title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P3_S371


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P3_S369

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

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

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.
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

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: breed

tag: strain

value: KrasLSL-G12D; Rosa26LSL-tdTomato

tag: tumor

tag: plate

tag: sack_timepoint (weeks)

tag: age (weeks)

tag: Sex

value: male


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P3_S368


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title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P3_S367


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title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S354


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S352


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S351


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S366


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S350


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S349


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S346


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S345


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S344


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S347


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S341


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S339


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S359


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S342


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S335


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S336


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S337


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S340


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S338


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S334


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S369


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S332


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S330


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S331


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S348


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S329


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S325


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S326


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S328


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S324


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S327


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S321


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S343


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S322


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S316


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S318


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S333


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S312


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S313


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S315


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S308


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S320


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S310


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S309


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S311


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S314


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S323


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S305


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S306


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S300


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S301


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S304


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S302


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S319


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S303


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S299


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title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S298


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title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S081


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title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S073


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S070


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S069


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S071


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S072


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S317


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S067


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S065


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S068


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S063


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S060


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S061


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S059


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S064


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S058


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S057


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S056


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S055


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S053


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S054


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S062


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S052


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S049


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S050


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S075


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S066


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S048


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S051


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S047


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S045


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S046


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S043


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S042


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S040


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S041


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S039


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S038


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S037


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S036


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S035


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S032


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S034


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S031


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S033


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S030


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S028


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S029


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S026


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S022


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S024


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S021


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S023


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S025


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S027


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S020


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S044


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S019


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S017


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S016


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S014


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S009


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S013


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S008


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S012


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S011


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S010


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S005


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S007


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S006


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S003


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S384


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S001


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S018


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S015


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S002


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S383


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S382


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S378


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S380


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S381


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S377


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S379


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S376


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S374


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S375


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S372


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P1_S004


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S370


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S371


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S373


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S366


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S365


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S362


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S367


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S364


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S360


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S363


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S361


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S307


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S359


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S356


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S358


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S354


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S353


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S357


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S355


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S351


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S352


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S368


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S369


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S348


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S349


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S350


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S347


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S345


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S346


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S344


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S343


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S342


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S341


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S340


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S339


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S337


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S336


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S333


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S332


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S330


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S331


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S328


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S326


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S327


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S329


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S325


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S338


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S321


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S318


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S322


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S319


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S323


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S317


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S311


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S312


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S315


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S320


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S310


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S313


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S334


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S335


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S324


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S309


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S307


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S306


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S308


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S305


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S304


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S303


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S316


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S301


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S300


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S314


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S299


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S302


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S298


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S296


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S297


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S294


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S293


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S292


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S295


title: Single-cell RNAseq of lung tumor: K_30w_ND_m1_T0_P2_S365


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S291


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S383


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S290


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S381


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S382


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S384


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S380


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S379


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S377


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S378


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S376


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S373


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S372


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S375


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S374


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S371


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S370


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S369


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S367


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S368


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S366


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S365


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S361


title: Single-cell RNAseq of lung tumor: K_2w_ND_m5_T0_P1_S289


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S360


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S358


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S359


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S356


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S354


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S352


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S351


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S350


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S348


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S349


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S343


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S345


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S344


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S338


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S342


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S340


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S339


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S347


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S363


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S357


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S334


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S333


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S336


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S364


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S353


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S341


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S331


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S346


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S329


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S362


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S355


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S335


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S328


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S327


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S326


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S325


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S337


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S322


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S323


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S321


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S320


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S319


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S332


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S330


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S316


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S315


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S311


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S313


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S314


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S312


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S310


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S309


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S308


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S304


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S305


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S302


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S307


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S303


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S306


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S324


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S301


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S299


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S317


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S300


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S297


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S296


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S318


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S294


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S295


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S291


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S292


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S293


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S290


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S289


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S288

value: female


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S286


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S283


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S284


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S280


title: Single-cell RNAseq of lung tumor: K_2w_ND_m4_T0_P1_S298


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S277


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S279


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S287


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S282


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S278


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S274


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S276


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S273


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S275


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S272


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S270


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S271


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S285


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S268


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S269


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S267


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S264


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S265


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S263


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S262


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S260


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S261


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S259


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S281


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S258


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S257


