title: MDA-MB-231-P

description: LncRNA expression

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA)

source_name: MDA-MB-231, Parental

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: Total RNA of breast cancer cells was prepared using TRIZOL (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: When cells growth with 70 percent confluence, cells were subjected for RNA extraction.

value: breast cancer cell line

value: Parental


title: MDA-MB-231-IV2-1

status: Public on May 26 2021

type: RNA

city: New Taipei

first: Kuo-Wang

last: Tsai

address: No. 289 Jianguo Road, Xindian District, New Taipei City

country: Taiwan

institute: Taipei Tzu Chi Hospital

description: LncRNA expression

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231, metastatic

growth_protocol: MDA-MB-231 cells and IV2-1 cells were culturein in Dulbecco’s modified Eagle’s medium supplemented with 10% inactivated FBS

tag: cell type

tag: treatment

value: highly metastatic breast cancer cells derived from MDA-MB-231-P


title: Au_20_COOH_1

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_1.txt

hyb_protocol: Labeled samples were randomly hybridized to Agilent SurePrint G3Human GE 8x60K DNA microarrays, according to the manufacturer’s protocol (Agilent).

scan_protocol: Hybridized slides were scanned using the Agilent microarray scanner (Model G2505C) and raw data were extracted using Agilent feature extraction software (version 12.0.1.1).

data_processing: mRNA expression raw intensity values were quality checked and exported from Agilent Feature Extraction software. The raw intensities were analysed with Bioconductor package Limma. Experiment was two-colour, but the data were analysed as a single-channel arrays.

organism: Mus musculus

label_protocol: RNA samples were labeled with Cy3 or Cy5 (Quick Amp Gene Expression Labelling kit, Agilent).

growth_protocol: Female C57BL/6 mice (7−8 weeks old) were purchased from Scanbur A/S (Karslunde, Denmark). They were housed in stainless steel cages with aspen chip bedding, in groups of four. The housing conditions were carefully controlled with temperature (20−21 °C) and humidity (40−45%) and 12 h dark/light cycles. Mice received food and water ad libitum.

extract_protocol: After sacrificing the lungs were removed, cut and transferred to RNALater stabilizing solution (Ambion, Life Technologies, CA, USA), and stored at −80 °C. Total RNA (totRNA) from the RNAlater-stabilized lung samples was isolated and purified by phenol/chloroform isolation method according to the instructions by Bioline Reagents.

treatment_protocol: Mice were exposed by oropharyngeal aspiration under isoflurane anesthesia to 10 μg of ENM per day in (50 μL) PBS for 4 consecutive days, mimicking a 1-week exposure scenario. Control mice received a corresponding vehicle, either plain  PBS or PBS supplemented with polyvinylpyrroline (Nanodiamnods NH control) or albumin (MWCNT control). BAL and tissue samples were collected 24 hours after the final exposure.

tag: tissue

value: lung

tag: age

value: 8 w/o

tag: gender

value: female

tag: strain

tag: exposure time

value: 4 days + 24 hours

tag: slide #

tag: functionalization

value: COOH

tag: nanomaterial


title: CuO_COOH_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_4.txt

value: CuO


title: CdTE_NH_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_3.txt

value: NH

value: CdTE


title: shAMPKa1/a2 rep2

type: SRA

city: Manchester

first: Michela

last: Garofalo

address: Wilmslow Road

country: United Kingdom

institute: University of Manchester

library_source: transcriptomic

data_processing:
Quality Check - Fastqc
Alignment was done with Rsubread Package with default parameters
Gene count generated with featureCounts program with Paired End (PE) mode
Gene model : Homo_sapiens.GRCh37.74
DESeq2 package was used for Differenatial gene expression
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files, Differentially expressed gene/LncRNA list and raw and normalized counts

source_name: H1299 cells

growth_protocol: H1299 cells were cultured in RPMI 1640 medium containing 10% FBS.

extract_protocol:
Total RNA was isolated from cells using TRIzol according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Samples were sequenced using a Nextseq500 instrument (Illumina) for 75bp. Sequencing was between 20 and 30 million reads per sample.

treatment_protocol: shRNA lentiviral transduction

value: AMPKa1/a2 knockdown


title: shAMPKa1/a2 rep1


title: shAMPKa1/a2 rep3


title: H1650 9291_rep 2

city: Aurora

first: Natalia

middle: J

last: Gurule

state: CO

department: Craniofacial Biology

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
PC9 and H1650 cells were suspended in 50% Matrigel/phosphate-buffered saline at 10 million cells per mL and 1 million cells were injected subcutaneously in both flanks of female nu/nu mice. When at least one of the tumors reached a volume of 100 mm3, the mice were randomized into treatment groups of diluent control (1% Polysorbate 80), AZD9291 (5 mg/kg). Drugs were delivered daily by oral gavage.
invivoH1650_ PC9 _AZD9291 _genes.fpkm_table.xlsx
H1650 in vivo

data_processing:
raw fastq files were processed with HISAT2
 Reads were mapped UCSC reference annotation GRCh37(hg19)
Transcripts were assembled against ensemble reference using Cufflinks.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file containing FPKMs

source_name: flank xenograft

extract_protocol:
total RNA was purified from cells using Quick-RNA MiniPrep kits (Zymo Research)
Illumina directional mRNA prep
per Novogene protocol for PE150 Illumina NGS

value: lung cancer cell line

value: osimertinib

tag: cell line


title: H1650 Control_rep2

value: diluent control


title: H1650 Control_rep 1


title: shAMPKa2 rep3

value: AMPKa2 knockdown


title: H1650 Control_rep 3


title: PC9 9291_rep 3

description:
PC9 and H1650 cells were suspended in 50% Matrigel/phosphate-buffered saline at 10 million cells per mL and 1 million cells were injected subcutaneously in both flanks of female nu/nu mice. When at least one of the tumors reached a volume of 100 mm3, the mice were randomized into treatment groups of diluent control (1% Polysorbate 80), AZD9291 (5 mg/kg). Drugs were delivered daily by oral gavage.
invivoH1650_ PC9 _AZD9291 _genes.fpkm_table.xlsx
PC9 in vivo


title: U2OS ABA treated Replicate 2

city: Menlo Park

first: Stephen

last: Shang

state: California

address: 297 Jane Stanford Way

institute: Stanford University

description: H3K9me3 ChIPseq

library_source: genomic

data_processing:
Library strategy: CRISPR-EChO
Alignment: Bowtie2
Duplicate Removal: samtools
Bigwig Generation: bedtools, bamCoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files *.bw contain indexed binary files

molecule: genomic DNA

source_name: U2OS Cells with CRISPR-ECHO

growth_protocol: Cells were grown with DMEM and split at 90% confluency.

extract_protocol:
Cell Lysis was performed as per standard ChIP protocol.  DNA was extracted via bead elution with Dynabeads Protein A.
Libraries were constructed as per standard ChIPseq library kit preparation with Novogene.

treatment_protocol: Cells were treated 1 day after splitting with ABA or DMSO in fresh DMSO media and, after reaching 80% confluency, subject to a standard ChIP protocol of 1% crosslinking followed by lysis, sonication, and pulldown with H3K9me3 antibodies.  Full protocol: Roughly 4 × 107 cells per sample were washed with PBS before addition of 1% formaldehyde in fresh media for crosslinking. After 15 minutes, the samples were quenched with glycine to a final concentration of 0.125 mol/L glycine. Cells were then lifted with a cell scraper, spun down, and resuspended in SDS lysis buffer (1% SDS, 10 mmol/L EDTA, 50 mmol/L Tris-HCl, pH 8.1) at a ratio of 1 mL per 2 × 107 cells and frozen at -80 before lysis at room temperature for 1h immediately before sonication. Pulse sonications were performed for 7 minutes at 40% amplitude with 1s on/1 s off on a Qsonica Q500 in 1mL aliquots in 1.5mL Eppendorf tubes with a total of 2 mL with maximum 50% SDS Lysis Buffer solution diluted with ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mmol/L EDTA, 16.7 mmol/L Tris-HCl, pH 8.1, 167 mmol/L NaCl). ChIPs were performed with antibodies for H3K9me3 (Abcam, ab8898). Pulldowns were performed with Dynabeads Protein A (10001D, Lot 00531421). DNA quantities were measured by Qubit 2.0 (Invitrogen Qubit dsDNA HS Assay Kit, Q32854) and Bioanalyzer before sequencing with Novogene targeting 20M reads / sample.

