title: RBG27570_Parental


title: RBG27606_Parental

status: Public on Feb 07 2020

type: SRA

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Raw reads were aligned to Mus musculus genome (GRCm38.81) using G-SNAP (version 2015-09-29) with the following parameters: –B 5 –n 1 –N 1 –Q. HTSeq-count (version 0.6.0) was run to assign mapped reads to Ensembl genes (GRCm38.81).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: Hoxb8 Cell line

growth_protocol: Conditionally immortalised early hematopoietic progenitor cells (Hoxb8-FL cells) (Redecke et al., 2013) were cultured in RPMI 1640 medium (Sigma-R8758) supplemented with 10% Fetal Bovine Serum (FBS) (HyCloneTM GE Healthcare), 5% Flt3L conditional medium, 1% Penicillin/Streptomycin (Sigma-P0781), 1% L-Glutamine (Sigma-G7513), 0.1% 2-Mercaptoethanol (50mM stock)(Gibco®), 0.001% β-estradiol (10mM stock) at 37 ̊C and 5% CO2.

extract_protocol:
GFP positive and DAPI negative cells were FACS sorted into individual wells of a 96 well plates containing lysis buffer and processed using Smart-Seq2 protocol as previously described (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
Libraries were prepared using the Illumina Nextera XT Libraries were prepared using the Illumina Nextera XT DNA preparation kit.

tag: treatment

tag: day

tag: batch

tag: condition

value: Parental


title: RBG27758_IL3_Day11_Parental


title: RBG27630_Parental


title: RBG27818_IL3_Day11_Parental


title: RBG27605_Parental


title: RBG27641_Parental


title: RBG27593_Parental


title: RBG27617_Parental


title: RBG27581_Parental


title: RBG27569_Parental


title: RBG28330_IL3_Day7_Parental


title: RBG28306_IL3_Day7_Parental


title: RBG28105_IL3_Day4_Parental


title: RBG28129_IL3_Day4_Parental


title: RBG28270_IL3_Day7_Parental


title: RBG28093_IL3_Day4_Parental


title: RBG28081_IL3_Day4_Parental


title: RBG28294_IL3_Day7_Parental


title: RBG28258_IL3_Day7_Parental


title: RBG28317_IL3_Day7_Parental


title: RBG28329_IL3_Day7_Parental


title: RBG28305_IL3_Day7_Parental


title: RBG28057_IL3_Day4_Parental


title: RBG28069_IL3_Day4_Parental


title: RBG28257_IL3_Day7_Parental


title: RBG28116_IL3_Day4_Parental


title: RBG28245_IL3_Day7_Parental


title: RBG28269_IL3_Day7_Parental


title: RBG28068_IL3_Day4_Parental


title: RBG28137_IL3_Day4_Parental


title: RBG28316_IL3_Day7_Parental


title: RBG28328_IL3_Day7_Parental


title: RBG28280_IL3_Day7_Parental


title: RBG28304_IL3_Day7_Parental


title: RBG28136_IL3_Day4_Parental


title: RBG28244_IL3_Day7_Parental


title: RBG28127_IL3_Day4_Parental


title: RBG28091_IL3_Day4_Parental


title: RBG28281_IL3_Day7_Parental


title: RBG28327_IL3_Day7_Parental


title: RBG28293_IL3_Day7_Parental


title: RBG28079_IL3_Day4_Parental


title: RBG28056_IL3_Day4_Parental


title: RBG28128_IL3_Day4_Parental


title: RBG28291_IL3_Day7_Parental


title: RBG28279_IL3_Day7_Parental


title: RBG28303_IL3_Day7_Parental


title: RBG28078_IL3_Day4_Parental


title: RBG28243_IL3_Day7_Parental


title: RBG28267_IL3_Day7_Parental


title: RBG28126_IL3_Day4_Parental


title: RBG28054_IL3_Day4_Parental


title: RBG28268_IL3_Day7_Parental


title: RBG28255_IL3_Day7_Parental


title: RBG28066_IL3_Day4_Parental


title: RBG28102_IL3_Day4_Parental


title: RBG28256_IL3_Day7_Parental


title: RBG28326_IL3_Day7_Parental


title: RBG28278_IL3_Day7_Parental


title: RBG28302_IL3_Day7_Parental


title: RBG28266_IL3_Day7_Parental


title: RBG28067_IL3_Day4_Parental


title: RBG28055_IL3_Day4_Parental


title: RBG28135_IL3_Day4_Parental


title: RBG28101_IL3_Day4_Parental


title: RBG28065_IL3_Day4_Parental


title: RBG28053_IL3_Day4_Parental


title: RBG28089_IL3_Day4_Parental


title: RBG28325_IL3_Day7_Parental


title: RBG28265_IL3_Day7_Parental


title: RBG28253_IL3_Day7_Parental


title: RBG28134_IL3_Day4_Parental


title: RBG28301_IL3_Day7_Parental


title: RBG28076_IL3_Day4_Parental


title: RBG28124_IL3_Day4_Parental


title: RBG28052_IL3_Day4_Parental


title: RBG28277_IL3_Day7_Parental


title: RBG28312_IL3_Day7_ME-Parental

value: ME-Parental


title: RBG28254_IL3_Day7_Parental


title: RBG28300_IL3_Day7_ME-Parental


title: RBG28288_IL3_Day7_ME-Parental


title: RBG28242_IL3_Day7_Parental


title: RBG28264_IL3_Day7_ME-Parental


title: RBG28240_IL3_Day7_ME-Parental


title: RBG28252_IL3_Day7_ME-Parental


title: RBG28075_IL3_Day4_ME-Parental


title: RBG28123_IL3_Day4_ME-Parental


title: RBG28051_IL3_Day4_ME-Parental


title: RBG28311_IL3_Day7_ME-Parental


title: RBG28275_IL3_Day7_ME-Parental


title: RBG28313_IL3_Day7_Parental


title: RBG28287_IL3_Day7_ME-Parental


title: RBG28086_IL3_Day4_ME-Parental


title: RBG28263_IL3_Day7_ME-Parental


title: RBG28074_IL3_Day4_ME-Parental


title: RBG28239_IL3_Day7_ME-Parental


title: RBG28241_IL3_Day7_Parental


title: RBG28050_IL3_Day4_ME-Parental


title: RBG28286_IL3_Day7_ME-Parental


title: RBG28250_IL3_Day7_ME-Parental


title: RBG28298_IL3_Day7_ME-Parental


title: RBG28062_IL3_Day4_ME-Parental


title: RBG28262_IL3_Day7_ME-Parental


title: RBG28064_IL3_Day4_Parental


title: RBG28238_IL3_Day7_ME-Parental


title: RBG28061_IL3_Day4_ME-Parental


title: RBG28049_IL3_Day4_ME-Parental


title: RBG28085_IL3_Day4_ME-Parental


title: RBG28073_IL3_Day4_ME-Parental


title: RBG28276_IL3_Day7_ME-Parental


title: RBG28097_IL3_Day4_ME-Parental


title: RBG28321_IL3_Day7_ME-Parental


title: RBG28297_IL3_Day7_ME-Parental


title: RBG28285_IL3_Day7_ME-Parental


title: RBG28249_IL3_Day7_ME-Parental


title: RBG28261_IL3_Day7_ME-Parental


title: RBG28237_IL3_Day7_ME-Parental


title: RBG28108_IL3_Day4_ME-Parental


title: RBG28120_IL3_Day4_ME-Parental


title: RBG28096_IL3_Day4_ME-Parental


title: RBG28048_IL3_Day4_ME-Parental


title: RBG28084_IL3_Day4_ME-Parental


title: RBG28236_IL3_Day7_ME-Parental


title: RBG28248_IL3_Day7_ME-Parental


title: RBG28131_IL3_Day4_ME-Parental


title: RBG28060_IL3_Day4_ME-Parental


title: RBG28308_IL3_Day7_ME-Parental


title: RBG28119_IL3_Day4_ME-Parental


title: RBG28107_IL3_Day4_ME-Parental


title: RBG28095_IL3_Day4_ME-Parental


title: RBG28059_IL3_Day4_ME-Parental


title: RBG28307_IL3_Day7_ME-Parental


title: RBG28283_IL3_Day7_ME-Parental


title: RBG28247_IL3_Day7_ME-Parental


title: RBG28130_IL3_Day4_ME-Parental


title: RBG28235_IL3_Day7_ME-Parental


title: RBG28106_IL3_Day4_ME-Parental


title: mTECs_AireKO_1_RNA-seq

city: bunkyo

first: Yoshihiko

last: Tomofuji

state: Tokyo

address: hongo 7-3-1

department: Immunology

country: Japan

institute: University of Tokyo

description:
mTECs_AireKO_1
mTECs from Aire KO mice
processed data file: RNA_seq_data_summary.txt

data_processing:
Data was trimmed and mapped to reference Mus musculus (mm10) genome by using CLC genomics Workbench v.9.0 (CLC).
RPKM was calculated by using CLC genomics Workbench v.9.0 (CLC).
log(RPKM) was calculated and DEGs were detected from total exon reads by using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNA_seq_data_summary.txt
Supplementary_files_format_and_content: Aire_KO_RNA_seq.csv, Chd4_cKO_RNA_seq.csv, Fezf2_KO_RNA_seq.csv

source_name: mTECs

extract_protocol:
Total RNA from sorted mTECs is extracted by Maxwell® 16 Automated Purification System (Promega).
Library for sequencing was synthesized using SMART-seq v4 Ultra Low Input RNA Kit.

tag: strain

tag: genotype/variation

value: AireKO

tag: cell type

value: TECs


title: mTECs_AireKO_2_RNA-seq

description:
mTECs_AireKO_2
mTECs from Aire KO mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_Fezf2KO_3_RNA-seq

description:
mTECs_Fezf2KO_3
mTECs from Fezf2 KO mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_Fezf2KO_2_RNA-seq

description:
mTECs_Fezf2KO_2
mTECs from Fezf2 KO mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_WT_6_RNA-seq

description:
mTECs_WT_6
mTECs from WT mice (CTL for Fezf2 KO)
processed data file: RNA_seq_data_summary.txt

value: WT


title: mTECs_Fezf2KO_1_RNA-seq

description:
mTECs_Fezf2KO_1
mTECs from Fezf2 KO mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_AireKO_3_RNA-seq

description:
mTECs_AireKO_3
mTECs from Aire KO mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_WT_5_RNA-seq

description:
mTECs_WT_5
mTECs from WT mice (CTL for Fezf2 KO)
processed data file: RNA_seq_data_summary.txt


title: mTECs_WT_4_RNA-seq

description:
mTECs_WT_4
mTECs from WT mice (CTL for Fezf2 KO)
processed data file: RNA_seq_data_summary.txt


title: RBG28094_IL3_Day4_ME-Parental


title: RBG28071_IL3_Day4_ME-Parental


title: RBG28234_IL3_Day11_Parental


title: RBG28046_IL3_Day4_ME-Parental


title: mTECs_WT_3_RNA-seq

description:
mTECs_WT_3
mTECs from WT mice (CTL for Aire KO)
processed data file: RNA_seq_data_summary.txt


title: RBG28070_IL3_Day4_ME-Parental


title: mTECs_WT_1_RNA-seq

description:
mTECs_WT_1
mTECs from WT mice (CTL for Aire KO)
processed data file: RNA_seq_data_summary.txt


title: mTECs_WT_2_RNA-seq

description:
mTECs_WT_2
mTECs from WT mice (CTL for Aire KO)
processed data file: RNA_seq_data_summary.txt


title: RBG28047_IL3_Day4_ME-Parental


title: BrTr11_1_CL2_022513

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). See platform.xls for a description of the IDs in readCounts.xls

organism: Homo sapiens

source_name: CTCs

extract_protocol:
RNA was extracted as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535).
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

treatment_protocol: Patients with a diagnosis of ER and/or PR positive metastatic breast cancer provided informed consent for de-identified blood collection, as per institutional review board approved protocol (DF/HCC 05-300) at Massachusetts General Hospital. Approximately 6-12 mL of fresh whole blood was processed through the microfluidic CTC-iChip as previously described [PMID: 24577360] within 4 hours from the blood draw. Before processing, whole blood samples were incubated with biotinylated antibodies against CD45 (R&D Systems, clone 2D1), CD66b (AbD Serotec, clone 80H3) and followed by incubation with Dynabeads MyOne Streptavidin T1 (Invitrogen) to achieve magnetic labelling of white blood cells. This mixture was processed through the CTC-iChip. To identify CTCs, the CTC-enriched product was stained with Alexa Fluor 488-conjugated antibodies against EpCAM (Cell Signaling Technology, #5198), Cadherin 11 (R&D Systems, FAB17901G), and HER2 (BioLegend, #324410). To identify contaminating white blood cells the product was stained with TexasRed-conjugated antibodies against CD45 (BD Biosciences, BDB562279), CD14 (BD Biosciences, BDB562334), and CD16 (BD Biosciences, BDB562320). The stained product was viewed under a fluorescent microscope where single CTCs were identified based on intact cellular morphology, Alexa Fluor 488-positive staining and lack of TexasRed staining. Cells of interest were individually micromanipulated with a 10 mm transfer tip on an Eppendorf Transfer-Man NK 2 micromanipulator and lysed.

