title: Post, R [S71]

city: Aurora

first: Sana

middle: D

last: Karam

state: CO

address: 1665 Aurora Ct.

department: Radiation Oncology

institute: CU Denver Anschutz

data_processing:
Reads were aligned and counts were generated using the BioSpyder TempoSeqr Platform. Genes with less than 1 mean raw count or less than 1 mean counts per million (CPM) were removed from the dataset. Reads were normalized to CPM using the edgeR R package. Differential expression was calculated using the voom function in the limma R package. Gene set enrichment analysis was performed using the fgsea R package, with the full list of genes sorted by log2-transformed fold changes as the ranking metric.
Assembly: NOT PROVIDED
Supplementary files format and content: excel and normalized CPM

source_name: Tumor

extract_protocol:
Tumor tissue collected from patients at time of initial biopsy and at time of surgery were used for RNA sequencing. A pathologist reviewed H&E stains of the tumor samples, and areas of tumor cellularity were identified and marked. Only the pathologist-marked areas of tumor cellularity were scraped and processed per BioSpyder kit instructions.
For the human RNA sequencing library preparation, a TempO-Seq Human Full Transcriptome FFPE Assay 96 sample Kit was used (BioSpyder, Carlsbad, CA).

value: Tumor

tag: response

value: R

value: HNSCC

tag: timepoint

value: Post

tag: treatment

value: SBRT + Durvalumab


title: ALF007D

status: Public on Nov 02 2022

type: SRA

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

country: Australia

institute: CSL Limited

library_source: transcriptomic

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using star (v2.6.1)13 with default parameters except for the --quantMode TranscriptomeSAM setting.
Reads were summarized at the gene level using featureCounts tool from the Subread package (v1.6.4)14, in a strand-specific manner.

molecule: polyA RNA

organism: Homo sapiens

source_name: Lung,ILD.Base,Whole lung

extract_protocol:
RNA was extracted from whole lung tissue according to manufacturer’s protocol (Fibrous Tissue Mini kit, Qiagen #74704). RNA quality was verified with the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Samples with RNA integrity numbers (RIN) over 6 were used for RNA sequencing.
cDNA libraries were prepared for sequencing using standard strand specific TrueSeq kits with ribosomal RNA and Globin mRNA depletion. At least 20 million 100 bp single-end reads were generated per sample using Illumina HiSeq 3000 (Illumina, California, USA) using standard protocols at the Australian Genome Research Facility (AGRF, Melbourne, Australia).

tag: tissue

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: CTD-ILD

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: Liver patient 17

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned with STAR (v.2.7.8a) to the human genome assembly (GRCh38, Ensembl release 101)
FeatureCounts (v.2.0) was employed for exon read counting
Quality of raw sequencing was assessed using FastQC (v.0.11.9) and MultiQC (v. v1.10.1)
Genetic variants were removed from raw sequencing reads using BAMboozle (v.0.5.0)
Assembly: GRCh38, Ensembl release 101
Supplementary files format and content: txt files with gene-level counts

molecule: total RNA

source_name: Liver biopsy

extract_protocol:
Needle biopsies of liver tissue were homogenized using FastPrep-24™ and RNA purified using TRIzol-RNA lysis reagent according to the manufacturer’s instructions. Purified RNA was quantified using Qubit 3.0 Fluorometer and RNA quality was assessed using Fragment Analyzer 5200
NEBNext Ultra RNA Library Prep Kit for Illumina were used for construction of libraries according to the manufacture's protocol. RNA was paired-end sequenced using the NovaSeqTM 6000 platform

tag: tissue

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: No-NAFLD

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Liver patient 20

value: NAFL


title: ALF027B

source_name: Lung,IPF.Base,Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul


title: Liver patient 19

tag: tissue


title: Pre, R [S70]

country: USA

value: Tumor

tag: response

value: R

tag: cell type

value: HNSCC

tag: timepoint

value: Pre

tag: treatment

value: SBRT + Durvalumab


title: ALF033B

source_name: Lung,CLAD.Base,Whole lung

value: Whole lung

value: Base

value: Unclassified

value: Disease

value: CLAD

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: CPFE

tag: smokingstatus

tag: severity

value: Severe

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Pre, R [S29]


title: NC-m6A-MeRIP-seq-Input2

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

country: China

institute: Qilu Hospital

data_processing:
QC check
Read mapping (hisat2)
Peakcalling (exome peak)
RNA methylaytion diffenetial analysis
Assembly: hg38
Supplementary files format and content: bigWig

source_name: THP-2-NC, input

extract_protocol:
For m6A-seq, total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2 and incubated with anti-m6A polyclonal antibody (Sigma Aldrich) for 3 h at 4℃. Then mix the products above with protein A/G magnetic beads (Thermo Fisher) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The beads were then separated and washed with IP buffer three times. A NEBNext Ultra RNA library prep kit (NEB) was used to establish the library for the purified mRNA fragments. Each group was sequenced with an Illumina NovaSeq 6000 sequencer, and the single-end sequencing length was 150 bp. Reads were compared with human genome version GRCH38 through TopHat. If a gene had more than one subtype, the longest subtype was retained. ExomePeak (P < 0.01) was used to identify differential m6A-modified peaks between IP and input samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
m6A-Seq

treatment_protocol: THP-1 cells were transfected with METTL3 and its negative control lentivirus.The positively infected cells were selected with 1 μg/mL puromycin.

tag: cell line

value: AML

tag: genotype

value: control

tag: rip antibody


title: Cre-_mice3

city: Novato

first: Lisa

last: Ellerby

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
Sequenced reads were trimmed for adaptor sequence and bases with quality score lower than 20 using Trim Galore! 0.6.4 with parameters trim_galore --fastqc --length 25 --cores 4 --paired --retain_unpaired
The external and internal rRNA contamination were filtered through SortMeRNA 2.1b with parameters sortmerna --ref $sortmernaREF --reads $merge --aligned $aligned --other $filtered -m 5120 --fastx --paired_out --log -a 30 -v
The filtered raw reads were mapped to the Genome Reference Consortium Mouse Build 38 striosome release 6(GRCm38.p6) assembly by GENCODE using STAR 2.7.2b with parameters STAR --runThreadN 15 --genomeDir Mus_musculus.GRCh38.p6.genome/ --sjdbGTFfile gencode.vM22.annotation.gtf --readFilesIn $read1 $read2 --outSAMtype BAM SortedByCoordinate
The raw counts of reads mapped to known genes were summarized by featureCounts, using GENECODE release M22 annotation with parameters featureCounts -a gencode.vM22.annotation.gtf -o final_counts.txt -g 'gene_name' -T 4 $dirlist
Then R Bioconductor package DESeq2 were used to normalize raw read counts logarithmically and perform differential expression analysis.
Genome_build: mm10(GRCm38.p6)
Supplementary_files_format_and_content: Microsoft excel table files include raw counts and log transformed values for each sample.

organism: Mus musculus

source_name: Striatum

extract_protocol:
Dissected striatum at 4 months of age was analyzed The collected cells were subject to  RNA extraction.
TruSeq RNA Sample Prep Kit v2 protocol  (Illumina, San Diego, CA, USA). Briefly, ribosomal RNA was removed using the Ribo-Zero rRNA  Removal Kit (Human/Mouse/Rat) (Illumina), the remaining RNA fragmented and cDNA  synthesized with random hexamers, end-repaired and ligated with appropriate adaptors for  sequencing. After size selection and purification using AMPure XP beads (Beckman Coulter,  CA, USA), 6 bp barcode bases were introduced at one end of the adaptors. The size and  concentration of the RNA-Seq libraries was measured by Bioanalyzer and Qubit fluorometry  (Life Technologies, Grand Island, NY, USA), and the rRNA-depleted libraries sequenced on the  Illumina HiSeq 2500 System with 100 nucleotide paired-end reads.

tag: strain

tag: tissue

value: Striatum

tag: age

value: 4 month

tag: gender

value: Female

tag: cre status

value: Negative


title: ALF010A

source_name: Lung,NDC.Apex,Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

value: M

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Ex-Smoker

value: Unknown

value: Senior Adult (>=60)


title: Liver patient 16

value: Liver biopsy

tag: Sex

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NAFL

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: NC-m6A-MeRIP-seq-Input1

tag: cell line

tag: cell type

value: AML

tag: genotype

tag: rip antibody


title: Post, R [S25]

tag: tissue

value: Tumor

tag: response

value: R

value: HNSCC

tag: timepoint

value: Post

tag: treatment

value: SBRT + Durvalumab


title: Liver patient 18

value: Female


title: Liver patient 21

value: No-NAFLD


title: ALF023C

source_name: Lung,IPF.Apex,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Never