value: Tumor Cell Line

value: ABA-treated

tag: chip antibody


title: shAMPKa2 rep2


title: shAMPKa2 rep1


title: PC9 9291_rep 1


title: PC9 9292_rep 2


title: shAMPKa1 rep3

value: AMPKa1 knockdown


title: PC9 Control_rep 3


title: shAMPKa1 rep2


title: PC9 Control_rep 2


title: shAMPKa1 rep1


title: PC9 Control_rep 1


title: MWCNT_prist_1

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_3.txt

value: core

value: MWCNT


title: MWCNT_PEG_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_3.txt

value: lung

value: 8 w/o

value: PEG


title: Ag_PEG_1

description: US11263921_257480912645_S01_GE2_1200_Jun14_1_3.txt

value: female

value: 4 days + 24 hours

value: Ag


title: Early Rebiopsy patient 8 rebiopsy

description:
Target lesions were biopsied prior to treatment and site matched upon re-biopsy. Histopathologic evaluation of the pre- and post-treatment biopsies was performed within 24-36 hours of collection. RNA extraction was performed on biopsy cores with a goal of obtaining at least 500 tumor cells to facilitate optimal RNA sequencing.
EarlyRebiopsy_genes.fpkm_table.xslx
Early Rebiopsy

source_name: core biopsy

value: EGFR TKI


title: CdTE_NH_1

description: US11263921_257480912645_S01_GE2_1200_Jun14_1_1.txt

value: NH

value: CdTE


title: MWCNT_NH_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_1_4.txt


title: ND_PEG_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_1.txt

value: ND


title: Ag_NH_2

description: US11263921_257480912634_S01_GE2_1200_Jun14_1_4.txt


title: ND_PEG_1

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_3.txt


title: Au_20_PEG_1

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_1.txt


title: TiO_core_prtcl_1

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_1.txt

value: TiO


title: TiO_core_rod_2

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_2.txt


title: CdTe_PEG_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_2.txt


title: shCTL rep2

value: control knockdown


title: shCTL rep3


title: Early Rebiopsy patient 8 baseline

value: treatment naïve


title: shCTL rep1


title: HEK293_Input_Rep2

city: Vandoeuvre-lès-Nancy

first: Sylvain

last: Maenner

address: 9 Avenue de la Forêt de Haye

department: CNRS-UL

country: France

institute: IMoPA

data_processing:
library strategy: ChIRP-seq
Fastq files of replicates 1 and 2 were aligned to the hg19 genome using bowtie2.
The aligned reads of both even and odd bam files of each replicate were intersected and merged using bedtools.
Peak calling was performed against LacZ negative control using MACS2 peak caller.
Peaks were further filtered based on the score ≥ 15, and FDR ≤ 0.05. Peaks located in blacklisted regions of the genome identified by ENCODE were discarded. Finally, only common peaks between both replicates were kept and considered as “True Peaks”.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using bamcoverage from deeptools; Scores represent RPKM.
Supplementary_files_format_and_content: peak bed files

growth_protocol: HEK293 cells were grown in Dulbecco’s Modified Eagle’s Medium-high glucose (DMEM) (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich), 1% penicillin/streptomycin (Sigma-Aldrich), and 1% L-glutamine (Sigma-Aldrich).

extract_protocol:
Lysates were clarified from sonicated chromatin and RNA-DNA complexes were isolated by antisense biotinylated oligos on streptavidin beads according to the protocol published by Chu et al., 2011. DNA was eluted using GeneJET Gel Extraction kit (Thermo Fisher Scientific).
High-throughput sequencing libraries were constructed using the NEBNext Ultra II DNA Kit according to the manufacturer’s recommendation. Paired-end sequencing was done on the NextSeq 500 with a read length of 43 bp and with 45 million reads per sample.

value: Human Embryonic Kidney cells


title: Early Rebiopsy patient 7 rebiopsy


title: Ctrl_PBS_PVP_ND_1

description: US11263921_257480912634_S01_GE2_1200_Jun14_1_3.txt

value: CTRL


title: HEK293_Input_Rep1


title: Au_20_COOH_3

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_4.txt

value: COOH


title: Early Rebiopsy patient 6 rebiopsy


title: LacZ_Odd_HEK293_Rep2

tag: genotype/variation

value: antisense biotinylated oligos against LacZ


title: Early Rebiopsy patient 6 baseline

value: lung


title: Early Rebiopsy patient 7 baseline


title: TiO_PEG_rod_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_2_4.txt

value: 8 w/o


title: Au_20_PEG_3

description: US11263921_257480912633_S01_GE2_1200_Jun14_2_1.txt

value: PEG


title: MWCNT_COOH_1

description: US11263921_257480912634_S01_GE2_1200_Jun14_1_1.txt

value: female

value: MWCNT


title: MSC_donor3_P10_OxBS

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: SAMPLE 16

hyb_protocol: Bisulfite converted or oxidized and bisulfite converted (OxBS) DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1).

label: Cy5 and Cy3

source_name: bone marrow

growth_protocol: Mesenchymal stem cells were isolated from the bone marrow of patients after orthopedic surgery. All samples were taken after written consent from donors and the study was approved by the ethics committee of RWTH Aachen University Medical School (permit number: EK300/13). Cells were flushed from bone marrow and cultured in Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) supplemented with 1% penicillin/streptomycin (PAA), 1% L-glutamine, 10% pooled human platelet lysate (Horn et al. 2010) and 0.1% heparin (5,000 lU/ml, Ratiopharm, Ulm, Germany). Human umbilical vein endothelial cells of three different donors (Lonza, Basel, Switzerland) were cultured in Endopan 3 medium (PAN-Biotech GmbH, Aidenbach, Germany) supplemented with 2% fetal bovine serum. All cells were grown at 37° C in an atmosphere with 5% CO2. Cells were harvested by trypsinization when reaching 90% confluency and re-seeded in a density of 10,000 cells /cm2

extract_protocol: Genomic DNA of MSCs was harvested with the NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germnay). To isolate DNA of HUVECs the cells were permeabilized (15mM Tris/HCl ph7.6, 60mM KCl, 15mM NaCl, 4mM CaCl2, 300mM sucrose, 0.2% NP-40, 0.5mM beta-Mercaptoethanol), lysed (50mM Tris/HCl ph8.0, 20mM EDTA, 1% SDS) with addition of RNase A for 2h at 37°C and subsequent proteinase K digestion overnight at 37°C. DNA of HUVECs was then purified by phenol/chloroform extraction.

treatment_protocol: oxidation and bisulfite treatment (OxBS)

value: bone marrow

value: mesenchymal stem cells

tag: passage

value: passage 10


title: Ctrl_anesth_2

description: US11263921_257480912633_S01_GE2_1200_Jun14_2_3.txt

value: 4 days + 24 hours


title: Hmb2-5 (miRNA-seq)

city: Regensburg

first: Norbert

last: Eichner

address: Universitätsstr. 31

institute: University of Regensburg

data_processing:
miRDeep2 Mapper: Trimming of 3'-Adapter, discarding resulting sequences shorter than 18nt and summing up reads that occured multiple times.
miRDeep2 Quantifier: Annotation of reads to human miRNAs listed in miRBAse (recognition window: 2nt's upstream, 5nt's downstream with 1 mismatch allowed).
Galaxy environment tools: Formatting output for further processing.
Analysis in R using DEseq2 package: Importing miRDeep2 readcounts of all samples in a list, set group design regarding to cell type (NHEMs, primary tumor cell lines, metastasis derived cell lines, MBrCs, other), normalization and differential expression analysis with standard parameters.
Genome_build: miRBase (version 22, March 2018)
Supplementary_files_format_and_content: Excel file (.xlsx) including: raw counts (miRDeep2 output), normalized counts (DEseq2), differential expression outputs between cell types (DEseq2).