tag: patient

tag: overall survival days

tag: overall survival event


title: RBG28222_IL3_Day11_Parental


title: RBG28210_IL3_Day11_Parental


title: RBG28295_IL3_Day7_ME-Parental


title: RBG28198_IL3_Day11_Parental


title: BrTr11_1_CL3_022513


title: RBG28118_IL3_Day4_ME-Parental


title: Brx17_CL2_020713


title: RBG28045_Parental


title: RBG28033_Parental


title: RBG28150_IL3_Day11_Parental


title: RBG28021_Parental


title: Reanalysis BrTr12_SC_022813


title: RBG27973_Parental


title: RBG27985_Parental


title: Reanalysis BrTr08_1_CL2_012913

description:
GSM1253381
GSM2314594


title: RBG27997_Parental


title: BrTr11_1_CL1_022513


title: Reanalysis Brx11_SC_020413


title: Reanalysis Brx11_CL_020413


title: Reanalysis Brx52_SC2_020413

description:
GSM1253379
GSM2314628


title: RBG28209_IL3_Day11_Parental


title: RBG28009_Parental


title: RBG28186_IL3_Day11_Parental


title: Reanalysis Brx17_SC1_020713


title: RBG28185_IL3_Day11_Parental


title: Reanalysis Brx52_CL5_020413

description:
GSM1253393
GSM2314624


title: RBG28197_IL3_Day11_Parental


title: RBG27961_Parental


title: RBG28173_IL3_Day11_Parental


title: Reanalysis Brx52_CL1_020413

description:
GSM1253394
GSM2314625


title: Reanalysis Brx52_CL4_020413


title: Reanalysis Brx52_SC1_020413

description:
GSM1253392
GSM2314627


title: RBG28233_IL3_Day11_Parental


title: RBG28161_IL3_Day11_Parental


title: Reanalysis Brx52_CL2_020413

description:
GSM1253395
GSM2314622


title: RBG28044_Parental


title: RBG28162_IL3_Day11_Parental


title: Reanalysis Brx53_SC_011513


title: Reanalysis Brx53_SC1_010313


title: Reanalysis Brx12_SC_012913


title: Reanalysis Brx52_CL3_020413


title: RBG28008_Parental


title: RBG28020_Parental


title: RBG28032_Parental


title: RBG28149_IL3_Day11_Parental


title: Reanalysis Brx53_CL2_010313

description:
GSM1253375
GSM2314632


title: RBG27996_Parental


title: Reanalysis Brx66_2_SC2_012913

description:
GSM1253386
GSM2314669


title: Reanalysis Brx66_2_CL3_012913


title: Reanalysis Brx53_CL2_011513


title: RBG28220_IL3_Day11_Parental


title: RBG28232_IL3_Day11_Parental


title: RBG27984_Parental


title: RBG27960_Parental


title: Reanalysis Brx66_1_012913


title: RBG27972_Parental


title: Reanalysis Brx66_2_SC1_012913

description:
GSM1253390
GSM2314667


title: RBG28208_IL3_Day11_Parental


title: RBG28172_IL3_Day11_Parental


title: Reanalysis Brx66_2_CL2_012913

description:
GSM1253385
GSM2314664


title: BR29_3_BYL_012913


title: Reanalysis Br29_2_012913


title: Brx03_CL1_012913


title: RBG28184_IL3_Day11_Parental


title: RBG28196_IL3_Day11_Parental


title: RBG28160_IL3_Day11_Parental


title: Brx164_1_SC3_091814


title: RBG28148_IL3_Day11_Parental


title: RBG28019_Parental


title: RBG28031_Parental


title: RBG28043_Parental


title: RBG28007_Parental


title: RBG27995_Parental


title: RBG27983_Parental


title: RBG28231_IL3_Day11_Parental


title: Brx164_1_SC1_091814


title: Brx117_2_SC1_091814


title: Brx146_2_relapse_SC2_082114


title: Brx164_1_SC4_091814


title: Brx116_1_SC1_092414


title: RBG28207_IL3_Day11_Parental


title: Brx163_1_SC2_090814


title: Brx90_1_SC1_101014


title: RBG28219_IL3_Day11_Parental


title: Brx146_2_relapse_SC3_082114


title: Brx90_1_SC3_101014


title: Brx90_1_SC2_101014


title: RBG28171_IL3_Day11_Parental


title: RBG28183_IL3_Day11_Parental


title: Brx146_2_relapse_SC1_082114


title: Brx116_2_TX_SC1_092414


title: RBG28195_IL3_Day11_Parental


title: RBG28042_Parental


title: RBG28159_IL3_Day11_Parental


title: Brx163_1_SC3_090814


title: Brx163_1_SC4_090814


title: RBG28030_Parental


title: Brx134_1_SC1_021914


title: Brx130_1_SC1_011714


title: RBG27959_Parental


title: RBG27971_Parental


title: RBG28006_Parental


title: RBG28018_Parental


title: RBG27994_Parental


title: RBG27970_Parental


title: Brx120_1_SC2_120513


title: RBG27958_Parental


title: RBG27982_Parental


title: RBG28158_IL3_Day11_Parental


title: Brx117_1_SC1_120613


title: RBG28146_IL3_Day11_Parental


title: RBG28206_IL3_Day11_Parental


title: RBG28218_IL3_Day11_Parental


title: Brx35_1_SC2_110713


title: RBG28041_Parental


title: Brx109_1_SC1_121613


title: Brx122_1_SC2_121213


title: RBG28029_Parental


title: Brx121_1_SC1_120913


title: RBG28017_Parental


title: RBG28005_Parental


title: Brx120_2_BYL_SC1_120613


title: Brx122_1_SC3_121213


title: RBG27993_Parental


title: RBG27981_Parental


title: RBG27957_Parental


title: RBG27969_Parental


title: Brx121_1_SC2_120913


title: Brx120_1_SC3_120513


title: Brx116_2_SC1_120213


title: Brx116_1_SC3_120213


title: RBG28229_IL3_Day11_Parental


title: Brx93_1_SC1_112113


title: RBG28193_IL3_Day11_Parental


title: Brx70_2_BYLrelapse_SC1_092413


title: RBG28217_IL3_Day11_Parental


title: Brx107_1_SC1_092013


title: RBG28169_IL3_Day11_Parental


title: RBG28016_Parental


title: RBG28040_Parental


title: Reanalysis Brx97_1_SC2_072313


title: RBG28028_Parental


title: Reanalysis Brx97_1_SC3_072313


title: RBG28205_IL3_Day11_Parental


title: Brx100_1_SC5_080113


title: RBG27992_Parental


title: RBG28004_Parental


title: RBG27980_Parental


title: Brx100_1_SC4_080113


title: Brx100_2_BYL_SC2_080213


title: Reanalysis Brx97_1_SC4_072313


title: RBG27968_Parental


title: RBG28204_IL3_Day11_ME-Parental


title: RBG28216_IL3_Day11_ME-Parental


title: Reanalysis Brx97_1_SC5_072313


title: RBG27956_Parental


title: RBG28192_IL3_Day11_ME-Parental


title: RBG28228_IL3_Day11_ME-Parental


title: RBG28181_IL3_Day11_Parental


title: RBG28180_IL3_Day11_ME-Parental


title: RBG28145_IL3_Day11_Parental


title: RBG28144_IL3_Day11_ME-Parental


title: RBG28168_IL3_Day11_ME-Parental


title: RBG28039_ME-Parental


title: Reanalysis Brx98_1_SC5_072313


title: Brx95_2_BYL_CL1_071813


title: Reanalysis Brx87_1_SC2_062113


title: RBG28015_ME-Parental


title: Reanalysis Brx82_1_SC1_051613


title: RBG27991_ME-Parental


title: RBG28027_ME-Parental


title: Brx86_2_BYL_SC3_052413


title: Brx86_2_BYL_SC2_052413


title: RBG28003_ME-Parental


title: RBG27967_ME-Parental


title: Brx86_2_BYL_SC1_052413


title: RBG27955_ME-Parental


title: Brx86_1_CL1_052313


title: Brx86_1_SC3_052313


title: RBG28227_IL3_Day11_ME-Parental


title: RBG27979_ME-Parental


title: RBG28215_IL3_Day11_ME-Parental


title: Reanalysis Brx83_1_SC3_051613


title: Reanalysis Brx83_1_SC4_051613


title: Reanalysis Brx83_1_SC2_051613


title: RBG28191_IL3_Day11_ME-Parental


title: RBG28179_IL3_Day11_ME-Parental


title: Reanalysis Br21_1_SC3_052113


title: RBG28167_IL3_Day11_ME-Parental


title: RBG28155_IL3_Day11_ME-Parental


title: RBG28143_IL3_Day11_ME-Parental


title: RBG28038_ME-Parental


title: RBG28014_ME-Parental


title: Brx72_2_BYL_SC3_031913


title: Reanalysis Brx72_1_SC6_031813


title: RBG28002_ME-Parental


title: RBG28203_IL3_Day11_ME-Parental


title: RBG27978_ME-Parental


title: RBG27966_ME-Parental


title: Reanalysis Brx10_1_SC3_041113


title: Reanalysis Br21_1_SC2_052113


title: Reanalysis Brx72_1_SC5_031813


title: Reanalysis Brx72_1_SC1_031813


title: Brx72_2_BYL_SC2_031913


title: RBG28226_IL3_Day11_ME-Parental


title: Brx72_2_BYL_SC1_031913


title: RBG28178_IL3_Day11_ME-Parental


title: Reanalysis Brx10_1_SC2_041113


title: Reanalysis Brx72_1_SC2_031813


title: RBG28166_IL3_Day11_ME-Parental


title: RBG28037_ME-Parental


title: RBG28190_IL3_Day11_ME-Parental


title: RBG28025_ME-Parental


title: RBG28142_IL3_Day11_ME-Parental


title: RBG28154_IL3_Day11_ME-Parental


title: RBG28013_ME-Parental


title: Reanalysis Brx73_1_SC1_032013


title: Reanalysis Brx61_1_SC4_032012

description:
GSM1253403
GSM2314645


title: Reanalysis Brx61_1_CL1_032012


title: RBG27990_ME-Parental


title: RBG27954_ME-Parental


title: RBG28001_ME-Parental


title: Reanalysis Brx72_1_SC4_031813


title: Reanalysis Brx61_1_CL5_032012

description:
GSM1253401
GSM2314644


title: RBG27989_ME-Parental


title: RBG28214_IL3_Day11_ME-Parental


title: RBG27953_ME-Parental


title: RBG28225_IL3_Day11_ME-Parental


title: Reanalysis Brx61_1_CL3_032012


title: Reanalysis Brx61_1_CL6_032012


title: Reanalysis Brx61_1_SC1_032012

description:
GSM1253387
GSM2314655


title: RBG28213_IL3_Day11_ME-Parental


title: RBG28201_IL3_Day11_ME-Parental


title: Reanalysis Brx61_1_CL4_032012

description:
GSM1253400
GSM2314651


title: RBG28177_IL3_Day11_ME-Parental


title: Reanalysis Brx71_SC2_031413


title: RBG28165_IL3_Day11_ME-Parental


title: Reanalysis Brx61_1_SC2_032012

description:
GSM1253402
GSM2314657


title: RBG28036_ME-Parental