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S255


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S256


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S252


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S253


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S250


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S247


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S254


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S249


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S246


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S251


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S245


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S266


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S248


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S242


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S244


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S239


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S241


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S238


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S235


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S234


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S236


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S232


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S233


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S237


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S231


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S229


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S230


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S228


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S226


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S227


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S224


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S243


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S225


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S223


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S219


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S221


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S218


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S220


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S216


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S214


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S240


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S213


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S222


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S215


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S211


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S212


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S210


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S209


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S208


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S205


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S204


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S203


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S207


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S206


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S202


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S200


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S195


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S199


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S198


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S287


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S197


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S201


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S288


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S194


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S217


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S286


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S278


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S281


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S280


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S196


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S285


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S284


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S283


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S275


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S282


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S279


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S277


title: Single-cell RNAseq of lung tumor: K_2w_ND_m3_T0_P1_S193


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S273


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S276


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S272


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S270


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S269


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S267


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S268


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S264


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S262


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S265


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S263


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S258


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S260


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S271


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S256


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S274


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S253


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S254


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S251


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S259


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S261


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S255


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S257


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S252


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S249


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S266


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S247


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S248


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S246


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S244


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S250


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S243


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S245


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S241


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S242


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S240


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S239


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S238


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S237


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S236


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S232


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S233


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S230


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S231


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S229


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S228


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S224


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S225


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S227


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S226


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S222


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S220


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S217


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S218


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S223


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S219


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S216


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S234


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S214


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S213


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S215


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S212


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S211


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S206


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S204


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S207


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S202


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S209


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S200


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S201


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S199


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S197


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S196


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S198


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S235


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S191


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S205


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S195


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S193


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S190


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S192


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S194


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S210


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S208


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S221


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S187


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S188


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S178


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S176


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S186


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S179


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S181


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S177


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S173


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S174


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S183


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S180


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S182


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S189


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S170


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S175


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S169


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S171


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S166


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S168


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S184


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S172


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S185


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S164


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S163


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P2_S203


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S165


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S167


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S160


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S159


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S154


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S155


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S162


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S157


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S149


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S158


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S156


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S152


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S150


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S151


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S147


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S148


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S146


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S143


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S141


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S142


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S144


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S153


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S145


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S139


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S161


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S137


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S134


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S135


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S138


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S136


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S133


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S131


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S127


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S128


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S126


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S124


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S140


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S122


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S123


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S115


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S116


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S114


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S117


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S120


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S110


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S107


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S132


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S111


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S106


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S105


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S109


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S104


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S113


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S129


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S103


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S112


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S130


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S119


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S121


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S125


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S100


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S102


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S098


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S101


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S108


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S118


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S378


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S381


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S380


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S377


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S379


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S375


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S376


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S368


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S372


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S373


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S374


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S371


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S370


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S369


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S097


title: Single-cell RNAseq of lung tumor: K_12w_ND_m3_T0_P1_S099


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S365


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S363


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S362


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S364


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S366


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S382


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S383


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S359


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S354


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S361


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S384


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S356


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S355


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S357


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S360


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S350


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S352


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S367


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S348


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S347


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S344


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S341


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S346


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S353


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S340


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S349


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S358


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S342


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S339


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S345


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S337


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S351


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S336


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S343


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S334


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S328


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S330


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S327


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S329


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S333


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S325


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S338


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S335


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S323


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S326


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S324


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S318


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S320


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S321


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S322


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S319


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S316


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S317


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S314


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S313


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S310


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S332


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S308


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S307


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S312


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S311


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S331


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S306


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S304


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S305


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S303


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S301


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S300


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S302


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S299


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S298


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S296


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S295


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S294


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S297


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S315


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S293


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S309


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S292


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S291


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S290


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P2_S289


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S287


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S288


title: MATa/a 4.5 hr sporulation media

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

country: USA

institute: UC Berkeley

data_processing:
library strategy: Ribosome profiling
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution. Because size distribution was 2nt longer than cycloheximide ribosome-profiling experiments (centered on 30nt vs 28nt), the a-site shift used was 2nt more. This returned results that centered peaks at known start codons. Alignments of raw reads to SK1 genome, bam files created.
ORF-RATER pipeline was run on bam files and those from NCBI GEO submission GSE108778
Genome_build: sk1_revised_100331 (fasta and gtf files provided here and also published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: ORFs called by ORF-RATER are listed in the csv file and a description of the columns is included in the readme file

organism: Saccharomyces cerevisiae

source_name: MATa/a 4.5 hr sporulation media, LTM pre-treated, footprints

growth_protocol: Vegetative: Strains were grown in YEPD(2%) at 30C, with shaking. Meiotic: Strains were grown in YEPD(2%) at 22C for 24 hours, then BYTA for 16 hours, then cells were washed one time with water and resuspended in sporulation media.