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Liver patient 15

tag: tissue

value: Liver biopsy

tag: Sex

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: ALF048A

source_name: Lung,CLAD.Apex,Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

tag: diseasenormal

tag: diseasegroup

value: CLAD

tag: gender

value: F

tag: diagnosis

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Ex-Smoker

value: Severe


title: Pre, NR [S22]

tag: tissue

value: Tumor

tag: response

value: NR

tag: cell type

value: HNSCC

tag: timepoint

value: Pre

tag: treatment


title: METTL3-RNA-seq-rep3

data_processing:
QC check
Read mapping (hisat2)
Peakcalling (exome peak)
RNA methylaytion diffenetial analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell lines

extract_protocol:
For RNA-seq, total RNA was isolated using TRIzol reagent and was extracted following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100. Qualified total RNA was further purified by RNAClean XP Kit. RNA-seq Library Prep Kit for Illumina® (Vazyme) was used to establish the library.Each group was sequenced with an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell lines

tag: cell line

value: AML

tag: genotype

value: WT

value: METTL3 overexpressing THP-1 cells


title: ALF044B

source_name: Lung,NDC.Base,Whole lung

value: Whole lung

tag: donorid

tag: group

value: Base

value: Right

value: Normal

value: NDC

tag: age

tag: lungweight mg

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Unknown

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: Pre, R [S21]

tag: tissue

tag: response

value: R

tag: cell type

value: SBRT + Durvalumab


title: Pre, R [S20]

value: Tumor

tag: timepoint

tag: treatment


title: NC-RNA-seq-rep3

tag: cell line

tag: genotype


title: Post, R [S19]

value: Post


title: NC-m6A-MeRIP-seq-IP3

source_name: THP-1-NC, IP

value: control

tag: rip antibody

value: anti-m6A polyclonal antibody


title: NC-m6A-MeRIP-seq-IP2


title: Liver patient 12

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NAFL

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: ALF046A

source_name: Lung,ILD.Apex,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: NSIP

tag: smokingstatus

tag: severity

value: Severe

tag: fvcprebd perc


title: Post, R [S17]

tag: tissue

tag: response

value: R

tag: cell type

value: HNSCC

tag: timepoint

tag: treatment

value: SBRT + Durvalumab


title: Post, NR [S23]

value: Tumor

value: NR

value: Post


title: NC-RNA-seq-rep2

value: cell lines

tag: cell line

value: AML

tag: genotype

value: WT


title: Pre, R [S24]

value: Pre


title: NC-m6A-MeRIP-seq-IP1

value: control

tag: rip antibody

value: anti-m6A polyclonal antibody


title: Liver patient 14

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NASH

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: ALF034A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Unknown

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: Liver patient 13

tag: tissue

tag: Sex

tag: tissue preservation

tag: steatosis, activity,_and_fibrosis_score

value: No-NAFLD

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Pre, NR [S13]

value: Tumor

tag: response

value: NR

tag: cell type

value: HNSCC

tag: timepoint

tag: treatment

value: SBRT + Durvalumab


title: METTL3-RNA-seq-rep1

value: cell lines

tag: cell line

value: AML

tag: genotype

value: WT

value: METTL3 overexpressing THP-1 cells


title: ALF031A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

value: HP

tag: smokingstatus

value: Never

tag: severity

value: Severe

tag: fvcprebd perc


title: ALF028C

tag: tissue

tag: donorid

value: Base

value: IPF

value: F

tag: diseasesubtype

value: Ex-Smoker

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: METTL3-RNA-seq-rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ALF035C

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

value: NSIP

value: Advanced

value: Senior Adult (>=60)


title: Post, R [S15]

tag: tissue

value: Tumor

tag: response

value: R

value: HNSCC

tag: timepoint

value: Post

value: SBRT + Durvalumab


title: ALF037A

value: Whole lung

tag: donorid

value: Disease

value: M

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: genomic DNA from aorta2

type: genomic

city: Beijing

first: Xiaohan Fan

address: 167 Beilishilu, Xicheng District

institute: Fuwai hospital

description:
aorta2_Grn.idat
aorta2_Red.idat
aortic dissection ascending aorta sample
SAMPLE 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infnium MethylationEPIC Array using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw intensity data were loaded to a biocondutor package “minfi”. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated).

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from normal and ascending aorta tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: male

value: ascending aorta tissue

tag: treatment

value: aortic dissection


title: Liver patient 11

value: Liver biopsy

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NAFL

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: genomic DNA from aorta7

description:
aorta7_Grn.idat
aorta7_Red.idat
normal ascending aorta sample
SAMPLE 7

tag: tissue

value: normal


title: genomic DNA from aorta8

description:
aorta8_Grn.idat
aorta8_Red.idat
normal ascending aorta sample
SAMPLE 8


title: genomic DNA from aorta6

description:
aorta6_Grn.idat
aorta6_Red.idat
normal ascending aorta sample
SAMPLE 6


title: ALF048D

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

value: CLAD

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

value: Ex-Smoker

value: Severe


title: Liver patient 10

tag: Sex

tag: tissue preservation

value: NASH


title: NC-RNA-seq-rep1

value: cell lines

tag: cell line

tag: cell type

value: AML

tag: genotype

value: WT

tag: treatment


title: Liver patient 9

tag: tissue

tag: steatosis, activity,_and_fibrosis_score

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: genomic DNA from aorta5

description:
aorta5_Grn.idat
aorta5_Red.idat
normal ascending aorta sample
SAMPLE 5

value: male

value: ascending aorta tissue


title: Liver patient 6

value: Liver biopsy


title: SKK-1 AZA treated 1

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Research

country: Spain

institute: Josep Carreras Leukaemia Research Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.9
Reads were trimmed keeping only the shRNA loop sequence using fastx_trimmer (-f 2, -l 22)
Reads were collapsed using fastx_collapser
Reads were aligned with the Epi9 reference
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files; aligned count data containing shRNA ID and gene symbol
Library strategy: Amplicon sequencing

source_name: peripheral blood

growth_protocol: Cells were maintained in RPMI 1640 (Gibco) supplemented with 10% of FBS, 1% penicillin-streptomycin and 1% L-Gutamine (Gibco) at 37ºC in 5% CO2.

extract_protocol:
gDNA was extracted from >8 x 10^6 cells using standard techniques
Libraries were prepared by PCR amplification of shRNA guide strands with custom primers (p7+loop, CAAGCAGAAGACGGCATACGATAGTGAAGCCACAGATGTA; p5+miR3’, AATGATACGGCGACCACCGACTAAAGTAGCCCCTTGAATTC) using AmpliTaq Gold polymerase (Thermofisher). PCR products were gel extracted (340bp band) and sequenced using a custom sequencing primer (miR30EcoRISeq, TAGCCCCTTGAATTCCGAGGCAGTAGGCA)

treatment_protocol: SKK-1 cells were transduced in triplicates with the Epi9 library containing 7296 shRNAs targeting 912 chromatin regulators. After puromycin treatment each replicate was split in two and one half treated with 0.075 µM AZA every two days. 21 days afterwards cells were harvested and gDNA extracted.

value: peripheral blood

value: SKK-1 cells

value: acute myeloid leukemia

tag: transduction

value: Epi9 shRNA

value: 21days azacitidine treatment


title: SKK-1 Untreated 3

value: untreated


title: Pre, NR [S11]

value: Tumor

tag: response

value: NR

value: HNSCC

tag: timepoint

value: Pre

value: SBRT + Durvalumab


title: ALF008A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Severe

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: SKK-1 AZA treated 3

tag: tissue

value: peripheral blood

tag: cell line

value: SKK-1 cells

tag: cell type

value: acute myeloid leukemia

tag: transduction

value: Epi9 shRNA

tag: treatment


title: Liver patient 8

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NASH

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Pre, R [S16]

value: Tumor

tag: response

value: R

value: HNSCC

tag: timepoint

value: Pre

value: SBRT + Durvalumab


title: SKK-1 AZA treated 2

value: 21days azacitidine treatment


title: Liver patient 7

value: NAFL


title: Post, NR [S12]

value: NR

value: Post


title: genomic DNA from aorta4

description:
aorta4_Grn.idat
aorta4_Red.idat
aortic dissection ascending aorta sample
SAMPLE 4

value: male

value: ascending aorta tissue

value: aortic dissection


title: genomic DNA from aorta3

description:
aorta3_Grn.idat
aorta3_Red.idat
aortic dissection ascending aorta sample
SAMPLE 3


title: SKK-1 Untreated 2

value: peripheral blood

value: SKK-1 cells

value: acute myeloid leukemia

value: Epi9 shRNA

value: untreated


title: ALF029D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Moderate

value: Senior Adult (>=60)


title: Liver patient 4

tag: tissue

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NAFL

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Liver patient 5


title: ALF019B

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

tag: gender

value: F

value: Never

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Pre, R [S9]

tag: tissue

value: Tumor

tag: response

value: R

tag: cell type

value: HNSCC

tag: timepoint

value: Pre

tag: treatment

value: SBRT + Durvalumab


title: Post, R [S10]

value: Post


title: SKK-1 Untreated 1

value: peripheral blood

tag: cell line

value: SKK-1 cells

value: acute myeloid leukemia

tag: transduction

value: Epi9 shRNA

value: untreated


title: ALF046B

value: Whole lung

tag: donorid

tag: group

value: Base

value: Disease

value: ILD

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: NSIP

tag: smokingstatus

value: Unknown

tag: severity

value: Severe


title: Liver patient 2

tag: tissue

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NASH

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Liver patient 3

value: NAFL


title: Post, NR [S8]

value: Tumor

tag: response

value: NR

tag: cell type

value: HNSCC

tag: timepoint

value: Post

tag: treatment

value: SBRT + Durvalumab


title: Pre, NR [S7]

value: Pre


title: ALF033A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Unclassified

tag: diseasenormal

tag: diseasegroup

value: CLAD

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

value: CPFE

value: Ex-Smoker

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: NB4 cells-PML/RARA

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

institute: SHANGH RUIJIN HOSPITAL

data_processing:
Library strategy: CUT&Tag
CUT&Tag-seq  reads were aligned to the human genome (hg38) by Bowtie2 (version 2.2.9) under the following parameters -D 15 -R 2 -N 0 -L 22 -i S,1,1.15, and uniquely mapped reads were retained for further analyses.
The sam files were converted to bam files and sorted with samtools.
High-confident binding sites were called by MACS (version 1.4.2) with a P-value cutoff of 1e-10. The tdf file was generated by igvtools under the following parameters -z 5 -w 25 -e 250. The bedgraph files were generated by macs with the -B command. The overlap of peaks from different ChIP–seq experiments was determined using the BEDTools2 suite
Genome_build: hg38

extract_protocol:
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library.
Libraries were prepared according to Illumina's instructions.