title: RBG28012_ME-Parental


title: RBG28024_ME-Parental


title: RBG27988_ME-Parental


title: RBG27977_ME-Parental


title: RBG27965_ME-Parental


title: Reanalysis Brx61_1_CL2_032012


title: Reanalysis Brx72_1_SC3_031813


title: RBG28000_ME-Parental


title: RBG28189_IL3_Day11_ME-Parental


title: RBG27976_ME-Parental


title: RBG27964_ME-Parental


title: RBG27952_ME-Parental


title: RBG28153_IL3_Day11_ME-Parental


title: RBG28212_IL3_Day11_ME-Parental


title: RBG28188_IL3_Day11_ME-Parental


title: RBG28224_IL3_Day11_ME-Parental


title: RBG28176_IL3_Day11_ME-Parental


title: RBG28152_IL3_Day11_ME-Parental


title: RBG28035_ME-Parental


title: Negative control mouse1 [CSU0030_NEG_M1]

type: RNA

city: Knoxville

first: Chunlei

last: Su

state: TN

address: 1311 Cumberland Avenue

department: Microbiology

institute: University of Tennessee

description: Gene expression data from mouse peritoneal cells

hyb_protocol: Five micrograms of fragmented cRNA was hybridized to the Affymetrix GeneChip. Arrays were processed using the Affymetrix Hyb/Stain kit PN900720.

scan_protocol: Arrays were scanned using the Affymetrix 7G scanner. The individual chip scans were quality checked for the presence of control genes and background signal values. All microarray procedures were done at the University of Tennessee Affymetrix Core Facility.

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis Console version 2.0.09. One-way between-subject ANOVA (unpaired). Default filter criteria: fold change >2 or <-2. ANOVA p-value <0.05 based on FDR analysis.

label: biotin

organism: Mus musculus domesticus

source_name: Cells from mouse peritoneal cavity

label_protocol: RNA samples were processed according to the Affymetrix protocol for one-cycle DNA synthesis using a Message Amp II-Biotin Enhanced Kit (P/N AM1791; Ambion, Austin, TX).

growth_protocol: 500 T. gondii parasites (tachyzoites) used to infect CD-1 outbred mice.

extract_protocol: Total RNA from peritoneal cells was extracted using Qiagen RNeasy Plus Mini Kit (catalog #74131; Qiagen,Valencia, CA) following the manufacturer’s instructions. The quality of RNA was tested by agarose gel electrophoresis, and the concentration of RNA was determined by reading the absorbance at 260/280 nm. Low quality RNA samples were not used for expression microarray.

treatment_protocol: Three different T. gondii strains with different virulence levels were used to infection CD-1 outbred mice. Four mice were euthanized on day 1, 2, 3, 4, 5 and 7 post infection. To collect peritoneal cells, 5 ml of ice-cold phosphate-buffered saline (PBS) was injected into the peritoneal cavity, and then peritoneal lavage was collected. The cells were collected by centrifugation at 1,000×g for 10 min at 4 °C, resuspended in 1 ml of RNAlater solution (Ambion, Austin, TX), incubated in 4°C for 1 h, and then stored at -70°C before RNA extraction.

tag: tissue

value: Cells from mouse peritoneal cavity

tag: agent

tag: age


title: RBG28140_IL3_Day11_ME-Parental


title: CTG infected mouse on day 5 [CSU014_CTG_PL_D5]

value: non-virulent T. gondii

value: Post infection


title: Negative control mouse2 [CSU049_Neg2]


title: CTG infected mouse on day 7 [CSU056_CTG_M1_D7]


title: Negative control mouse3 [CSU065_Neg_M2_D7]


title: CTG infected mouse on day 5 [CSU006_CTG_M1_D5]


title: RBG28023_ME-Parental


title: CTG infected mouse on day 7 [CSU058_CTG_M4_D7]


title: RBG27999_ME-Parental


title: CTG infected mouse on day 4 [CSU047_CTG_M1_D4]


title: RBG27987_ME-Parental


title: Negative control mouse4 [CSU066_Neg_M3_D7]


title: CTG infected mouse on day 7 [CSU057_CTG_M3_D7]


title: CTG infected mouse on day 5 [CSU010_CTG_M3_D5]


title: CTG infected mouse on day 3 [CSU0032_CTG_D3_M4]


title: CTG infected mouse on day 4 [CSU048_CTG_M2_D4]


title: RBG27951_ME-Parental


title: RBG28223_IL3_Day11_ME-Parental


title: RBG27963_ME-Parental


title: RBG28211_IL3_Day11_ME-Parental


title: CTG infected mouse on day 2 [CSU046_CTG_M2_D2]


title: RBG28199_IL3_Day11_ME-Parental


title: CTG infected mouse on day 3 [CSU0025_CTG_M1_D3]


title: RBG28187_IL3_Day11_ME-Parental


title: PTG infected mouse on day 7 [CSU063_PTG_M3_D7]

value: Intermediate virulent T. gondii


title: CTG infected mouse on day 2 [CSU045_CTG_M4_D2]


title: PTG infected mouse on day 5 [CSU012_PTG_2PL_D5]


title: RBG28175_IL3_Day11_ME-Parental


title: CTG infected mouse on day 1 [CSU0031_CTG_D1_M4]


title: PTG infected mouse on day 5 [CSU011_PTG_PL_D5]


title: PTG infected mouse on day 7 [CSU062_PTG_M2_D7]


title: CTG infected mouse on day 1 [CSU0024_CTG_M2_D1]


title: PTG infected mouse on day 4 [CSU044_PTG_M2_D4]


title: PTG infected mouse on day 4 [CSU043_PTG_M1_D4]


title: RBG28163_IL3_Day11_ME-Parental


title: RBG27975_ME-Parental


title: PTG infected mouse on day 1 [CSU0026_PTG_M1_D1]


title: PTG infected mouse on day 3 [CSU0034_PTG_D3_M4]


title: RBG28139_IL3_Day11_ME-Parental


title: PTG infected mouse on day 2 [CSU042_PTG_M2_D2]


title: RBG28010_ME-Parental


title: RBG27998_ME-Parental


title: PTG infected mouse on day 1 [CSU0033_PTG_D1_M4]


title: PTG infected mouse on day 2 [CSU041_PTG_M1_D2]


title: RBG27974_ME-Parental


title: PTG infected mouse on day 3 [CSU0027_PTG_M2_D3]


title: RBG27950_ME-Parental


title: RBG18224_Flt3L_Day7_ME-Parental


title: GT1 infected mouse on day 7 [CSU061_GT1_M4_D7]

value: virulent T. gondii genotype


title: RBG18248_Flt3L_Day7_ME-Parental


title: RBG18236_Flt3L_Day7_ME-Parental


title: RBG18212_Flt3L_Day7_ME-Parental


title: RBG28151_IL3_Day11_ME-Parental


title: RBG18200_Flt3L_Day7_ME-Parental


title: RBG18344_IL3_Day7_MLL-ENL2


title: GT1 infected mouse on day 5 [CSU007_GT_M2_D5]


title: RBG27962_ME-Parental


title: RBG18188_Flt3L_Day7_ME-Parental


title: GT1 infected mouse on day 7 [CSU060_GT1_M3_D7]


title: GT1 infected mouse on day 7 [CSU059_GT1_M1_D7]


title: GT1 infected mouse on day 5 [CSU005_GT_M1_D5]


title: RBG18176_Flt3L_Day7_ME-Parental


title: RBG28011_ME-Parental


title: GT1 infected mouse on day 4 [CSU039_GT1_M1_D4]


title: GT1 infected mouse on day 2 [CSU038_GT1_M2_D2]


title: GT1 infected mouse on day 4 [CSU040_GT1_M2_D4]


title: GT1 infected mouse on day 3 [CSU0036_GT1_D3_M4]


title: GT1 infected mouse on day 5 [CSU009_GT1_M3_D5]


title: GT1 infected mouse on day 1 [CSU0035_GT1_D1_M4]


title: GT1 infected mouse on day 3 [CSU0029_GT1_M2_D3]


title: RBG18320_IL3_Day7_MLL-ENL2


title: dsRNAIP_EndoUmut_3

city: MAYWOOD

first: Susan

last: Baker

state: IL

address: 2160 S. 1st Ave, Bldg 115 Rm 270B Baker

department: Microbiology & Immunology

institute: Loyola University Chicago

description: dsRNAip_mock_v_endoumut, dsRNAIP_wt_v_endoumut, dsRNAIP_viral_reads

data_processing:
Differential gene expression perfomed using Galaxy, usegalaxy.org
Reads aligned to GRCm38 Ensembl build of C57bl/6J genome using HISAT2 v2.1.0
Mapped reads were quantified with Featurecounts v1.6.3
Differential Gene expression calculated with DESeq2 v2.11.40.2
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel Spreadsheets, contains either differential gene expression analyses or normalized read counts of individual genes for each triplicate at indicated timepoints

source_name: C57Bl/6 BMDMs

growth_protocol: BMDMs were plated in DMEM with 20% FBS, then infected and incubated at 37C, 5% CO2 for indicated time

extract_protocol:
Total RNA was collected using Rneasy columns from Qiagen
Libraries were constructed according to Illumina Total RNA sequencing library prep with Ribozero subtraction

treatment_protocol: BMDMs were infected with WT or mutant MHV-A59 for 1 hr, then infectious media was removed and fresh media added for remainder of incubation

tag: virus

value: EndoUmut

tag: hours post infection


title: GT1 infected mouse on day 5 [CSU013_GT1_PL_D5]


title: RBG18296_IL3_Day7_MLL-ENL2


title: dsRNAIP_WT_3

description: dsRNAip_mock_v_wt, dsRNAIP_wt_v_endoumut, dsRNAIP_viral_reads


title: dsRNAIP_EndoUmut_1


title: dsRNAIP_WT_2


title: GT1 infected mouse on day 1 [CSU0028_GT1_M1_D1]


title: RBG18284_IL3_Day7_MLL-ENL1


title: dsRNAIP_WT_1


title: RBG18332_IL3_Day7_MLL-ENL2


title: RBG18272_IL3_Day7_MLL-ENL1


title: GT1 infected mouse on day 2 [CSU037_GT1_M1_D2]


title: dsRNAIP_Mock_3

description: dsRNAip_mock_v_wt, dsRNAIP_mock_v_endoumut, dsRNAIP_viral_reads


title: dsRNAIP_Mock_2


title: RBG18260_IL3_Day7_MLL-ENL1


title: RBG18247_Flt3L_Day7_ME-Parental


title: Input_EndoUmut_3

description: Input_viral_reads, Input_mock_v_endoumut, Input_wt_v_endoumut, Input_normalizedcounts


