title: WT_H2AZ_ZT0_WL

description:
histone variant
Sample 6


title: BR1_T1_plus

status: Public on Apr 30 2021

type: SRA

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
IonXpressRNA_008_R_2015_03_11_14_18_53_user_PRI-173-Boonstra_800253_chip1_Auto_user_PRI-173-Boonstra_800253_chip1_252
IonXpressRNA_008_R_2015_03_12_13_05_45_user_PRI-174-Boonstra_800253_chip1_Auto_user_PRI-174-Boonstra_800253_chip1_254

library_source: transcriptomic

data_processing:
mapping of reads was done using: bowtie2  --local using Escherichia coli K12 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus subtilis subsp. subtilis str. 168, circular BCT 15-JAN-2018, AL009126.3
Supplementary_files_format_and_content: Tab delimited text file

molecule: total RNA

organism: Bacillus subtilis

source_name: compT1 (bioreplicate 1)

growth_protocol: The following competence medium was used: 18 ml demineralized water, 2 ml 10× competence medium stock [0.615 M K2HPO4•3H2O, 0.385 M KH2PO4, 20% glucose, 10 ml 300 mM Tri‐Na‐citrate, 1 ml 2% ammonium ferric citrate, 1 g casein hydrolysate (oxoid), 2 g potassium glutamate], 100 μl 2 mg ml-1 tryptophan, 67 μl 1 M MgSO4 (Spizizen, 1958; Konkol et al., 2013). Strains were streaked out from -80 stocks on Luria Bertani (LB) agar plates with antibiotics and grown overnight at 37°C. A single colony (sc) was diluted 1000× in PBS or 1× Spizizen solution 100 μl of the sc colony solution was added to 20 ml medium in 100 ml Erlenmeyer flasks and grown at 37°C 220 rpm. Exponential/early stationary overnight cultures were diluted to an OD600 of 0.05 in 20 ml medium without antibiotics. Antibiotic concentrations used were chloramphenicol (cm) 5 μg ml-1, spectinomycin (sp) 50 μg ml-1, erythromicin (ery) 0.5 μg ml-1, and lincomycin 12.5 μg ml-1. Growth conditions in CDSM (Vasantha and Freese, 1980; Hageman et al., 1984) + alanine (10 mM) + tryptophan 1 mM. Strains were grown overnight at 37°C on LB agar + chloramphenicol (control) or chloramphenicol + erythromycin (BFA1698), single colonies were diluted and incubated in 2 ml LB 37°C 220 rpm in test tubes. The diluted cultures were mid‐exponential after overnight growth. The overnight cultures were diluted to OD600 0.05 in 2 ml CDSM + alanine + tryptophan and chloramphenicol (control) or chloramphenicol + erythromycin (BFA1698) in test tubes and grown to mid‐exponential growth at 37°C 220 rpm. Cultures were diluted to OD600 0.1 in 100 μl CDSM + alanine + tryptophan without antibiotics in a 96 wells plate and grown at 37°C, 240 rpm, 10 min measuring interval for 20 h in a Thermo Fisher Varioskan Lux. The remainder of the cultures was grown for 24 h after which the cultures were kept in the dark at 4°C without shaking for 4 days. Spores were harvested by centrifugation at 10 000 g and washed 3× with double distilled water. The spore crops were diluted to the same OD and heated for 10 min at 80°C and dilutions were plated on LB agar with chloramphenicol and grown overnight at 37°C. Colonies were counted and measured with ImageJ. Statistics were done in Sigmaplot using a Rank Sum Test.

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: Bacillus subtilis 168 PcomG‐gfp chloramphenicol resistant variant PcomG‐gfp was grown as described in growth conditions Samples for protein analysis and RNA‐seq analysis were taken at 5.5 and 6.5 h respectively. One hour of sorting through FACS yields approximately 3 × 10^7 GFP‐negative (non‐competent cells) and 1.5 × 10^7 GFP‐positive (competent) cell

tag: strain

value: str 168

tag: genotype/variation


title: RNA-seq_shFto-2_CD8T_rep1

city: Beijing

first: Dali

last: Han

state: 北京

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences

description: processed data file: RNA-seq_CD8T_gene_count.csv

data_processing:
For RNA-seq, adaptor and low quality bases were trimmed by Trim Galore version 0.6.0 with command "trim_galore -q 20 --three_prime_clip_R1 3 --clip_R2 3 --phred33 --illumina --stringency 3 --paired --length 36". Ribosomal RNA was removed by Bowtie2 version 2.3.5 and reads didn't align concordantly were retained. Clean reads were then aligned to mm10 genome with STAR version 2.7.0f in default setting. Only alignments with mapping quality more than 20 were used for downstream analysis. Aligned reads were converted into bigwig format based on BPM normalization in 1bp bin size with deepTools and visualized with Integrative Genomics Viewer (IGV).
For ATAC-seq, adaptor and low-quality bases were trimmed by Trim Galore version 0.6.0 with command "trim_galore -q 20 --phred33 --nextera --stringency 3 --paired". Clean reads were then aligned to mm10 genome by Bowtie2 version 2.3.5 with parameter "-X 2000 --no-mixed --no-discordant" and alignments with mapping quality more than 20 were retained. Picard toolkit was used to remove duplicates and reads mapped to blacklist regions were discarded. Fragments below 100 bps were considered as originated from nucleosome-free regions and retained for downstream analysis. Reads were then converted into bigwig format based on BPM normalization in 1bp bin size with deepTools and visualized with IGV. MACS2 v2.1.3 was applied to call peak with parameter "-g mm --nomodel --shift -100 --extsize 200 -f BAM --keep-dup all"
For m6A-seq, basic sequencing quality control, sequence alignment, and visualization were performed as described in RNA-seq data analysis. m6A peaks were called by exomePeak v2.16.0.
Genome_build: mm10
Supplementary_files_format_and_content: peaks, gene counts

organism: Mus musculus

growth_protocol: B16-OVA-shNC or shFto cells were cultured with complete DMEM medium containing 10% FBS, 1% NEAA, 1% HEPES and 5μg/mL puromycin. Naïve CD8+ OTI T cells were purified using EasySep Mouse CD8+ T Cell Isolation Kit (Stemcell). CD8+ T cells for sequencing were co-cultured with B16-OVA-shNC or shFto tumor cells for 8 hours in RPMI 1640 medium containing 10%FBS, 0.1mM NEAA, 1% HEPES, 2 mM L-glutamine and 50U IL-2.