source_name: melanoma cell line derived from RRID:CVCL_6646

growth_protocol: The melanocytes were grown either in melanocyte serum-free M2 medium without PMA (phorbol-myristate acetate) from PromoCell (Heidelberg, Germany) or in melanocyte serum-free medium with PMA from Lonza (Basel, Swiss) at 37°C and 5% CO2. The melanoma cell lines were grown in DMEM or RPMI-1640 Medium (Sigma-Aldrich, Steinheim, Germany) supplemented with penicillin (400 units/ml), streptomycin (50 mg/ml), and 10% FBS (Sigma-Aldrich, Steinheim, Germany) at 37°C and 8% CO2. RPMI was additionally supplemented with 0.2 % Sodiumbicarbonate.

extract_protocol:
Cells were trypsinized from a T75 cell culture flask and total RNA including small RNAs was isolated using the miRNeasy Mini Kit from Qiagen (Hilden, Germany) according to the manufacturer's manual.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.

treatment_protocol: Melanocytes and melanoma cell lines were untreated, the dedifferentiation procedure of melanocytes to MBrCs was performed as described by Cook et al 2003, journal of investigative dermatology: NHEM were grown for three passages and subsequently cultivated in MCBD 153 medium (Sigma Aldrich, Steinheim, Germany) containing 2% FBS (PAA Laboratories, Pasching, Austria), 8% chelated FBS, 2 mM glutamine, 1.66 ng/ml cholera toxin B, 10 ng/ml SCF, 100 nM endothelin-3 and 2.5 ng/ml bFGF. Chelated FBS was prepared by mixing 1.2 g of Chelex-100 (Sigma Aldrich, Steinheim, Germany) per 40 ml of FBS for 1.5 h at 4°C with gentle stirring.

tag: genotype

value: MIA deficient

value: untreated


title: LacZ_Even_HEK293_Rep2


title: MSC_donor1_P4_OxBS

description: SAMPLE 11

label_protocol: Standard Infinium HD Methylation Assay protocol

value: passage 4


title: Early Rebiopsy patient 5 rebiopsy

value: EGFR TKI


title: MSC_donor2_P10_OxBS

description: SAMPLE 15


title: LacZ_Odd_HEK293_Rep1

value: Human Embryonic Kidney cells


title: MBrC_rep2 (miRNA-seq)

source_name: melanoblast related cells

value: MBrC

value: wildtype

value: dedifferentiated from normal human epidermal melanocytes according Cook et al 2003, journal of investigative dermatology


title: ND_NH_2

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_3.txt

value: lung

value: NH

value: ND


title: MSC_donor3_P4

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.


title: MSC_donor1_P10


title: MSC_donor1_P10_OxBS

description: SAMPLE 14


title: Early Reboipsy patient 5 baseline

description:
Target lesions were biopsied prior to treatment and site matched upon re-biopsy. Histopathologic evaluation of the pre- and post-treatment biopsies was performed within 24-36 hours of collection. RNA extraction was performed on biopsy cores with a goal of obtaining at least 500 tumor cells to facilitate optimal RNA sequencing.
EarlyRebiopsy_genes.fpkm_table.xslx
Early Rebiopsy

value: treatment naïve


title: MSC_donor2_P4_OxBS

description: SAMPLE 12


title: Au_20_NH_2

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_4.txt

value: 8 w/o

value: female


title: MBrC_rep1 (miRNA-seq)


title: MSC_donor3_P10

value: bone marrow

value: mesenchymal stem cells


title: LacZ_Even_HEK293_Rep1

value: antisense biotinylated oligos against LacZ


title: MSC_donor3_P4_OxBS

description: SAMPLE 13


title: MSC_donor2_P10

value: passage 10


title: Ctrl_PBS_CdTe_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_2.txt

value: 4 days + 24 hours

value: CTRL


title: Early Rebiopsy patient 4 rebiospy

value: EGFR TKI


title: Hmb2 (miRNA-seq)

source_name: melanoma cell line RRID:CVCL_6646

tag: tumor stage

value: melanoma cell line derived from melanoma metastasis

value: untreated


title: ANRIL_Even_HEK293_Rep2

value: Human Embryonic Kidney cells

value: antisense biotinylated oligos against ANRIL


title: ANRIL_Odd_HEK293_Rep2


title: Mel_Im (miRNA-seq)

source_name: melanoma cell line RRID:CVCL_3980

value: wildtype


title: MSC_donor2_P4

value: passage 4


title: HUVEC_donor1_P15

source_name: umbilical cord

value: umbilical cord

value: human umbilical vein endothelial cells

value: passage 15


title: Mel_Ju (miRNA-seq)

source_name: melanoma cell line RRID:CVCL_3979


title: Early Rebiopsy patient 4 baseline

value: lung

value: treatment naïve


title: HUVEC_donor3_P8

value: passage 8


title: Early Rebiopsy patient 3 rebiopsy


title: HUVEC_donor2_P12

value: passage 12


title: ANRIL_Odd_HEK293_Rep1


title: Mel_Wei (miRNA-seq)

source_name: melanoma cell line RRID:CVCL_3981

value: melanoma cell line derived from primary cutananeous melanoma


title: Mel_Ei (miRNA-seq)

source_name: melanoma cell line RRID:CVCL_3978


title: 69_T_2

city: Dallas

first: Mingrui

last: zhu

state: TX

address: 5323 Harry Hines Blvd

department: Pathology

institute: UTSouthwestern Medical Center

data_processing:
Raw FASTQ ﬁles were analyzed using FastQC v0.11.2 (Andrews, 2010) and FastQ Screen v0.4.4 (Wingett, 2011), and reads were quality-trimmed using fastq-mcf. (ea-utils/1.1.2-806) (Aronesty, 2013).
The trimmed reads were mapped to the hg19 assembly of the human genome (the University of California, Santa Cruz, version from igenomes) using STAR v2.5.3a (Dobin et al., 2013). Duplicated reads were marked using Picard tools (v1.127; https://broadinstitute.github.io/picard/), the RNA counts generated from FeatureCounts (Liao et al., 2014) were TMM normalized (Robinson and Oshlack, 2010), and differential expression analysis was performed using edgeR (Robinson et al., 2010). For differential expression analysis, statistical cutoffs of FDR ≤ 0.05 and log2CPM ≥ 0 and were used to identify statistically signiﬁcant and possibly biologically relevant differentially regulated genes.

source_name: H69 cell line

growth_protocol: Cells were grown in RPMI media supplemented with 10% FBS

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit and following the kits protocol
Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring  only high quality RNA is used (RIN Score 8 or higher).   Qubit® 4.0 Fluorimeter from ThermoFisher is used to determine the concentration prior to staring library prep.  One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina.  Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated.   After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.  Before being normalized and pooled, samples are quantified by Qubit then run on the Illumina NextSeq 500 using V2.5 reagents.