extract_protocol:
Cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009.
As described in Ingolia et al, Science 2009

treatment_protocol: Vegetative cells were harvested in exponential growth phase (OD600=0.6) or saturated growth (OD600=10). Meiotic cells were harvested at times indicated, with 0 hr being the time that the cells were transferred into sporulation media.

tag: growth condition

value: meiotic

tag: molecule type

value: ribosome footprints


title: 10 hr sporulation media

source_name: 10 hr sporulation media, LTM pre-treated, footprints


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S286


title: 22 hr sporulation media

source_name: 22 hr sporulation media, LTM pre-treated, footprints


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S285


title: Residual Lesion GFP Plus 3

type: RNA

city: Philadelphia

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, mogene10st_Mm_ENTREZG; R 3.0.2

label: Biotin

source_name: Residual Lesion GFP Plus

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

value: nu/nu

tag: gender

value: Female

tag: tissue

value: Isolated Orthotopic Residual Lesion Tumor Cells

tag: cell genotype

tag: treatment

value: HER2/neu inhibition

tag: time point

value: 28d after doxycycline withdrawal


title: Recurrent Tumor GFP Minus 3

source_name: Recurrent Tumor GFP Minus

value: Isolated Orthotopic Recurrent Tumor Stromal Cells

value: Recurrent Tumor


title: Recurrent Tumor GFP Plus 1

source_name: Recurrent Tumor GFP Plus

value: Isolated Orthotopic Recurrent Tumor Tumor Cells


title: Recurrent Tumor GFP Minus 1


title: Recurrent Tumor GFP Plus 2


title: 6 hr sporulation media

source_name: 6 hr sporulation media, LTM pre-treated, footprints


title: 8 hr sporulation media

source_name: 8 hr sporulation media, LTM pre-treated, footprints


title: Primary Tumor GFP Plus 3

source_name: Primary Tumor GFP Plus

value: Isolated Orthotopic Primary Tumor Tumor Cells

value: Untreated

value: Primary Tumor


title: Residual Lesion GFP Plus 1


title: Primary Tumor GFP Plus 2


title: Primary Tumor GFP Plus 1


title: Recurrent Tumor GFP Plus 3


title: 4.5 hr sporulation media

source_name: 4.5 hr sporulation media, LTM pre-treated, footprints


title: Recurrent Tumor GFP Minus 2


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S283


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S282


title: Residual Lesion GFP Plus 2


title: 3 hr sporulation media

source_name: 3 hr sporulation media, LTM pre-treated, footprints


title: 1.5 hr sporulation media

source_name: 1.5 hr sporulation media, LTM pre-treated, footprints


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S284


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S281


title: 0 hr sporulation media

source_name: 0 hr sporulation media, LTM pre-treated, footprints


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S279


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S277


title: vegetative exponential

source_name: vegetative exponential, LTM pre-treated, footprints

value: vegetative


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S276

value: KrasLSL-G12D; Rosa26LSL-tdTomato


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S273

value: male


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S272


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S271


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S275


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S270


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S278


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S280


title: vegetative saturated

source_name: vegetative saturated, LTM pre-treated, footprints


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S274


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S268


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S267


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S266


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S269


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S264


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S265


title: human adult dermal fibroblasts_biological rep2

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

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

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

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

label: biotin

organism: Homo sapiens

source_name: human adult dermal fibroblasts_donor-02

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

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

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

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

tag: donor id

value: female

tag: status

value: healthy

tag: cell type

value: primary cell line

tag: passage

value: passage 2-4


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S263

source_name: Lung tissue, AT2 cells

tag: timepoint

tag: breed

tag: strain


title: human adult menstrual derived stromal cells_biological rep2

source_name: human adult menstrual derived stromal cells_donor02


title: human adult dermal fibroblasts_biological rep1

source_name: human adult dermal fibroblasts_donor-01


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S262

tag: tumor

tag: plate

tag: sack_timepoint (weeks)