extract_protocol:
For RNA-seq, total RNAs were extracted using Trizol reagent (invitrogen). For m6A-seq, total RNAs in tumor cells were extracted using Trizol and polyadenylated RNAs were purified using the Dynabeads mRNA Purification Kit (Invitrogen). RNAs were fragmented into ~100-nucleotide-long fragments by using 10X Fragmentation Reagent(Invitrogen) at 94℃ for 45s and stopped by the 10X Stop Solution(Invitrogen). EpiMark N6-methyladenosine enrichment kit (NEB E1610S) was used for m6A immunoprecipitation (m6A-IP) to enrich the m6A marked RNAs followed by RNA extraction by Trizol. For ATAC-seq, 5 × 104 B16-OVA-shNC or shFto cells were first lysed with ATAC RSB buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin on ice for 3 minutes. Then cell lyates were centrifuged to collecte the cell nuclei. After a wash step, the cell nuclei were ready for library construction.
For RNA-seq and m6A-seq, the library construction was performed with SMARTer Stranded Total RNA-Seq Kit (Takara). For ATAC-seq, the libraries were constructed by using TruePrep DNA Library Prep Kit V2 for illumine (Vazyme).

treatment_protocol: For m6A-seq, B16-OVA-shNC or shFto cells were treated with DMSO and shNC cells in Dac51 group were treated with 5μM Dac51 for 48 hours.  CD8+ T cells used for sequencing were co-cultured with B16-OVA-shNC or shFto for 8 hours and then sorted by BD Aria III.

tag: strain background

tag: genotype

value: OT-I

tag: cell type

value: OT-1 CD8+ T cell

tag: treatment

value: co-culture with shFto-2 B16-OVA cells


title: RD DMSO #1

type: genomic

city: Los Angeles

first: Katherine

middle: K

last: Slemmons

state: CA

address: 4650 Sunset Blvd

department: Hematology/Oncology

country: USA

institute: Children's Hospital Los Angeles

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium EPIC Beadarrays using standard Illumina protocol

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

data_processing: The raw signal intensities are extracted from the *.IDAT files using the ‘noob’ function in the minfi R package. The ‘noob’ function corrects for background fluorescence intensities and red-green dye-bias as described by Triche et al. The beta value was c

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: RD cell line

label_protocol: Genomic DNA (1000 ng) was bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s recommendations. The amount of bisulfite-converted DNA as well as the completeness of bisuflite conversion for

growth_protocol: The cell lines were cultured in RPMI-1640, 100_units/ml penicillin and 100__g/ml streptomycin, 2_mM glutamine, and 10% heat inactivated fetal bovine serum at 37ºC in an atmosphere of 5% CO2.

extract_protocol: Total genomic DNA was extracted using the KingFisher (ThermoFisher) per manufacturer’s recommendations.

treatment_protocol: SGI-110 was obtained from AdooQ and resuspended in DMSO at 10mM. Cells were treated with DMSO or 0.5µM SGI-110 for 5 days.

tag: sample type

value: Control

tag: disease

value: embryonal rhabdomyosarcoma


title: LCL161_4 (vivo)

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description: CD45+ CD11b+ cells from LCL161-treated mouse pancreatic tumor

data_processing:
FASTQs were aligned using STAR (v2.7.3a) against the GRCm38 genome with ENSEMBL 97 exon annotations.
Gene-level counts were obtained from the alignments using the R package "Rsubread" (v1.32.4).
Count normalization and differential expression analysis was performed with the R package "DESeq2" (v1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated text file of raw (unnormalized) gene-level counts for each sample

source_name: orthotopic 6694c2 pancreatic tumor

extract_protocol:
Pancreatic tumors were excised, minced, digested in RPMI containing collagenase and anti-trypsin, filtered through a 40 um cell strainer, washed with PBS, and sorted by FACS for CD45+ CD11b+ cells. Total RNA was prepared from those cells using a Qiagen RNeasy kit according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: orthotopic 6694c2 pancreatic tumor


title: LCL161_1 (vivo)


title: HIBEC_P300i_5

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Tophat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for differential gene expression
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene_Counts.tsv

source_name: Biliary Epithelial Cells

growth_protocol: Cells grown in H69 media used for cholangiocyte cell lines

extract_protocol:
Qiagen Kit was utilized to isolate mRNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SGC-CBP30 added to 4 hour serum starved HiBEC cells for 24 hours

tag: cell line

value: Human Intrahepatic Biliary Epithelial Cells (HIBEC)

tag: passage

tag: agent

value: SGC-CBP30 (10uM)


title: Rh30 SGI-110 #1

source_name: Rh30 cell line

value: Drug treated

value: alveolar rhabdomyosarcoma


title: pif457_PIF7:PIF7:4xMYC_ZT4_lowR:FR_MYC_rep2

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
transcription factor
Sample 4

library_source: genomic

data_processing:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
ChIP-seq peak identification with GEM
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig; The file processed_data_file_descriptions.txt includes the samples used for bamCompare for each .bw file.