title: dsRNAIP_Mock_1


title: dsRNAIP_EndoUmut_2


title: RBG18235_Flt3L_Day7_ME-Parental


title: RBG18199_Flt3L_Day7_ME-Parental


title: RBG18223_Flt3L_Day7_ME-Parental


title: RBG18187_Flt3L_Day7_ME-Parental


title: Input_EndoUmut_2


title: Input_EndoUmut_1


title: Input_WT_3

description: Input_viral_reads, Input_mock_v_wt, Input_wt_v_endoumut, Input_normalizedcounts


title: RBG18211_Flt3L_Day7_ME-Parental


title: RBG18163_Flt3L_Day7_ME-Parental


title: Input_Mock_3

description: Input_viral_reads, Input_mock_v_wt, Input_mock_v_endoumut, Input_normalizedcounts


title: Input_WT_1


title: RBG18175_Flt3L_Day7_ME-Parental


title: RBG18331_IL3_Day7_MLL-ENL1


title: RBG18343_IL3_Day7_MLL-ENL2


title: RBG18319_IL3_Day7_MLL-ENL2


title: Input_Mock_1


title: Input_WT_2


title: Input_Mock_2


title: EndoUmut_12hpi_3

description: 12hpi_normalized_counts, 12hpi_DUBmut_v_EndoUmut, 12hpi_mock_v_EndoUmut, 12hpi_WT_v_EndoUmut

data_processing:
Differential gene expression perfomed using Galaxy, usegalaxy.org
Reads aligned to GRCm38 Ensembl build of C57bl/6J genome using HISAT2 v2.1.0
Mapped reads were quantified with Featurecounts v1.6.3
Differential Gene expression calculated with DESeq2 v2.11.40.2
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel Spreadsheets, contains normalized read counts of individual genes for each triplicate at indicated timepoints

molecule: polyA RNA

extract_protocol:
Total RNA was collected using Rneasy columns from Qiagen
Libraries were constructed according to Illumina Poly-A sequencing library prep


title: RBG18307_IL3_Day7_MLL-ENL2


title: EndoUmut_12hpi_2


title: RBG18295_IL3_Day7_MLL-ENL2


title: EndoUmut_12hpi_1


title: RBG18283_IL3_Day7_MLL-ENL1


title: RBG18271_IL3_Day7_MLL-ENL1


title: DUBmut_12hpi_2

description: 12hpi_normalized_counts, 12hpi_mock_v_DUBmut, 12hpi_WT_v_DUBmut, 12hpi_DUBmut_v_EndoUmut

value: DUBmut


title: RBG18259_IL3_Day7_MLL-ENL1


title: DUBmut_12hpi_3


title: RBG18234_Flt3L_Day7_ME-Parental


title: DUBmut_12hpi_1


title: RBG18246_Flt3L_Day7_ME-Parental


title: WT_12hpi_3

description: 12hpi_normalized_counts, 12hpi_mock_v_WT, 12hpi_WT_v_EndoUmut, 12hpi_WT_v_DUBmut


title: RBG18210_Flt3L_Day7_ME-Parental


title: RBG18222_Flt3L_Day7_ME-Parental


title: RBG18198_Flt3L_Day7_ME-Parental


title: EndoUmut_9hpi_3


title: WT_12hpi_1


title: WT_12hpi_2


title: DUBmut_9hpi_3


title: RBG18162_Flt3L_Day7_ME-Parental


title: DUBmut_9hpi_1


title: RBG18308_IL3_Day7_MLL-ENL1


title: EndoUmut_9hpi_1


title: RBG18186_Flt3L_Day7_ME-Parental


title: RBG18318_IL3_Day7_MLL-ENL1


title: WT_9hpi_2


title: RBG18294_IL3_Day7_MLL-ENL2


title: WT_9hpi_3


title: WT_9hpi_1


title: RBG18282_IL3_Day7_MLL-ENL2


title: DUBmut_9hpi_2


title: RBG18270_IL3_Day7_MLL-ENL2


title: EndoUmut_6hpi_3


title: RBG18258_IL3_Day7_MLL-ENL1


title: RBG18245_Flt3L_Day7_ME-Parental


title: DUBmut_6hpi_3


title: EndoUmut_6hpi_1


title: EndoUmut_9hpi_2


title: RBG18221_Flt3L_Day7_ME-Parental


title: RBG18209_Flt3L_Day7_ME-Parental


title: DUBmut_6hpi_1


title: RBG18233_Flt3L_Day7_ME-Parental


title: RBG18330_IL3_Day7_MLL-ENL2


title: WT_6hpi_2


title: RBG18197_Flt3L_Day7_ME-Parental


title: RBG18185_Flt3L_Day7_ME-Parental


title: WT_6hpi_1


title: RBG18306_IL3_Day7_MLL-ENL2


title: EndoUmut_3hpi_3


title: RBG18161_Flt3L_Day7_ME-Parental


title: RBG18341_IL3_Day7_MLL-ENL1


title: EndoUmut_6hpi_2


title: EndoUmut_3hpi_1


title: DUBmut_3hpi_3


title: EndoUmut_3hpi_2


title: RBG18317_IL3_Day7_MLL-ENL2


title: RBG18329_IL3_Day7_MLL-ENL2


title: RBG18174_Flt3L_Day7_ME-Parental


title: DUBmut_3hpi_2


title: DUBmut_6hpi_2


title: RBG18293_IL3_Day7_MLL-ENL2


title: RBG18257_IL3_Day7_MLL-ENL1


title: DUBmut_3hpi_1


title: WT_3hpi_2


title: Mock_3

description: 3hpi_normalized_counts, 6hpi_normalized_counts, 9hpi_normalized_counts, 12hpi_normalized_counts, 12hpi_mock_v_EndoUmut, 12hpi_mock_v_WT, 12hpi_mock_v_DUBmut


title: RBG18269_IL3_Day7_MLL-ENL2


title: RBG18244_Flt3L_Day7_ME-Parental


title: WT_3hpi_3


title: RBG18220_Flt3L_Day7_ME-Parental


title: Mock_1


title: WT_3hpi_1


title: RBG18208_Flt3L_Day7_ME-Parental


title: WT_6hpi_3


title: RBG18173_Flt3L_Day7_ME-Parental


title: RBG18196_Flt3L_Day7_ME-Parental


title: RBG18232_Flt3L_Day7_ME-Parental


title: RBG18340_IL3_Day7_MLL-ENL1


title: RBG18160_Flt3L_Day7_ME-Parental


title: RBG18184_Flt3L_Day7_ME-Parental


title: RBG18316_IL3_Day7_MLL-ENL1


title: RBG18304_IL3_Day7_MLL-ENL1


title: RBG18172_Flt3L_Day7_ME-Parental


title: RBG18292_IL3_Day7_MLL-ENL2


title: Mock_2


title: RBG18280_IL3_Day7_MLL-ENL2


title: RBG18243_Flt3L_Day7_ME-Parental


title: Patient_3_H_Tm

city: Toronto

first: Igor

last: Jurisica

state: Ontario

address: 60 Leonard Avenue

department: Krembil Research Institute

country: Canada

institute: University Health Network

hyb_protocol: As described in Reis et al. 2011 [PMID: 21549012]

scan_protocol: According to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)

data_processing: Raw data extracted from the RCC files were assembled into matrix

source_name: Tumour

label_protocol: Using 400 ng total RNA, gene transcrpts levels were assayed using Nanostring nCounter assay kits by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA).

extract_protocol: RNA from FFPE samples was isolated using the RecoverAll Total Nucleic Acid Isolation kit (Ambion/Life Technologies, Carlsbad, CA, USA), following our previously reported protocol with modifications to improve RNA yield [PMID: 23835716]. RNA was stored at -80ºC until RNA extraction

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: Tongue SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

value: bilat ND, excision FOM

tag: rtx

value: N

tag: qtx

tag: recurrence status

value: no recurrence

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_3_E_Tm

tag: batch

tag: patient id

tag: gender

tag: treatment


title: Patient_3_K_Nr

source_name: Normal

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Posterior left margin


title: Patient_3_G_Nr

value: Anterior right margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx


title: RBG18256_IL3_Day7_MLL-ENL1

tag: day

tag: condition

value: ME-Parental


title: Patient_3_E_Nr

value: Anterior to Posterior margin

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_3_G_Tm

tag: batch

tag: patient id

tag: gender

tag: treatment

tag: last follow-up

tag: date of death


title: RBG18231_Flt3L_Day7_ME-Parental


title: Patient_3_J_Nr

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Left margin

tag: tumor size at maximum dimension

tag: Stage


title: RBG18219_Flt3L_Day7_ME-Parental

tag: day

tag: condition


title: Patient_39_H_Tm

value: F

value: never

tag: grade

value: left partial glossectomy

tag: rtx

tag: qtx

tag: recurrence status

value: local recurrence and possible neck & lung mets

tag: date of diagnosis

tag: date of 1st recurrence


title: RBG18207_Flt3L_Day7_ME-Parental

tag: treatment

tag: batch


title: Patient_39_H_Nr

tag: patient id

tag: gender

value: Posterior margin

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_39_I_Nr

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Left tongue margin

tag: tumor size at maximum dimension

tag: Stage


title: Patient_39_J_Nr

tag: grade

tag: rtx

tag: qtx

tag: recurrence status


title: Patient_39_G_Tm

tag: batch

tag: treatment

tag: date of diagnosis

tag: date of 1st recurrence


title: Patient_39_F_Tm

tag: patient id

tag: gender

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_39_E_Tm

tag: age at diagnosis

tag: smoker

tag: last follow-up

tag: date of death


title: Patient_38_O_Tm

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

value: bilat ND, composite resection tongue & FOM, free forearm flap


title: RBG18159_Flt3L_Day7_ME-Parental

tag: day

tag: condition


title: RBG18183_Flt3L_Day7_ME-Parental

tag: treatment

tag: batch


title: RBG18171_Flt3L_Day7_ME-Parental


title: Patient_39_E_Nr

value: Anterior margin

tag: grade

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: RBG18315_IL3_Day7_MLL-ENL2


title: RBG18327_IL3_Day7_MLL-ENL1


title: Patient_3_F_Tm

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: current

value: Y

value: Tongue SCC

value: moderate

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_38_N_Tm

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

value: N

value: no recurrence

tag: last follow-up

tag: date of death


title: RBG18195_Flt3L_Day7_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition

value: ME-Parental


title: RBG18267_IL3_Day7_MLL-ENL1


title: RBG18279_IL3_Day7_MLL-ENL1


title: RBG18291_IL3_Day7_MLL-ENL1


title: RBG18303_IL3_Day7_MLL-ENL2


title: RBG18230_Flt3L_Day7_Parental

value: Parental


title: RBG18158_Flt3L_Day7_Parental


title: Patient_38_K_Nr

value: F

tag: grade

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: RBG18182_Flt3L_Day7_Parental


title: Patient_38_L_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

value: Deep margin

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_38_K_Tm

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: last follow-up

tag: date of death


title: Patient_38_L_Tm

tag: batch

tag: grade

tag: treatment

tag: rtx


title: Patient_38_M_Tm

value: Lateral and deep margins

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: Patient_38_J_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker


title: Patient_38_O_Nr

tag: drinker

tag: pathology report

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_38_I_Nr

value: Medial margin

tag: tumor size at maximum dimension

tag: Stage

tag: last follow-up

tag: date of death


title: Patient_38_G_Tm

tag: batch

tag: grade

tag: treatment

tag: rtx


title: RBG18326_IL3_Day7_Parental

tag: day

tag: condition


title: Patient_38_F_Tm

tag: patient id

tag: gender

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: RBG18314_IL3_Day7_Parental