tag: cell line

tag: cut&tag antibody

value: PML/RARA

value: Treatment


title: Liver patient 1

tag: tissue

value: Liver biopsy

tag: Sex

value: Female

tag: tissue preservation

value: RNAlater

tag: steatosis, activity,_and_fibrosis_score

value: NASH

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: genomic DNA from aorta1

description:
aorta1_Grn.idat
aorta1_Red.idat
aortic dissection ascending aorta sample
SAMPLE 1

value: male

value: ascending aorta tissue

tag: treatment

value: aortic dissection


title: ALF039A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

tag: diagnosis

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Never

tag: severity

value: Severe


title: ALF007A

tag: tissue

value: Apex

value: ILD

value: F

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

value: CTD-ILD

value: Ex-Smoker

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: RNA_HCT116-pcDNA-R3_S54

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

data_processing:
RNA-seq reads were aligned to the GRCh38/hg38 build of the human genome using the Subread aligner (ver 2.0.0). Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts (ver 2.0.0). Reads overlapping exons in annotation build 38.2 of NCBI RefSeq database were included.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million) value of 0.5 or greater in at least three libraries. Read counts were converted to log2 CPM, quantile-normalised and precision weighted with the limma voom function. Log2 CPM values were then converted to log2 FPKM (fragments per kilobases per million) values. A linear model was fitted to each gene. Differentially expressed genes were assessed using the limma treat function, which tested against a 1.5 fold change of gene expression based on empirical Bayes moderated t-statistics. The differentially expressed genes were called with an FDR cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in each sample.

growth_protocol: Human cell lines were grown in DMEM-F12 with 10% FCS

extract_protocol:
Transfection protocol: Cell lines were trasfected with EHF expression plasmid and retrovirally transduced with CDX1 expression plasmid. Cells were selected with G418 for EHF and GFP positivity for CDX1.
RNA was extracted from cell lines using the High Pure RNA Isolation Kit (Roche)
RNA libraries were prepared by the Australian Genome Research Facility (AGRF)

tag: cell type

value: Human colorectal cancer

value: Colon

tag: cell line

tag: infection


title: NB4 cells-IgG (ppara)

tag: cut&tag antibody

value: IgG

tag: treatment

value: Control


title: Pre, NR [S5]

value: Tumor

tag: response

value: NR

value: HNSCC

tag: timepoint

value: Pre

value: SBRT + Durvalumab


title: RNA_HCT116-pcDNA-R2_S53


title: ALF022B

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: HP

tag: smokingstatus

value: Never


title: NB4 cells-PPARa

tag: cell line

tag: cut&tag antibody

value: PPARα

value: Treatment


title: ALF042D

tag: tissue

value: ILD

value: F

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

value: IPF

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: HPVpos12

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

institute: University of Michigan

data_processing:
The adaptors were trimmed from raw WBGS sequences by Trim Galore (v0.4.1) (https://github.com/FelixKrueger/TrimGalore) and Cutadapt (v1.10).
The trimmed sequences were aligned to human genome (hg19) and the percentage of methylated reads at each CpG was calculated using Bisma rk (v0.16.1) with the ‘--directional -q --score-min L,0,-0.2 --ignore-quals’ options.
The significant (FDR<0.05 and absolute methylation difference >= 20%) differentially methylated regions (DMRs) were calculated using MethylSig (v0.99) with 100 bp tiling window, ‘min.group.num >= 80%’ and controlling for sex, age, stage and smoking status. In total, 270,326 DMRs were identified between IMU and KRT subgroups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file include differentially methylated regions (FDR<0.05 and absolute methylation difference >= 20%)

source_name: HNSCC tissue

extract_protocol:
Samples were quantitated using Qubit, and quality was assessed on the TapeStation 2200 with the genomic DNA tapescreen kit. 300ng of gDNA was sheared with a Covaris S220 (Duty factor 5%, Peak incident 105, Cycle/burst 200, time 80s, temperature 4-8C) in a 130ul volume. Sheared DNA was cleaned using Qiagen PCR Purification columns, with an elution volume of 32ul EB. Sheared DNA was end-repaired, A-tailed, and ligated with Illumina Methylation adapters overnight at 16C. The enzyme was heat inactivated at 65C for 10 min before clean up of DNA using Qiagen MinElute PCR Purification columns and elution in 20ul EB. Ligated DNA samples ran on a 1% agarose gel to select fragments 200-650bp and clean up with Qiagen Gel Extraction kit. The samples were next processed for bisulfite treatment using Zymo’s EZ DNA Methylation kit. The reactions were prepared according to the manufacturer’s instructions, but incubated in a thermocycler as follows: 55 cycles of 95C for 30sec, 50C for 15 min.
After cleanup of the DNA from bisulfite reaction, the libraries were amplified using Roche FastStart Hi-Fidelity DNA polymerase, and PCR PE primers for 16 cycles. The PCR products were cleaned using Agencourt AMPure XP bead 1.8:1 bead:DNA ratio. Final libraries were quantified with Qubit BR dsDNA kit, and the library size was assessed on a TapeStation 2200 using a HS HD1000 screentape kit.

value: head and neck cell carcinoma

tag: hpv type

tag: hpv integration

value: HPVintpos

tag: hpv-positive subtype

value: IMU


title: HCT116-EV-e3_S9

data_processing:
ATAC-seq reads were mapped to the GRCh38/hg38 build of the human genome using the Subread aligner (ver 2.0.0). Only uniquely mapped reads were retained. ATAC peaks were called using Homer (ver 4.7) with an FDR cutoff of 1E-5. Overlapping peaks from different samples were merged into a single peak region that covers all the overlapping peaks. Mapped reads were assigned to all the merged regions for each sample using featureCounts (ver 2.0.0).
Regions were removed from analysis if they failed to achieve a counts per million (CPM) value of at least 3.0 in any sample. Read counts for regions were converted to log2 CPM, quantail-normalised and precision weighted with the limma voom function. An MDS plot was generated on the voom results. Log2 CPM values were calculated from the reads mapped to each 50-bp bin in the 5kbp – TSS – 5kbp regions of the genes. Z-scores were then calculated for each gene to generate the heatmaps showing the chromatin accessibility around the TSS sites of the genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized log2-CPM values for each library. The supplementary file, ATAC_Raw_Counts.txt, includes raw read counts for genes in each sample.

extract_protocol:
Transfection protocol: Cell lines were trasfected with EHF expression plasmid and retrovirally transduced with CDX1 expression plasmid. Cells were selected with G418 for EHF and GFP positivity for CDX1.
Nulcei extracted from 5x10^4 cells by resuspension in ATAC-Seq lysis buffer. Digestion of DNA and ligation of adapter was performed using the Nextera Kit (Illumina). DNA was digested with Tn5 transposase enzyme and purified by the Qiagen MinElute PCR purification kit.

tag: cell type

value: Human colorectal cancer

value: Colon

tag: infection


title: NB4 cells-IgG (pmlrara)

value: IgG

tag: treatment

value: Control


title: RNA_HCT116-pcDNA-R1_S52

tag: cell line


title: HCT116-EV-e2_S5


title: RNA_HCT116-EHF-R3_S57


title: HCT116-EV-e1_S1


title: HPVneg11

value: neg

value: HPVneg

value: HPV(-)


title: Post, NR [S6]

value: Tumor

tag: response

value: NR

value: HNSCC

tag: timepoint

value: Post

value: SBRT + Durvalumab


title: RNA_HCT116-EHF-R2_S56

tag: tissue


title: HPVneg3


title: ALF021B

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: HP

tag: smokingstatus

value: Never

value: Moderate


title: HCT116-EHF-e3_S10

tag: cell type

value: Human colorectal cancer

value: Colon

tag: cell line

tag: infection


title: RNA_HCT116-EHF-R1_S55

tag: tissue


title: HPVneg10

value: head and neck cell carcinoma

tag: hpv type

value: neg

tag: hpv integration

value: HPVneg

tag: hpv-positive subtype

value: HPV(-)


title: ALF026D

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Right

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

value: M

tag: rnaconcentration ngul

value: Ex-Smoker

tag: severity

value: Unknown

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: HPVneg6


title: ALF019C

value: Whole lung

value: Apex

value: Disease

value: IPF

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Advanced


title: HCT116-EHF-e1_S2

tag: cell type

value: Human colorectal cancer

tag: tissue

tag: cell line

tag: infection


title: HPVpos18

tag: hpv type

tag: hpv integration

value: HPVintneg

tag: hpv-positive subtype

value: KRT


title: RNA_HCT116-EHF-CDX1-R3_S63

value: Colon


title: RNA_HCT116-EHF-CDX1-R2_S62


title: HCT116-EHF-e2_S6


title: ALF043B

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

value: F

tag: rnaconcentration ngul

tag: severity

value: Moderate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: HCT116-E-C-e3_S12