organism: Arabidopsis thaliana

source_name: light-grown seedlings

growth_protocol: light-grown seedlings were grown on Linsmaier and Skoog medium

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: low R:FR exposure

value: seedlings

value: low R:FR

tag: antibodies

value: MYC (Cell Signaling Technology, 2276)


title: BR1_T1_minus

description:
IonXpressRNA_009_R_2015_03_11_14_18_53_user_PRI-173-Boonstra_800253_chip1_Auto_user_PRI-173-Boonstra_800253_chip1_252
IonXpressRNA_009_R_2015_03_12_13_05_45_user_PRI-174-Boonstra_800253_chip1_Auto_user_PRI-174-Boonstra_800253_chip1_254

source_name: nonT1 (bioreplicate 1)


title: HIBEC_P300i_6


title: Cultured Neoparamoeba perurans floating trophozoites biological replicate 3

city: St Lucia

first: Natasha

last: Botwright

state: QLD

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were mapped to the Atlantic salmon genome with HISAT2 v2.1.0.
Reads counts were extracted using HTSeq v 0.7.2
Differential expression was completed with EdgeR
Genome_build: ICSASG_v2 Salmo salar
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values for each sample

organism: Paramoeba perurans

source_name: Culture

growth_protocol: Neoparamoeba perurans were grown in a 1x MYB (1 g malt, 1 g yeast in 1 L sterile seawater) at 32 ppm

extract_protocol:
Rneasy mini kit (QIAGEN) with Turbo-DNase treatment
TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Amoebic gill disease was induced with Neoparamoeba perurans at 100 cells/L

tag: type

value: primary culture

value: amoeba cells

tag: disease state

value: culture


title: Rh30 DMSO #2


title: WT_IgG_I

description:
control
Sample 3

value: white light

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: RD SGI-110 #2


title: BR1_T2_plus

description:
IonXpressRNA_010_R_2015_03_11_14_18_53_user_PRI-173-Boonstra_800253_chip1_Auto_user_PRI-173-Boonstra_800253_chip1_252
IonXpressRNA_010_R_2015_03_12_13_05_45_user_PRI-174-Boonstra_800253_chip1_Auto_user_PRI-174-Boonstra_800253_chip1_254

source_name: compT2 (bioreplicate 1)

value: str 168


title: WT_H2AZ_ZT0_lowR:FR

description:
histone variant
Sample 7

data_processing:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig; The file processed_data_file_descriptions.txt includes the samples used for bamCompare for each .bw file.

value: H2A.Z (Active Motif, 39647)


title: HIBEC_Ctrl_3

value: DMSO


title: Rh30 SGI-110 #3


title: RD DMSO #3

value: Control

value: embryonal rhabdomyosarcoma


title: HIBEC_Ctrl_2

value: Human Intrahepatic Biliary Epithelial Cells (HIBEC)


title: RD DMSO #2


title: HIBEC_Ctrl_1


title: Rh30 SGI-110 #2


title: LCL161_2 (vivo)

value: orthotopic 6694c2 pancreatic tumor


title: WT_IgG_II

description:
control
Sample 5


title: Rh30 DMSO #3


title: Vehicle_4 (vivo)

description: CD45+ CD11b+ cells from vehicle-treated mouse pancreatic tumor

value: Vehicle


title: HIBEC_P300i_4

value: SGC-CBP30 (10uM)


title: Cultured Neoparamoeba perurans floating trophozoites biological replicate 2


title: pif457_PIF7:PIF7:4xMYC_ZT4_WL_MYC

description:
transcription factor
Sample 2

value: seedlings


title: Vehicle_2 (vivo)


title: Cultured Neoparamoeba perurans floating trophozoites biological replicate 1


title: Vehicle_3 (vivo)


title: pif457_PIF7:PIF7:4xMYC_ZT4_lowR:FR_MYC_rep1

description:
transcription factor
Sample 1

value: low R:FR


title: Vehicle_1 (vivo)


title: CTRL-C4_Replicate_3

status: Public on Apr 29 2021

type: RNA

city: London

first: Steve

last: West

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression data from CTRL-C4

hyb_protocol: All fragmented and biotin labeled cDNA samples were hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays for 16 hr at 45C. Arrays were washed using the Affymetrix Fluidics Station 450 according to the manufacturer’s recommendations.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 7G scanner with autoloader running Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Affymetrix gene expression data was analyzed using Bioconductor 2.5 running on R version 2.10.0. Probeset expression measures were calculated using RMA with the oligo package.

label: Biotin

source_name: Lymphoblastoid Cell Line from Control Healthy Individual. Age- and Sex-matched Control  for AOA2-P4.

label_protocol: RNA samples were amplified and biotin labeled using the WT-Ovation Pico target prep v1.0 protocol, which was derived from the NuGEN WT-Ovation Pico RNA Amplification system and the NuGEN FL-Ovation cDNA Biotin Module v2.

growth_protocol: Lymphoblastoid cell lines (LCLs) from control and AOA2 patients were cultured in RPMI 1640 medium (ThermoFisher) containing 20% FBS (Sigma-Aldrich), 1% Penicillin/Streptomycin (P/S; Sigma-Aldrich), 2 mM L-glutamine (ThermoFisher) and 1% Non-Essential Amino Acids (ThermoFisher). All LCLs were grown at 37°C and in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from cultured human and mouse cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.

treatment_protocol: Cells were harvested by trypsinization followed by two washes with ice-cold PBS.

value: Lymphoblastoid Cell Line transformed by Epstein-Barr Virus

tag: morphology

value: Lymphoblast

value: Normal


title: CTRL-C4_Replicate_2

description: Gene expression data from CTRL-C4


title: CTRL-C2_Replicate_3

description: Gene expression data from CTRL-C2

source_name: Lymphoblastoid Cell Line from Control Healthy Individual. Age- and Sex-matched Control  for AOA2-P2.


title: CTRL-C1_Replicate_2

description: Gene expression data from CTRL-C1

source_name: Lymphoblastoid Cell Line from Control Healthy Individual. Age- and Sex-matched Control  for AOA2-P1.


title: Rh30 DMSO #1

value: alveolar rhabdomyosarcoma


title: AOA2-P3_Replicate_2

description: Gene expression data from AOA2-P3

source_name: Lymphoblastoid Cell Line from AOA2 Patient with SETX Mutation

value: Homozygous mutation in SETX gene, c.3466delG


title: AOA2-P3_Replicate_3

description: Gene expression data from AOA2-P3


title: CTRL-C2_Replicate_2

description: Gene expression data from CTRL-C2


title: CTRL-C3_Replicate_2

description: Gene expression data from CTRL-C3

source_name: Lymphoblastoid Cell Line from Control Healthy Individual. Age- and Sex-matched Control  for AOA2-P3.