title: Patient_38_F_Nr

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_37_2F_Tm

tag: batch

value: former

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: left ND, hemiglossectomy, free forearm flap

value: local recurrence

tag: last follow-up

tag: date of death


title: Patient_38_N_Nr

tag: patient id

tag: gender

tag: treatment

value: bilat ND, composite resection tongue & FOM, free forearm flap

tag: rtx


title: RBG18255_IL3_Day7_MLL-ENL2

tag: day

tag: condition


title: RBG18290_IL3_Day7_Parental


title: Patient_37_2E_Tm

tag: age at diagnosis

tag: smoker

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: Patient_37_2C_Nr

tag: batch

tag: drinker

tag: pathology report

value: Superior medial margin

tag: tumor size at maximum dimension

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RBG18266_IL3_Day7_Parental


title: RBG18278_IL3_Day7_Parental


title: RBG18194_Flt3L_Day7_Parental


title: Patient_37_2A_Nr

tag: patient id

tag: gender

value: Anterior margin

tag: Stage

tag: grade

tag: last follow-up

tag: date of death


title: RBG18181_Flt3L_Day7_Parental

tag: treatment

tag: day

tag: condition


title: RBG18193_Flt3L_Day7_Parental


title: RBG18254_IL3_Day7_Parental


title: Patient_36_1E_Nr

value: M

tag: age at diagnosis

tag: smoker

value: current

value: Remaining normal tissue

value: partial glossectomy

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis


title: RBG18157_Flt3L_Day7_Parental

tag: batch


title: Patient_36_1A_Nr

tag: drinker

value: N

tag: pathology report

tag: tumor size at maximum dimension

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_35_2H_Tm

tag: patient id

tag: gender

value: never

value: Retromolar SCC

tag: Stage

tag: grade

value: moderate

value: right ND, marginal mandibulectomy, resection buccal ca, free forearm flap

tag: last follow-up

tag: date of death


title: Patient_36_1C_Tm

tag: age at diagnosis

tag: smoker

value: Tongue SCC and tongue base SCC

tag: treatment

tag: rtx


title: RBG18338_IL3_Day7_Parental

tag: day

tag: batch

tag: condition

value: Parental


title: RBG18325_IL3_Day7_Parental


title: Patient_36_1C_Nr

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: qtx

tag: recurrence status

tag: date of diagnosis


title: RBG18302_IL3_Day7_Parental


title: Patient_35_2G_Nr

tag: patient id

tag: gender

value: F

value: Posterior margin

tag: Stage

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RBG18277_IL3_Day7_Parental

tag: treatment


title: Patient_37_2F_Nr

tag: age at diagnosis

tag: smoker

value: former

value: Y

value: Normal

tag: grade

value: left ND, hemiglossectomy, free forearm flap

tag: rtx

value: local recurrence

tag: last follow-up

tag: date of death


title: RBG18313_IL3_Day7_Parental

tag: day

tag: batch

tag: condition


title: RBG18301_IL3_Day7_Parental


title: Patient_35_2H_Nr

tag: drinker

tag: pathology report

value: Posterior inferior margin

tag: tumor size at maximum dimension

tag: qtx

tag: recurrence status

tag: date of diagnosis


title: RBG18265_IL3_Day7_Parental


title: Patient_35_2F_Tm

tag: patient id

tag: gender

tag: Stage

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_35_2E_Nr

tag: age at diagnosis

tag: smoker

value: Anterior margin

tag: grade

tag: treatment

tag: rtx

tag: last follow-up


title: RBG18253_IL3_Day7_Parental

tag: day

tag: batch

tag: condition


title: RBG18241_Flt3L_Day7_Parental


title: RBG18216_Flt3L_Day7_Parental


title: RBG18204_Flt3L_Day7_Parental


title: RBG18180_Flt3L_Day7_Parental


title: Patient_35_2D_Tm

tag: drinker

value: N

tag: pathology report

tag: tumor size at maximum dimension

tag: qtx

tag: recurrence status

tag: date of death


title: RBG18336_IL3_Day7_Parental


title: Patient_35_2D_Nr

tag: patient id

tag: gender

value: Antero-inferior margin

tag: Stage

value: no recurrence

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: RBG18156_Flt3L_Day7_Parental

tag: treatment


title: Patient_35_2C_Tm

tag: age at diagnosis

tag: smoker

value: never

value: Retromolar SCC

tag: grade

tag: rtx

tag: date of 3rd recurrence

tag: last follow-up


title: RBG18324_IL3_Day7_Parental

tag: day

tag: batch

tag: condition


title: RBG18312_IL3_Day7_Parental


title: Patient_34_6E_Nr

tag: drinker

tag: pathology report

value: Anterior medial margin

tag: tumor size at maximum dimension

value: well

value: right ND, mandibulectomy with composite resection, free fibula flap

tag: qtx

tag: recurrence status

tag: date of death


title: Patient_34_6E_Tm

tag: patient id

tag: gender

value: F

value: Mandibular gingiva SCC

tag: Stage

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: Patient_35_2F_Nr

tag: age at diagnosis

tag: smoker

value: Superior margin

tag: grade

value: moderate

tag: treatment

value: right ND, marginal mandibulectomy, resection buccal ca, free forearm flap

tag: rtx

tag: date of 3rd recurrence


title: Patient_34_6C_Tm

tag: batch

value: former

tag: drinker

tag: pathology report

value: Y

tag: last follow-up


title: Patient_34_6D_Nr

value: Posterior lateral margin

tag: tumor size at maximum dimension

tag: qtx

tag: recurrence status

tag: date of death


title: Patient_34_6B_Nr

tag: patient id

tag: gender

value: Posterior mucosal and soft tissue margin

tag: Stage

tag: date of diagnosis


title: RBG18288_IL3_Day7_Parental

tag: day

tag: condition

value: Parental


title: RBG18191_Flt3L_Day7_Parental

tag: treatment


title: RBG18276_IL3_Day7_Parental


title: Patient_34_6A_Nr

tag: age at diagnosis

tag: smoker

value: N

value: Anterior mucosal and soft tissue margin

tag: grade

tag: rtx

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: RBG18335_IL3_Day7_Parental

tag: batch


title: Patient_33_5J_Nr

value: M

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

value: bilat ND, mandibulotomy with glossectomy, free forearm flap

tag: qtx

value: local & regional recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_33_5K_Nr

tag: patient id

tag: gender

tag: Stage

tag: recurrence status

tag: date of diagnosis

tag: date of death


title: RBG18192_Flt3L_Day7_Parental

tag: treatment

tag: day

tag: condition


title: RBG18323_IL3_Day7_Parental


title: Patient_34_6F_Nr

tag: age at diagnosis

tag: smoker

value: Posterior medial margin

tag: grade

value: well

tag: rtx

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: Patient_33_5I_Tm

tag: batch

tag: drinker

tag: pathology report

value: Tongue SCC

tag: tumor size at maximum dimension

tag: qtx

tag: date of 3rd recurrence


title: RBG18311_IL3_Day7_Parental


title: Patient_33_5I_Nr

tag: patient id

tag: gender

value: Superior margin

tag: Stage

tag: recurrence status

tag: date of diagnosis

tag: last follow-up


title: Patient_33_5H_Nr

tag: age at diagnosis

tag: smoker

value: Anterior lateral margin

value: moderate

tag: treatment

tag: date of death


title: Patient_33_5G_Tm

value: former

tag: grade

tag: rtx

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: RBG18300_IL3_Day7_Parental

tag: day

tag: batch

tag: condition


title: RBG18275_IL3_Day7_Parental


title: RBG18263_IL3_Day7_Parental


title: RBG18154_Flt3L_Day7_Parental


title: RBG18251_IL3_Day7_Parental


title: Patient_33_5E_Nr

tag: patient id

tag: drinker

value: Y

tag: pathology report

value: Lateral posterior margin

tag: tumor size at maximum dimension

tag: qtx

tag: date of 3rd recurrence


title: Patient_33_5K_Tm

tag: gender

tag: age at diagnosis

tag: Stage

tag: recurrence status

tag: date of diagnosis

tag: last follow-up


title: RBG18310_IL3_Day7_Parental

tag: treatment


title: Patient_32_2E_Tm

tag: smoker

value: current

value: Mandible and FOM SCC

tag: grade

value: bilat ND, mandibulectomy with composite resection FOM & mandible; free fibula flap

tag: rtx

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Patient_33_5C_Nr

tag: batch

tag: patient id

tag: drinker

tag: pathology report

value: Anterior margin

value: N


title: Patient_33_5C_Tm

tag: gender

value: M

tag: tumor size at maximum dimension

value: bilat ND, mandibulotomy with glossectomy, free forearm flap

tag: qtx

tag: date of 3rd recurrence


title: Patient_33_5J_Tm

tag: age at diagnosis

tag: Stage

tag: recurrence status

value: local & regional recurrence

tag: date of diagnosis


title: RBG18298_IL3_Day7_Parental

tag: treatment

tag: day

tag: condition

value: Parental


title: Patient_33_5D_Nr

tag: smoker

value: Posterior margin

tag: grade

tag: rtx

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: RBG18274_IL3_Day7_Parental

tag: batch


title: RBG18286_IL3_Day7_Parental


title: RBG18287_IL3_Day7_Parental


title: Patient_32_2D_Tm

tag: patient id

tag: gender

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

value: no recurrence

tag: date of death


title: RBG18250_IL3_Day7_Parental


title: Patient_32_2D_Nr

tag: age at diagnosis

value: Posterior FOM margin

tag: Stage

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 3rd recurrence


title: RBG18297_IL3_Day7_Parental

tag: treatment

tag: day

tag: condition


title: Patient_31_3H_Tm

tag: smoker

value: Tongue SCC

tag: grade

value: bilat ND, glossectomy, advancement flap

tag: rtx

value: local recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_32_2C_Tm

tag: batch

tag: patient id

tag: gender

tag: drinker

value: Y

tag: pathology report

tag: tumor size at maximum dimension

value: moderate


title: RBG18178_Flt3L_Day7_Parental


title: RBG18322_IL3_Day7_Parental


title: Patient_32_2I_Tm

tag: age at diagnosis

value: current

tag: Stage

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of death


title: Patient_31_3G_Tm

tag: smoker

tag: grade

tag: treatment

tag: date of 3rd recurrence


title: RBG18261_IL3_Day7_Parental

tag: day

tag: condition


title: BRx142-RPL15-overexpression-2

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters.
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu.
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had fewer than 100,000 uniquely aligned reads were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: rnaSeqBRx142_readCounts.xlsx contains the counts as determined by the last data processing step above.

source_name: circulating tumor cell - derived cell line

growth_protocol: CTCs were grown in suspension in ultra-low attachment plates (Corning) in tumor sphere media, consisting of RPMI-1640 with GlutaMAX supplemented with EGF (20ng/mL), FGF (20ng/mL), 1X B27, and 1X antibiotic/antimycotic (Life Technologies), in 4% O2, as previously described (PUBMED IDs  27556950 and 25013076). CTC lines were routinely checked for mycoplasma (MycoAlert, Lonza), and were authenticated by RNA-seq and DNA-seq.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
The SMART-Seq HT Kit (Takara Bio USA) was used according to the manufacturer’s instructions.

treatment_protocol: Control or a CMV promoter-driven, lentiviral encoded vector to ectopically express RPL15. Lentiviral expression constructs for RPL15 (Accession: BC071672) were obtained from the CCSB-Broad Lentiviral Expression Library.