treatment_protocol: Cells were treated with either DMSO or TSA

value: HSA treated


title: ANRIL_Even_HEK293_Rep1


title: Early Rebiopsy patient 1 rebiopsy


title: 69_T_3


title: Early Rebiopsy patient 2 rebiopsy


title: Early Rebiopsy patient 3 baseline


title: Ctrl_PBS_CuO_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_1.txt

value: 8 w/o

value: female

value: 4 days + 24 hours

value: CTRL


title: MSC_donor1_P4

value: bone marrow

value: mesenchymal stem cells


title: Early Rebiopsy patient 2 baseline


title: NHEM_rep4 (miRNA-seq)

source_name: normal human epidermal melanocytes obtained from PromoCell (Heidelberg, Germany)

value: NHEM

value: wildtype

value: untreated


title: HUVEC_donor1_P10

value: umbilical cord

value: human umbilical vein endothelial cells

value: passage 10


title: 69_T_1


title: Ctrl_PBS_CuO_2

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_3.txt

value: lung


title: H1975 AZD7day

description:
cells were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C in a humidified 5% CO2 incubator
H1975_in_vitro_genes.fpkm_table.xlsx
H1975 in vitro

source_name: cell line

value: lung cancer cell line

value: osimertinib


title: Early Rebiopsy patient 1 baseline

value: treatment naïve


title: ND_NH_1

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_2.txt

value: NH

value: ND


title: Mel_Juso (miRNA-seq)

source_name: melanoma cell line RRID:CVCL_1403

value: melanoma cell line derived from primary cutananeous melanoma


title: NHEM_rep3 (miRNA-seq)


title: 69_D_3

value: vehicle


title: CdTE_NH_2

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_4.txt

value: 8 w/o

value: female

value: 4 days + 24 hours

value: CdTE


title: 69_D_2


title: MWCNT_PEG_1

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_3.txt

value: PEG

value: MWCNT


title: H1975 AZD5day


title: NHEM_rep1 (miRNA-seq)

source_name: normal human epidermal melanocytes obtained from Lonza (Basel, Swiss)

value: NHEM

value: wildtype

value: untreated


title: Ctrl_PBS_CdTe_2

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_4.txt

value: lung

value: CTRL


title: H1975 AZD3day

value: lung cancer cell line

value: osimertinib


title: OCI-AML5 OTX015 treated input DNA

city: Houston

first: Kapil

last: Bhalla

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the human genome build UCSC hg19 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in TDF format

source_name: AML cultured cell line

growth_protocol: SET-2 and SET-2-OTX P/R cells were cultured in 20% FBS containing RPMI1640 media. OCI-AML5 cells were cultured in MEM Alpha media with 20% FBS and 10 ng/mL of GM-CSF.

extract_protocol:
AML cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes or BRD4-containing complexes were isolated with H3K27Ac or BRD4 antibody, respectively. Following ChIP washes, the  immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation. For ATAC-Seq analysis, isolated nuclei were treated with Tn5 transposase in tagmentation buffer at 37°C for 30 minutes. Tagmented, eluted DNA was purified over a column and utilized for library preparation.
Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 15 cycles (12 cycles for ATAC-Seq) and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. For ATAC-Seq, fragments larger than 200 bp were isolated utilizing AMP-XP beads.  The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

treatment_protocol: OCI-AML5 cells were transduced with Cas9 and sgRNA molecules and incubated for 8 days to knockout out KDM1A/LSD1 expression.  For drug treatments, OCI-AML5 cells were treated with 1000 nM of INCB059872 for 16 hours or 1000 nM of OTX015 for 8 hours prior to sample collection. SET2 and SET OTX P/R cells were treated with 250 nM of INCB059872 for 16 hours before sample collection.

value: leukemia blast cells

value: 1000 nM of OTX015


title: H1975 AZD2day


title: H1975 AZD1day


title: NHEM_rep2 (miRNA-seq)


title: OCI-AML5 OTX015 treated BRD4 ChIP Seq

value: BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs)  catalog #A700-004


title: Hdac3fl/+ PS rep3

city: Nanjing

first: Lan

last: Ye

state: Jiangsu

address: B112 Xuehai Building,101 Longmian Avenue, Jiangning district

country: China

institute: Nanjing Medical University

data_processing:
Clean data were obtained by trimming the adaptor sequence and removing sequences with low quality.
Clean reads were mapped to the mouse genome (mm10) with HISAT2 (v.2.1.0; Johns Hopkins University, Baltimore, MD, USA) with a GTF file download from the UCSC database (University of California, Santa Cruz).
The aligned reads of genes were counted using HTSeq followed by DESeq2 normalization to evaluate gene expression as normalized counts per million.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts for every gene and every sample

source_name: pachytene spermatocytes (PS)

extract_protocol:
Testes were collected, pachytene spermatocytes and round spermatids were isolated from wild-type and HDAC3 KO testes , and RNA was harvested using Trizol reagent.
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina).

value: wild type

value: pachytene spermatocytes (PS)


title: Stra8-cre/Hdac3fl/- PS rep3

value: HDAC3 KO


title: H1975 AZD8hr


title: Hdac3fl/+ RS rep3

source_name: round spermatids (RS)

value: round spermatids (RS)


title: H1975 AZD4hr


title: Ag_PEG_2

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_2.txt

value: 8 w/o

value: female

value: 4 days + 24 hours

value: Ag


title: Au_20_NH_1

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_1.txt

value: NH


title: ND_COOH_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_4.txt

value: COOH

value: ND


title: Au_20_NH_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_3.txt

value: lung


title: OCI-AML5 Control (BETi) BRD4 ChIP Seq

value: Control


title: TiO_PEG_prtcl_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_2.txt

value: PEG

value: TiO


title: OCI-AML5 Control (BETi) input DNA

value: leukemia blast cells


title: Stra8-cre/Hdac3fl/- RS rep2


title: 69_D_1

value: vehicle


title: Stra8-cre/Hdac3fl/- RS rep3


title: H1975 AZD1hr

value: lung cancer cell line

value: osimertinib


title: Hdac3fl/+ RS rep2

value: wild type


title: OCI-AML5 INCB BRD4 ChIP Seq

value: BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs)  catalog #A700-004


title: OCI-AML5 Control BRD4 ChIP Seq


title: H1975 DMSO7day

value: DMSO


title: Stra8-cre/Hdac3fl/- PS rep2

value: HDAC3 KO

value: pachytene spermatocytes (PS)


title: H1975 DMSO4hr


title: OCI-AML5 Cas9 BRD4 ChIP Seq


title: Hdac3fl/+ PS rep2


title: OCI-AML5 LSD1 Knockout BRD4 ChIP Seq

value: LSD1 Knockout


title: HCC4006 AZD11day

description:
cells were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C in a humidified 5% CO2 incubator
4006_ in vitro_genes.fpkm_table.xlsx
HCC4006 in vitro


title: ND_COOH_1

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_3.txt

value: 8 w/o

value: female

value: 4 days + 24 hours


title: Stra8-cre/Hdac3fl/- RS rep1

value: round spermatids (RS)


title: Ag_NH_1

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_4.txt

value: lung

value: NH

value: Ag


title: Ctrl_PBS_Ag_2

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_2.txt

value: CTRL


title: OCI-AML5 INCB input DNA

value: leukemia blast cells


title: Au_5_NH_2

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_1.txt


title: Hdac3fl/+ RS rep1


title: MWCNT_prist_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_4.txt

value: core

value: MWCNT


title: HCC4006 AZD9day

value: lung cancer cell line

value: osimertinib


title: OCI-AML5 INCB H3K27Ac ChIP Seq

value: H3K27Ac (Active Motif) RRID:AB_2793305


title: OCI-AML5 Control input DNA

value: Control


title: HCC4006 AZD7day


title: Ctrl_PBS_Au_20_1

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_1.txt


title: Stra8-cre/Hdac3fl/- PS rep1

value: HDAC3 KO

value: pachytene spermatocytes (PS)