title: human adult bone marrow mesenchymal stem cells_biological rep2

source_name: human adult bone marrow mesenchymal stem cells_donor02


title: human Embryonic Stem Cells-WA01

value: hESC

value: passage 57


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S261

tag: age (weeks)

tag: Sex


title: human Embryonic Stem Cells-WA09_p67

source_name: hESC-H9 p67

tag: gender

value: passage 67


title: human adult bone marrow mesenchymal stem cells_biological rep1

source_name: human adult bone marrow mesenchymal stem cells_donor01


title: human adult dermal fibroblasts_biological rep4

source_name: human adult dermal fibroblasts_donor-04


title: human adult menstrual derived stromal cells_biological rep3

source_name: human adult menstrual derived stromal cells_donor03


title: human adult menstrual derived stromal cells_biological rep4

source_name: human adult menstrual derived stromal cells_donor04


title: human adult dermal fibroblasts_biological rep3

source_name: human adult dermal fibroblasts_donor-03


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S260


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S259


title: human adult menstrual derived stromal cells_biological rep1

source_name: human adult menstrual derived stromal cells_donor01


title: human Embryonic Stem Cells-WA09_p33

source_name: hESC-H9 p33

value: passage 33


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S258


title: human adult bone marrow mesenchymal stem cells_biological rep3

source_name: human adult bone marrow mesenchymal stem cells_donor03


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S257


title: iPS_AOX5_biological rep4

source_name: MnSC-donor-04 reprogrammed to iPSC  with AOX5

value: iPSC reprogrammed from primary MnSC cell lines

value: Passage 10-20 of iPSC


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S256


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S254


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S253


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S252


title: iPS_AOX5_biological rep3

source_name: MnSC-donor-03 reprogrammed to iPSC  with AOX5


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S255


title: iPS_AOX5_biological rep2

source_name: MnSC-donor-02 reprogrammed to iPSC  with AOX5


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S251


title: iPS_AOX5_biological rep5


title: iPS_OSK_biological rep5

source_name: MnSC-donor-04 reprogrammed to iPSC  with OSK


title: iPS_OSK_biological rep3

source_name: MnSC-donor-03 reprogrammed to iPSC  with OSK


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S248

source_name: Lung tissue, AT2 cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S250


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S247


title: iPS_OSK_biological rep2

source_name: MnSC-donor-02 reprogrammed to iPSC  with OSK


title: iPS_AOX5_biological rep1

source_name: MnSC-donor-01 reprogrammed to iPSC  with AOX5


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S245


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S244


title: iPS_OSK_biological rep1

source_name: MnSC-donor-01 reprogrammed to iPSC  with OSK


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S246


title: Subject 32_non-SS_Batch 3

city: Oklahoma City

first: A. Darise

last: Farris

state: OK

address: 825 NE 13th Street, MS 24

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

hyb_protocol: The Cy3-labeled cDNAs were hybridized overnight (17 hours, 65 degrees C) to an Agilent Whole Human Genome Oligo Microarray 8x60K using Agilent's recommended hybridization chamber and oven. The microarrays were washed once with Agilent Gene Expression Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37 degrees C) Agilent Gene Expression Wash Buffer 2 for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out  the microarray image files. Amplified cDNA samples from 17 pSS and 15 nSS subjects were hybridized to Agilent Whole Human Genome 8x60K microarrays in three batches. All data were pooled to assess potential batch effects by principal components analysis, and gene expression data were quality checked using the arrayQualityMetrics R package. Batch effects were equalized via ComBat analysis (sva R package v 3.8.0; manual specification of batches). Low-variability genes (defined as <50% of the overall variability distribution) were filtered using the function varFilter in R to reduce the false positive rate. The data were quantile normalized, and differentially expressed genes were detected using the limma R package v3.3. P-values were corrected for multiple testing using the Benjamin-Hochberg procedure. The significance threshold was set at a false discovery rate (FDR) of 0.1 resulting in adjusted p-values less than 0.1. Genes with log fold-change values of at least 1.5 were included in the list of differentially expressed genes (DEG). Data from multiple probes for the same gene were collapsed to one by maximum expression level.