tag: tissue

tag: rpl15 overexpressing

value: RPL15 overexpressing


title: RBG18249_IL3_Day7_Parental

tag: batch


title: BRx142-RPL15-overexpression-1

value: circulating tumor cell - derived cell line

value: control


title: BRx142-pLX304-2


title: Patient_31_3G_Nr

tag: patient id

tag: gender

tag: drinker

tag: pathology report

value: Deep margin

tag: rtx

value: N

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_31_3F_Tm

value: M

tag: age at diagnosis

tag: smoker

tag: tumor size at maximum dimension

tag: Stage

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of death


title: BRx142-pLX304-1

tag: tissue

tag: rpl15 overexpressing


title: Patient_31_3F_Nr

tag: batch

tag: patient id

tag: gender

tag: grade

tag: treatment

tag: date of 3rd recurrence


title: Patient_31_3D_Nr

tag: drinker

tag: pathology report

tag: rtx

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_31_3C_Tm

tag: age at diagnosis

tag: smoker

tag: tumor size at maximum dimension

tag: Stage

tag: qtx

tag: recurrence status


title: RBG18140_GM-CSF_Day7_ME-Parental

value: GM-CSF

tag: day

tag: batch

tag: condition

value: ME-Parental


title: RBG18152_GM-CSF_Day7_ME-Parental

tag: treatment


title: Patient_31_3D_Tm

tag: patient id

tag: gender

tag: grade

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RPL15_overexpressing_BRx142_batch2

data_processing:
Library strategy: ribo-Seq
Trim_galore was used to remove adapters and low-quality base-calls with quality set to 20, stringency set to 3, and length set to 25.
Bowtie2 was used to attempt to align the resulting reads to the hg19_rmsk rRNA FASTA file from the UCSC table browser. Reads that aligned were discarded.
The remaining reads were aligned to the hg19 refGene transcriptome from UCSC with additions for ERCC92 and RGC spike-ins using tophat with the no-novel-juncs option set.
Only uniquely aligned reads were kept and then duplicates were removed using samtools rmdup.
Read counts for all the genes were then created using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: riboSeq_readCounts.xlsx contains the counts as determined by the last data processing step above.

extract_protocol:
Ribosome profiling was performed as previously described (PUBMED ID 22836135). Briefly, 10 million RPL15- or control-expressing Brx-142 cells were treated with 0.1 mg/ml cyclohexamide for 1 minute, washed with cold PBS containing cycloheximide and lysed. A range of RNase I (Thermofisher) concentrations was tested, and an optimal concentration was chosen that did not lead to degradation of the ribosome protected fragments. RNase I (Thermofisher) treatment was performed and the monosomes were isolated by gel filtration MicroSpin S-400 HR Columns (GE Healthcare). After RNA extraction using RNA Clean & Concentrator-25 kit (Zymo Research), rRNA was depleted (Ribo-Zero Gold rRNA Removal Kit, Illumina), and ribosome-protected fragments were purified by PAGE. The fragments were end- repaired with PNK (NEB).
Libraries were prepared using a TruSeq small RNA Library Prep Kit (Illumina) and sequenced on a NextSeq 500 Illumina (76 bp single-end reads).

tag: tissue

tag: rpl15 overexpressing

tag: molecule subtype

value: ribosome-bound mRNA


title: Patient_31_3B_Tm

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: rtx

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_31_3H_Nr

tag: batch

tag: patient id

tag: gender

tag: Stage

tag: treatment

tag: qtx

tag: recurrence status


title: Patient_31_3C_Nr

value: Left margin

tag: grade

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RBG18128_GM-CSF_Day7_ME-Parental

tag: day

tag: condition


title: RBG18116_GM-CSF_Day7_ME-Parental


title: RBG18285_IL3_Day7_Parental

value: Parental


title: Patient_30_1E_Tm

value: F

tag: age at diagnosis

tag: smoker

value: never

tag: drinker

tag: pathology report

value: Maxila SCC

tag: tumor size at maximum dimension

value: right partial maxillectomy

tag: rtx


title: RPL15_overexpressing_BRx142_batch1

tag: tissue

tag: rpl15 overexpressing

tag: batch

tag: molecule subtype


title: Patient_30_1D_Tm

tag: patient id

tag: gender

tag: Stage

value: moderate

tag: treatment

tag: qtx

tag: recurrence status

value: local recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_30_1D_Nr

tag: age at diagnosis

tag: smoker

tag: drinker

value: Medial margin

tag: grade

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RBG18104_GM-CSF_Day7_ME-Parental

tag: day

tag: batch

tag: condition


title: Patient_30_1E_Nr

tag: patient id

tag: gender

tag: pathology report

value: section through the tumor with the margin in block 1E

tag: tumor size at maximum dimension

tag: Stage

tag: rtx


title: control_BRx142_batch2

tag: tissue

value: circulating tumor cell - derived cell line

tag: rpl15 overexpressing

value: control

tag: molecule subtype


title: Patient_30_1C_Tm

tag: age at diagnosis

tag: smoker

tag: drinker

value: N

tag: treatment

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: control_BRx142_batch1

tag: batch


title: RBG18092_GM-CSF_Day7_ME-Parental

tag: day

tag: condition


title: RBG18080_GM-CSF_Day7_ME-Parental


title: Patient_31_3B_Nr

tag: patient id

tag: gender

value: M

value: current

value: Y

tag: pathology report

value: Right margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: bilat ND, glossectomy, advancement flap

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RBG18068_GM-CSF_Day7_ME-Parental

tag: treatment

value: GM-CSF

value: ME-Parental


title: Patient_2_Y_Tm

tag: age at diagnosis

tag: smoker

value: former

tag: drinker

value: Retromolar SCC

value: rigth ND, marginal mandibulectomy, resection or oral ca

tag: rtx

tag: qtx

tag: recurrence status

value: local & regional recurrence


title: Patient_30_1B_Nr

tag: batch

value: F

value: never

value: Lateral margin

value: moderate

value: right partial maxillectomy

value: local recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: vehicle-treated B cells from mouse M3

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

data_processing:
Base calling and demultiplexing was performed with bcl2fastq v2.18.0.12.
Residual adapter sequences present in sequencing reads were removed with Cutadapt version 1.12.
Reads were aligned to the mouse reference sequence GENCODE M8 using STAR version 2.5.2b using the --quantMode parameter setting to output read couts per gene.
Genome_build: GENCODE M8
Supplementary_files_format_and_content: Count tables were assembled from STAR --quantMode output in R (v3.3.1); scores represent raw read counts per gene.

source_name: B cells from mouse M3

growth_protocol: Female B6 mice were housed according to the German Law on the Protection of Animals; mice were fed with standard rodent diet and had free access to pathogen-free water.

extract_protocol:
B cells were isolated following the protocol of the B Cell Isolation Kit, mouse (Miltenyi Biotec) and RNA thereof was extrated with the Rneasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared with the TruSeq stranded mRNA kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Mice received a daily oral dose of 1 mg/kg body weight FTY720 (Sigma-Aldrich) diluted in 20 µl of 25 % ethanol in Aqua dest.. Control mice were MP4-immunized and treated with vehicle solution only.

tag: mouse

value: vehicle

tag: strain


title: FTY720-treated B cells from mouse M3


title: Patient_30_1A_Nr

tag: patient id

tag: gender

value: N

tag: pathology report

value: Posterior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade


title: vehicle-treated B cells from mouse M2

source_name: B cells from mouse M2

tag: treatment


title: RBG18056_ME-Parental

value: Untreated

tag: day

tag: condition


title: Patient_2_Y_Nr

value: M

tag: age at diagnosis

tag: smoker

tag: drinker

value: Y

value: Anterior gingival margin

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: Patient_2_X_Tm

tag: batch

tag: patient id

value: former

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_2_X_Nr

tag: gender

tag: pathology report

value: Medial alveolar mucosa

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment


title: Patient_2_W_Tm

tag: age at diagnosis

tag: smoker

tag: drinker

value: Retromolar SCC

value: rigth ND, marginal mandibulectomy, resection or oral ca

tag: rtx


title: Patient_2_W_Nr

value: Lateral anterior margin

tag: qtx

value: local & regional recurrence

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: FTY720-treated B cells from mouse M2

tag: mouse

tag: strain


title: Patient_2_V_Tm

tag: batch

tag: patient id

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_30_1C_Nr

tag: gender

value: F

value: never

tag: pathology report

value: Anterior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment


title: FTY720-treated B cells from mouse M1

source_name: B cells from mouse M1


title: RBG18020_ME-Parental

tag: day

tag: condition

value: ME-Parental


title: Patient_2_V_Nr

tag: age at diagnosis

tag: smoker

tag: drinker

value: Medial margin

value: moderate

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RBG18032_ME-Parental

tag: batch


title: Patient_2_U_Tm

tag: patient id

tag: gender

value: N

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_2_U_Nr

tag: pathology report

value: Lateral margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment


title: Patient_2_T_Tm

value: M

tag: age at diagnosis

tag: smoker

tag: drinker

tag: rtx


title: Patient_2_S_Tm

value: Y

tag: qtx

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: Patient_2_T_Nr

tag: batch

tag: patient id

tag: gender

value: Posterior retromolar trigone margin

tag: recurrence status


title: RBG18008_ME-Parental

value: Untreated

tag: day

tag: condition


title: RBG17996_ME-Parental


title: RBG17984_ME-Parental


title: RBG18044_ME-Parental


title: Patient_2_S_Nr

value: former

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_29_1C_Tm

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Tongue SCC

tag: grade

value: well

tag: treatment

value: left ND, transoral resection tongue

tag: rtx

value: no recurrence


title: Patient_29_1E_Tm

tag: batch

tag: patient id

tag: qtx

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: Patient_29_1B_Nr

tag: gender

tag: pathology report

value: Posterior margin

tag: tumor size at maximum dimension

tag: recurrence status


title: Patient_29_1A_Nr

value: Anterior margin

tag: Stage

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_29_1D_Nr

tag: age at diagnosis

tag: smoker

tag: drinker

tag: grade


title: Patient_28_1D_Nr

tag: batch

tag: patient id

value: never

value: Medial lateral margin from anterior to posterior

tag: treatment

value: partial maxillectomy, free forearm flap

tag: rtx


title: Patient_28_1E_Nr

value: N

tag: qtx

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RBG18127_GM-CSF_Day7_ME-Parental

value: GM-CSF

tag: day

tag: condition

value: ME-Parental


title: Patient_28_1B_Tm

tag: gender

value: M

value: Y

tag: pathology report

value: Maxillary alveolus SCC

tag: tumor size at maximum dimension

tag: Stage

tag: recurrence status

tag: date of 1st recurrence


title: vehicle-treated B cells from mouse M1

tag: mouse

value: vehicle

tag: strain


title: RBG18151_GM-CSF_Day7_ME-Parental

tag: batch


title: Patient_27_4A_Nr

tag: patient id

value: F

tag: age at diagnosis

tag: smoker

tag: drinker

value: Posterior commisure margin QS

tag: grade

tag: treatment

value: left ND, resection buccal ca, free forearm flap

value: local recurrence

tag: date of 2nd recurrence

tag: last follow-up


title: Patient_27_1J_Tm

tag: gender

value: Buccal SCC

value: well

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of 3rd recurrence

tag: date of death


title: RBG18079_GM-CSF_Day7_ME-Parental

tag: day

tag: condition


title: Patient_27_3A_Nr

tag: batch

tag: pathology report

value: Superior anterior commisure margin QS

tag: tumor size at maximum dimension

tag: Stage

tag: recurrence status

tag: date of 1st recurrence


title: RBG18115_GM-CSF_Day7_ME-Parental

tag: treatment


title: RBG18103_GM-CSF_Day7_ME-Parental


title: Patient_27_5A_Nr

tag: patient id

tag: age at diagnosis

tag: smoker

value: never

tag: drinker

value: tongue margin QS

tag: grade

tag: date of 2nd recurrence


title: RBG18091_GM-CSF_Day7_ME-Parental


title: Patient_28_1A_Nr

tag: gender

value: Medial lateral margin from anterior to posterior

value: partial maxillectomy, free forearm flap

tag: rtx

tag: qtx

value: no recurrence

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_27_1I_Nr

tag: batch

value: N

tag: pathology report

value: Superior margin

tag: tumor size at maximum dimension

tag: date of death


title: RBG18067_GM-CSF_Day7_ME-Parental

tag: treatment

value: GM-CSF

tag: day

tag: condition

value: ME-Parental


title: Patient_27_1H_Nr

tag: patient id

tag: age at diagnosis

tag: smoker

value: Posterior margin

tag: Stage

tag: recurrence status

tag: date of 1st recurrence


title: Patient_27_1H_Nr_1

tag: gender

value: F

tag: drinker

tag: grade

tag: rtx

tag: qtx

tag: date of 2nd recurrence


title: Patient_27_1G_Tm

tag: batch

tag: pathology report

tag: tumor size at maximum dimension

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Mouse 3b Thy

city: Palo Alto

first: Pablo

last: Domizi

state: CA

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

description: -JUN.2 Thy

hyb_protocol: Carried out through the PAN (Protein and Nucleic Acid Facility) Stanford

source_name: Bones (femur, tibia, fibula, humerus, ulna, radius, calotte, scapula, vertebrae, ribs)

label_protocol: No specific labeling was used instread of labeling the submitted tubes.