title: HCC4006 AZD5day


title: OCI-AML5 Control H3K27Ac ChIP Seq


title: HCC4006 AZD3day


title: ND_NH_3

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_1.txt

value: 8 w/o

value: ND


title: OCI-AML5 LSD1 Knockout H3K27Ac ChIP Seq

value: LSD1 Knockout


title: HCC4006 AZD1day


title: Hdac3fl/+ PS rep1

value: wild type


title: Sox30 KO testes Sox30

data_processing:
ChIP-seq reads were aligned to the mouse genome (mm10) using BOWTIE software (bowtie2 version 2.3.4.3)
The aligned reads were further filtered to remove those with low mapping quality and duplicated arising as an artefact of sample amplification or sequencing
Peak calling was carried out by using MACS2 (version 2.1.2, with options'-mfold 5, 50 –p 0.0001') on ChIP file against the input file.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.3.0) and visualized in the Integrative Genomics Viewer (IGV version 2.5.0).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: mouse testes

extract_protocol:
Lysates were sonicated, antibody-bound DNA complexes were immunoprecipitated, washed, and DNA was extracted.
DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers

value: testes

value: Sox30 KO

tag: chip antibodies

value: ABclonal, A11759


title: HCC4006 AZD8hr


title: OCI-AML5 Cas9 input DNA

tag: cell type


title: Sox30 KO testes HDAC3

value: Abcam, ab7030


title: HCC4006 AZD1hr

tag: treatment


title: HCC4006 DMSO11d

tag: tissue

value: DMSO


title: CdTe_PEG_1

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_2.txt

value: lung

tag: age

value: female

value: 4 days + 24 hours

value: PEG

value: CdTE


title: wild-type testes input


title: HCC4006 AZD4hr

value: lung cancer cell line

value: osimertinib


title: wild-type testes Sox30


title: CuO_core_1

description: US11263921_257480912703_S01_GE2_1200_Jun14_1_2.txt

tag: gender

value: core

value: CuO


title: HCC4006 DMSO1day


title: CuO_NH3_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_1.txt

value: 8 w/o

tag: strain

value: NH


title: SET2-OTX P/R INCB ATAC Seq 1

description: Tn5 transposase treated cells

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ATAC-Seq reads were mapped to the human genome build UCSC hg19 using bowtie2 and duplicate reads were removed.
ATAC-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-Seq tracks represented normalized to reads per million mapped in TDF format

source_name: sAML cultured cell line

tag: sample type

value: leukemia blast cells

value: SET2-OTX P/R


title: Ag_COOH_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_1_1.txt

tag: exposure time

tag: slide #

value: COOH

value: Ag


title: Sox30 KO testes NCOR

value: testes

value: Sox30 KO

value: Abcam, ab3482


title: TiO_NH_rod_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_3.txt

value: lung

value: female

tag: functionalization

tag: nanomaterial

value: TiO


title: CuO_PEG_2

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_4.txt

value: 4 days + 24 hours

value: PEG


title: Au_20_COOH_2

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_2.txt


title: MWCNT_NH_3

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_3.txt

value: MWCNT


title: ND_PEG_2

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_1.txt

value: ND


title: wild-type testes NCOR

value: wild type


title: Sox30 KO testes input


title: SET2-OTX P/R Control ATAC Seq 2

description: Tn5 transposase treated cells

value: control


title: HCC4006 DMSO4hr

description:
cells were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C in a humidified 5% CO2 incubator
4006_ in vitro_genes.fpkm_table.xlsx
HCC4006 in vitro

value: lung cancer cell line

value: DMSO

tag: cell line


title: OCI-AML5 Cas9 H3K27Ac ChIP Seq

value: leukemia blast cells

tag: chip antibody

value: H3K27Ac (Active Motif) RRID:AB_2793305

tag: genotype/variation


title: wild-type testes HDAC3

tag: genotype

value: Abcam, ab7030


title: H1650 AZD14day

description:
cells were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C in a humidified 5% CO2 incubator
4006_ in vitro_genes.fpkm_table.xlsx
H1650 in vitro

value: osimertinib


title: CdTe_COOH_2

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_3.txt

value: 8 w/o

value: COOH

value: CdTE


title: Stra8-cre/Hdac3fl/- RS input

value: round spermatids (RS)

value: HDAC3 KO


title: SET2 INCB ATAC Seq 1

description: Tn5 transposase treated cells


title: SET2 INCB ATAC Seq 2

description: Tn5 transposase treated cells


title: Stra8-cre/Hdac3fl/- RS H3K27ac

value: Abcam ab4729


title: SET2-OTX P/R INCB ATAC Seq 2

description: Tn5 transposase treated cells

value: SET2-OTX P/R


title: H1650 AZD7day

description:
cells were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C in a humidified 5% CO2 incubator
H1650_in_vitro_genes.fpkm_table.xlsx
H1650 in vitro


title: TiO_COOH_rod_1

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_4.txt

value: lung

value: female

value: 4 days + 24 hours

value: TiO


title: OCI-AML5 LSD1 Knockout input DNA

value: LSD1 Knockout


title: H1650 AZD5day

value: lung cancer cell line


title: SET2 Control ATAC Seq 2

description: Tn5 transposase treated cells

value: leukemia blast cells

value: control


title: SET2-OTX P/R Control ATAC Seq 1

description: Tn5 transposase treated cells


title: Stra8-cre/Hdac3fl/- PS input

value: pachytene spermatocytes (PS)


title: H1650 AZD3day

value: osimertinib


title: Stra8-cre/Hdac3fl/- PS H3K27ac


title: TiO_PEG_prtcl_1

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_2.txt

value: 8 w/o

value: PEG


title: Hdac3fl/+ RS input

value: wild type


title: Ctrl_PBS_TiO-rod_2

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_4.txt

value: CTRL


title: Ag_NH_3

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_1.txt

value: NH

value: Ag


title: CdTe_COOH_1

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_3.txt

value: COOH

value: CdTE


title: H1650 AZD1day


title: SET2 Control ATAC Seq 1

description: Tn5 transposase treated cells


title: OCI-AML5 INCB-treated ATAC Seq

description: Tn5 transposase treated cells


title: OCI-AML5 Control ATAC Seq

description: Tn5 transposase treated cells


title: Hdac3fl/+ RS H3K27ac

value: round spermatids (RS)

value: Abcam ab4729


title: H1650 AZD8hr


title: CuO_COOH_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_2.txt

value: lung

value: female

value: 4 days + 24 hours

value: CuO


title: Hdac3fl/+ PS input


title: OCI-AML5 LSD1 knockout ATAC Seq 2

description: Tn5 transposase treated cells

value: leukemia blast cells

value: knockout out KDM1A/LSD1 expression


title: OCI-AML5 LSD1 knockout ATAC Seq 1

description: Tn5 transposase treated cells


title: H1650 AZD6hr

value: lung cancer cell line

value: osimertinib


title: H1650 AZD4hr


title: Hdac3fl/+ PS H3K27ac

value: pachytene spermatocytes (PS)


title: H1650 AZD10day


title: MWCNT_COOH_2

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_1.txt

value: 8 w/o

value: MWCNT


title: Stra8-cre/Hdac3fl/- RS input for KO H3K9ac

value: HDAC3 KO


title: Ctrl_PBS_Au_20_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_4.txt

value: CTRL


title: OCI-AML5 Cas9 ATAC-Seq 2

description: Tn5 transposase treated cells

value: transduced with Cas9


title: Ctrl_PBS_TiO-prtcl_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_3.txt


title: H1650 AZD2hr


title: OCI-AML5 Cas9 ATAC-Seq 1

description: Tn5 transposase treated cells


title: Stra8-cre/Hdac3fl/- RS H3K9ac

value: Milipore, 07-352


title: Stra8-cre/Hdac3fl/- PS input for KO H3K9ac


title: Stra8-cre/Hdac3fl/- PS H3K9ac


title: SW480_pooled Input_CHIPseq

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Basecalls performed using BWA algorithm with default settings
ChIP-seq reads were aligned to the human genome (hg38) using the BWA algorithm.
The tags are extended in silico at their 3 ́- ends to a length of 200bp. To identify the density of fragments  along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peaks were callled using Model-based Analysis of ChIP-Seq (MACS) to identify significant enrichments in the ChIP/IP data file when compared to the Input data file.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files contains the density of fragments in every 32-nt bin of the genome.