tag: cell type

tag: tissue

tag: cell line


title: HPVneg18

value: head and neck cell carcinoma

tag: hpv type

value: neg

tag: hpv integration

value: HPVneg

value: HPV(-)


title: HCT116-E-C-e2_S8

tag: infection


title: RNA_HCT116-EHF-CDX1-R1_S61


title: ALF011B

value: Whole lung

tag: donorid

tag: group

value: Unclassified

value: ILD

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: HP

tag: smokingstatus

value: Ex-Smoker

value: Severe


title: HPVneg17

tag: hpv-positive subtype


title: ALF007B

tag: tissue

tag: lunglocation

tag: leftright

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: rnaconcentration ngul

value: CTD-ILD

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: RNA_HCT116-CDX-R3_S60

tag: cell type

value: Human colorectal cancer

value: Colon

tag: cell line

tag: infection


title: HCT116-E-C-e1_S4


title: ALF041A

tag: donorid

tag: group

value: Apex

value: Left

value: IPF

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Never

value: Moderate

value: Senior Adult (>=60)


title: RNA_HCT116-CDX-R2_S59

tag: tissue


title: ALF025A

value: Whole lung

tag: lunglocation

tag: leftright

value: Right

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: rnaconcentration ngul

tag: smokingstatus

value: Unknown

tag: severity

tag: fvcprebd perc

tag: dlco perc


title: ALF028A

tag: donorid

tag: group

value: Disease

tag: gender

tag: diagnosis

value: Ex-Smoker

value: Severe

tag: dlco perc_corrected

tag: age group


title: HPVneg15

value: head and neck cell carcinoma

tag: hpv type

value: neg

tag: hpv integration

value: HPVneg

tag: hpv-positive subtype

value: HPV(-)


title: ALF023A

tag: tissue

tag: lunglocation

value: Apex

tag: leftright

value: Left

value: IPF

value: M

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Advanced


title: HCT116-CDX1-e3_S11

tag: cell type

value: Human colorectal cancer

value: Colon

tag: cell line

tag: infection


title: RNA_HCT116-CDX-R1_S58


title: A549, FOXM1, rep2

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description: A549 FOXM1 ChIP-seq rep2

data_processing:
The ChIP-seq libraries were sequenced to have at least 20 million read pairs using an Illumina NovaSeq. According to ENCODE ChIP-seq guideline, two biological replicates of A549 MYBL2 and FOXM1 ChIP-seq data were generated.
ChIP-seq reads were aligned to the hg38 genome using BWA v0.7.17 and the raw alignment bam file was marked duplicates using picard v2.20.8 and removed duplicates using samtools v1.10.
The library complexity is computed to get quanlity matrix using bedtoools v2.19.1
The control tagAlign files of A549 were downloaded from ENCODE (ID: ENCFF821HQW and ENCFF302AJZ) and combined as the control for analysis. Peaks were called using MACS2 v2.2.7.1 with the deafault parametter settings.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were grown to 70%-90% confluence and cross-linked with 1% formaldehyde for 10 minutes and quenched with 125nM glycine for 5 minutes at RT. Nuclei were lysed in nuclei lysis buffer, and performed snap-freeze using liquid nitrogen. Chromain was sonicated to an approximate length of 200 bp - 500 bp using bioruptor sonicator.
Libraries were prepared using the KAPA Hyper Prep Kit from KAPA Biosystems. End-Repair and A-Tailing Buffers, DNA ligase, and ligation buffer were used. Ampure beads were used for post-ligation clean up, and KAPA HiFi HotStart Ready Mix and Nextflex Primer Mix were used for amplification of adapter modified DNA fragments.

value: Lung adenocarcinoma cell

tag: chip antibody

value: FOXM1 (CST)


title: ALF029B

value: Whole lung

tag: donorid

tag: group

value: Base

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: rnaconcentration ngul

tag: smokingstatus

tag: severity

value: Moderate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: HPVpos16

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

tag: hpv integration

value: HPVintpos

tag: hpv-positive subtype

value: KRT


title: ALF020C

tag: donorid

tag: lunglocation

tag: leftright

value: Normal

value: NDC

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Ex-Smoker

value: Unknown


title: HPVpos17


title: HPVpos15


title: A549, FOXM1, rep1

description: A549 FOXM1 ChIP-seq rep1

tag: cell line

tag: cell type

tag: chip antibody


title: 254T Esophageal Squamous Cell Carcinoma

city: Taoyuan City

first: Hsuan

last: Liu

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
RNA sequencing data were trimmed reads and aligned to hg38 reference by by using BaseSpace app: RNA-Seq Alignment v1.0 with STAR and hg38 reference
Aligned RNA-seq reads were quantified and annotated using the Partek® Flow® Genomic Analysis Software (Partek) with GENCODE release 27.
The number of reads for each mRNA was normalized to read counts per million (CPM+0.0001) and quantified across all samples
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene counts (CPM+0.0001) for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: tumor tissue

extract_protocol:
ESCC tumor tissues were homogenized in liquid nitrogen and subjected to total RNA extraction using RNAzol B (Tel-Test, INC.), according to the manufacturer's protocol.
For RNA sequencing, libraries were prepared using the TruSeq RNA Access Library Prep Guide (Part # 15049525 Rev. B; Illumina) according to the manufacturer’s instructions. Equal concentrations of each library were sequenced using a NextSeq 500 (Illumina) platform. F

tag: ccrt response

value: poor

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: 333T Esophageal Squamous Cell Carcinoma


title: A549, MYBL2, rep2

description: A549 MYBL2 ChIP-seq rep2

value: MYBL2 (PT)


title: ALF019D

tag: tissue

tag: group

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: F

tag: diagnosis

tag: rnaconcentration ngul

tag: smokingstatus

value: Never

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF034B

value: Whole lung

tag: donorid

tag: lunglocation

value: Base

tag: leftright

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Senior Adult (>=60)


title: HPVneg14

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

value: neg

tag: hpv integration

value: HPVneg

tag: hpv-positive subtype

value: HPV(-)


title: HPVpos14

value: HPVintpos

value: KRT


title: 238T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: poor

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: HPVneg16


title: ALF043C

tag: group

value: Apex

value: Right

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: rnaconcentration ngul

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Moderate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: A549, control_FDI6, rep3

description: A549 Control for FDI-6 experiment RNA-seq rep3

data_processing:
RNA-seq reads were aligned to the human reference genome hg38 using in-house mRNA-seq analysis pipeline, which is adapted from NCI Genomic Data Commons bioinformatic pipieline (https://gdc.cancer.gov/).
Reads were first trimmed using Trimgalore to filter out low quality reads and the adapter sequences. The trimmed reads were then aligned to human reference genome version 38 (hg38) with the annotation GENCODE V29 using STAR to generate bam files.
HTseq was used to quantify the reads counts for each gene, with the bam files as the input.
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited textt files include Htseq-counts values for each samples

growth_protocol: DMEM or RPMI, 10% fetal bovine serum, 1% penicillin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Extraction was done using the Direct-zol RNA MiniPrep Kit (Zymo Research), with phenol. RNA was extracted in 3 replicates for each condition.
Libraries were prepared by polyA capture, and reverse transcription of cDNA. A 150 bp paired-end sequencing strategy was used to sequence the samples.

treatment_protocol: The expressions of MYBL2 and FOXM1 were knocked down using 25nM of small interfering RNAs (siRNAs). Negative control siRNA, and siRNAs targeting MYBL2 and FOXM1 were purchased from Dharmacon(Horizon Discovery, Cambridge, UK). A549 cells were transfected with control scrambled siRNA or siRNAs targeting MYBL2 or FOXM1 using DharmaFECT1TM transfecction reagent (Dharmacon), according to the manufacturer’s instructions. For FDI-6 treatment, cells were treated with 20μM FDI-6 for 24h.

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

value: WT

tag: treatment


title: 250T Esophageal Squamous Cell Carcinoma

tag: ccrt response


title: A549, MYBL2, rep1

description: A549 MYBL2 ChIP-seq rep1

tag: chip antibody

value: MYBL2 (PT)


title: HPVpos13

tag: tissue

tag: hpv type

tag: hpv integration

value: HPVintneg

tag: hpv-positive subtype

value: IMU


title: A549, control_FDI6, rep2

description: A549 Control for FDI-6 experiment RNA-seq rep2


title: 189T Esophageal Squamous Cell Carcinoma

tag: disease state


title: ALF027A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Advanced

tag: age group


title: HPVneg13

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

value: neg

tag: hpv integration

value: HPVneg

tag: hpv-positive subtype

value: HPV(-)


title: 177T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: poor

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: A549, control_FDI6, rep1

description: A549 Control for FDI-6 experiment RNA-seq rep1

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

tag: treatment


title: HCT116-CDX1-e1_S3

value: Human colorectal cancer

value: Colon

tag: infection


title: ALF026E

source_name: Lung,NDC.NA,Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Unclassified

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Unknown

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: HPVneg12

tag: tissue

tag: hpv type

tag: hpv integration

tag: hpv-positive subtype


title: ALF030D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

value: F

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: age group


title: ALF014B

value: Apex

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: CLAD

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: smokingstatus

value: Never

tag: severity

value: Severe


title: 168T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: poor

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: A549, FDI6, rep3

description: A549 FDI-6 RNA-seq rep3

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

value: FDI6 treatment

tag: treatment


title: A549, FDI6, rep2

description: A549 FDI-6 RNA-seq rep2


title: HCT116-CDX1-e2_S7

value: Human colorectal cancer

tag: tissue

value: Colon

tag: infection


title: 163T Esophageal Squamous Cell Carcinoma


title: 321T Esophageal Squamous Cell Carcinoma

value: good


title: 317T Esophageal Squamous Cell Carcinoma


title: ALF018C

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

tag: diseasenormal

value: IPF

value: M

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Ex-Smoker

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: ALF045A

value: Apex

value: Right

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: smokingstatus

tag: severity


title: HPVpos9

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

tag: hpv integration

value: HPVintneg

tag: hpv-positive subtype

value: IMU


title: ALF043A

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Moderate


title: A549, siControl_Both, rep2

description: A549 siControl for siBoth RNA-seq rep2

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

value: WT

tag: treatment


title: HPVneg8

tag: tissue

value: neg

value: HPVneg

value: HPV(-)


title: HPVneg9

tag: hpv type


title: ALF012A

value: Whole lung

value: Normal

tag: diseasegroup

value: NDC

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: smokingstatus

value: Current

tag: severity

value: Unknown

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: 253T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: good

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: A549, siBoth, rep3

description: A549 siBoth RNA-seq rep3

tag: cell line

tag: cell type

tag: genotype

value: MYBL2 & FOXM1 knockdown

tag: treatment

value: siBoth (siMYBL2 & siFOXM1)


title: A549, siControl_Both, rep3

description: A549 siControl for siBoth RNA-seq rep3


title: HPVneg7

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

tag: hpv integration

tag: hpv-positive subtype


title: HPVpos11

value: HPVintneg

value: IMU


title: 170T Esophageal Squamous Cell Carcinoma

value: poor


title: A549, siControl_Both, rep1

description: A549 siControl for siBoth RNA-seq rep1

value: Lung adenocarcinoma cell

value: WT


title: ALF016B

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Ex-Smoker

value: Severe

value: Senior Adult (>=60)


title: A549, siBoth, rep2

description: A549 siBoth RNA-seq rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HPVpos10

tag: tissue

tag: hpv type

tag: hpv integration

tag: hpv-positive subtype

value: KRT


title: A549, FDI6, rep1

description: A549 FDI-6 RNA-seq rep1

value: FDI6 treatment


title: 244T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: good

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: HPVneg4

value: head and neck cell carcinoma

value: neg

value: HPVneg

value: HPV(-)


title: 239T Esophageal Squamous Cell Carcinoma


title: A549, siBoth, rep1

description: A549 siBoth RNA-seq rep1

value: Lung adenocarcinoma cell

value: MYBL2 & FOXM1 knockdown

value: siBoth (siMYBL2 & siFOXM1)


title: ALF035D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

value: NSIP

tag: smokingstatus

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF012F

tag: tissue

value: Left

value: Normal

value: NDC

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Current

value: Unknown

value: Senior Adult (>=60)


title: HPVneg2

value: head and neck cell carcinoma

tag: hpv type

value: neg

tag: hpv integration

value: HPVneg

tag: hpv-positive subtype

value: HPV(-)


title: A549, siControl, rep4

description: A549 siControl RNA-seq rep4

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

value: WT

tag: treatment

value: siControl


title: 196T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: good

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: A549, siControl, rep3

description: A549 siControl RNA-seq rep3


title: HPVpos8

value: HPVintpos

value: KRT


title: ALF007C

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

tag: gender

value: F

tag: diagnosis

tag: age

value: CTD-ILD

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: A549, siControl, rep2

description: A549 siControl RNA-seq rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HPVpos6

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

tag: hpv integration

tag: hpv-positive subtype


title: 249T Esophageal Squamous Cell Carcinoma

tag: ccrt response

tag: disease state


title: 179T Esophageal Squamous Cell Carcinoma


title: HPVpos7

value: HPVintneg

value: IMU


title: ALF018A

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Severe

value: Senior Adult (>=60)


title: HPVpos4

tag: tissue

tag: hpv type

tag: hpv integration

tag: hpv-positive subtype


title: ALF044A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Normal

value: NDC

tag: smokingstatus

value: Unknown

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: HPVpos3

value: HPVintpos


title: 173T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: good

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: 176T Esophageal Squamous Cell Carcinoma


title: 164T Esophageal Squamous Cell Carcinoma


title: ALF023B

value: Base

tag: leftright

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

value: Never


title: HPVpos1

tag: tissue

value: head and neck cell carcinoma

tag: hpv type

tag: hpv integration

value: HPVintneg

tag: hpv-positive subtype


title: 301T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: poor


title: HPVneg5

value: neg

value: HPVneg

value: HPV(-)


title: ALF032D

tag: donorid

tag: group

tag: lunglocation

value: Right

value: IPF

value: M

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF038B

value: Whole lung

tag: leftright

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Senior Adult (>=60)


title: A549, siControl, rep1

description: A549 siControl RNA-seq rep1

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

value: WT

tag: treatment

value: siControl


title: HPVneg1

tag: tissue

tag: hpv type

tag: hpv integration

tag: hpv-positive subtype


title: A549, siFOXM1, rep3

description: A549 siFOXM1 RNA-seq rep3

value: FOXM1 knockdown


title: 198T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: good

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: 278T Esophageal Squamous Cell Carcinoma

value: poor


title: HPVpos5

value: head and neck cell carcinoma

value: HPVintneg

value: KRT


title: A549, siFOXM1, rep1

description: A549 siFOXM1 RNA-seq rep1


title: 299T Esophageal Squamous Cell Carcinoma


title: A549, siMYBL2, rep4

description: A549 siMYBL2 RNA-seq rep4

value: MYBL2 knockdown


title: HPVpos2

value: HPVintpos


title: A549, siMYBL2, rep3

description: A549 siMYBL2 RNA-seq rep3


title: 242T Esophageal Squamous Cell Carcinoma


title: ALF048C

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: CLAD

tag: gender

value: F

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

tag: severity

value: Severe

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF041B

tag: tissue

value: Whole lung

value: Base

value: IPF

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Never

value: Moderate

value: Senior Adult (>=60)


title: A549, siFOXM1, rep4

description: A549 siFOXM1 RNA-seq rep4

tag: cell line

tag: cell type

value: Lung adenocarcinoma cell

tag: genotype

value: FOXM1 knockdown

tag: treatment


title: ALF008B

tag: donorid

tag: group

tag: lunglocation

tag: leftright

tag: diseasenormal

tag: diseasegroup

tag: gender

value: M

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker


title: 294T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: poor

tag: disease state

value: Esophageal Squamous Cell Carcinoma


title: A549, siMYBL2, rep2

description: A549 siMYBL2 RNA-seq rep2

value: MYBL2 knockdown


title: ALF030C

tag: tissue

value: Apex

value: Right

value: Normal

value: NDC

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Unknown

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF018D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: processingdate

value: Severe


title: A549, siFOXM1, rep2

description: A549 siFOXM1 RNA-seq rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ALF047C

tag: tissue

value: IPF

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

value: Never

tag: severity

value: Senior Adult (>=60)


title: A549, siMYBL2, rep1

description: A549 siMYBL2 RNA-seq rep1

value: Lung adenocarcinoma cell


title: 306T Esophageal Squamous Cell Carcinoma

tag: ccrt response

value: good

tag: disease state


title: 298T Esophageal Squamous Cell Carcinoma


title: LN_AMP-CpG_72h_2

type: RNA

city: Boston

first: Martin

middle: P

last: Steinbuck

state: Massachusetts

address: 451D Street, Ste 501

institute: Elicio Therapeutics

description: AMP-CpG 72h - 2

hyb_protocol: Performed by Canopy Biosciences following the NanoString protocols.

data_processing: NanoString generated raw values of CpG and AMP-CpG samples were analyzed against Mock samples using Rosalind software. Volcano plots show Rosalind-generated p-values (log2) and fold-changes (-log10). For heat maps, Z-scores were calculated for the raw expression data. These were then averaged among biological duplicates and mock-subtracted.

label: NanoString Probes

extract_protocol: Inguinal lymph nodes were harvested from immunized C57BL/6J mice at the indicated time points, processed into single cell suspensions, and lysed with RLT buffer (Qiagen, cat# 79216).

treatment_protocol: In vivo - vaccine injection into mouse.

tag: strain

value: Lymph node

tag: vaccine

value: AMP-CpG

tag: time


title: LN_AMP-CpG_72h_1

description: AMP-CpG 72h - 1

scan_protocol: Performed by Canopy Biosciences following the NanoString protocols.


title: ALF026A

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

tag: gender

value: M

tag: processingdate

value: Ex-Smoker

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Overexpressing OspC3, beta-treated [ALP4689A36]

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
ALP4689A36
Gene expression in cell line
mRNA

data_processing:
nf-core/rnaseq pipeline (version 3.5) was used to perform the primary analysis.
Gene counts per gene per sample were obtained using RSEM-STAR.
Differential gene expression carried out with DESeq.
Assembly: Human GRCh38 genome downloaded from Ensembl (release 95).
Supplementary files format and content: Normalizedcounts.txt: Tab-delimited text file includes normalized counts per gene per sample.

source_name: human cell line

growth_protocol: Cells were seeded in DMEN+10% FBS in 24 well plates at 2.10^5/mL. 24 hours later, cells were transfected with GFP-tagged plasmids and the medium was changed 24 hours later.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit from QIAGEN (Ref 74106) following manufacturer’s protocols.
RNA libraries were prepared for sequencing using polyA_KAPA_mRNA_Hyper_Prep, following manufacturer’s protocols.