source_name: non-SS_Batch 3_Minor salivary gland memory CD4 T cells

label_protocol: 250 ng of each cDNA sample was used as template for Cy3 labeling which was performed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: Samples were shipped on dry ice to Miltenyi Biotec where mRNA isolated with paramagnetic oligo(dT) microbeads underwent proprietary bead-bound cDNA synthesis, 3′-end tailing and labeling, followed by single-primer amplification of cDNA and cDNA purification.

treatment_protocol: SG biopsy tissue (4-6 minor salivary glands/subject) was minced, digested with 750 U/mL Collagenase I (Sigma), 500 U/mL Hyaluronidase IV (Sigma) and 0.1 mg/mL DNAse I (Roche) in RPMI/10mM Hepes/5% fetal calf serum (FCS) for 1 hour at 37°C, then dissociated with program “B” on a gentleMACS instrument (Miltenyi Biotec) or processed as described in PMID27358913. Cells were stained with monoclonal antibodies (CD3-PE, CD4-PECy5, CD8-Alexa 488 and CD45RA-V450, Becton Dickinson, Franklin Lakes, NJ, USA). CD3+CD4+CD45RA- cells excluding propidium iodide were first bulk sorted at high purity using doublet discrimination on a FACSAria (Becton Dickinson). Then 200 cells in ~1 µL were sorted into 6.7 µL SuperAMP buffer (Miltenyi Biotec, Auburn, CA, USA) using a MoFlo-XDP (Beckman-Coulter Indianapolis, IN, USA) and stored at -80 degrees C.

tag: subject id

value: Subject 32

tag: aecg disease classification

value: non-SS

tag: age

value: F

tag: race

value: Black

tag: batch

value: Batch 3

value: Minor salivary gland memory CD4 T cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S243

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S249


title: Subject 31_non-SS_Batch 3

value: Subject 31

value: M

value: More Than One


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S242


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S240


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S239


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S241


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S237


title: Subject 28_non-SS_Batch 3

value: Subject 28

value: White


title: Subject 26_non-SS_Batch 3

value: Subject 26


title: Subject 27_non-SS_Batch 3

value: Subject 27


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S236


title: Subject 30_non-SS_Batch 3

value: Subject 30


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S235


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S234


title: Subject 29_non-SS_Batch 3

value: Subject 29


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S232


title: Subject 24_Primary SS_Batch 3

source_name: Primary SS_Batch 3_Minor salivary gland memory CD4 T cells

value: Subject 24

value: Primary SS


title: Subject 21_Primary SS_Batch 3

value: Subject 21

value: F


title: Subject 25_Primary SS_Batch 3

value: Subject 25

value: Batch 3


title: Subject 23_Primary SS_Batch 3

value: Subject 23

value: Minor salivary gland memory CD4 T cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S233

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: Subject 19_Primary SS_Batch 3

value: Subject 19

value: More Than One


title: iPS_OSK_biological rep4

tag: donor id

value: female

tag: status

value: healthy

value: iPSC reprogrammed from primary MnSC cell lines

value: Passage 10-20 of iPSC


title: Subject 16_non-SS_Batch 2

source_name: non-SS_Batch 2_Minor salivary gland memory CD4 T cells

value: Subject 16

value: non-SS

value: Native American

value: Batch 2

tag: cell type


title: Subject 17_Primary SS_Batch 3

value: Subject 17

value: Primary SS

value: F


title: Subject 22_Primary SS_Batch 3

value: Subject 22

value: Black

value: Batch 3


title: Subject 18_Primary SS_Batch 3

value: Subject 18

value: White

value: Minor salivary gland memory CD4 T cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S238

tag: timepoint

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: Subject 14_non-SS_Batch 2

value: Subject 14

value: More Than One


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S231

tag: breed


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S230

tag: strain


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S229

tag: tumor


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S228

tag: plate


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S227

tag: sack_timepoint (weeks)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S225

tag: age (weeks)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S224

tag: Sex


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S223


title: Subject 15_non-SS_Batch 2

value: Subject 15

value: M


title: Subject 20_Primary SS_Batch 3

value: Subject 20


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S220


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S222


title: Subject 12_non-SS_Batch 2

value: Subject 12

value: non-SS

value: Batch 2


title: Subject 7_Primary SS_Batch 2

source_name: Primary SS_Batch 2_Minor salivary gland memory CD4 T cells

value: Subject 7

value: Primary SS

value: F


title: Subject 11_Primary SS_Batch 2

value: Subject 11


title: Subject 2_Primary SS_Batch 1

source_name: Primary SS_Batch 1_Minor salivary gland memory CD4 T cells

value: Subject 2

value: Batch 1


title: Subject 8_Primary SS_Batch 2

value: Subject 8

value: White

value: Minor salivary gland memory CD4 T cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180148 scDNA

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

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,

tag: animal


title: Subject 6_Primary SS_Batch 2

tag: subject id

value: Subject 6


title: Subject 10_Primary SS_Batch 2

value: Subject 10

tag: aecg disease classification


title: Subject 9_Primary SS_Batch 2

value: Subject 9

tag: age


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S221

value: KrasLSL-G12D; Rosa26LSL-tdTomato

value: male


title: Subject 3_non-SS_Batch 1

source_name: non-SS_Batch 1_Minor salivary gland memory CD4 T cells

value: Subject 3

tag: race


title: Subject 13_non-SS_Batch 2

value: Subject 13

value: non-SS

tag: batch


title: Subject 5_non-SS_Batch 1

value: Subject 5

value: More Than One


title: Subject 4_non-SS_Batch 1

value: Subject 4

value: F


title: KP_30w_ND_m3_T9_170907Amo_D17-180150 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180147 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S217


title: KP_30w_ND_m3_T9_170907Amo_D17-180149 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S219


title: Subject 1_Primary SS_Batch 1

value: Subject 1

value: Primary SS

value: M


title: KP_30w_ND_m3_T9_170907Amo_D17-180145 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180143 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S214


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S215


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S218


title: KP_30w_ND_m3_T9_170907Amo_D17-180144 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180146 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180140 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180142 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S211


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S210


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S216


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S213


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S208


title: KP_30w_ND_m3_T9_170907Amo_D17-180141 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180139 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S207


title: KP_30w_ND_m3_T9_170907Amo_D17-180135 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S212


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S209


title: KP_30w_ND_m3_T9_170907Amo_D17-180136 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180137 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S206


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S205


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S204


title: KP_30w_ND_m3_T9_170907Amo_D17-180132 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S226


title: KP_30w_ND_m3_T9_170907Amo_D17-180131 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S201


title: KP_30w_ND_m3_T9_170907Amo_D17-180138 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180130 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S199


title: KP_30w_ND_m3_T9_170907Amo_D17-180128 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S198


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S200


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S197


title: KP_30w_ND_m3_T9_170907Amo_D17-180126 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180134 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S196


title: KP_30w_ND_m3_T9_170907Amo_D17-180125 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S194


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S203


title: KP_30w_ND_m3_T9_170907Amo_D17-180122 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180121 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S195


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S193


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S191


title: KP_30w_ND_m3_T9_170907Amo_D17-180123 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S192


title: KP_30w_ND_m3_T9_170907Amo_D17-180119 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m2_T0_P1_S202


title: KP_30w_ND_m3_T9_170907Amo_D17-180120 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180118 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S189


title: KP_30w_ND_m3_T9_170907Amo_D17-180127 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180117 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S188


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S187


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S186


title: KP_30w_ND_m3_T9_170907Amo_D17-180124 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180133 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S185


title: KP_30w_ND_m3_T9_170907Amo_D17-180116 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180114 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S184


title: KP_30w_ND_m3_T9_170907Amo_D17-180115 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S183


title: KP_30w_ND_m3_T9_170907Amo_D17-180129 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180113 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180111 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180112 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S182


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S181


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S190


title: KP_30w_ND_m3_T9_170907Amo_D17-180110 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S180


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S179


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S177


title: KP_30w_ND_m3_T9_170907Amo_D17-180107 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S178


title: KP_30w_ND_m3_T9_170907Amo_D17-180106 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S176