title: CTRL-C3_Replicate_1

description: Gene expression data from CTRL-C3


title: CTRL-C1_Replicate_3

description: Gene expression data from CTRL-C1


title: CTRL-C3_Replicate_3

description: Gene expression data from CTRL-C3


title: CTRL-C1_Replicate_1

description: Gene expression data from CTRL-C1


title: CTRL-C2_Replicate_1

description: Gene expression data from CTRL-C2


title: AOA2-P4_Replicate_3

description: Gene expression data from AOA2-P4

value: Homozygous mutation in SETX gene, c.1669C>T


title: AOA2-P1_Replicate_2

description: Gene expression data from AOA2-P1

value: Homozygous mutation in SETX gene, c.6106+3393_7101-22del20648ins25


title: AOA2-P4_Replicate_2

description: Gene expression data from AOA2-P4


title: AOA2-P1_Replicate_1

description: Gene expression data from AOA2-P1


title: AOA2-P1_Replicate_3

description: Gene expression data from AOA2-P1


title: AOA2-P4_Replicate_1

description: Gene expression data from AOA2-P4


title: CTRL-C4_Replicate_1

description: Gene expression data from CTRL-C4


title: MD11991

city: Edinburgh

first: Peter

middle: G

last: Vaughan-Shaw

address: Crewe Road

department: IGMM

institute: University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol  Standard Illumina scanning protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Perform normexp background correction using negative control probes and quantile normalization using negative and positive control probes. Limma bioconductor package

label: biotin

source_name: Normal mucosa

label_protocol: For HT12 analysis, total RNA was converted to double-stranded cDNA, followed by in vitro transcription amplification to generate labelled cRNA (Illumina TotalPrep™ RNA Amplification Kit).  Gene expression profiling was undertaken using the HumanHT-12 v4.0 Expression BeadChip Arrays (Illumina) and IScan NO660 scanner, providing coverage of 47,231 transcripts and >31,000 annotated genes derived from the National Centre for Biotechnology Information Reference Sequence RefSeq Release 38 (November 7, 2009).

extract_protocol: RNA was extracted from mucosa and blood PBMC using a proprietary RNA extraction kit (Ribopure kit, Applied Biosystems) according to the manufacturer’s protocol. This process initially involved homogenising the sample in 1 mL TRIzol. The homogenates were then incubated for 5 minutes at room temperature to enable the nucleoprotein complexes to completely dissociate. 200 μl of chloroform was added and the tubes vortexed at 2800 rpm for 15 seconds. After 5 minutes’ incubation at room temperature, the homogenate was centrifuged at 12,000 x g for 10 min at 4°C. This separated the homogenate into a lower, red, organic phase (phenol-BCP phase); an interphase; and a colourless, upper, aqueous phase. 400 μl of the aqueous phase was withdrawn to which 200 μl of ethanol was added. The mixture was vortexed at maximum speed for 5 seconds and added to a filter cartridge-collection tube. This was centrifuged at 12,000 x g for 30 seconds at room temperature and the flow-through discarded. Two wash cycles using 500 μl of provided wash solution were undertaken, with a final spin of 12,000 x g for 30 seconds to ensure all wash solution had left the filter. Finally, 50 μl of provided elution buffer was added to the filter cartridge within a new collection tube and spun at 12,000 x g for 30 seconds to elute the RNA. RNA purity (A260/A280 and A260/A230) and concentration was assessed by the Nanodrop 800 spectrophotometer. The RNA yield and integrity of samples to be submitted for microarray expression analysis was assessed using the 2100 Bioanalyzer®.  cDNA synthesis of RNA samples was performed prior to qRT-PCR. RNA was first treated with DNase. 1µg RNA was treated with 1µl (1 unit) DNase 1 (commercial RQ1 RNase-free DNase in 10mM HEPES (pH 7.5), 50% glycerol (v/v), 10mM CaCl2 and 10mM MgCl2; Promega), with 1µl of 10x RQ1 reaction buffer (400mM Tris-HCl (pH 8.0), 100mM MgSO4 and 10mM CaCl2; Promega) and RNase-free DNase-free water (Gibco) to make a 10µl reaction. Following incubation at 37°C for 30 minutes, 1µl DNase STOP (20mM EGTA, pH 8.0, Promega) was added and incubation at 65°C for 10 minutes performed to inactivate the DNase.  DNase treated RNA samples were then reversed transcribed to cDNA. Samples were added to a solution containing 1µl (200 units) Moloney Murine Leukemia Virus Reverse Transcriptase (in 20mM Tris-HCl (pH 7.5), 200mM NaCl, 0.1mM EDTA, 1mM DTT, 0.01% Nonidet® P-40 and 50% glycerol; Promega), 4µl M-M:VRT buffer (50mM Tris-HCl (pH 8.3 at 25°C; Promega), 75mM KCl, 3mM MgCl2 and 10mM DTT; Promega), 2µl dNTP (10mM, containing dATP, dCTP, dGTP and dTTP; Promega), 1µl (20 units) Recombinant RNasin Ribonuclease Inhibitor (in 20mM HEPES-KOH (pH 7.6), 50mM KCl, 8mM DTT, 50% (v/v) glycerol; Promega), 2µl of 0.25µg/µl random primers (Promega) and 1µl RNase-free DNase-free water. This was incubated at 37°C for 30 minutes and 95°C for 5 minutes.

treatment_protocol: Human subjects were sampled at baseline. No interventions were investigated in this study

value: Normal mucosa

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: RIGHT

tag: label - sentrix barcode

tag: label - section

value: E

tag: batchnumber


title: AOA2-P2_Replicate_2

description: Gene expression data from AOA2-P2

tag: cell type

tag: morphology

tag: genotype

value: Compound heterozygous mutation in SETX gene, c.7240C>T; c.7626delG


title: AOA2-P2_Replicate_3

description: Gene expression data from AOA2-P2


title: MD16173

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

value: LEFT

value: K


title: AOA2-P3_Replicate_1

description: Gene expression data from AOA2-P3


title: AOA2-P2_Replicate_1

description: Gene expression data from AOA2-P2


title: MD16601

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: B


title: Day 1 HKLs from Fish 1

city: St. John's

first: Nicole

last: Smith

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences

country: Canada

institute: Memorial University

description: Biological replicate 1 of 4. Day 1 HKL culture.