treatment_protocol: Cells were treated or not with IFN beta at 10ng/mL for 18 hours.

tag: cell line

tag: overexpression

tag: treatment

value: IFNbeta


title: Overexpressing OspC1, beta-treated [ALP4689A35]

description:
ALP4689A35
Gene expression in cell line
mRNA


title: ALF030B

tag: tissue

value: Normal

value: NDC

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

tag: severity


title: LN_AMP-CpG_24h_1

description: AMP-CpG 24h - 1

label_protocol: Performed by Canopy Biosciences following the NanoString protocols.

tag: strain

tag: vaccine

tag: time


title: LN_AMP-CpG_24h_2

description: AMP-CpG 24h - 2


title: ALF039B

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: processingdate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Overexpressing OspC1, UT [ALP4689A32]

description:
ALP4689A32
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

tag: treatment

value: untreated


title: Overexpressing GFP, UT [ALP4689A31]

description:
ALP4689A31
Gene expression in cell line
mRNA

value: GFP


title: LN_AMP-CpG_6h_1

description: AMP-CpG 6h - 1

tag: strain

tag: tissue

tag: vaccine


title: LN_AMP-CpG_6h_2

description: AMP-CpG 6h - 2

tag: time


title: ALF046C

tag: donorid

tag: group

tag: lunglocation

value: Apex

value: Right

value: Disease

value: ILD

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: diseasesubtype

value: NSIP

tag: smokingstatus

value: Unknown

tag: severity

value: Severe


title: ALF001

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: processingdate

value: Never

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: Overexpressing OspC3, beta-treated [ALP4689A30]

description:
ALP4689A30
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

tag: treatment

value: IFNbeta


title: LN_AMP-CpG_2h_2

description: AMP-CpG 2h - 2

tag: strain

tag: tissue

value: Lymph node

tag: vaccine

value: AMP-CpG

tag: time


title: ALF014D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

value: CLAD

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

tag: severity


title: Overexpressing OspC1, beta-treated [ALP4689A29]

description:
ALP4689A29
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

tag: treatment


title: CA6

city: Winston Salem

first: Dan

last: Zhao

state: NC

address: 1 Medical Center Blvd

department: Cancer Biology

institute: Wake Forest University School of Medicine

data_processing:
Libraries were prepared using the CleanTag Library kit (Trilink Biotechnology) and purified with the AMPure XP beads.
The quantity of each library was measured using the Qubit 3.0 (Thermo Fisher, USA) and sequenced using the Illumina NextSeq 500.
The adaptor removal was performed using Trim_Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
miRDeep2 was used to map the reads to miRBase v.22 and to get counts of the microRNAs in different samples.
Gene expression, which were converted from counts based on negative binominal model, was analyzed using R package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.xlsx: Matrix table with raw gene counts for every gene and every sample.

source_name: breast cancer serum exosomes

extract_protocol:
Exosomes from serum samples were extracted by Exoquick kit (System Biosciences). RNA was extracted by miRNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. RNA quantity and integrity were confirmed with a NanoDrop spectrophotometer (NanoDrop Technologies) and Agilent 2100 Bioanalyser (Agilent Technologies).
Libraries were prepared using the CleanTag TM library kit (TriLink Biotechnologies).

value: Breast cancer

tag: race

value: Caucasian American

tag: cell type

value: Serum Exosomes


title: LN_CpG_72h_2

description: CpG 72h - 2

tag: strain

tag: tissue

tag: vaccine

value: CpG

tag: time


title: ALF014A

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using star (v2.6.1)13 with default parameters except for the --quantMode TranscriptomeSAM setting.
Reads were summarized at the gene level using featureCounts tool from the Subread package (v1.6.4)14, in a strand-specific manner.

extract_protocol:
RNA was extracted from whole lung tissue according to manufacturer’s protocol (Fibrous Tissue Mini kit, Qiagen #74704). RNA quality was verified with the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Samples with RNA integrity numbers (RIN) over 6 were used for RNA sequencing.
cDNA libraries were prepared for sequencing using standard strand specific TrueSeq kits with ribosomal RNA and Globin mRNA depletion. At least 20 million 100 bp single-end reads were generated per sample using Illumina HiSeq 3000 (Illumina, California, USA) using standard protocols at the Australian Genome Research Facility (AGRF, Melbourne, Australia).

tag: donorid

tag: group

tag: lunglocation

tag: leftright

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: processingdate

value: Severe

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: LN_CpG_72h_1

description: CpG 72h - 1

tag: strain

tag: tissue


title: Overexpressing GFP, beta-treated [ALP4689A28]

description:
ALP4689A28
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

value: GFP

tag: treatment


title: CA4

tag: race

tag: cell type


title: Overexpressing GFP, beta-treated [ALP4689A34]

description:
ALP4689A34
Gene expression in cell line
mRNA


title: ALF020D

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Normal

value: NDC

value: M

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Unknown


title: Overexpressing OspC3, UT [ALP4689A27]

description:
ALP4689A27
Gene expression in cell line
mRNA

tag: cell line

value: untreated


title: CA5

tag: diagnosis


title: ALF018B

source_name: Lung,IPF.Base,Whole lung

tag: tissue

value: Whole lung

value: Base

tag: diseasegroup

value: IPF

tag: gender

tag: age

tag: processingdate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: CA3

value: Breast cancer

tag: race

value: Caucasian American

tag: cell type


title: Overexpressing OspC3, UT [ALP4689A33]

description:
ALP4689A33
Gene expression in cell line
mRNA

tag: overexpression

tag: treatment


title: LN_AMP-CpG_2h_1

description: AMP-CpG 2h - 1

tag: strain

value: Lymph node

tag: vaccine

value: AMP-CpG

tag: time


title: LN_CpG_6h_2

description: CpG 6h - 2

value: CpG


title: ALF016A

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

tag: diseasenormal

value: Disease

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

tag: severity

value: Severe


title: Overexpressing OspC1, UT [ALP4689A26]

description:
ALP4689A26
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

tag: treatment


title: ALF050A

tag: tissue

value: Left

value: Normal

tag: diseasegroup

value: NDC

tag: gender

tag: age

tag: processingdate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Overexpressing OspC3, beta-treated [ALP4689A24]

description:
ALP4689A24
Gene expression in cell line
mRNA

value: IFNbeta


title: ALF009C

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Unclassified

tag: diseasenormal

value: M

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

value: Ex-Smoker

value: Unknown


title: ALF013A

tag: tissue

value: Whole lung

tag: diseasegroup

value: F

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

tag: severity


title: LN_CpG_2h_2

description: CpG 2h - 2

tag: strain

tag: vaccine

tag: time


title: Overexpressing OspC1, beta-treated [ALP4689A23]

description:
ALP4689A23
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

tag: treatment


title: CA2

value: Breast cancer

tag: race

value: Caucasian American

tag: cell type

value: Serum Exosomes


title: CA1

tag: diagnosis


title: LN_CpG_6h_1

description: CpG 6h - 1

value: Lymph node

value: CpG


title: LN_CpG_24h_2

description: CpG 24h - 2


title: ALF026B

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

tag: diseasenormal

tag: gender

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: processingdate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: LN_CpG_2h_1

description: CpG 2h - 1

tag: strain

tag: tissue

tag: vaccine

tag: time


title: AA6

tag: diagnosis

tag: race

value: African American

tag: cell type


title: Overexpressing GFP, beta-treated [ALP4689A22]

description:
ALP4689A22
Gene expression in cell line
mRNA

tag: cell line

tag: overexpression

value: GFP

tag: treatment


title: LN_CpG_24h_1

description: CpG 24h - 1


title: AA5


title: AA4


title: LN_Mock_72h_2

description: Mock 72h - 2

value: Mock


title: LN_Mock_72h_1

description: Mock 72h - 1


title: Overexpressing OspC3, UT [ALP4689A21]

description:
ALP4689A21
Gene expression in cell line
mRNA

value: untreated


title: ALF009B

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: gender

tag: age

tag: lungweight mg

tag: rin

tag: volum ul

tag: diseasesubtype

tag: smokingstatus

tag: severity


title: Overexpressing GFP, UT [ALP4689A25]

description:
ALP4689A25
Gene expression in cell line
mRNA

tag: cell line


title: ALF012E

tag: tissue

value: Apex

tag: diagnosis

tag: rnaconcentration ngul

tag: processingdate

value: Current

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: Overexpressing OspC1, UT [ALP4689A20]

description:
ALP4689A20
Gene expression in cell line
mRNA

tag: overexpression

tag: treatment


title: ALF008D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: age

tag: lungweight mg

value: Ex-Smoker

value: Severe


title: AA3

tag: diagnosis

value: Breast cancer

tag: race

value: African American

tag: cell type

value: Serum Exosomes


title: Overexpressing GFP, UT [ALP4689A19]

description:
ALP4689A19
Gene expression in cell line
mRNA

tag: cell line

value: GFP

value: untreated


title: AA2


title: Pt40

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR (v2.7.8) and quantified with HT-Seq (v0.13.5) using the GRCh38 human assembly
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Genome_build: GRCh38

source_name: APL

extract_protocol:
About 1μg of total RNA was used, and polyA-tailed mRNAs were purified from total RNA using oligo-dT attached magnetic beads. The purified library was quantified using a Qubit 4 Fluorometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: bone marrow

value: Female

tag: genotype

value: Low-risk

value: Untreated


title: LN_Mock_24h_1

description: Mock 24h - 1

tag: strain

value: Lymph node

tag: vaccine

value: Mock

tag: time


title: ALF031C

value: Whole lung

tag: donorid

tag: group

value: Apex

value: Right

value: ILD

value: F

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: HP

tag: smokingstatus

value: Never

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: Pt39

tag: tissue

tag: age

tag: gender

value: Male

tag: genotype

tag: treatment


title: SUM-149PT_2_Paclitaxel_resistant_synergy_7.5e-9M_Paclitaxel_+_10uM_INC424_2

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: SUM2-149PT_Paclitaxel_resistant_7.5e-9M_Paclitaxel_+_10uM_INC424_2

data_processing:
Illumina Bcl2fastq v2.18
Reads were aligned to hg19 using STAR
For rpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of RPKM table

growth_protocol: For RNA-seq, cells were seeded in 100mm plates at 1x10^6 cells/plate for SUM149 and 7.5x10^5 cells/plate for FCIBC02, and treatments added after 24 or 48h respectively

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits and the Kapa Biosystems library quantification kit

treatment_protocol: Treatments were added in 0.5ml/100mm-plate non-FBS containing DMEM/F12 and cells incubated for 72h

tag: cell line

value: 7.5E-9M Paclitaxel + 10uM INC424


title: LN_Mock_6h_2

description: Mock 6h - 2

tag: strain

tag: vaccine

tag: time


title: ALF050D

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

value: M

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

value: Unknown


title: ALF047D

tag: tissue

value: Disease

value: IPF

tag: gender

tag: age

tag: diseasesubtype

tag: smokingstatus

tag: severity

value: Severe

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: Pt38

value: bone marrow

tag: genotype

value: Intermediate-risk

tag: treatment

value: Untreated


title: LN_Mock_2h_2

description: Mock 2h - 2

tag: strain

value: Lymph node

tag: vaccine

value: Mock

tag: time


title: ALF040A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

tag: diseasegroup

value: F

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Never


title: LN_Mock_6h_1

description: Mock 6h - 1

tag: tissue


title: Pt37

tag: age

tag: gender

value: Male

tag: genotype


title: LN_Mock_24h_2

description: Mock 24h - 2

tag: strain

tag: vaccine


title: SUM-149PT_2_Paclitaxel_resistant_synergy_10uM_INC424_2

tag: cell line

tag: treatment

value: 10uM INC424


title: ALMND.PPV.GRR

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description:
smallRNA
G2

data_processing:
Illumina adapter removal: To remove Illumina adapters in 50 nt short reads, in FASTQ format, the sequence of the first 8 nucleotides of the adapter used (TGAATTC) was searched and, when detected, reads were 3’ truncated at that position. Remaining sequences, between 18 and 42 nt were considered “smallRNAs” (sRNAs)
sRNA count and filtering: For each sample, a table of unique sRNA sequences and their number of occurrences per sample (raw counts), was prepared. Only sRNA sequences appearing 3 or more times in, at least one sample, were considered for ulterior analysis. At the end, a total of 1,248,316 unique 18-42 nt sRNAs remained
Annotation of sRNAs with miRBase: Each sRNA was compared with mature miRNAs from miRBase. Only exact matches were considered. Raw counts of these known miRNAs were used to calculate normalization factors.
Normalization of sRNA counts based on known miRNA counts: To make sRNA abundances comparable between samples, raw count of each sRNA in each sample was multiplied by the average raw counts of known miRNAs detected in the previuos step, for all samples, and divided by the average sRNA raw counts of that sample
Differential expression of sRNAs: To detect differentially expressed sRNAs between two samples (experiment vs control) DEGexp function of DEGseq package was used. Normalized counts, as calculated in the previous step, were used as expression values. For each sRNA, log2(fold changes) an q-values were obtained
Genome_build: Peach v2.0.a1 (v2.1) https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1
Supplementary_files_format_and_content: Text-tabulated table containing more than 1 000 000 rows (one per smallRNA detected) with smallRNA sequences and their abundances in each sample

organism: Prunus dulcis

source_name: Leaf

growth_protocol: Plants were subjected to growth cycles in the greenhouse and rest periods in cold chamber. Leaf samples were collected after cycle 2 pooling leaves from 5 different plants

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen) and RNA samples were sent to the Centre for Genomic Regulation (CRG, Barcelona, Spain) for library preparation and RNA sequencing
The cDNA libraries of miRNA were prepared using the TruSeq Small RNA Library Preparation Kit of Illumina (following the manufactures protocol), cDNA libraries were sequenced using an Illumina GAII machine to perform 50 bp single sequencing

treatment_protocol: Control (A) and PPV-infected “GF305” peaches (B), “GF305” peach grafted with “Garrigues” almond (C and F), PPV-infected “GF305” peach grafted with “Garrigues” almond (D and G) and “GF305” peach grafted with “Garrigues” almond and the inoculated with PPV (E)

tag: cultivar

value: Garrigues

value: Leaf

tag: infection

value: PPV-infected

tag: grafted

value: Graft

value: Garrigues grafted in PPV-infected GF305


title: Pt36

value: bone marrow

value: Female


title: SUM-149PT_2_Paclitaxel_resistant_synergy_7.5e-9M_Paclitaxel_+_10uM_INC424_1

description: SUM2-149PT_Paclitaxel_resistant_7.5e-9M_Paclitaxel_+_10uM_INC424_1

value: 7.5E-9M Paclitaxel + 10uM INC424


title: LN_Mock_2h_1

description: Mock 2h - 1

value: Lymph node

tag: time


title: ALF036A

tag: donorid

tag: group

tag: lunglocation

tag: leftright

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

tag: diagnosis

tag: processingdate

tag: diseasesubtype

value: CTD-ILD

tag: smokingstatus

value: Unknown

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: SUM-149PT_2_Paclitaxel_resistant_synergy_10uM_INC424_1

tag: cell line

tag: treatment


title: ALF018E

source_name: Lung,IPF.NA,Whole lung

tag: tissue

value: Whole lung

tag: donorid

value: Unclassified

value: IPF

tag: gender

value: M

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Ex-Smoker

value: Severe

value: Senior Adult (>=60)


title: ALMND.GRR

description:
smallRNA
F2

tag: cultivar

value: Garrigues

value: Leaf

tag: infection

value: Not infected

tag: grafted

value: Graft

value: Garrigues grafted in Wild Type GF305


title: siRUNX2-3

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Typically, base call quality diminishes toward the end of a read. This is characteristic to first- and second-generation sequencing technologies (Sanger, Illumina, SOLiD, 454)
SOAPnuke, a filtering software independently developed by BGI, is used for filtering.
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts or in FPKM (fragments per thousand nucleotides per million mapped reads).
Genome_build: hg19_ucsc
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: breast cancer cell

growth_protocol: MDA-MB-231 cells were cultured in a humidified incubator equilibrated with 5% CO2 at 37 °C. The media (Dulbecco Modified Eagle Medium (DMEM)) was supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 48h in adherent conditions with siRUNX2 or NC.

tag: cell type


title: ALF020B

first: Katherine

address: 30 Flemington Rd, Parkville

institute: CSL Limited

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: diagnosis

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

tag: severity

tag: fvcprebd perc

tag: dlco perc


title: Pt35

tag: tissue

value: bone marrow

tag: age

tag: gender

value: Male

tag: genotype

value: Low-risk

tag: treatment

value: Untreated


title: Pt34

value: Female

value: Intermediate-risk


title: SUM-149PT_2_Paclitaxel_resistant_synergy_7.5e-9M_Paclitaxel_1

description: SUM2-149PT_Paclitaxel_resistant_7.5e-9M_Paclitaxel_1

tag: cell line

value: 7.5E-9M Paclitaxel


title: Pt33


title: SUM-149PT_2_Paclitaxel_resistant_synergy_Vehicle_2

description: SUM2-149PT_Paclitaxel_resistant_Vehicle_2

value: Vehicle


title: ALF036B

source_name: Lung,ILD.Base,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Disease

value: ILD

value: F

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: CTD-ILD

value: Unknown

tag: dlco perc_corrected

tag: age group


title: Pt32


title: ALF015B

value: Base

tag: leftright

value: Left

tag: diseasenormal

tag: diseasegroup

value: IPF

value: M

tag: diagnosis

tag: processingdate

tag: diseasesubtype

value: NSIP

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Moderate

tag: fvcprebd perc


title: siRUNX2-1

tag: cell type

tag: treatment


title: Pt31

tag: tissue

value: bone marrow

tag: age

tag: gender

value: Male

tag: genotype

value: Untreated


title: Control3

value: Control


title: SUM-149PT_2_Parental_synergy_2.5e-9M_Paclitaxel_+_10uM_INC424_2

description: SUM2-149PT_Parental_2.5e-9M_Paclitaxel_+_10uM_INC424_2

tag: cell line

value: 2.5E-9M Paclitaxel + 10uM INC424


title: SUM-149PT_2_Paclitaxel_resistant_synergy_Vehicle_1

description: SUM2-149PT_Paclitaxel_resistant_Vehicle_1

value: Vehicle


title: Control2


title: ALF035A

source_name: Lung,IPF.Apex,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

value: Disease

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Advanced

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: ALF024B

value: Base

tag: leftright

value: Left

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

value: F

tag: diagnosis

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Unknown

tag: severity

tag: fvcprebd perc


title: Pt29

tag: tissue

value: bone marrow

tag: age

tag: gender

value: Female

tag: genotype

value: Low-risk

tag: treatment


title: SUM-149PT_2_Paclitaxel_resistant_synergy_7.5e-9M_Paclitaxel_2

description: SUM2-149PT_Paclitaxel_resistant_7.5e-9M_Paclitaxel_2

tag: cell line

value: 7.5E-9M Paclitaxel


title: AA1

value: Breast cancer

tag: race

value: African American

tag: cell type

value: Serum Exosomes


title: Control1

value: Control


title: Pt28

value: Male

value: Intermediate-risk

value: Untreated


title: SUM-149PT_2_Parental_synergy_10uM_INC424_2

value: 10uM INC424


title: SUM-149PT_2_Parental_synergy_10uM_INC424_1


title: SUM-149PT_2_Parental_synergy_2.5e-9M_Paclitaxel_+_10uM_INC424_1

description: SUM2-149PT_Parental_2.5e-9M_Paclitaxel_+_10uM_INC424_1

value: 2.5E-9M Paclitaxel + 10uM INC424


title: ALF032A

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

value: Disease

value: IPF

value: M

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Ex-Smoker

value: Advanced

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF047B

tag: tissue

value: Base

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Never

tag: severity

value: Severe

tag: fvcprebd perc

value: Senior Adult (>=60)