growth_protocol: JUN inducible mice were kept on a regular diet.

extract_protocol: FACS purified cells were sorted into trizol (ThermoFisher Scientific). For RNA extraction, we added chloroform and centrifuged the tubes. We transferred the upper phase to a new tube and added 70 % EtOH. Afterwards, the complete volume was added to the columns of the RNEasy MiniElute Cleanup Kit (Qiagen). Between the next three centrifugation steps, we washed the columns with 80% EtOH (+H2O), 80% EtOH (+RPE) and 70%EtOH. After letting the membranes slightly dry, we added water onto the membranes, centrifuged the columns and measured the RNA quantity and quality of the flow through with a NanoDrop 2000 (ThermoFisher Scientific).

treatment_protocol: JUN in pubs were induced through administration of doxycycline to the mum's drinking water

tag: tissue

tag: osteoprogenitor

value: Thy


title: Mouse 3b CSP

description: -JUN.2 CSP

scan_protocol: Carried out through the PAN (Protein and Nucleic Acid Facility) Stanford

value: Bones (femur, tibia, fibula, humerus, ulna, radius, calotte, scapula, vertebrae, ribs)

value: CSP


title: Mouse 4 Thy

description: JUN.1 Thy


title: Mouse 4 CSP

description: JUN.1 CSP


title: Mouse 4 SSC

description: JUN.1 SSC

value: SSC


title: Patient_27_1F_Tm

tag: patient id

tag: age at diagnosis

tag: smoker

value: Buccal SCC

tag: Stage

value: well

tag: treatment

value: left ND, resection buccal ca, free forearm flap

value: local recurrence

tag: date of death


title: Mouse 7 CSP

description: JUN.2 CSP


title: Mouse 3 CSP

description: -JUN.1 CSP


title: RBG18043_ME-Parental

value: Untreated

tag: day

tag: condition


title: RBG18055_ME-Parental


title: Patient_27_1E_Tm

tag: gender

value: never

tag: drinker

tag: grade

tag: rtx

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: Mouse 7 Thy

description: JUN.2 Thy

tag: tissue

tag: osteoprogenitor


title: Patient_27_1D_Nr

tag: batch

tag: patient id

tag: age at diagnosis

tag: pathology report

value: Anterior margin

tag: tumor size at maximum dimension

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Fibroblast-like early clone 2

city: Ramat-Gan

first: Tomer

last: Kalsiky

state: Israel

address: Ramat-Gan

country: Israel

institute: Bar-Ilan University

data_processing:
TopHat
DESeq
HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: Table 1 is an assembling of all *.count files generated by HTseq

source_name: Fibroblast-like early clone

growth_protocol: Collected tissues were washed with cold HBSS (Invitrogen) and minced into ~1 mm cubes using sterile surgical scalpels. The dissected tissue was then incubated for two hours in 37°C with Iscoves' Mod Dulbecco's Medium (IMDM) (Invitrogen) supplemented with 0.1% collagenase IV (Invitrogen). The digested tissue was then gradually forced through 100 µm, 70 µm and 50 µm cell strainers to achieve a single cell suspension. After the digesting medium was removed, the cells were resuspended in a growth medium and plated in flasks. Serum-free medium (SFM) was comprised of N2 medium (Biological Industries) supplemented with 1% Pen-strep 100M, 1% L-glutamine, 0.4% B27 supplement (Gibco), 4µg/ml heparin sodium (Intramed), 1% non-essential amino acids, 1% sodium pyruvate, 0.2% CD Lipid concentrate (all from Invitrogen), 2.4mg/ml glucose, 0.4mg/ml transferrin, 10mg/ml insulin, 38.66µg/ml putrescine, 0.04% sodium selentine, 12.6µg/ml progesterone (all from Sigma-Aldrich), 10ng/ml FGF and 20ng/ml EGF. For passaging, cells were detached using non-enzymatic cell dissociation solution (Sigma-Aldrich).

extract_protocol:
Zymo Research's RNA Isolation kit (the Direct-zol™-96 RNA) - purification of RNA directly from samples in TRIZOL.
Illumina TruSeq RNA

value: adult kidney

tag: source

value: colony

tag: passage

value: early

tag: morphology

value: Fibroblast-like

tag: clone number


title: RBG18031_ME-Parental

tag: treatment

tag: day

tag: condition

value: ME-Parental


title: Fibroblast-like early clone 3

tag: tissue


title: Fibroblast-like early clone 1


title: Patient_27_1C_Tm

tag: gender

value: F

tag: smoker

tag: drinker

value: N

tag: Stage

tag: grade

tag: rtx

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Mouse 10, 9-29-17

value: Bones (femur, tibia, fibula, humerus, ulna, radius, calotte, scapula, vertebrae, ribs)

tag: osteoprogenitor


title: Patient_27_1B_Tm

tag: batch

tag: patient id

tag: age at diagnosis

tag: pathology report

tag: tumor size at maximum dimension

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Mouse 7, 9-29-17

tag: tissue


title: Patient_27_1B_Nr

tag: gender

tag: smoker

tag: drinker

value: Anterior SCC

tag: Stage

tag: grade

tag: treatment


title: Patient_26_5I_Tm

value: former

value: Tongue SCC

value: rigth ND, manibulotomy with resection oral cavity ca; free forearm flap

tag: rtx

tag: qtx

tag: recurrence status

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Mouse 3, 9-29-17

description: -JUN.1 SSC

tag: osteoprogenitor

value: SSC


title: RBG18019_ME-Parental

value: Untreated

tag: day

tag: batch

tag: condition


title: Mouse 3 Thy

description: -JUN.1 Thy

tag: tissue

value: Thy


title: RBG18139_GM-CSF_Day7_ME-Parental

value: GM-CSF


title: RBG18007_ME-Parental


title: Epithelial-like early clone 5

source_name: Epithelial-like early clone

value: adult kidney

tag: source

tag: passage

tag: morphology

value: Epithelial-like

tag: clone number


title: Epithelial-like early clone 6

value: colony

value: early


title: Patient_27_1C_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

value: never

tag: drinker

tag: pathology report

value: Anterior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: well

value: left ND, resection buccal ca, free forearm flap

value: local recurrence

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: RBG17995_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition

value: ME-Parental


title: Epithelial-like early clone 4

tag: tissue

tag: source

tag: passage

tag: morphology

tag: clone number


title: RBG17983_ME-Parental


title: Patient_26_5F_Nr

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: former

tag: drinker

value: N

value: Lateral margin

tag: rtx

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Patient_26_5F_Tm

tag: batch

tag: pathology report

value: Tongue SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

value: rigth ND, manibulotomy with resection oral cavity ca; free forearm flap

value: no recurrence

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_26_5G_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker


title: Patient_26_5H_Nr

tag: drinker

value: FOM mucosa

tag: rtx

tag: qtx

tag: recurrence status


title: Patient_26_5C_Nr

tag: batch

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Epithelial-like early clone 3

tag: tissue

value: adult kidney

tag: source

tag: passage

tag: morphology

value: Epithelial-like

tag: clone number


title: Epithelial-like late clone 3

source_name: Epithelial-like late clone

value: colony

value: late


title: RBG18150_GM-CSF_Day7_ME-Parental

tag: treatment

value: GM-CSF

tag: day

tag: condition


title: Patient_26_5B_Nr_1

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: pathology report

value: Medial margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: well

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: RBG18138_GM-CSF_Day7_ME-Parental

tag: batch


title: Epithelial-like late clone 2

tag: tissue

tag: source

tag: passage

tag: morphology


title: Patient_25_1H_Tm

value: M

value: current

tag: drinker

value: Y

value: FOM SCC

value: poor

tag: treatment

value: right ND, mandibulectomy with resection oral cavity & oropharynx ca, free scapula flap

tag: rtx

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Patient_25_1G_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: pathology report

value: Buccal mucosal lateral margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: N


title: Epithelial-like early clone 2

tag: tissue

tag: source

tag: passage

value: early

tag: morphology

tag: clone number


title: Patient_25_1E_Nr

tag: batch

tag: drinker

value: Medial FOM mucosal margin

tag: treatment

tag: rtx

tag: qtx

tag: recurrence status

value: no recurrence

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_25_1E_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: pathology report

tag: tumor size at maximum dimension

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Patient_25_1D_Nr

tag: batch

tag: drinker

value: Anterior margin

tag: Stage

tag: grade


title: RBG18126_GM-CSF_Day7_ME-Parental

tag: treatment

tag: day

tag: condition

value: ME-Parental


title: Patient_24_4A_Nr

value: QS resubmitted left superior alveolar margin

value: moderate

value: bilat ND, mandibulotomy, partial glossectomy, free thigh flap

tag: rtx

tag: qtx

tag: recurrence status

value: local recurrence

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: RBG18114_GM-CSF_Day7_ME-Parental

value: GM-CSF


title: Epithelial-like late clone 1

tag: tissue

value: adult kidney

tag: source

value: colony

tag: passage

value: late

tag: morphology

value: Epithelial-like

tag: clone number


title: Patient_25_1C_Tm

tag: batch

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: FOM SCC

tag: tumor size at maximum dimension

value: poor

value: right ND, mandibulectomy with resection oral cavity & oropharynx ca, free scapula flap