hyb_protocol: The Cy5-labelled aRNA (825 ng) from each experimental sample was mixed with an equal quantity of Cy3-labelled aRNA from the common reference, and the resulting pool was fragmented using the Gene Expression Hybridization Kit, following the manufacturer's instructions (Agilent, Mississauga, ON, Canada). Each labelled aRNA pool was co-hybridized to the microarray (8 arrays in total, Figure 1A) for 17 h at 65°C with rotation using an Agilent hybridization oven.

scan_protocol: The microarray slides were scanned at 5 µm resolution using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer, Waltham, MA, USA), and the Cy3 and Cy5 channel photomultiplier tube (PMT) settings were adjusted to balance the fluorescence signal. The raw data were saved as TIFF images, and the signal intensity data were extracted using Imagene 9.0 (BioDiscovery, El Segundo, CA, USA).

data_processing: R and the Bioconductor package ‘marray’ were used to flag (remove from the data set) low-quality spots on the microarray and to log2-transform and Loess-normalize the data. Probes with more than 25% missing values were omitted from the dataset, and the missing values were imputed using the least sqare methods  (‘EM_array’) and the ‘LSimpute’ package

organism: Salmo salar

source_name: Atlantic salmon HKLs cultured for 1 day

label_protocol: A consortium for Genomic Research on All Salmonids Project (cGRASP)-designed 44K Atlantic salmon oligonucleotide array (GEO accession: GPL11299; Agilent Technologies) that comprises 60mer probes was used as the microarray platform. 500 ng of RNA were in vitro transcripted into aRNA following the manufacturer's instructions. The quality and quantity of the aRNAs were checked by agarose gel electrophoresis and NanoDrop spectrophotometry, respectively. Amplified RNA from all samples was pooled and used as a common reference. Twenty micrograms of aRNA were ethanol precipitated overnight and re-suspended in coupling buffer. The experimental samples were then labelled with Cy5 (GE Healthcare Life Sciences, Buckinghamshire, UK), while the common reference was labelled with Cy3 (GE Healthcare Life Sciences), following the manufacturer’s instructions. The efficiency of labelling and aRNA concentration were assessed using NanoDrop spectrophotometry.

growth_protocol: Atlantic salmon HKLs were isolated using a Percoll density gradient and cultured in L-15 media (supplemented with FBS and antibiotic) for 1 day or 5 days.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were rinsed with L-15 media 24 h after seeding to remove non-adherent cells and every 48 h thereafter. Cells were sampled with Trizol immediately after rinsing at 24h (Day 1) and again at 120 h (Day 5).

tag: primary cells

value: Atlantic salmon adherent HKLs

tag: culture duration

value: 1 day

source_name: Pooled Day 1 and Day 5 adherent HKLs

value: Pooled adherent HKLs cultured for 1 day and 5 days


title: MD18234

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: Day 5 HKLs from Fish 1

description: Biological replicate 1 of 4. Day 5 HKL culture.

source_name: Atlantic salmon HKLs cultured for 5 days

value: 5 days


title: MD13170

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

value: J


title: MD14394

tag: tissue

tag: age

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: F


title: MD16170

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: label - sentrix barcode

tag: label - section

value: G

tag: batchnumber


title: MD12368

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9


title: Day 5 HKLs from Fish 4

description: Biological replicate 4 of 4. Day 5 HKL culture.

tag: primary cells

tag: culture duration


title: Day 5 HKLs from Fish 3

description: Biological replicate 3 of 4. Day 5 HKL culture.


title: Day 1 HKLs from Fish 3

description: Biological replicate 3 of 4. Day 1 HKL culture.


title: Day 1 HKLs from Fish 2

description: Biological replicate 2 of 4. Day 1 HKL culture.


title: Day 1 HKLs from Fish 4

description: Biological replicate 4 of 4. Day 1 HKL culture.


title: Day 5 HKLs from Fish 2

description: Biological replicate 2 of 4. Day 5 HKL culture.