source_name: Colon carcinoma

growth_protocol: Cells were cultured as adherent monolayers in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich #D5796) supplemented with 10% (v/v) fetal bovine serum (Bovogen #SFBS-AU), 2mM L-glutamine (Life technologies #25030081), 100 units/mL penicillin and 0.1% (w/v) streptomycin (Life technologies #15140122) (complete DMEM, C-DMEM). Cells were grown at 37°C in a 5% CO2 humidified incubator, and passaged every 2-3 days (30-80% confluency).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on a NexSeq 500 (100 bp, single end reads).

value: SW480 colorectal cancer cell line

tag: crispr knockout

value: control & KMT2A knockout


title: H1650 DMSO7day

value: DMSO


title: SW480_KO_H3K4m34_CHIPseq

value: KMT2A knockout

value: H3K4me3 (Active motif, #39159)


title: Hdac3fl/+ RS input for control H3K9ac

value: round spermatids (RS)

value: wild type

tag: chip antibodies


title: PC9 AZD3day

description:
cells were cultured in RPMI-1640 growth medium supplemented with 10% fetal bovine serum at 37 °C in a humidified 5% CO2 incubator
PC9_ in vitro_genes.fpkm_table.xlsx
PC9  in vitro


title: H1650 DMSO4hr


title: SW480_H3K4me3_CHIPseq

value: control


title: SW480_KO_bCatenin_CHIPseq

value: anti-beta-catenin (Cell Signalling, #9581)


title: CdTe_PEG_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_2.txt

value: lung

value: female

value: 4 days + 24 hours

value: PEG

value: CdTE


title: Ctrl_PBS_Au_5_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_1.txt

value: 8 w/o

value: CTRL


title: PC9AZD2day

value: lung cancer cell line

value: osimertinib


title: H1650 AZD1hr


title: Hdac3fl/+ PS input for control H3K9ac

value: pachytene spermatocytes (PS)


title: Ctrl_PBS_PVP_ND_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_3.txt


title: Au_5_NH_1

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_2.txt

value: NH


title: PC9AZD1day


title: TiO_COOH_prtcl_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_1.txt

value: COOH

value: TiO


title: Au_20_PEG_2

description: US11263921_257480912645_S01_GE2_1200_Jun14_2_4.txt


title: Hdac3fl/+ PS H3K9ac

value: Milipore, 07-352


title: SW480_bCatenin_CHIPseq

value: SW480 colorectal cancer cell line


title: PC9 AZD8hr


title: TiO_core_rod_3

description: US11263921_257480912645_S01_GE2_1200_Jun14_1_3.txt

value: core


title: PC9AZD4hr


title: BMDMs, KO-Ctrl_2

city: Taipei

first: Li-Chung

last: Hsu

address: No.7, ChungShan S. Rd., ZhongZheng Dist.

department: Graduate institute of Molecular Medicine

institute: National Taiwan University

data_processing:
Basecalls performed using Illumina HiSeq PE150
Total of 4.45-11.8 million clean reads (Reads Per Kilo bases per Million reads, RPKMs) were obtained from each sample. RPKMs were compared to mouse RefSeq-RNA mm10 and quantitated using FANSe3 (Fast and Accurate mapping algorithm for Next-generation Sequencing, the 3rd generation (Rajkumar, A.P. et al., 2015 and Zhang, G. et al., 2012)).
The differential genes expression of each stimulation (including control and LPS)  of each genotype was quantified using edgeR  (Robinson, M.D., McCarthy, D.J. & Smyth, G.K., 2010) and FANSe3.
Genome_build: mm10
Supplementary_files_format_and_content: DiffExprAnalysis includes CK_ctrl-vs-WT_ctrl, CK_LPS-vs-WT_LPS,  WT_LPS-vs-WT_ctrl and venn.
Supplementary_files_format_and_content: RC_RPKM.xlsx

growth_protocol: Bone marrow-derived macrophages (BMDMs) were prepared from femurs and tibia bones of 7-week old mice and bone marrow was flushed out with DMEM medium using a 25-gauge syringe. The bone marrow progenitor cells were harvested, and differentiated in high-glucose DMEM medium containing 20% L929 cell-conditioned medium for 7 days. Adherent BMDMs were collected and cultured in DMEM containing 10 ng/ml M-CSF overnight for further experiments.

extract_protocol:
Total RNAs of BMDMs were harvested using Trizol reagent.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LPS stimulation for 4 hour

value: male

tag: agent

value: Ctrl

value: Bone marrow

tag: cell type

value: BMDMs


title: Hdac3fl/+ RS H3K9ac

tag: tissue

value: round spermatids (RS)

value: wild type


title: DLD1 Input_CHIPseq

value: DLD1 colorectal cancer cell line

value: control


title: BMDMs, KO-LPS_2

tag: age

value: LPS


title: BMDMs, KO-LPS_1

tag: gender


title: DLD1_H3K4me3_CHIPseq

value: H3K4me3 (Active motif, #39159)


title: DLD1_KO_H3K4m34_CHIPseq

value: KMT2A knockout


title: PC9 DMSO2day

value: lung cancer cell line

tag: treatment

value: DMSO


title: BMDMs, KO-Ctrl_1

tag: strain


title: PC9 DMSO4hr


title: DLD1_KO Input_CHIPseq


title: DLD1_KO_bCatenin_CHIPseq

value: anti-beta-catenin (Cell Signalling, #9581)


title: Ctrl_PBS_serum_MWCNT_3

description: US11263921_257480912645_S01_GE2_1200_Jun14_1_1.txt

value: lung

value: 8 w/o

value: female

tag: exposure time

value: 4 days + 24 hours

value: CTRL


title: TiO_COOH_rod_3

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_4.txt

tag: slide #

value: COOH

value: TiO


title: TiO_NH_prtcl_1

description: US11263921_257480912645_S01_GE2_1200_Jun14_1_4.txt

tag: functionalization

value: NH


title: Au_5_COOH_2

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_3.txt

tag: nanomaterial


title: BMDMs, WT-LPS_2

value: male

value: WT

value: Bone marrow

value: BMDMs


title: DLD1_bCatenin_CHIPseq

tag: cell line

value: DLD1 colorectal cancer cell line

value: control


title: BMDMs, WT-LPS_1

value: LPS


title: CuO_core_3

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_1.txt

value: core

value: CuO


title: input late

description:
pooled samples 4-6
Input_late_S2

data_processing:
Quality of the resulting reads was checked by FastQC before reads were aligned to the hg19 genome assembly using bowtie2
We used MACS2 for peakcalling on each sample with the default parameters against the input control.
All the peaks were filtered by signal > 50 and selected with the overlapping of potential CTCF binding motif, which was obtained by RGT motif analysis (http://www.regulatory-genomics.org/motif-analysis).
The normalized coverage of each sample was calculated by Deeptools bamCoverage with normalization of Reads Per Kilobase per Million mapped reads (RPKM), these normalized coverages were used for down-stream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain the normalized coverage of each sample calculated by Deeptools bamCoverage with normalization of Reads Per Kilobase per Million mapped reads (RPKM)
Supplementary_files_format_and_content: bed files contain MACS2 peaks filtered by signal > 50 and selected with the overlapping of potential CTCF binding motif, these CTCF binding peaks were further divided into “early” or “late” CTCF peaks, derived from proliferating and senescent samples respectively

source_name: input late

growth_protocol: Cells were flushed from bone marrow and cultured in Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) supplemented with 1% penicillin/streptomycin (PAA), 1% L-glutamine, 10% pooled human platelet lysate and 0.1% heparin (5,000 lU/ml, Ratiopharm, Ulm, Germany) at 37° C in an atmosphere with 5% CO2. Cells were harvested by trypsinization when reaching 90% confluency, counted, and re-seeded in a density of 10,000 cells /cm2.

extract_protocol:
Chromatin Immunoprecipitation of CTCF was performed using the ChIP-IT PBMC kit with the fixation protocol of the ChIP-IT High Sensitivity kit (both Active Motife, Carlsbad, CA, USA). In brief, MSCs of early passage (P 2, n = 3) and late passage (P 8 – 14, n = 3) were cross-linked with 1.2 % formaldehyde (Applichem, Darmstadt, Germany) for 15 min at room temperature. After cell lysis, chromatin fragmentation was performed by sonication for 20 min (20 cycles a´ 30 sec on/30 sec off, total on-time 10 min) in a water bath sonicator (Biorupter® Pico Sonicator Device, Diagenode). 5 - 33 µg of sonicated chromatin was incubated with 4 µg ChIP-validated CTCF antibody (Active Motif) overnight on an end-to-end rotator at 4°C. For immunoprecipitation, samples were incubated with protein G agarose beads (Active Motife) at 4°C for 3 hours. Finally, the cross-link was reversed, the DNA was proteinase K digested and purified.
Sequencing and library preparation were conducted by the IZKF Sequencing Core Facility of RWTH Aachen University Medical school.

value: bone marrow

value: mesenchymal stromal cells

tag: passage

tag: chip antibody


title: G471-G471-2

city: Madison

first: Ming-Song

last: Lee

state: WI

address: 2715 Marshall CT., Apt 319

institute: UW-Madison

data_processing:
BBDuk (REF) was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) (REF) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq (REF) by supplementing Ensembl gene annotation (GRCh38.78). Gene expression values were calculated as counts per million (CPM). Genes with no detected CPM in all samples were filtered out.
Genome_build: GRCh38

source_name: iPSC-NCC-Ch

extract_protocol:
Total RNA was extracted using Direct-zol™ RNA Miniprep Kit (Zymo Research) as per the manufacturer's instructions. Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
The cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.

value: derived from iPSCs


title: PC9 AZD1hr

value: lung cancer cell line

value: osimertinib


title: BMDMs, WT-Ctrl_2

tag: genotype

value: Ctrl


title: G362-9-P

source_name: Chondrocyte

value: Primary cells


title: G362-7-310-1


title: input early

description:
pooled samples 1-3
Input_early_S1

source_name: input early


title: G362-8-310-2


title: G362-6-O


title: CTCF_ChIPSeq_donor3_P14

value: CTCF antibody (Active Motif)


title: MWCNT_NH_1

description: US11263921_257480912634_S01_GE2_1200_Jun14_2_2.txt

data_processing: mRNA expression raw intensity values were quality checked and exported from Agilent Feature Extraction software. The raw intensities were analysed with Bioconductor package Limma. Experiment was two-colour, but the data were analysed as a single-channel arrays.

value: lung

value: 8 w/o

value: female

value: 4 days + 24 hours

value: NH

value: MWCNT


title: CTCF_ChIPSeq_donor1_P8


title: G362-5-N


title: CTCF_ChIPSeq_donor2_P14


title: Ctrl_anesth_1

description: US11263921_257480912634_S01_GE2_1200_Jun14_1_3.txt

value: CTRL


title: G362-4-M

source_name: iPSC-MC-Ch


title: BMDMs, WT-Ctrl_1

value: male

value: WT

value: Bone marrow

value: BMDMs


title: CTCF_ChIPSeq_donor3_P2

value: bone marrow

value: mesenchymal stromal cells


title: CTCF_ChIPSeq_donor2_P2


title: CTCF_ChIPSeq_donor1_P2


title: TiO_core_prtcl_2

description: US11263921_257480912634_S01_GE2_1200_Jun14_1_4.txt

value: core

value: TiO


title: G362-2-K

value: derived from iPSCs


title: Ctrl_anesth_3

description: US11263921_257480912634_S01_GE2_1200_Jun14_1_1.txt


title: Ctrl_PBS_Au_5_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_2_4.txt


title: Ctrl_PBS_serum_MWCNT_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_2_1.txt


title: CuO_COOH_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_2_3.txt

value: COOH

value: CuO


title: MYB123 silenced 2

status: Public on May 25 2021

city: Cordoba

first: Antonio

middle: Rodriguez

last: Franco

state: CORDOBA

address: Rabanales. Ed Severo Ochoa

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

data_processing:
2x150 paired fastq files sequenced in a Hiseq-4000 Illumina device
Raw sequences filtered with Trim-Galore by quality Q>=30 and automatic detection of adapters
As reference for mapping of reads, a multi fasta file containing only cds sequences corresponding to Fragaria vesca v2.0 genome was used
Kallisto v 0.45.0 version was used for mapping
Example of command included in json file: kallisto quant -t 8 -b 100 -i TercerArrayKallisto_2.index --rf-stranded -o MYB86_1 filter_Sample_4_1_1.fq.gz filter_Sample_4_1_2.fq.gz
The abundance files were created by the Kallisto pseudomapper.
Data imported into R using tximport
Differential expression analysis done with DESeq2 under R 3.6.1
DE data filtered with a p-adjusted value <=0.05, and a Log2FoldChange >= 1, or <= -1
Genome_build: Fragaria vesca v2.0
Supplementary_files_format_and_content: Abundance files were created by the Kallisto:
abundance.h5  A binary file with the abundance that contains boostrapping. This is the one imported by tximport for the DESeq2 analysis
abundance.tsv Is a text version of the above, but lacking boostrapping (target_ids searchable at https://www.rosaceae.org/species/fragaria_vesca/genome_v2.0.a1)
run_info.json is a statistical file than also contains the command line executed

organism: Fragaria x ananassa

source_name: RNA from strawberry receptacles

growth_protocol: Plants grown in growth chambers

extract_protocol:
Receptacles were frozen in liquid nitrogen, grounded with a morter and pestle and RNA isolates according regular protocols established in our lab. mRNA isolated with magnetic poly(T) tails
Stranded libraries following TruSeq Illumina protocol
rf-stranded (dUTP method)

treatment_protocol: Transgenic plants transformed with empty pRFN vector (control) and pFRN contain MYB123 for RNAi intereference silencing

tag: variety

value: Chandler

value: MYB123 silenced

value: receptacles


title: MYB123 silenced 1


title: Transgenic control 1

value: control


title: G362-3-L


title: Transgenic control 3


title: tissue as old, biological rep3

city: Beijing

first: Tingyi

last: Sun

state: Beijing

address: No.10 Xitoutiao, You'anmenwai, Fengtai District

institute: Capital Medical University

description: clinical colon mucosa tissue samples from old colorectal cancer patients

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: normal clinical colon mucosa tissue samples from colorectal cancer patients were collected immediately