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S175


title: KP_30w_ND_m3_T9_170907Amo_D17-180104 scDNA

description: DNA sequencing of tumor cells


title: Monomac6_Input

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

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

source_name: Monomac6 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

value: AML

tag: genome variation

value: CTRL

tag: chip antibody

value: none (input)


title: KP_30w_ND_m3_T9_170907Amo_D17-180105 scDNA

description: DNA sequencing of tumor cells

tag: timepoint


title: KP_30w_ND_m3_T9_170907Amo_D17-180103 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S174

tag: breed


title: Molm13_Input

source_name: Molm13 cell line

tag: cell type


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S173

tag: strain

tag: tumor


title: AMU-AML1_Input

source_name: AMU-AML1 cell line


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S172

tag: plate

tag: sack_timepoint (weeks)


title: KP_30w_ND_m3_T7_170907Amo_D17-180100 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180099 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180108 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180109 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180096 scDNA

description: DNA sequencing of tumor cells


title: UCSD-AML1_Input

source_name: UCSD-AML1 cell line


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S171

tag: age (weeks)

tag: Sex


title: Monomac6_MED1

value: Mediator1 (Bethyl A300-793A)


title: KP_30w_ND_m3_T7_170907Amo_D17-180097 scDNA

description: DNA sequencing of tumor cells

tag: animal


title: KP_30w_ND_m3_T7_170907Amo_D17-180098 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S170


title: Monomac6_H3K4me1_rep2

value: H3K4me1 (abcam ab8895)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S169

value: KrasLSL-G12D; Rosa26LSL-tdTomato


title: KP_30w_ND_m3_T9_170907Amo_D17-180101 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180092 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180093 scDNA

description: DNA sequencing of tumor cells


title: Monomac6_H3K4me1_rep1


title: KP_30w_ND_m3_T7_170907Amo_D17-180091 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T9_170907Amo_D17-180102 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S168

value: male


title: KP_30w_ND_m3_T7_170907Amo_D17-180090 scDNA

description: DNA sequencing of tumor cells


title: Monomac6_H3K27ac_rep2

value: H3K27ac (abcam ab4729)


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S167


title: KP_30w_ND_m3_T7_170907Amo_D17-180088 scDNA

description: DNA sequencing of tumor cells


title: Monomac6_H3K27ac_rep1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S166


title: Molm13_MED1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S165


title: KP_30w_ND_m3_T7_170907Amo_D17-180095 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180086 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S164


title: KP_30w_ND_m3_T7_170907Amo_D17-180094 scDNA

description: DNA sequencing of tumor cells


title: Molm13_H3K27ac_rep2


title: KP_30w_ND_m3_T7_170907Amo_D17-180084 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180082 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180083 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180081 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180080 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180079 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180085 scDNA

description: DNA sequencing of tumor cells


title: Molm13_H3K4me1


title: Molm13_H3K27ac_rep1


title: KP_30w_ND_m3_T7_170907Amo_D17-180078 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180089 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S163


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S162


title: KP_30w_ND_m3_T7_170907Amo_D17-180075 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180076 scDNA

description: DNA sequencing of tumor cells


title: AMU-AML1_MED1


title: AMU-AML1_H3K4me1


title: KP_30w_ND_m3_T7_170907Amo_D17-180077 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S161


title: AMU-AML1_H3K27ac


title: KP_30w_ND_m3_T7_170907Amo_D17-180087 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S156


title: UCSD-AML1_MED1


title: KP_30w_ND_m3_T7_170907Amo_D17-180072 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180073 scDNA

description: DNA sequencing of tumor cells


title: KP_30w_ND_m3_T7_170907Amo_D17-180074 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S158


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S159


title: UCSD-AML1_H3K4me1_rep1


title: KP_30w_ND_m3_T7_170907Amo_D17-180070 scDNA

description: DNA sequencing of tumor cells


title: UCSD-AML1_H3K4me1_rep2


title: KP_30w_ND_m3_T7_170907Amo_D17-180071 scDNA

description: DNA sequencing of tumor cells


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S157


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S155


title: UCSD-AML1_H3K27ac_rep1


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S154


title: Single-cell RNAseq of lung tumor: K_12w_ND_m1_T0_P4_S160


title: KP_30w_ND_m3_T7_170907Amo_D17-180068 scDNA

description: DNA sequencing of tumor cells