title: MD18761

tag: tissue

tag: age

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site


title: MD12552

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: label - sentrix barcode

tag: label - section

value: H

tag: batchnumber


title: MD13845

tag: tissue

tag: age

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

value: L


title: RNA-seq_shFto-1_CD8T_rep2

tag: strain background

tag: genotype

value: OT-I

tag: cell type

value: OT-1 CD8+ T cell

tag: treatment

value: co-culture with shFto-1 B16-OVA cells


title: MD11021

value: Normal mucosa

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site


title: MD17135

tag: tissue

tag: age

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: MD16829

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 9

tag: peer 10

tag: peer 11

value: RIGHT

value: E


title: MD17466

tag: tissue

tag: age

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: LEFT


title: MD2335

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: label - sentrix barcode


title: MD7851

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 9

tag: label - section

value: B

tag: batchnumber


title: MD18565

tag: tissue

tag: age

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

value: K


title: MD13451

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site

value: A


title: MD13846

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 9

tag: label - sentrix barcode


title: MD13839

tag: tissue

tag: age

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - section

tag: batchnumber


title: MD18243

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD18562

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site

value: D


title: MD13834

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD18552

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

value: C

tag: batchnumber


title: MD18553

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14

value: I


title: MD18564

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD18567

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD18566

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD18561

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD18563

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site

value: F


title: MD18249

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD18560

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD18559

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14

value: J


title: MD18554

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD18240

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD18555

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD18551

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD18238

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD18557

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD18228

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD18231

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD18237

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD18248

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13830

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD18229

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD18233

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site

value: G


title: MD18232

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode

value: H


title: MD18230

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17835

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17802

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17793

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD18236

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17797

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17831

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17792

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17798

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17801

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17796

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17790

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD17791

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17789

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17788

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17794

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD17786

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17477

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17476

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17478

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17795

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17787

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17479

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD18239

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode

value: L


title: MD17300

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17473

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17253

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17465

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD17467

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17470

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17255

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17305

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17243

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17240

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17469

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17472

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD17239

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17471

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17463

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17464

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD17236

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17302

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17247

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17474

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17304

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17468

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17241

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17237

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD17257

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17234

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17238

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17235

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD17233

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17229

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17225

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD18247

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17142

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17224

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17151

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17227

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD17226

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17146

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17141

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17147

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD17231

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17156

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17228

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17149

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17138

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17212

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17154

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17140

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD17115

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17125

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17128

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17139

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD17131

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17129

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

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tag: peer 14


title: MD17117

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17134

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD17106

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD17130

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD17105

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17108

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD17096

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17094

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17102

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17104

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD16819

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17110

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD17076

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD17083

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD16824

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD16831

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD16760

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17099

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD16997

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD17088

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17095

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD17098

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD16759

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD17093

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD16619

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD16632

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD16616

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD16612

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD16608

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD17064

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD16602

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD16661

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD16605

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD16662

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD16603

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD16598

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD16596

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD16600

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD16593

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD16587

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD16595

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD16597

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD16586

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD16584

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD16588

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD16183

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD16185

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD16590

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD16585

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD16184

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD16186

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD16180

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD16175

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD16177

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD16174

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD16168

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD16176

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD16178

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD16179

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD16172

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD16167

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD16171

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD14403

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD16169

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD15039

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD15040

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD14501

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD16147

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD17133

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD14509

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD15037

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD15049

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD15042

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD16182

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD14513

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD15036

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD14502

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD15038

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD15041

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD14498

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD14402

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD14398

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD14396

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD14400

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD14399

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD14397

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD14393

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD14392

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD14076

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD14391

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD14063

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD14390

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD14386

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD13887

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD13896

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD13849

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13850

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD14384

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD14059

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13897

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD14388

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD14385

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD13900

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD14383

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD14058

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD14056

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD14064

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD14387

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13882

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD13847

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13842

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13848

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD13841

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD13844

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD13843

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD13840

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD13838

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD13467

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD13836

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD13833

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13831

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD13837

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13455

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD16181

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD13447

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD13422

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD13425

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD13453

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD13427

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD13429

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD13458

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD13446

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13441

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD13443

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13454

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13452

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD13430

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD13417

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD13419

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD13420

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD13414

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD13412

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD13411

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD13408

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13421

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD13403

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13402

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13394

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD13379

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD13375

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD14395

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD13158

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD13160

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD13401

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD13393

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD13166

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13389

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD13153

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13104

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13378

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD13167

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD13165

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD13386

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD13043

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD13101

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD13097

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD13103

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD13381

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD12884

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD12996

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD13159

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13041

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD13100

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD12854

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD12775

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD12755

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD13156

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD12810

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD12741

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD12751

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD13046

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD12779

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD12812

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12726

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD12668

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD12669

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD12659

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD12660

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD12650

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD12647

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD12639

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD12637

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD12856

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD12631

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD12645

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD13399

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD12634

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD12626

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD12568

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD12562

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD12481

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD12520

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD12587

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD12529

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD12619

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD12555

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD12813

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12586

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD12475

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD12633

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD12519

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD12602

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD12477

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD12597

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD12609

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD12483

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD12624

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD12646

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD12584

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12473

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: MD12464

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 15

tag: label - sampling site


title: MD12630

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sentrix barcode


title: MD12446

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - section

tag: batchnumber


title: MD12468

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 13

tag: peer 14


title: MD12451

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site


title: MD12433

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 12

tag: label - sentrix barcode


title: MD12435

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: label - section

tag: batchnumber


title: MD12419

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 13

tag: peer 14


title: MD12412

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 15

tag: label - sampling site


title: MD12415

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: label - sentrix barcode


title: MD12421

tag: tissue

tag: age

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12409

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 13

tag: peer 14


title: HuT-ctrl-rep3

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: Hybridization according to Affymetrix protocol, performed at the NCI-Frederick LMT Microarray Center (Frederick, MD)

scan_protocol: GeneArray scanner, according to Affymetrix protocol, performed at the NCI-Frederick LMT Microarray Center (Frederick, MD)

data_processing: MAS5.0 normalization method, according to Affymetrix protocol. All intensity values were log2 transformed before further analysis.

label_protocol: Biotin labeling according to Affymetrix protocol, performed at the NCI-Frederick LMT Microarray Center (Frederick, MD)

growth_protocol: Cells were cultured in appropriate cell culture medium (Gibco Laboratories) supplemented with 10% fetal bovine serum (Gibco Laboratories), 100-units/L penicillin-streptomycin and 1% glutamine (Gibco Laboratories).

extract_protocol: Total RNA was isolated from all seven cell lines using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: HUT78, LOXIMVI, M14, A549, MDA231, ACHN, MiaPaca and PC3 cell lines were treated with 25 ng/ml of romidepsin for 6 hours. A549, ACHN, and MiaPaca were also treated for 18 hours. Controls were treated with DMSO. Treatment was followed by a 42-hours incubation in drug-free medium.