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of death


title: Patient_24_2U_Tm

value: Mandibular + Tongue SCC

tag: Stage

tag: grade

tag: treatment

tag: rtx

value: N

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_24_2W_Nr

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

value: Anterior to posterior margins


title: RBG17971_ME-Parental

value: Untreated

tag: day

tag: condition

value: ME-Parental


title: Patient_26_5B_Nr

value: F

tag: smoker

value: former

tag: drinker

tag: pathology report

value: Medial margin

tag: tumor size at maximum dimension

value: well

value: rigth ND, manibulotomy with resection oral cavity ca; free forearm flap

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: RBG18102_GM-CSF_Day7_ME-Parental

tag: treatment

value: GM-CSF


title: Patient_24_2U_Nr

value: M

value: current

tag: Stage

tag: grade

value: moderate

value: bilat ND, mandibulotomy, partial glossectomy, free thigh flap

tag: rtx

tag: qtx

tag: recurrence status

value: local recurrence

tag: date of death


title: Epithelial-like early clone 1

tag: tissue

value: adult kidney

tag: source

value: colony

tag: passage

value: early

tag: morphology

value: Epithelial-like

tag: clone number


title: Patient_24_2T_Tm

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

value: Y

value: Mandibular + Tongue SCC

value: N

tag: date of diagnosis

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_24_2R_Tm

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: rtx

tag: qtx

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: early bulk human adult kidney

source_name: early bulk human adult kidney

tag: tissue

tag: source

value: bulk

tag: passage

tag: morphology

tag: clone number


title: Patient_24_2Q_Nr

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

value: Anterior to posterior margins

tag: recurrence status

tag: date of diagnosis

tag: date of death


title: RBG18090_GM-CSF_Day7_ME-Parental

tag: treatment

tag: day

tag: condition

value: ME-Parental


title: Patient_24_2Q_Tm

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

tag: qtx

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: RBG18078_GM-CSF_Day7_ME-Parental

tag: batch


title: Patient_24_2P_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: recurrence status


title: BRx-82-3--01-20-15

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had fewer than 100,000 reads were discarded. Samples for which PTPRC expression was greater than 10 reads-per-million were deemed possible white blood cells and were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows).

source_name: candidate CTC

extract_protocol:
Single CTCs were isolated from fresh whole blood following leukocyte depletion using the microfluidic CTC-iChip as described in PMID 23552373. Single cells were individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer, and flash frozen in liquid nitrogen.
Clontech SMARTer Ultra Low Input Kit for RNA v3 for cDNA synthesis and the Nextera XT kit for library construction

tag: patient

tag: clinical hormone receptor

value: HR+

tag: clinical her2

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: BRx-82-4--01-20-15


title: Patient_24_2N_Tm

value: M

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of death


title: Patient_24_2N_Nr

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

value: current

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_24_2M_Tm

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

value: moderate

tag: recurrence status


title: RBG18042_ME-Parental

source_name: Hoxb8 Cell line

tag: treatment

value: Untreated

tag: day

tag: condition


title: late bulk human adult kidney

source_name: late bulk human adult kidney

tag: tissue

tag: source

tag: passage

value: late

tag: morphology

tag: clone number


title: Patient_24_2B_Tm

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: Stage

tag: grade

value: bilat ND, mandibulotomy, partial glossectomy, free thigh flap

tag: rtx

tag: qtx

value: local recurrence

tag: date of diagnosis

tag: date of death


title: BRx-47-2--08-14-15

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression

value: fail


title: RBG18030_ME-Parental

tag: treatment

tag: day

tag: condition


title: BRx-47-1--08-14-15


title: Patient_24_2B_Nr

tag: batch

tag: patient id

tag: gender

tag: drinker

tag: pathology report

value: Lateral margin

tag: tumor size at maximum dimension

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_24_2M_Nr

tag: age at diagnosis

tag: smoker

value: Y

tag: Stage

tag: grade

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of death


title: RBG18018_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition


title: BRx-278-8--01-21-16

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: Patient_24_2A_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker

tag: pathology report

value: Inferior margin

tag: tumor size at maximum dimension

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: RBG18006_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition


title: RBG18066_GM-CSF_Day7_ME-Parental

value: GM-CSF


title: Patient_23_4B_Nr

tag: smoker

value: Anterior medial margin

tag: Stage

tag: grade

value: bilat ND, mandibulectomy, composite resection, free fibula flap

tag: rtx

tag: qtx

value: N

tag: date of diagnosis

tag: date of death


title: RBG17994_ME-Parental

value: ME-Parental


title: BRx-278-6--01-21-16

tag: patient

tag: clinical hormone receptor

value: HR+

tag: clinical her2

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: BRx-278-7--01-21-16


title: Patient_23_2G_Nr

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: drinker

tag: pathology report

value: Midi-lateral FOM margin

tag: tumor size at maximum dimension

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: Patient_23_2J_Nr

tag: batch

tag: smoker

value: Mid transverse section

tag: Stage

tag: grade

tag: treatment

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of death


title: Patient_23_2G_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker

value: FOM + Tongue SCC


title: RBG17982_ME-Parental

value: Untreated

tag: day

tag: condition


title: Patient_23_2F_Tm

tag: pathology report

tag: tumor size at maximum dimension

tag: recurrence status

value: local recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_23_2K_Tm

tag: batch

tag: smoker

tag: Stage

tag: grade

tag: treatment

tag: last follow-up


title: RBG18149_GM-CSF_Day7_ME-Parental


title: RBG18137_GM-CSF_Day7_ME-Parental


title: Patient_23_2D_Nr

tag: patient id

tag: gender

tag: rtx

tag: qtx

tag: date of diagnosis

tag: date of death


title: Patient_23_2D_Tm

tag: age at diagnosis

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension


title: BRx-278-4--01-21-16

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression

value: fail


title: Patient_22_6J_Nr

tag: batch

tag: smoker

value: current

value: Superior margin

tag: Stage

tag: grade

value: moderate

tag: treatment

value: right ND, mandibulotomy with resection of tongue, free forearm flap

tag: recurrence status

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: BRx-278-3--01-21-16


title: Patient_22_6I_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker

value: Y

value: Anterior margin

tag: rtx

tag: qtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: Patient_23_4A_Nr

tag: batch

tag: smoker

tag: pathology report

value: Anterior medial margin

tag: tumor size at maximum dimension

value: bilat ND, mandibulectomy, composite resection, free fibula flap

value: N


title: RBG18125_GM-CSF_Day7_ME-Parental

tag: treatment

value: GM-CSF

tag: day

tag: condition

value: ME-Parental


title: BRx-278-2--01-21-16

tag: patient

tag: clinical hormone receptor

value: HR+

tag: clinical her2

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: Patient_22_6F_Tm

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: drinker

value: Tongue SCC

tag: Stage

tag: grade

tag: rtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_22_6E_Tm

tag: batch

tag: smoker

tag: pathology report

tag: tumor size at maximum dimension

tag: treatment

tag: qtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: Patient_22_6D_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker


title: BRx-278-1--01-21-16

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: RBG18101_GM-CSF_Day7_ME-Parental

tag: day

tag: batch

tag: condition


title: BRx-267-2--12-30-15


title: BRx-278-5--01-21-16

value: fail


title: Patient_21_5L_Tm

tag: smoker

value: current

tag: pathology report

value: Buccal mucosa SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

value: left ND, resection oral ca, free forearm flap

tag: rtx

tag: recurrence status

value: local & regional recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_21_5J_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker

value: Buccal mucosa SCC close to deep margin

value: moderate

tag: qtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: Patient_23_2F_Nr

tag: batch

tag: smoker

tag: pathology report

value: Posterior FOM margin

tag: tumor size at maximum dimension

value: Y

value: local recurrence


title: RBG17970_ME-Parental

tag: treatment

value: Untreated

tag: day

tag: condition


title: Patient_21_5J_Nr

value: N

value: Inferior margin

tag: Stage

tag: grade

tag: rtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: Patient_21_5I_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker

tag: qtx

tag: date of 3rd recurrence


title: BRx-267-1--12-30-15

tag: patient

tag: clinical hormone receptor

value: HR+

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: RBG18077_GM-CSF_Day7_ME-Parental

tag: treatment

value: GM-CSF

tag: day

tag: batch

tag: condition

value: ME-Parental


title: Patient_21_5I_Nr

value: M

tag: smoker

tag: pathology report

value: Superior posterior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: last follow-up

tag: date of death


title: RBG18065_GM-CSF_Day7_ME-Parental


title: BRx-267-1--12-15-15

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

value: pass

value: fail


title: RBG18053_ME-Parental

tag: treatment

tag: day

tag: batch


title: Patient_21_5G_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

tag: pathology report

value: Buccal mucosa SCC

value: left ND, resection oral ca, free forearm flap

tag: qtx

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Reanalysis Brx-245-2--09-04-15

value: HR-

tag: ptprc expression


title: Patient_21_5F_Tm

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

tag: rtx

tag: recurrence status

value: local & regional recurrence

tag: date of diagnosis

tag: date of 1st recurrence

tag: last follow-up

tag: date of death


title: RBG18089_GM-CSF_Day7_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition


title: Patient_21_5K_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: qtx


title: BRx-245-1--09-04-15

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: Patient_21_5B_Tm

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_20_2G_Tm

tag: batch

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: never

tag: drinker

tag: pathology report

value: Tumor

tag: treatment

value: bilat ND, mandibulotomy with resection FOM & inner mandible, parotidectomy, free forearm flap

value: Y

tag: qtx

value: probable recurrence


title: Patient_21_5A_Tm

value: N

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx


title: Patient_20_2G_Nr

value: Superior Posterior maxillary margin

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence


title: Patient_28_1B_Nr

tag: batch

value: M

value: Medial lateral margin from anterior to posterior

value: well

value: partial maxillectomy, free forearm flap

value: no recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RBG18041_ME-Parental

value: Untreated

tag: day

tag: condition

value: ME-Parental


title: RBG18029_ME-Parental


title: BRx-267-2--12-15-15

tag: patient

tag: clinical hormone receptor

value: HR+

tag: clinical her2

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: Patient_28_1C_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Maxillary alveolus SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: qtx


title: BRx-239-2--09-17-15

value: fail


title: RBG18017_ME-Parental

tag: day

tag: batch

tag: condition


title: Patient_20_2D_Tm

value: F

value: never

value: Buccal alveolar SCC

value: moderate

tag: rtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_20_2E_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

value: N

tag: pathology report

value: bilat ND, mandibulotomy with resection FOM & inner mandible, parotidectomy, free forearm flap

value: Y

value: probable recurrence


title: Patient_20_2D_Nr

value: Mid inferior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: qtx


title: Patient_20_2B_Tm

tag: batch

value: Anterior margin

tag: rtx

tag: recurrence status

tag: date of diagnosis


title: RBG18005_ME-Parental

tag: day

tag: condition


title: Patient_20_2C_Nr

tag: patient id

value: Inferior anterior mandibular mucosal margin

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RBG17993_ME-Parental

value: Untreated


title: BRx-233-3--09-16-15

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: Patient_1_V_Tm

tag: batch

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Tongue + FOM SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

value: bilta ND, mandibulotomy with resection of tongue & FOM, free forearm flap

tag: qtx

value: no recurrence


title: Patient_1_V_Nr

tag: patient id

value: Posterior medial margin

tag: rtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_1_U_Nr

tag: batch

tag: gender

tag: age at diagnosis

tag: smoker

value: Posterior lateral margin


title: RBG17981_ME-Parental

tag: day

tag: condition

value: ME-Parental


title: RBG17969_ME-Parental

tag: treatment


title: BRx-233-1--10-13-15

tag: patient

tag: clinical hormone receptor

value: HR+

tag: clinical her2

tag: number uniquely mapped reads

value: fail

tag: ptprc expression

value: pass


title: BRx-233-2--09-16-15


title: Patient_1_T_Nr

tag: patient id

value: F

value: never

tag: drinker

tag: pathology report

value: Normal margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

tag: rtx

tag: qtx

value: N

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: Patient_1_S_Nr

tag: batch

tag: gender

tag: age at diagnosis

tag: smoker

value: Y

value: Anterior margin

tag: treatment

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RBG18148_GM-CSF_Day7_ME-Parental

value: GM-CSF

tag: day

tag: condition


title: BRx-239-1--09-17-15

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: RBG18136_GM-CSF_Day7_ME-Parental


title: Patient_1_R_Nr

tag: patient id

tag: drinker

tag: pathology report

value: Anterior lateral margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence