sorting buffer (Miltenyi Biotec) to determine the cell number and viability using trypan blue dye, prior to further applications. For blood collection, tumor-bearing mice were bled using a 1 ml syringe via a cardiac puncture and collected in EDTA containing tubes. The blood was then diluted 1:1 with PBS1x, and carefully layered upon 1 volume of Ficoll‐Paque Plus (VWR International Eurolab) and centrifuged for 30 to 40 minutes at 400g, without brake, at room temperature. The mononuclear cell layer was then collected, washed in PBS1x, counted and prepared for further application. Human tumor cells from the mouse peripheral tissues were purified by autoMACS Pro Separator using MS columns (Miltenyi Biotec) in accordance with the manufacturer’s instructions. Before loading, the single-cell suspension was filtered through a 40-μm cell strainer (BD Biosciences). Human tumor cells were enriched by two-step process: first incubating with a PE-conjugated primary antibody for the human antigen HLA-ABC (clone G46-2.6, BD Pharmingen), followed by incubation with Anti-PE MicroBeads UltraPure (Miltenyi Biotec). The enriched human tumor cells were imaged using a confocal microscope (Leica SP5-MP) and representative images were captured with ImageJ software.
Library preparation was performed following provider manufacturer instructions. Briefly, Single-Cell Auto Prep System (Fluidigm, South San Francisco, CA,USA) and cDNA amplification was generated  using the SMARTer®Ultra™ Low RNA kit for the Fluidigm C1™ System (Clontech, Mountain View, CA, USA). Libraries were generated from 300 pg of amplified cDNA using the Nextera XT DNA Sample Prep Kit (Illumina) and sequenced on the HiSeq 2500 sequencer (Illumina)

tag: cell type

value: Single Primary Tumor Cell

value: Pancreas

tag: pdx

value: positive

value: negative


title: Anti-YAP replicate2

value: non-small cell lung cancer

tag: antibodies

value: Anti-YAP


title: KP_30w_ND_m3_T1_170907Amo_D17-180036 scDNA

description: DNA sequencing of tumor cells


title: PT35


title: SBcl2_No_S47_L007 [SBcl2.Ctrl]


title: KP_30w_ND_m3_T1_170907Amo_D17-180038 scDNA

description: DNA sequencing of tumor cells


title: PT36


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S121

tag: breed

tag: strain

tag: plate

tag: sack_timepoint (weeks)

tag: age (weeks)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S122

tag: timepoint

tag: tumor

tag: Sex


title: Me252_Yes_S9_L005 [Me252.Expt]

tag: cell line

value: IFNG 6hr


title: PT34


title: PB_No_S1 [PB.Ctrl]

description: PB.Ctrl

value: PB

tag: tissue/cell type


title: KP_30w_ND_m3_T1_170907Amo_D17-180034 scDNA

description: DNA sequencing of tumor cells

tag: animal


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S119


title: PT33


title: KP_30w_ND_m3_T1_170907Amo_D17-180033 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S118


title: Me252_No_S44_L007 [Me252.Ctrl]

tag: genotypes


title: KP_30w_ND_m3_T1_170907Amo_D17-180032 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S117


title: Me215_No_S45_L007 [Me215.Ctrl]

tag: treatment


title: KP_30w_ND_m3_T1_170907Amo_D17-180035 scDNA

description: DNA sequencing of tumor cells


title: PT31


title: PT32


title: Me215_Yes_S10_L005 [Me215.Expt]

tag: molecule subtype


title: KP_30w_ND_m3_T1_170907Amo_D17-180037 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S116


title: PT30

tag: cell type


title: M418_Yes_S1_L005 [M418.Expt]


title: KP_30w_ND_m3_T1_170907Amo_D17-180031 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S115


title: KP_30w_ND_m3_T1_170907Amo_D17-180030 scDNA

description: DNA sequencing of tumor cells


title: M418_No_S36_L006 [M418.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S120


title: PT28

tag: pdx


title: KP_30w_ND_m3_T1_170907Amo_D17-180029 scDNA

description: DNA sequencing of tumor cells


title: PB_Yes_S2 [PB.Expt]

description: PB.Expt


title: KP_30w_ND_m3_T1_170907Amo_D17-180028 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S113


title: M417_Yes_S20_L007 [M417.Expt]


title: PT27


title: M417_No_S35_L006 [M417.Ctrl]


title: KP_30w_ND_m3_T1_170907Amo_D17-180027 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S112


title: PT25


title: M414_Yes_S19_L007 [M414.Expt]


title: PT26


title: M414_No_S34_L006 [M414.Ctrl]


title: KP_30w_ND_m3_T1_170907Amo_D17-180025 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180026 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S108


title: PT23


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S110


title: KP_30w_ND_m3_T1_170907Amo_D17-180023 scDNA

description: DNA sequencing of tumor cells


title: PT24


title: M410_Yes_S15_L006 [M410.Expt]


title: M411_Yes_S18_L007 [M411.Expt]


title: PT29


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S109


title: PT22


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S107


title: KP_30w_ND_m3_T1_170907Amo_D17-180022 scDNA

description: DNA sequencing of tumor cells


title: M410_No_S16_L006 [M410.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S114


title: KP_30w_ND_m3_T1_170907Amo_D17-180021 scDNA

description: DNA sequencing of tumor cells


title: PT20


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S106


title: M409_Yes_S17_L007 [M409.Expt]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S111


title: KP_30w_ND_m3_T1_170907Amo_D17-180020 scDNA

description: DNA sequencing of tumor cells


title: PT19


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S105


title: KP_30w_ND_m3_T1_170907Amo_D17-180024 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180019 scDNA

description: DNA sequencing of tumor cells


title: M411_No_S33_L006 [M411.Ctrl]


title: PT18


title: PT17


title: KP_30w_ND_m3_T1_170907Amo_D17-180018 scDNA

description: DNA sequencing of tumor cells


title: M407_Yes_S16_L007 [M407.Expt]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S102


title: KP_30w_ND_m3_T1_170907Amo_D17-180017 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S103


title: M407_No_S17_L007 [M407.Ctrl]


title: M407.JAK2.KO_Yes_S6_L005 [M407.JAK2.KO.Expt]

source_name: Melanoma_JAK2 KO_IFNG 6hr

value: JAK2 KO


title: PT15


title: PT21


title: KP_30w_ND_m3_T1_170907Amo_D17-180016 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S101


title: M407.JAK2.KO_No_S41_L007 [M407.JAK2.KO.Ctrl]

source_name: Melanoma_JAK2 KO_IFNG Control


title: M409_No_S32_L006 [M409.Ctrl]