tag: cell line

value: HuT

tag: treatment

value: control

tag: time (h)


title: HuT-Dp 6h-rep3

source_name: HuT-Dp 6h-rep3

value: Romidepsin


title: MD12408

tag: tissue

value: Normal mucosa

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: LOX-Dp 6h-rep3

source_name: LOX-Dp 6h-rep3

value: LOX


title: MD12316

tag: age

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11

value: RIGHT

tag: label - section

tag: batchnumber


title: MD12369

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 7

tag: peer 13

tag: peer 14

value: LEFT


title: PC3-ctrl-rep3

tag: cell line

tag: treatment

tag: time (h)


title: PC3-Dp 6h-rep3

source_name: PC3-Dp 6h-rep3


title: MD12385

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 8

tag: peer 12

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: MD12370

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

value: E

tag: batchnumber


title: MDA-ctrl-rep3

tag: cell line

value: MDA

tag: treatment

tag: time (h)


title: HuT-Dp 6h-rep2

source_name: HuT-Dp 6h-rep2


title: MD12312

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 12

tag: peer 13

tag: peer 14

value: K


title: M14-ctrl-rep3


title: MD12407

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: M14-Dp 6h-rep3

source_name: M14-Dp 6h-rep3

tag: cell line

tag: treatment

tag: time (h)


title: MDA-Dp 6h-rep3

source_name: MDA-Dp 6h-rep3


title: LOX-ctrl-rep3


title: MD12307

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12400

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 12

tag: peer 13

tag: peer 14


title: HuT-ctrl-rep2

tag: cell line

tag: treatment

tag: time (h)


title: MD12305

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: MD12259

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12304

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 12

tag: peer 13

tag: peer 14


title: LOX-Dp 6h-rep2

source_name: LOX-Dp 6h-rep2

tag: cell line

tag: treatment

tag: time (h)


title: MD12255

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: MD12260

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: LOX-ctrl-rep2

tag: cell line

tag: treatment

tag: time (h)


title: PC3-Dp 6h-rep2

source_name: PC3-Dp 6h-rep2


title: MD12256

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 12

tag: peer 13

tag: peer 14


title: M14-ctrl-rep2


title: M14-Dp 6h-rep2

source_name: M14-Dp 6h-rep2


title: MD12254

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: MD12272

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 11

tag: label - section

tag: batchnumber


title: MD12454

tag: age

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 12

tag: peer 13

tag: peer 14

value: D


title: MD12236

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 15


title: MD12253

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 11

tag: label - sampling site

tag: label - sentrix barcode


title: MD12234

tag: age

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 12

tag: label - section

value: I

tag: batchnumber


title: PC3-ctrl-rep2

tag: cell line

tag: treatment

tag: time (h)


title: MDA-Dp 6h-rep2

source_name: MDA-Dp 6h-rep2


title: MD12202

tag: tissue

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15

value: C


title: MD12071

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 11

tag: label - sampling site

tag: label - sentrix barcode

value: B


title: MD12147

tag: tissue

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 12

tag: label - section

tag: batchnumber


title: MD12208

tag: age

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15


title: MD12114

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 7

tag: peer 8

tag: peer 11

value: A


title: LOX-Dp 6h-rep1

source_name: LOX-Dp 6h-rep1

tag: cell line

tag: treatment

tag: time (h)


title: MD12100

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 12

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: MD12201

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15


title: MDA-ctrl-rep1

tag: cell line

tag: treatment

tag: time (h)


title: PC3-ctrl-rep1


title: MD12095

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

tag: peer 11

tag: peer 12

tag: label - sampling site

value: H


title: HuT-Dp 6h-rep1

source_name: HuT-Dp 6h-rep1


title: MD12069

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: M14-Dp 6h-rep1

source_name: M14-Dp 6h-rep1

tag: cell line

tag: treatment

tag: time (h)


title: ACHN-Dp 6h-rep3

source_name: ACHN-Dp 6h-rep3

value: ACHN


title: HuT-ctrl-rep1

value: HuT


title: M14-ctrl-rep1

value: control


title: MDA-ctrl-rep2


title: LOX-ctrl-rep1


title: MD12070

source_name: Normal mucosa

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

tag: peer 13

tag: peer 14

tag: peer 15

value: L


title: MD12088

value: Normal mucosa

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: label - sampling site


title: ACHN-ctrl-rep3

tag: cell line

tag: treatment

tag: time (h)


title: MDA-Dp 6h-rep1

source_name: MDA-Dp 6h-rep1

value: Romidepsin


title: PC3-Dp 6h-rep1

source_name: PC3-Dp 6h-rep1


title: MD12068

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

value: RIGHT

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: ACHN-Dp 6h-rep2

source_name: ACHN-Dp 6h-rep2


title: ACHN-ctrl-rep2


title: ACHN-ctrl-rep1


title: MD12065

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15

value: LEFT


title: ACHN-Dp 6h-rep1

source_name: ACHN-Dp 6h-rep1

tag: cell line

tag: treatment

tag: time (h)


title: HEK293 FS mutant NUP98-HOXA9 (HA)  H3K27ac Input

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: Dept of Biochemistry and Biophysics

institute: UNC Lineberger Comprehensive Cancer Center

data_processing:
All reads were mapped to the human genome (hg19), drosophila (dm3) or mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools. We filter out reads with a mapping quality score of < 20 for downstream analysis.
Profiles of ChIP-seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: GRCh37/hg19 or GRCm38/mm10

source_name: HEK 293 cells

growth_protocol: HEK 293 cells were grown in DMEM base medium plus 10% FBS and 1% antibiotics. The fusion-transformed mouse HSPCs (leukemia-causing cells) were grown in Opti-MEM base medium plus 10% FBS, 2% of supernatant containing home-made murine stem cell factor (from mSCF-producing CHO cells), 1% of supernatant containing murine FLT3 ligand (from FLT3L-producing cells), 1% antibiotics and 50uM of beta-mercaptoethanol.

extract_protocol:
Fixed cells were sonicated in a Bioruptor sonication device for 45 cycles at a high-energy setting to enrich the sonicated DNA to be ~300bp as described in our method. The sonicated samples were incubated with the indicated antibodies pre-bound to the protein-G/A beads for overnight. Across 293 cell samples with GFP-tagged chimera, the cleared cell lysates from sonicated nuclei were added with the same fraction of the sonicated and cleared chromatin of Drosophila S2 cells (see our Method), and then protein-DNA complexes were isolated with antibodies against GFP and those against Drosophila-specific histone H2Av (Active Motif cat# 39715). Beads were then washed with various washing buffers (please see our method). Bead-bound DNA was eluted and subject to reverse crosslinking and sequential treatments of RNase and protease K. Finally, ChIP DNA was purified with a PCR cleanup kit (Qiagen) and used for library construction.
Multiplexed ChIP-seq sequencing libraries were prepared using the NEBNext Ultra II kit (NEB, #E7645L) following the manufacture’s instruction. ChIP-seq libraries were pooled together and sequenced on a Nextseq 550 system using a Nextseq 550 High Output Kit v2.5 or sent to UNC High-Throughput Sequencing Facility (HTSF) for sequencing by using an Illuminia Hiseq 2500/4000 system.

treatment_protocol: For ChIP-seq experiments, HEK293 cells with stable expression of IDR-WT or IDR-mutated NUP98-HOXA9 and FUS-HOXA9 (GFP-tagged or 3XHA-3XFLAG-tagged) were grown in DMEM medium and fixed with 1% of formaldehyde in PBS for 10 min at room temperature. For 1,6-Hexanediol treatment, growth medium was removed and cells then incubated with 10% of 1,6-hexanediol in PBS for 1 min. Then, formaldehyde was added directly to make up the final concentration formaldehyde to be 1%, followed by incubation at room temperature for 10 min.

tag: antibody used

value: n/a (input)

tag: treatment condition


title: HEK293 FS mutant NUP98-HOXA9 (HA) H3K27ac IP

value: Rabbit anti-H3K27Ac antibody (Ab4729)


title: HEK293 WT NUP98-HOXA9 (HA) H3K27ac Input

value: 3XHA-3XFLAG-tagged, IDR-WT NUP98-HOXA9


title: HEK293 WT NUP98-HOXA9 (HA) H3K27ac IP


title: MD12056

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

tag: peer 11

tag: peer 12

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section

value: G


title: A549-ctrl-rep2

tag: cell line


title: MD12064

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15

tag: batchnumber


title: HEK293 EV control cell  (matched for H3K27ac IP)

tag: antibody used

tag: treatment condition

value: Empty vector (EV) control


title: MD12067

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

tag: peer 11

tag: peer 12

tag: label - sampling site


title: A549-Dp 6h-rep3

source_name: A549-Dp 6h-rep3

tag: cell line

tag: treatment

tag: time (h)


title: A549-ctrl-rep3


title: MD12054

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sentrix barcode

tag: label - section

value: J


title: MD12052

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

tag: peer 11

tag: peer 12

value: I

tag: batchnumber


title: MD12051

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 9

tag: label - sampling site


title: MD12050

tag: tissue

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sentrix barcode

tag: label - section

value: F


title: MD12057

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 8

tag: peer 11

value: D


title: MD12059

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 12

value: B

tag: batchnumber


title: MD12063

tag: tissue

tag: peer 9

tag: peer 10

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: C


title: MD12061

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: label - sentrix barcode

tag: label - section


title: A549-ctrl-rep1

tag: cell line

tag: treatment

value: control

tag: time (h)


title: A549-Dp 6h-rep2

source_name: A549-Dp 6h-rep2


title: HEK293 EV control cell H3K27ac

tag: antibody used

tag: treatment condition


title: MD12048

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: batchnumber


title: HEK293 WT NUP98-HOXA9 (HA) HA IP

value: Rabbit anti-HA antibody (ab9110)


title: HEK293 EV control cell Input (matched for HA IP)


title: MD12053

value: Normal mucosa

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section


title: MD12049

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 8

value: A


title: HEK293 WT NUP98-HOXA9 (HA) Input (matched for HA IP)

tag: antibody used

tag: treatment condition


title: HEK293 FS mutant NUP98-HOXA9 (HA) HA IP


title: HEK293 FS mutant NUP98-HOXA9 (HA) Input (matched for HA IP)


title: HEK293 EV control cell HA IP


title: ORS

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Reads were trimmed with Atropos.
Mapping and gene quantification were performed with STAR version 2.5.3 against human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab: Tab-delimited files with raw counts for each genes.

molecule: polyA RNA

source_name: Ewing sarcoma cell line

growth_protocol: Cells were grown as previously described (Kovar et al., 1997, Dauphinot et  al., 2001) and recommended by ATCC, DSMZ, or COG Repository.

extract_protocol:
RNA was extracted using RNeasy plus mini kit (74134, Qiagen).
RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library.

tag: cell line

value: ORS

tag: cell type

value: Ewing sarcoma cell line

tag: genotype

value: STAG2 mut


title: POE

value: POE


title: MD12047

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

value: RIGHT

tag: batchnumber


title: MD12041

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 8

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section


title: SKES1

tag: cell line

tag: cell type

tag: genotype


title: MD12039

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

value: LEFT


title: MD12042

tag: tissue

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 8

tag: peer 14

tag: peer 15

tag: batchnumber


title: MD12046

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section

value: G


title: MD12032

tag: tissue

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

value: J


title: MD12045

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 8

tag: peer 14


title: MHH-ES1

tag: cell line

tag: cell type

tag: genotype


title: EW3


title: EW7

value: STAG2 WT


title: STA-ET-8.1


title: EW22


title: MD12040

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: TC-252


title: RM82


title: A549-Dp 6h-rep1

source_name: A549-Dp 6h-rep1

tag: treatment

value: Romidepsin

tag: time (h)


title: STA-ET-11


title: MD12037

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

value: E


title: MD12033

tag: tissue

tag: age

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

value: I


title: MD12003

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: label - section

tag: batchnumber


title: MD11990

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13


title: STA-ET-1

tag: cell line

tag: cell type

tag: genotype


title: EW16


title: MD12038

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

value: L


title: SK-N-MC

value: SK-N-MC


title: STA-ET-7.2


title: MD12002

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: label - section

value: C

tag: batchnumber


title: VH64

tag: cell line

tag: cell type

tag: genotype


title: CHLA-10


title: MD11986

tag: tissue

value: Normal mucosa

tag: age

tag: gender

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14


title: MD11915

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: WE-68

tag: cell line

tag: cell type

tag: genotype


title: MD11588

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 10

tag: peer 11

tag: label - section

value: D

tag: batchnumber


title: MD11981

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 12

tag: peer 13

tag: peer 14


title: MD11481

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

value: B


title: WE_M2_68

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

tag: genotype


title: MD11868

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: STA-ET-2.1


title: EW1