title: SUM-149PT_2_Parental_synergy_2.5e-9M_Paclitaxel_2

description: SUM2-149PT_Parental_2.5e-9M_Paclitaxel_2

tag: cell line

tag: treatment

value: 2.5E-9M Paclitaxel


title: Pt27

value: bone marrow

value: Male

tag: genotype

value: Intermediate-risk


title: siRUNX2-2

tag: cell type


title: Pt26

value: Female

value: Low-risk

value: Untreated


title: ALF049A

source_name: Lung,NDC.Apex,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

value: Normal

value: NDC

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

value: Unknown

tag: dlco perc

tag: dlco perc_corrected


title: SUM-149PT_2_Parental_synergy_2.5e-9M_Paclitaxel_1

description: SUM2-149PT_Parental_2.5e-9M_Paclitaxel_1


title: ALF028B

tag: tissue

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: F

tag: diagnosis

tag: age

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

tag: age group


title: SUM-149PT_2_Parental_synergy_Vehicle_2

tag: cell line

tag: treatment

value: Vehicle


title: Pt30

value: bone marrow

tag: genotype


title: Pt25

value: Intermediate-risk


title: Pt24

value: Male

value: High-risk


title: ALF024C

tag: donorid

tag: group

tag: lunglocation

tag: leftright

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: severity

tag: fvcprebd perc


title: SUM-149PT_2_Parental_synergy_Vehicle_1


title: ALF035B

tag: tissue

value: Base

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: volum ul

value: NSIP

value: Advanced

tag: dlco perc

tag: dlco perc_corrected

value: Senior Adult (>=60)


title: Pt23

tag: genotype

tag: treatment

value: Untreated


title: KF20_P10

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA with Transcriptome analysis Console software

label: biotin

source_name: Wilms tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Thermo Fisher Scientific).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: histotype

value: WT


title: SUM-149PT_Doxorubicin_resistant_synergy_2e-7M_Doxorubicin_+_10uM_INC424_2

description: SUM-149PT_Doxorubicin_resistant_2e-7M_Doxorubicin_+_10uM_INC424_2

tag: cell line

value: 2E-7M Doxorubicin + 10uM INC424


title: KF19_P10


title: ALF050C

city: Melbourne

last: Monaghan

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

value: Normal

value: NDC

value: M

tag: lungweight mg

tag: rnaconcentration ngul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Unknown

tag: age group


title: KF21_P10


title: ALF026C

tag: tissue

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: rin

tag: volum ul

value: Ex-Smoker

tag: severity

tag: fvcprebd perc


title: ALF017A

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: dlco perc

tag: dlco perc_corrected


title: SUM-149PT_Doxorubicin_resistant_synergy_2e-7M_Doxorubicin_+_10uM_INC424_1

description: SUM-149PT_Doxorubicin_resistant_2e-7M_Doxorubicin_+_10uM_INC424_1

tag: cell line

tag: treatment


title: Pt22

tag: tissue

value: bone marrow

value: Male

tag: genotype

value: High-risk


title: Pt21

tag: gender

value: Female


title: KF18_P10

tag: histotype


title: SUM-149PT_Doxorubicin_resistant_synergy_10uM_INC424_2

description: SUM-149PT_Doxorubicin_resistant_10uM_INC424_2

value: 10uM INC424


title: ALF049B

source_name: Lung,NDC.Base,Whole lung

value: Base

tag: diseasenormal

tag: diseasegroup

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

tag: age group

value: Senior Adult (>=60)


title: Pt20

value: Intermediate-risk

value: Untreated


title: KF17_P09

value: WT


title: Pt19


title: SUM-149PT_Doxorubicin_resistant_synergy_2e-7M_Doxorubicin_2

description: SUM-149PT_Doxorubicin_resistant_2e-7M_Doxorubicin_2

value: 2E-7M Doxorubicin


title: KF15_P09


title: ALF025D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Normal

tag: rin

tag: volum ul

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: SUM-149PT_Doxorubicin_resistant_synergy_10uM_INC424_1

description: SUM-149PT_Doxorubicin_resistant_10uM_INC424_1

tag: cell line

tag: treatment


title: ALF043D

tag: tissue

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

value: Moderate


title: SUM-149PT_Doxorubicin_resistant_synergy_2e-7M_Doxorubicin_1

description: SUM-149PT_Doxorubicin_resistant_2e-7M_Doxorubicin_1


title: KF16_P09

tag: histotype


title: SUM-149PT_Doxorubicin_resistant_synergy_Vehicle_2

description: SUM-149PT_Doxorubicin_resistant_Vehicle_2

value: Vehicle


title: KF13_P08


title: Pt17

value: bone marrow

tag: genotype

value: Low-risk


title: Pt18

value: Female


title: Pt16

value: Male


title: ALF027C

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: M

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

value: Advanced

tag: age group


title: Pt15

tag: tissue

tag: gender

value: Intermediate-risk

tag: treatment

value: Untreated


title: KF14_P09

value: WT


title: KF11_P08


title: KF12_P08


title: ALF048B

source_name: Lung,CLAD.Base,Whole lung

value: Whole lung

value: Base

value: Right

tag: diseasenormal

tag: diseasegroup

value: CLAD

tag: diagnosis

tag: age

tag: lungweight mg

tag: severity

value: Severe

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: SUM-149PT_Doxorubicin_resistant_synergy_Vehicle_1

description: SUM-149PT_Doxorubicin_resistant_Vehicle_1

tag: cell line

value: Vehicle


title: ALF028D

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Disease

value: IPF

value: F

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate


title: SUM-149PT_Parental_synergy_1e-8M_Doxorubicin_+_10uM_INC424_2

description: SUM-149PT_Parental_1e-8M_Doxorubicin_+_10uM_INC424_2

tag: treatment

value: 1E-8M Doxorubicin + 10uM INC424


title: SUM-149PT_Parental_synergy_1e-8M_Doxorubicin_+_10uM_INC424_1

description: SUM-149PT_Parental_1e-8M_Doxorubicin_+_10uM_INC424_1


title: ALF023D

tag: tissue

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: diseasesubtype

tag: smokingstatus

value: Never

tag: age group

value: Senior Adult (>=60)


title: KF10_P08

tag: histotype


title: SUM-149PT_Parental_synergy_10uM_INC424_2

tag: cell line

value: 10uM INC424


title: Pt13

value: bone marrow

tag: age

value: Male

tag: genotype

value: Low-risk


title: ALF011A

source_name: Lung,ILD.Apex,Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Unclassified

value: ILD

value: M

tag: lungweight mg

tag: rnaconcentration ngul

value: HP

value: Ex-Smoker

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: KF09_P07

value: WT


title: Pt12

tag: tissue

tag: gender

value: Female

tag: treatment

value: Untreated


title: ALF046D

value: Whole lung

value: Base

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: F

tag: diagnosis

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: NSIP

tag: smokingstatus

value: Unknown

value: Severe

tag: age group


title: SUM-149PT_Parental_synergy_10uM_INC424_1

tag: cell line

value: 10uM INC424


title: ALF050B

tag: donorid

tag: group

tag: lunglocation

tag: leftright

value: Left

value: Normal

value: NDC

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: severity


title: Pt11

tag: tissue

value: bone marrow

tag: gender

tag: genotype

value: Intermediate-risk

tag: treatment


title: KF08_P07

tag: histotype

value: WT


title: ALF017B

value: Apex

tag: diseasenormal

tag: diseasegroup

value: M

tag: diagnosis

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: SUM-149PT_Parental_synergy_1e-8M_Doxorubicin_2

tag: cell line

value: 1E-8M Doxorubicin


title: Pt10

tag: age

value: Female

value: Untreated


title: Pt14

tag: tissue

value: Low-risk


title: ALF027D

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Right

value: Disease

value: IPF

tag: gender

tag: lungweight mg

tag: rnaconcentration ngul

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Advanced

tag: age group


title: SUM-149PT_Parental_synergy_1e-8M_Doxorubicin_1

tag: treatment


title: ALF025B

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: diagnosis

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Unknown

tag: fvcprebd perc


title: Pt08

tag: tissue

value: bone marrow

tag: age

value: Male

tag: genotype

value: Intermediate-risk


title: SUM-149PT_Parental_synergy_Vehicle_2

tag: cell line

value: Vehicle