title: M407.JAK1.KO_No_S40_L006 [M407.JAK1.KO.Ctrl]

source_name: Melanoma_JAK1 KO_IFNG Control

value: JAK1 KO


title: PT14


title: M407.JAK1.KO_Yes_S5_L005 [M407.JAK1.KO.Expt]

source_name: Melanoma_JAK1 KO_IFNG 6hr

value: Melanoma


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S098


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S099


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S100


title: KP_30w_ND_m3_T1_170907Amo_D17-180015 scDNA

description: DNA sequencing of tumor cells


title: M406_Yes_S18_L008 [M406.Expt]

value: wild type


title: PT16


title: KP_30w_ND_m3_T1_170907Amo_D17-180014 scDNA

description: DNA sequencing of tumor cells


title: PT12


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S104


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S096


title: PT11


title: M399_Yes_S16_L007 [M399.Expt]


title: KP_30w_ND_m3_T1_170907Amo_D17-180013 scDNA

description: DNA sequencing of tumor cells


title: PT09


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S097


title: KP_30w_ND_m3_T1_170907Amo_D17-180012 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180010 scDNA

description: DNA sequencing of tumor cells


title: M398_Yes_S12_L007 [M398.Expt]


title: M399_No_S31_L006 [M399.Ctrl]

value: IFNG Control


title: KP_30w_ND_m3_T1_170907Amo_D17-180011 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S095


title: PT08


title: PT06


title: M397_Yes_S15_L007 [M397.Expt]

value: poly-A selected


title: PT05


title: PT13


title: M398_No_S13_L007 [M398.Ctrl]


title: KP_30w_ND_m3_T1_170907Amo_D17-180009 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T1_170907Amo_D17-180007 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S094

value: KrasLSL-G12D; Rosa26LSL-tdTomato


title: M397_No_S30_L006 [M397.Ctrl]


title: PT04


title: KP_30w_ND_m3_T1_170907Amo_D17-180008 scDNA

description: DNA sequencing of tumor cells


title: PT07


title: M406_No_S19_L008 [M406.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S092

value: male


title: PT10


title: M397.AR_Yes_S4_L005 [M397.AR.Expt]

tag: cell line modification

value: AR cell lines treated with BRAF until resistant


title: KP_30w_ND_m3_T1_170907Amo_D17-180005 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S090

tag: breed


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S091

tag: strain


title: PT03

value: Single Primary Tumor Cell


title: KP_30w_ND_m3_T1_170907Amo_D17-180004 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S093

tag: plate


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S089

tag: sack_timepoint (weeks)


title: PT02

value: Pancreas


title: M397.AR_No_S39_L006 [M397.AR.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S088

tag: age (weeks)


title: M395_Yes_S2 [M395.Expt]


title: KP_30w_ND_m3_T1_170907Amo_D17-180006 scDNA

description: DNA sequencing of tumor cells

tag: timepoint


title: PT01

value: positive


title: KP_30w_ND_m3_T1_170907Amo_D17-180002 scDNA

description: DNA sequencing of tumor cells

tag: tumor


title: KP_30w_ND_m3_T1_170907Amo_D17-180003 scDNA

description: DNA sequencing of tumor cells


title: M395_No_S1 [M395.Ctrl]


title: LM24

description: Single tumor cell isolated from a disgregated liver metastasis tumor of a Highly metastatic pancreatic ductal adenocarcinoma Patient-Derived Xenograft model

source_name: Metastatic Tumor Cell (Liver)

value: Single Metastatic Tumor Cell

value: Liver

value: negative


title: KP_30w_ND_m3_T1_170907Amo_D17-180001 scDNA

description: DNA sequencing of tumor cells

source_name: Lung tissue, AT2 cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S087

tag: Sex


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S086


title: M383_Yes_S20_L008 [M383.Expt]

tag: cell line

value: IFNG 6hr


title: LM23


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S085


title: WT rep3

city: Haikou

first: Pingjuan

last: Zhao

address: XueYuan Road 4

department: Institute of Tropical Bioscience and Biotechnology

country: China

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

tag: genotype/variation


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S084


title: W303 sen1-1 dbr1∆ + pTet-i-CUT rep2

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
Sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Reads demultiplexing with bcl2fastq2-2.18.12, Quality-trimming with trimmomatic, Mapping with bowtie2, Count reads mapping to protein-coding genes with htseq-counts
Genome_build: R64
Supplementary_files_format_and_content: Bigwig files providing coverage for all samples.

organism: Saccharomyces cerevisiae W303

source_name: W303 sen1-1 dbr1∆ + pTet-i-CUT

growth_protocol: Cells were grown to OD600=0.3-0.5 in YPD at 30°C  (wild-type and rrp6∆) or in DO-Ura at 34°C (dbr1∆ and sen1-1 dbr1∆) .

extract_protocol:
Hot phenol RNA extraction followed by rRNA depletion using the Ribominus kit
NextSeq 500/550 High Output Kit

treatment_protocol: dbr1∆ and sen1-1 dbr1∆ cells grown in DO-Ura + Doxycycline were washed and left to grow in the absence of Doxycycline to induce expression of the decoy or control RNA.

value: W303-derived strain

tag: tissue

value: S.cerevisiae culture

value: 6h 34°C

tag: genotype

value: sen1-1 dbr1D::HIS3, pTet-i-CUT


title: M383_No_S21_L008 [M383.Ctrl]

tag: tissue/cell type

value: Melanoma

tag: genotypes

value: wild type

tag: treatment

value: IFNG Control

tag: molecule subtype


title: M381_Yes_S14_L007 [M381.Expt]

value: poly-A selected


title: LM22

tag: cell type

tag: pdx


title: LM21


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S083

tag: breed

tag: strain

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: plate

value: male


title: W303 sen1-1 dbr1∆ + pTet-i-CUT rep1


title: M381_No_S29_L006 [M381.Ctrl]


title: LM20


title: W303 sen1-1 dbr1∆ + pTet-i rep2

source_name: W303 sen1-1 dbr1∆ + pTet-i

value: sen1-1 dbr1D::HIS3, pTet-i


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S082

tag: timepoint

tag: sack_timepoint (weeks)

tag: age (weeks)


title: M376_Yes_S4_L007 [M376.Expt]

tag: cell line


title: LM19

value: positive


title: LM18

value: Single Metastatic Tumor Cell


title: W303 sen1-1 dbr1∆ + pTet-i rep1


title: M376_No_S5_L007 [M376.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S081

tag: tumor

tag: Sex


title: W303 dbr1∆ + pTet-i-CUT rep2

source_name: W303 dbr1∆ + pTet-i-CUT

tag: tissue

value: dbr1D::HIS3, pTet-i-CUT


title: M375_Yes_S13_L007 [M375.Expt]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S080


title: LM17

value: Liver

value: negative


title: LM16


title: M375_No_S28_L006 [M375.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S079


title: W303 dbr1∆ + pTet-i-CUT rep1

tag: genotype


title: M370_Yes_S12_L007 [M370.Expt]

tag: tissue/cell type

value: IFNG 6hr


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S078


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S077


title: W303 dbr1∆ + pTet-i rep1

source_name: W303 dbr1∆ + pTet-i

value: W303-derived strain

value: dbr1D::HIS3, pTet-i


title: LM15


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S076


title: W303 rrp6∆

source_name: W303 rrp6∆

value: S.cerevisiae culture


title: LM14


title: LM13


title: M370_No_S27_L006 [M370.Ctrl]

source_name: Melanoma_wild type_IFNG Control

tag: genotypes


title: W303 dbr1∆ + pTet-i rep2

tag: treatment

value: 6h 34°C


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S075


title: M368_No_S26_L006 [M368.Ctrl]

value: Melanoma

tag: molecule subtype


title: Dropseq_Circ_Infested_120hAEL_3

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

description:
Drop-seq
HYU_6-3_4

data_processing:
Raw paired-end fastq files were merged into a single bam file using picard FastqToSam
An unaligned bam file was then preprocessed and aligned to fly reference genome using  Drop-seq_alignment.sh pipeline in the Drop-seq alignment toolkit. The aligner used in this pipeline was STAR (2.5.3a).
Aligned reads were quantified using BAMTagHistogram provided in the Dorp-seq alignment toolkit.
A cutoff value for proper cell number was determined by calculating cumulative read fractions.
UMI count matrix was generated using DigitalExpression provided in the Drop-seq alignment toolkit with aligned read count cutoff determined in the previous step.
Genome_build: BDGP 6.02 (September 2014)
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample.

molecule: polyA RNA

organism: Drosophila melanogaster

growth_protocol: To synchronize larval stages, one hundred adult flies were kept on grape-juice agar plate for two hours. Hatched larvae were discarded at 23 hours after egg laying (AEL), and those at 24 hours AEL were collected and reared on normal corn-meal yeast media.

extract_protocol:
100 to 150 primary LGs were dissected and kept in 200 µl ice-cooled Schneider’s medium (Gibco, 21720024). After dissection, centrifugation at 3,000 rpm and 4 ℃ for 5 minutes was done. Supernatant was discarded and 300 µl of room-temperature Schneider’s medium was added to the lymph gland primary lobes. 300 µl of Papain (Worthington, LK003178) pre-heated to 37 ℃, and 4.1 µl of Liberase TM (Roche, 5401119001) were added and gently mixed. The samples were incubated for 20 minutes with gentle nutation. At 5-, 10-, and 15-minute time points of incubation, samples were mixed using 200p pipette. Enzymes were inactivated with 100 µl of ice-cooled Schneider’s medium, and samples were kept on ice. Suspended cells were passed through a 40 µm cell strainer (Corning, 352340). After, centrifugation at 3,000 rpm and 4 ℃ for 5 minutes was done. Supernatant was discarded, and 1X filtered sterile PBS was added to cells. Final concentration of cells was fixed to 300 cells/µl for a total of 600 µl.
All the Drop-seq and cDNA synthesis methods were followed by previous study (Macosko, Evan Z., et al. "Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets." Cell 161.5 (2015): 1202-1214.). The concentration of beads was fixed to 300 beads/u.  Around 10 minutes Drop-seq run performed for each experiment.
single-cell RNA-seq (Drop-seq)

value: Oregon-R

tag: condition

value: wasp infestation at 72 h AEL

value: Circulation

tag: biological replicates


title: M318_Yes_S10_L007 [M318.Expt]

source_name: Melanoma_wild type_IFNG 6hr

value: wild type

value: poly-A selected


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S072

tag: breed

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: LM12

tag: cell type

value: Single Metastatic Tumor Cell

tag: pdx

value: positive


title: M318_No_S25_L006 [M318.Ctrl]

value: IFNG Control


title: LM08

value: Liver

value: negative


title: W303 wt

source_name: W303 wt

tag: strain

value: W303-derived strain


title: LM10


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S073

tag: timepoint

tag: plate

tag: sack_timepoint (weeks)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S074

tag: tumor

tag: age (weeks)


title: M308_No_S18_L006 [M308.Ctrl]

tag: cell line


title: M308_Yes_S17_L006 [M308.Expt]

value: IFNG 6hr


title: M368_Yes_S11_L007 [M368.Expt]


title: LM07


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S071

tag: Sex


title: Dropseq_Circ_Infested_120hAEL_1

description:
Drop-seq
DropSeq_Infested_Circ_120hAEL_lib1

tag: tissue


title: LM09


title: Dropseq_Circ_Infested_120hAEL_2

description:
Drop-seq
DropSeq_Infested_Circ_120hAEL_lib2


title: Dropseq_Circ_Infested_96hAEL_2

description:
Drop-seq
DropSeq_Infested_Circ_96hAEL_lib2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S070


title: LM06


title: M299_Yes_S9_L007 [M299.Expt]

tag: tissue/cell type

tag: genotypes


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S069


title: LM05


title: M299_No_S24_L006 [M299.Ctrl]

tag: treatment

tag: molecule subtype


title: Dropseq_Circ_Infested_96hAEL_1

description:
Drop-seq
DropSeq_Infested_Circ_96hAEL_lib1

tag: condition

tag: biological replicates


title: Dropseq_Circ_Normal_120hAEL_3

description:
Drop-seq
DropSeq_Normal_Circ_120hAEL_lib3

value: steady state


title: Dropseq_Circ_Infested_96hAEL_3

description:
Drop-seq
DropSeq_Infested_Circ_96hAEL_lib3


title: LM04

tag: cell type


title: M297_No_S23_L006 [M297.Ctrl]


title: Dropseq_Circ_Normal_120hAEL_2

description:
Drop-seq
DropSeq_Normal_Circ_120hAEL_lib2


title: M297_Yes_S8_L007 [M297.Expt]


title: Dropseq_Circ_Normal_120hAEL_1

description:
Drop-seq
DropSeq_Normal_Circ_120hAEL_lib1


title: LM03

tag: pdx


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S067

tag: breed

tag: strain


title: M285_No_S22_L006 [M285.Ctrl]


title: M285_Yes_S7_L007 [M285.Expt]


title: LM01


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S065

tag: timepoint

tag: plate


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S066

tag: tumor

tag: sack_timepoint (weeks)


title: LM02


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S064

tag: age (weeks)


title: M263_Yes_S10_L007 [M263.Expt]

tag: cell line


title: Dropseq_Circ_Normal_96hAEL_2

description:
Drop-seq
DropSeq_Normal_Circ_96hAEL_lib2

tag: tissue


title: CTC14

description: Single tumor cell isolated from the bloodstream using a human HLA antibody (Circulating Tumor Cell) of a Highly metastatic pancreatic ductal adenocarcinoma Patient-Derived Xenograft model

source_name: Circulating Tumor Cell (Bloodsteam)

value: Single Circulating Tumor Cell

value: Blood


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S068

tag: Sex


title: Dropseq_Circ_Normal_96hAEL_3

description:
Drop-seq
DropSeq_Normal_Circ_96hAEL_lib3

value: Oregon-R


title: Dropseq_Circ_Normal_96hAEL_1

description:
Drop-seq
DropSeq_Normal_Circ_96hAEL_lib1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S063


title: M263_No_S11_L007 [M263.Ctrl]

tag: tissue/cell type

value: Melanoma

tag: genotypes


title: CTC12


title: Dropseq_LG_Infested_96hAEL_3

description:
Drop-seq
HYU_5-5_3

value: wasp infestation at 72 h AEL

value: Lymph gland


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S062


title: CTC10


title: Dropseq_LG_Infested_96hAEL_4

description:
Drop-seq
HYU_5-6_6


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S061


title: M262_No_S20_L005 [M262.Ctrl]

value: wild type

tag: treatment

tag: molecule subtype

value: poly-A selected


title: Dropseq_LG_Infested_96hAEL_2

description:
Drop-seq
HYU_5-4_2

tag: condition

tag: biological replicates


title: M257_No_S19_L005 [M257.Ctrl]


title: Dropseq_LG_Infested_96hAEL_1

description:
Drop-seq
HYU_5-3_1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S059

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S060


title: M257_Yes_S4_L007 [M257.Expt]


title: CTC08

tag: cell type

tag: pdx

value: positive


title: CTC07


title: M249_Yes_S24_L008 [M249.Expt]


title: CTC05


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S058

tag: breed

tag: strain


title: Dropseq_LG_Normal_120hAEL_4

description:
Drop-seq
DropSeq_120hAEL_lib4


title: CTC06


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S057

tag: timepoint

tag: plate


title: Dropseq_LG_Normal_120hAEL_3

description:
Drop-seq
DropSeq_120hAEL_lib3


title: Dropseq_LG_Normal_120hAEL_2

description:
Drop-seq
DropSeq_120hAEL_lib2


title: M262_Yes_S5_L007 [M262.Expt]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S056

tag: tumor

tag: sack_timepoint (weeks)


title: M249.AR_Yes_S32_L008 [M249.AR.Expt]

tag: cell line

tag: cell line modification

value: AR cell lines treated with BRAF until resistant


title: Dropseq_LG_Normal_120hAEL_1

description:
Drop-seq
DropSeq_120hAEL_lib1

tag: tissue


title: CTC03


title: CTC02


title: Dropseq_LG_Normal_96hAEL_5

description:
Drop-seq
DropSeq_96hAEL_lib5


title: M244_Yes_S3_L007 [M244.Expt]

tag: tissue/cell type


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S054

tag: age (weeks)

tag: Sex


title: CTC01


title: Dropseq_LG_Normal_96hAEL_4

description:
Drop-seq
DropSeq_96hAEL_lib4


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S053


title: Heart_NC_2 weeks

city: Qingdao

first: Kun

last: Wang

state: Shandong

address: 308 Ningxia Road

institute: Qingdao University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: Ensembl genes (GRCm38)
Supplementary_files_format_and_content: Matrix table with FPKM of gene in samples

source_name: NC overexpressed heart

extract_protocol:
Total RNAs were extracted from CHAPIR mimic and negative control (NC) mice hearts using Trizol reagent (Invitrogen). RNA were quantified using a NanoDrop ND-1000 instrument.
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: CHAPIR mimic (30 mg/kg) was administered using implanted osmotic minipumps (Alzet model 1002; Alza Corp.). A scrambled mimic served as a negative control (NC) and it was administered using the same procedure of mimic treatment. Pumps were dorsally implanted in the mice for 14 days.

value: heart


title: Heart_CHAPIR_2 weeks

source_name: CHAPIR overexpressed heart


title: Dropseq_LG_Normal_96hAEL_3

description:
Drop-seq
DropSeq_96hAEL_lib3


title: M249_No_S25_L008 [M249.Ctrl]

tag: genotypes

tag: treatment

value: IFNG Control

tag: molecule subtype


title: Heart_NC_2 weeks_input

data_processing:
Illumina HiSeq raw sequencing read data that passed the Illumina chastity flter were used for the following analysis. The IP and Input trimmed reads (with 5’, 3’-adaptor bases removed) were aligned to genome reference sequences using HISAT2 software (v2.1.0). Aligned reads were used for peak calling of the MeRIP regions, statistically signifcant MeRIP enriched regions (peaks) were identifed for each sample at a p value threshold of 0.05. The MeRIP enriched regions (peaks) were annotated by the overlapped gene using the newest Ensembl database. The alignment statistical analysis was applied to retain the valid sequences for subsequent signifcant diﬀerentially methylated regions identifed. Hierarchical clustering, scatter plots and volcano plots were performed for the methylated enriched regions analysis in R or Python environment for statistical computing and graphics.
Genome_build: Ensembl genes (GRCm38)
Supplementary_files_format_and_content: The fold enrichment within the peak in the IP sample compared with the input sample

extract_protocol:
Total RNAs were extracted from CHAPIR mimic and negative control (NC) mice hearts using Trizol reagent (Invitrogen). RNA were quantified using a NanoDrop ND-1000 instrument. mRNAs were isolated from total RNA sample and they were chemically fragmented to 100-nucleotides-long fragments. MeRIP was performed to enrich m6A methylated mRNAs using Anti-N6-methyladenosine (m6A) antibody (Abcam, ab208577).
We used KAPA Stranded mRNA-seq Kit (Illumina) for RNA-seq library preparation of both m6A enriched RNAs and input mRNAs. The libraries were subjected to denaturation to obtain single-stranded DNA molecules and captured on Illumina flow cells. Then, they were amplified in situ as sequencing clusters and sequenced for 150 cycles on Illumina HiSeq 4000 system as per the manufacturer’s instructions. The image analysis and base calling were carried out using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). The sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter, trimmed adaptor bases by cutadapt) were aligned to genome sequences from Ensembl using HISAT2 software (v2.1.0). The aligned reads were used for peak calling by exomePeak and a statistically significant MeRIP enriched regions (peaks) were identified for each transcript and compared by exomePeak. The MeRIP enriched regions (peaks) were annotated by the overlapped gene using the newest version of Ensembl database. Then the statistical analysis of m6A peak in each transcript region was done.

tag: strain background

tag: genotype/variation

value: NC-overexpressed


title: Dropseq_LG_Normal_96hAEL_2

description:
Drop-seq
DropSeq_96hAEL_lib2

tag: condition

tag: biological replicates


title: M243_No_S10_L006 [M243.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S051

tag: timepoint

tag: breed

tag: strain


title: Heart_NC_2 weeks_IP

tag: antibody

value: Anti-N6-methyladenosine (m6A) antibody (Abcam, ab208577)


title: Dropseq_LG_Normal_96hAEL_1

description:
Drop-seq
DropSeq_96hAEL_lib1

value: steady state


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S050

tag: tumor

tag: plate

tag: sack_timepoint (weeks)


title: M238_Yes_S2_L007 [M238.Expt]

tag: cell line

tag: tissue/cell type

value: IFNG 6hr


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S049

tag: age (weeks)

tag: Sex


title: M238_No_S17_L005 [M238.Ctrl]

tag: genotypes

tag: treatment


title: Heart_CHAPIR_2 weeks_input

tag: strain background

value: CHAPIR-overexpressed

tag: tissue


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S055


title: M249.AR_No_S33_L008 [M249.AR.Ctrl]

tag: cell line modification

tag: molecule subtype


title: Heart_CHAPIR_2 weeks_IP

tag: genotype/variation


title: Dropseq_LG_Normal_72hAEL_5

description:
Drop-seq
DropSeq_72hAEL_lib5

value: Oregon-R

tag: condition

tag: biological replicates


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S048

tag: timepoint

tag: breed

tag: strain


title: M238.AR_Yes_S3_L005 [M238.AR.Expt]

value: Melanoma


title: Dropseq_LG_Normal_72hAEL_3

description:
Drop-seq
DropSeq_72hAEL_lib3


title: CPT_36hrs_Rep4

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description: CPT injected DRG tissue 36 hrs after injury Rep4

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to  mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 Ensembl as reference
Normalization (VST) and differential expression analysis using limma.
Genome_build: mm10

source_name: Primary DRG

extract_protocol:
Total RNA from whole DRG tissues were extracted and purified using Qiagen RNeasy Plus Mini Kit. The RNA quality was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Nano Chip (Whole Chip). RNA concentration was determined using  NanoDrop.
cDNA was generated from 5ng of IP or FT RNA using the Nugen Ovation® 2 RNA-Seq Sytstem V2 kit (Nugen). 1 ug of cDNA was fragmented using the Covaris M220. Paired-end libraries for multiplex sequencing were generated from 300 ng of fragmented cDNA using the Apollo 324 automated library preparation system (Wafergen Biosystems), enriched over 10 cycles of PCR cycles and purified with Agencourt AMPure XP beads (Beckman Coulter).

treatment_protocol: 2 mg/kg Camptothecin treatment

value: Primary DRG after sciatic nerve injury

value: camptothecin treatment after 36hrs after injury


title: M238.AR_No_S38_L006 [M238.AR.Ctrl]

value: wild type


title: M243_Yes_S9_L006 [M243.Expt]

value: poly-A selected


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S047

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: tumor

tag: plate

tag: sack_timepoint (weeks)


title: Dropseq_LG_Normal_72hAEL_4

description:
Drop-seq
DropSeq_72hAEL_lib4

value: Lymph gland


title: CPT_36hrs_Rep3

description: CPT injected DRG tissue 36 hrs after injury Rep3


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S052

tag: age (weeks)

value: male


title: M244_No_S18_L005 [M244.Ctrl]

tag: cell line

tag: tissue/cell type


title: Dropseq_LG_Normal_72hAEL_2

description:
Drop-seq
DropSeq_72hAEL_lib2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S046

tag: Sex


title: CPT_36hrs_Rep1

description: CPT injected DRG tissue 36 hrs after injury Rep1

tag: treatment


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S044


title: CPT_36hrs_Rep2

description: CPT injected DRG tissue 36 hrs after injury Rep2

tag: tissue


title: M233.JAK2.KO_c8_Yes_S14 [M233.JAK2.KO.Expt]

source_name: Melanoma_JAK2 KO_IFNG 6hr

tag: genotypes

value: JAK2 KO


title: GRL13866-4B

city: Blacksburg

first: Robert

last: Settlage

state: VA

address: 1 Washington St

department: Advanced Research Computing

institute: Virginia Tech

data_processing:
ea-utils clipping of sequencing adaptor from sequencing reads
btrim quality trimming of reads
map data to genome using tophat
count reads mapping to genes using htseq
Genome_build: GCF_000054005.1_ASM5400v1_genomic
Supplementary_files_format_and_content: csv of HTSeq gene counts

organism: Brucella abortus

source_name: Bacterial cells

growth_protocol: Bacteria were cultured in brucella broth to late exponential phase.

extract_protocol:
RNA was isolated using Trizol reagent, and the RNA was then treated with DNase prior to library preparation.
Illumin TruSeq libraries were prepped according to Illumina protocols

treatment_protocol: Cultures were terminated by the addition of an equal volume of ethanol:acetone (50:50 mixture)

tag: genotype

value: genotype LS044 (Deletion of gene encoding RNaseJ)


title: CPT_24hrs_Rep4

description: CPT injected DRG tissue 24 hrs after injury Rep4

value: camptothecin treatment after 24hrs after injury


title: M233.JAK2.KO_c8_No_S13 [M233.JAK2.KO.Ctrl]

source_name: Melanoma_JAK2 KO_IFNG Control

value: IFNG Control

tag: molecule subtype


title: M233_Yes_S8 [M233.Expt]


title: GRL13864-3C

value: genotype LS042 (Truncation of rne, encoding RNaseE; Removal of approximately 200 AA of C-terminus)


title: M233.JAK1.KO_c2_Yes_S12 [M233.JAK1.KO.Expt]

source_name: Melanoma_JAK1 KO_IFNG 6hr

value: JAK1 KO


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S045

source_name: Lung tissue, AT2 cells


title: CPT_24hrs_Rep3

description: CPT injected DRG tissue 24 hrs after injury Rep3


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S043


title: CPT_24hrs_Rep2

description: CPT injected DRG tissue 24 hrs after injury Rep2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S042


title: GRL13865-4A


title: GRL13863-3B


title: CPT_24hrs_Rep1

description: CPT injected DRG tissue 24 hrs after injury Rep1


title: M233.JAK1.KO_c2_No_S11 [M233.JAK1.KO.Ctrl]

source_name: Melanoma_JAK1 KO_IFNG Control


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S041


title: GRL13862-3A


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S040


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S039


title: M233_No_S7 [M233.Ctrl]


title: M233.B2M.KO_Yes_S10 [M233.B2M.KO.Expt]

source_name: Melanoma_B2M KO_IFNG 6hr

value: B2M KO

value: IFNG 6hr


title: Dropseq_LG_Normal_72hAEL_1

description:
Drop-seq
DropSeq_72hAEL_lib1

value: Oregon-R

tag: condition

value: steady state


title: GRL13861-2C

value: genotype CC138 (deletion of gene encoding small RNA, Bsr8)


title: M233.B2M.KO_No_S9 [M233.B2M.KO.Ctrl]

source_name: Melanoma_B2M KO_IFNG Control

value: Melanoma


title: M207_Yes_S1_L007 [M207.Expt]

value: wild type


title: CPT_18hrs_Rep3

description: CPT injected DRG tissue 18 hrs after injury Rep3

value: Primary DRG after sciatic nerve injury

value: camptothecin treatment after 18hrs after injury


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S038

value: KrasLSL-G12D; Rosa26LSL-tdTomato


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S037

value: male


title: CPT_18hrs_Rep2

description: CPT injected DRG tissue 18 hrs after injury Rep2


title: GRL13858-1C

value: genotype WT2308


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S036


title: GRL13859-2A


title: M207_No_S16_L005 [M207.Ctrl]

value: poly-A selected


title: HeMa_Yes_S8_L007 [HeMa.Expt]

description: HeMa.Expt

source_name: Melanocytes_wild type_IFNG 6hr

value: HeMa

value: Melanocytes


title: GRL13857-1B


title: CPT_18hrs_Rep1

description: CPT injected DRG tissue 18 hrs after injury Rep1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S035


title: VEH_36hrs_Rep3

description: VEH injected DRG tissue 36 hrs after injury Rep3

value: vehicle treatment 36hrs after injury


title: GRL13856-1A1


title: HeMa_No_S9_L007 [HeMa.Ctrl]

description: HeMa.Ctrl

source_name: Melanocytes_wild type_IFNG Control

value: IFNG Control


title: VEH_36hrs_Rep4

description: VEH injected DRG tissue 36 hrs after injury Rep4


title: CPT_18hrs_Rep4

description: CPT injected DRG tissue 18 hrs after injury Rep4


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S034


title: VEH_36hrs_Rep2

description: VEH injected DRG tissue 36 hrs after injury Rep2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S033


title: M420_No_S36_L007 [M420.Ctrl]

source_name: Melanoma_wild type_IFNG Control


title: M420_Yes_S37_L007 [M420.Expt]

source_name: Melanoma_wild type_IFNG 6hr


title: M420.JAK2.KO_Yes_S41_L007 [M420.JAK2.KO.Expt]

value: JAK2 KO


title: GRL13860-2B


title: VEH_36hrs_Rep1

description: VEH injected DRG tissue 36 hrs after injury Rep1


title: VEH_24hrs_Rep4

description: VEH injected DRG tissue 24 hrs after injury Rep4

value: vehicle treatment 24hrs after injury


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S032


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S031


title: VEH_24hrs_Rep3

description: VEH injected DRG tissue 24 hrs after injury Rep3


title: 9-PB1-0

city: MINNEAPOLIS

first: Ryan

last: Langlois

state: MN

institute: University of Minnesota

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.0_S9

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

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

value: A549 cells

tag: cell type

value: lung carcinoma

tag: deltaha or deltapb1 infected

tag: hours post deltaha or deltapb1 infection (hpi)


title: 8-PB1-0

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.0_S8


title: 7-PB1-0

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.0_S7


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S030

tag: timepoint

tag: breed

tag: strain


title: VEH_24hrs_Rep2

description: VEH injected DRG tissue 24 hrs after injury Rep2


title: 5-HA-0

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.0_S5

value: deltaHA


title: M420.JAK1.KO_Yes_S39_L007 [M420.JAK1.KO.Expt]

value: Melanoma

value: JAK1 KO

value: IFNG 6hr


title: VEH_24hrs_Rep1

description: VEH injected DRG tissue 24 hrs after injury Rep1

value: Primary DRG after sciatic nerve injury


title: 4-HA-0

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.0_S4


title: M420.JAK1.KO_No_S38_L007 [M420.JAK1.KO.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S028

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: tumor

tag: plate

tag: sack_timepoint (weeks)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S029

tag: age (weeks)

value: male


title: M202_No_S28_L007 [M202.Ctrl]

tag: cell line

tag: tissue/cell type

value: wild type


title: 3-naive

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
naive_S3


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S027

tag: Sex


title: VEH_18hrs_Rep3

description: VEH injected DRG tissue 18 hrs after injury Rep3

tag: tissue

tag: treatment

value: vehicle treatment 18hrs after injury


title: M202.JAK2.KO_Yes_S33_L007 [M202.JAK2.KO.Expt]

tag: genotypes

tag: molecule subtype

value: poly-A selected


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S026


title: 33-PB1-12

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.12_S33

tag: cell type


title: 32-PB1-12

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.12_S32

tag: deltaha or deltapb1 infected


title: M420.JAK2.KO_No_S40_L007 [M420.JAK2.KO.Ctrl]


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S025


title: VEH_18hrs_Rep2

description: VEH injected DRG tissue 18 hrs after injury Rep2


title: VEH_18hrs_Rep1

description: VEH injected DRG tissue 18 hrs after injury Rep1


title: 6-HA-0

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.0_S6

tag: hours post deltaha or deltapb1 infection (hpi)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S024

tag: timepoint


title: 30-HA-12

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.12_S30


title: M202.JAK1.KO_Yes_S31_L007 [M202.JAK1.KO.Expt]


title: M202.JAK1.KO_No_S30_L007 [M202.JAK1.KO.Ctrl]


title: 2-naive

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
naive_S2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S023

tag: breed


title: M202.B2M.KO_Yes_S35_L007 [M202.B2M.KO.Expt]

value: B2M KO


title: Wnt1 GFP plus Recurrent 3

type: RNA

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

hyb_protocol: Affymetrix Generic Hybridization

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner

data_processing: RMA using Brainarray custom CDF, mogene20st_Mm_ENTREZG; R 3.0.2

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: H2B-eGFP-labeled tumor cells were grown orthotopically in nu/nu mice on doxycycline

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Doxycycline withdrawal was used in order to inactivate oncogene and lead to tumor regression

tag: strain

value: nu/nu

tag: gender

value: Female

value: Isolated Orthotopic Recurrent Tumor Tumor Cells

tag: cell genotype

value: Wnt1 inhibition

tag: time point

value: Recurrent Tumor


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S021

tag: tumor

tag: plate

tag: sack_timepoint (weeks)

tag: age (weeks)


title: Wnt1 GFP plus Recurrent 4

tag: tissue


title: 28-HA-12

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.12_S28

tag: cell line

value: A549 cells

value: lung carcinoma


title: 27-PB1-9

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.9_S27


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S019

tag: Sex


title: Wnt1 GFP plus Recurrent 1

tag: treatment


title: M202.JAK2.KO_No_S32_L007 [M202.JAK2.KO.Ctrl]

tag: tissue/cell type

value: Melanoma

tag: genotypes

value: JAK2 KO

value: IFNG Control

tag: molecule subtype


title: Wnt1 GFP plus Recurrent 2


title: LB192b

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

value: PFM2 (MG1655 derivative)

tag: time incubated

value: 192 hours

tag: growth medium

value: LB Lenox


title: LB192c

tag: strain


title: LB192a


title: Wnt1 GFP plus Primary 4

tag: gender

value: Isolated Orthotopic Primary Tumor Tumor Cells

value: Untreated

value: Primary Tumor


title: 31-PB1-12

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.12_S31

tag: cell type

tag: deltaha or deltapb1 infected

tag: hours post deltaha or deltapb1 infection (hpi)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S018

data_processing:
bcl2fastq was used to extract invidual cell read files
Transcript/gene counts estimated using RSEM, using STAR for alignment
Picard-Tools CollectRNASeqMetrics is applied to each bam
QC filtering
Sequencing depth normalization
log2(transcripts/100K + 1)
Genome_build: Gencode GRCm38.p5 (M15)
Supplementary_files_format_and_content: Raw count matrices are in HDF5 Feature Barcode Matrix Format, and metadata files are comma-delimited text:
mmLungPlate_fQC_dSp_normTPM.h5 (hdf5, (i,j,v, sparse matrix), Log2 (transcript/100K+1))
mmLungPlate_fQC_dSp_rawCount.h5 (hdf5, (i,j,v, sparse matrix), Raw counts, after depth normalization.)
mmLungPlate_fQC_dSp_rawCountOrig.h5 (hdf5, (i,j,v, sparse matrix), Raw counts )
mmLungPlate_fQC_dZ_QCstat_smpTable.csv (csv, QC table)
mmLungPlate_fQC_dZ_annot_smpTable.csv (csv, sample annotations)
mmLungPlate_fQC_geneTable.csv (csv, gene ids)
mmLungPlate_fQC_smpTable.csv (csv, sample ids)

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.
Cells were dissociated as above, stained with DAPI and live cells were sorted as described above into 96 well plates containing 5 ml of TCL Buffer (Qiagen, catalog #1031576) with 1% beta-mercaptoethanol. Plates were processed by a modified SMART-Seq2 protocol (Picelli et al., 2013), with the following modifications: RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter, catalog #A63881) using Bravo Automated Liquid Handling Platform prior to oligo-dT primed reverse transcription with Maxima reverse transcriptase (Thermo Fischer, catalog #EP0752) and locked TSO oligonucleotide (Exiqon, custom made), which was followed by a 21 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, catalog #KK2601). The WTA product was purified using Agencourt AMPure XP beads (Beckman-Coulter, catalog #A63881) and a Bravo Automated Liquid Handling Platform. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina, catalog #FC-131-1096) with custom barcode adapters. Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina, catalog #FC-404-2005) at the Broad Genomics Platform.
SmartSeq2

tag: timepoint

tag: breed

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: tumor

tag: plate

value: male


title: VEH_18hrs_Rep4

description: VEH injected DRG tissue 18 hrs after injury Rep4

tag: tissue

value: Primary DRG after sciatic nerve injury

value: vehicle treatment 18hrs after injury


title: M202_Yes_S29_L007 [M202.Expt]

tag: cell line

value: wild type

value: IFNG 6hr

value: poly-A selected


title: 26-PB1-9

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.9_S26

value: A549 cells

value: lung carcinoma


title: 25-PB1-9

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.9_S25


title: Wnt1 GFP plus Primary 3

value: nu/nu

value: Female

tag: cell genotype

tag: treatment

tag: time point


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S017

tag: sack_timepoint (weeks)

tag: age (weeks)

tag: Sex


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S022

tag: strain


title: 24-HA-9

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.9_S24

value: deltaHA


title: 29-HA-12

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.12_S29


title: LB144c

value: PFM2 (MG1655 derivative)

tag: time incubated

value: 144 hours

tag: growth medium


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S020


title: Wnt1 GFP plus Primary 1

tag: gender

value: Isolated Orthotopic Primary Tumor Tumor Cells


title: LB144b

value: LB Lenox


title: 22-HA-9

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.9_S22

tag: cell type

tag: deltaha or deltapb1 infected

tag: hours post deltaha or deltapb1 infection (hpi)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S015

tag: timepoint

tag: breed

tag: tumor


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S014

tag: plate


title: Wnt1 GFP plus Residual Lesion 3

tag: tissue

value: Isolated Orthotopic Residual Lesion Tumor Cells

tag: cell genotype

value: Wnt1 inhibition

value: 28d after doxycycline withdrawal


title: LB72c

value: 72 hours


title: 21-PB1-6

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.6_S21

tag: cell line


title: 20-PB1-6

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.6_S20


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S013

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: sack_timepoint (weeks)

value: male


title: Wnt1 GFP plus Primary 2

tag: treatment

value: Untreated

tag: time point

value: Primary Tumor


title: minusAA_RNAseq

city: University Park

first: Laura

last: Ritchey

address: 203 Althouse Lab

department: Chemistry

institute: Pennsylvania State University

description: ribosomal depleted, combined triplicates

data_processing:
Cutadapt (1.16)
Bowtie2 (2.3.4.1)
StructureFold2, sam_filter.py
StructureFold2, sam_to_rtsc.py
StructureFold2, rtsc_to_react.py
Genome_build: custom build as described in citation
Supplementary_files_format_and_content: rtsc files indicate the reverse transcription stop count on each nucleotide

organism: Bacillus subtilis

source_name: PLBS338 cells

growth_protocol: PLBS338 cells were grown to mid-esponential phase in a shaking water bath. Growth was stopped by using frozen slurry killing buffer (containing 10 mM Tris-HCl, 5 mM MgCl2, 25 mM NaN3, 1.5 mM chloramphenicol, and 12.5% ethanol)

extract_protocol:
Cells were pelleted and frozen, and RNA was extracted using RNeasy Mini Kit, then ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit
RNA-seq: RNA from three replicates of -DMS treatment were combined and sent to the Genomics Core Facility at Penn State University for standard RNA-seq library preparation and next generation sequencing. This was performed separately for +AA samples (Samples A-C) and -AA samples (Samples G-I). Structure-seq2: Reverse transcription with a random hexamer was performed, followed by ligation, and then amplification with Illumina-specific primers.

treatment_protocol: For + DMS treatments, DMS was added to a final concentration of 50 mM for 5 min. For all samples, DTT was added to quench the reaction.

tag: media

value: min + glutamine

value: control (no DMS)


title: LB72a

tag: strain

tag: time incubated


title: LB72b

tag: growth medium


title: Wnt1 GFP plus Residual Lesion 2

value: nu/nu

tag: gender


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S016

first: Matan

last: Hofree

institute: The Hebrew University of Jerusalem

tag: age (weeks)

tag: Sex


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S012

tag: timepoint


title: plusAA_RNAseq

value: ACH + tryptophan (all amino acids)


title: LB24c

value: 24 hours


title: 1-naive

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
naive_S1

value: A549 cells

tag: cell type

value: lung carcinoma

tag: deltaha or deltapb1 infected

tag: hours post deltaha or deltapb1 infection (hpi)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S011

tag: breed

tag: tumor

tag: plate


title: 23-HA-9

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.9_S23

tag: cell line

value: deltaHA


title: minusAA_plusDMS_rep3

description:
ribosomal depleted
minusAA_plusDMS.rtsc
minusAA_plusDMS_targeted.rtsc

data_processing:
Library strategy: Structure-seq2
Cutadapt (1.16)
Bowtie2 (2.3.4.1)
StructureFold2, sam_filter.py
StructureFold2, sam_to_rtsc.py
StructureFold2, rtsc_to_react.py
Genome_build: custom build as described in citation
Supplementary_files_format_and_content: rtsc files indicate the reverse transcription stop count on each nucleotide

tag: treatment

value: 50 mM DMS


title: Wnt1 GFP plus Residual Lesion 1

value: Female

tag: tissue

value: Isolated Orthotopic Residual Lesion Tumor Cells

tag: cell genotype

tag: time point


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S010

tag: strain

tag: sack_timepoint (weeks)


title: 19-PB1-6

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.6_S19


title: LB24b

value: PFM2 (MG1655 derivative)

tag: time incubated

tag: growth medium

value: LB Lenox


title: LB144a

value: 144 hours


title: minusAA_plusDMS_rep2

tag: media


title: 18-HA-6

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.6_S18


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S009

tag: timepoint

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: age (weeks)

tag: Sex

value: male


title: LB24a


title: 17-HA-6

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.6_S17

tag: cell type

tag: deltaha or deltapb1 infected

tag: hours post deltaha or deltapb1 infection (hpi)


title: minusAA_plusDMS_rep1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S008

tag: breed

tag: tumor

tag: plate


title: LB8c

value: 8 hours


title: 16-HA-6

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.6_S16

tag: cell line


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S007


title: minusAA_minusDMS_rep3

description:
ribosomal depleted
minusAA_minusDMS.rtsc
minusAA_minusDMS_targeted.rtsc

value: min + glutamine

tag: treatment


title: minusAA_minusDMS_rep2

value: control (no DMS)


title: 15-PB1-3b

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.3_S15


title: LB8b


title: LB8a


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S006


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S005


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S004


title: plusAA_plusDMS_rep3

description:
ribosomal depleted
plusAA_plusDMS.rtsc
plusAA_plusDMS_targeted.rtsc


title: plusAA_plusDMS_rep2


title: minusAA_minusDMS_rep1


title: M202.B2M.KO_No_S34_L007 [M202.B2M.KO.Ctrl]

tag: tissue/cell type

value: Melanoma

tag: genotypes

value: B2M KO

value: IFNG Control

tag: molecule subtype

value: poly-A selected


title: LB4a

tag: strain

tag: time incubated

value: 4 hours


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S003

tag: sack_timepoint (weeks)


title: 13-PB1-3b

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.3_S13

value: A549 cells

value: lung carcinoma


title: 14-PB1-3b

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
PB1.3_S14


title: LB4c

tag: growth medium


title: plusAA_plusDMS_rep1

tag: media

value: ACH + tryptophan (all amino acids)

value: 50 mM DMS


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S002

tag: timepoint

tag: age (weeks)

tag: Sex


title: 12-HA-3b

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.3_S12

tag: cell type

tag: deltaha or deltapb1 infected

value: deltaHA

tag: hours post deltaha or deltapb1 infection (hpi)


title: 11-HA-3b

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.3_S11


title: 10-HA-3b

description:
A549 cells
Proj024_flu-forwardreads.txt
Proj024_flu-reversereads.txt
sample name:
HA.3_S10


title: plusAA_minusDMS_rep3

description:
ribosomal depleted
plusAA_minusDMS.rtsc
plusAA_minusDMS_targeted.rtsc


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P1_S001

tag: breed

tag: tumor

tag: plate


title: plusAA_minusDMS_rep2

tag: treatment


title: 9-NTC-PB1

description:
A549 cells
Project_018.txt
sample name:
9.NTC.PB1_S9

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

tag: cell line

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


title: Tigit_pos_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: Positive

tag: genotype

value: Kras mut, Trp53 null


title: Tigit_neg_post 10xRNA-seq

value: Post-transplant

value: Negative


title: Tigit_pos_pre_2 10xRNA-seq


title: 8-NTC-PB1

description:
A549 cells
Project_018.txt
sample name:
8.NTC.PB1_S8


title: Tigit_pos_post 10xRNA-seq


title: 7-NTC-PB1

description:
A549 cells
Project_018.txt
sample name:
7.NTC.PB1_S7


title: plusAA_minusDMS_rep1