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: colorectal cancer colon mucosa tissue


title: MYB123 silenced 3


title: TiO_core_rod_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_2.txt

value: lung

value: 8 w/o

value: female

value: 4 days + 24 hours


title: tissue as young, biological rep3

description: clinical colon mucosa tissue samples from young colorectal cancer patients


title: tissue as young, biological rep2


title: The ovotestes of zig-zag eel

city: Fuzhou

first: Zhen

last: Huang

state: Fujian

address: 1 keji road, college of life science, Fujian Normal University (Qishan campus)

institute: Fujian Normal University

data_processing:
Cell Ranger mkfastq pipeline was performed to demultiplex BCL files and to convert barcode and read data to FASTQ files for analysis  Cell Ranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting
Genome_build: NCBI Accession No. PRJNA489256
Supplementary_files_format_and_content: matrix.mtx.gz (tab-delimited text file, the rows of which report the genes in the order they are presented along rows in matrix.mtx.gz)

organism: Mastacembelus armatus

source_name: ovotestes

extract_protocol:
The dissected ovotestes were cut into pieces in phosphate-buffered saline solution and digested with 0.25% trypsin (Invitrogen, Carlsbad, CA, USA) in Hanks balanced salt solution (Invitrogen) for 30 min at 37 °C. After that, DMEM containing 10% serum was used to terminate digestion. The tissue and cells were gently triturated, centrifuged at 200 g for 5 min, and resuspended with PBS. Cells were filtered with a 0.45-μm cell-strainer to discard any undigested tissue.
Single-cell RNA seq (scRNA-seq) libraries were constructed using a 10X Genomics kit (ChromiumTM Single Cell 3’v2) following the manufacturer’s instructions

value: ovotestes


title: tissue as young, biological rep1


title: Transgenic control 2


title: tissue as old, biological rep2


title: MWCNT_PEG_3

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_4.txt

extract_protocol: After sacrificing the lungs were removed, cut and transferred to RNALater stabilizing solution (Ambion, Life Technologies, CA, USA), and stored at −80 °C. Total RNA (totRNA) from the RNAlater-stabilized lung samples was isolated and purified by phenol/chloroform isolation method according to the instructions by Bioline Reagents.

value: PEG

value: MWCNT


title: tissue as old, biological rep1


title: Ctrl_PBS_TiO-prtcl_1

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_3.txt

value: CTRL


title: Osteosarcoma NC3

city: Shijiazhuang

first: Mengke

last: Fan

address: Ziqiang Road, Qiaoxi District

department: Bone research institute

institute: The Third Hospital of Hebei Medical University

data_processing:
Illumina NovaSeq 6000 software used for basecalling
The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .
HISAT package used for aligning reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome
StringTie used for the map reads of each sample
StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.

source_name: osteosarcoma

growth_protocol: 143B cells was obtained from CellCook (Guangzhou, China). The cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) (Gibco, USA) and 1% penicillin/streptomycin. All of them were at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina NovaSeq 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
A cDNA library constructed by technology from the pooled RNA from brain samples of pig was sequenced run with Illumina 4000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of 80 nmol/L siRNA with Hiperfect® Transfection Reagent (QIAGEN, Germany). After 36 h, total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) .

value: osteosarcoma cells

value: Negative control


title: Osteosarcoma NC2


title: Osteosarcoma SI2

value: Siglec-15 knockdown


title: Osteosarcoma NC1


title: Osteosarcoma SI3


title: Au_5_PEG_2

city: Tampere

first: Dario

last: Greco

institute: Tampere University

description: US11263921_257480912633_S01_GE2_1200_Jun14_1_1.txt


title: Osteosarcoma SI1


title: ACHN_Flag_eclip

city: guangzhou

first: yuntan

last: qiu

state: guangdong

address: 107 Yanjiang West Road, Guangzhou City, Guangdong Province

department: Research Center of Medicine

institute: Sun Yat-Sen Memorial Hospital

data_processing:
Library strategy: eCLIP-Seq
eCLIP data processing was conducted using eCLIP pipeline version 0.2.1a (https://github.com/YeoLab/eclip/releases/tag/0.2.1a).
adapter were removed by using cutadapter version 2.10. RNA adapter sequences:AUAUAGGNNNNNAGAUCGGAAGAGCGUCGUGUAG; DNA adapter sequences:NNNNNNNNNNAGATCGGAAGAGCACACGTCTG  .
eCLIP-seq reads were aligned to the hg19 genome assembly using STAR version 3.2.
peaks were called using clipper version 2.1.0.  High-confidence eCLIP peaks were called by selecting MEX3A-binding peaks with a minimum IP count ≥10 and a minimum log2FC（IP/ Input value)≥ 1.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using deeptools version 3.5.0

source_name: ACHN

extract_protocol:
Input and Flag antibody IP fractions were run on an NuPAGE Bis-Tris protein gels (Thermo Fisher, USA). Protein-RNA complexes between 72kDa and 150kDa were collected for RNA isolation followed by library generation.
eCLIP libraries were constructed, following the protocol previously published [PMID:27018577].

tag: overexpression

tag: antibody

value: FLAG

value: ACHN


title: ACHN_Input_eclip

value: input


title: Cancer sample patient M4-4

city: Seoul

first: Sang Kil

address: 50-1 Yonsei-ro, Seodeamun-gu

department: Internal Medicine

country: South Korea

institute: Yonsei University Colloge of Medicine

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit

scan_protocol: Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)

data_processing: Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library.  The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Data was quantile normalized followed by log2 transform.  Signals from probes measuring same ncRNA were averaged.

source_name: cancer tissue

label_protocol: Labbeling was done according to Nimblegen one color DNA Labeling kit.

extract_protocol: Total RNA extracted using Total RNA Purification Kit from Norgen Biotek corp following manufacturer's instructions

value: gastric tissue

tag: surgical indication

value: advanced gastric cancer

tag: Sex

value: f

tag: t stage

tag: n stage

tag: stage(tnm)

value: IIIa

tag: treatement after surgery

value: no

tag: recurrence

tag: disease free survival (months)

tag: death

tag: overall survial duration (months)


title: Cancer sample patient P3-1

tag: tissue

tag: age

value: m

value: IIb

value: IV Chemo


title: ACHN_IgG

data_processing:
RIP-Seq data were aligned and quantified using RSEM as well as STAR against the GRCh37 human reference genome and annotation (GTF format) downloaded from GENCODE official website. Gene counts were then used for downstream analysis ).
Genome_build: hg19
Supplementary_files_format_and_content: The targets were selected according to IP fold-enrichment (IP gene count >=100, Log2FC(IP/IgG) >= 1).

extract_protocol:
Briefly, 1 x 107 cells that stably expressing Flag-tagged MEX3A were treated with 0.3% formaldehyde and the cross-linked reaction was stopped by adding 0.125 M glycine. The complexes of RNA and protein were enriched by 5μg of anti-Flag antibody with Dynabeads protein G (Invitrogen, #10004D) in cell lysis buffer overnight at 4 ºC. Then, total RNA was isolated by the phenol-chloroform method after treated with proteinase K (thermo fisher). Then, the library construction and sequencing were finished by BGI.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters.

value: IgG

tag: cell line


title: Normal sample patient P3-1

source_name: adajacent non-cancer gastric tissue


title: Cancer sample patient M1-1

value: Ib


title: HCC213L_m2_CD4

city: Rotterdam

first: Lucia

last: Campos Carrascosa

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Short reads alignment was performed with the ENSEMBL Homo_sapiens. GRCh37 chosen as the reference genome
The corresponding annotation (ENSEMBL v76) was also retrieved from the ENSEMBL FTP website. The STAR aligner (version 2.4.0b) was used to perform mapping to the reference genome
Alignments were processed with the featureCounts66 function of the Rsubread package, using the annotation file, also used for supporting the alignment. STAR/RSEM (available on Github) was used to quantitate expression levels
Genome_build: hg19
Supplementary_files_format_and_content: CSV file contains log2 transformed TPM counts

source_name: TIL

growth_protocol: TILs were isolated from fresh HCC patient-derived tumor samples.

extract_protocol:
2 TIL subsets were sorted according to the expression of CD45/CD3/CD4/CD8. CD8+ (CD45+CD3+CD8+CD4-) TILs and CD4+ (CD45+CD3+CD4+CD8-) TILs were sorted directly into RLT+ lysis buffer. RNA was immediately isolated using RNeasy micro kit (Qiagen) according to manufacturer's instructions
Barcoded mRNA-seq cDNA libraries were prepared using TruSeq RNA Access Libraryprep Kit (Illumina) according to the manual
Barcoded RNA-Seq libraries were onboard clustered using HiSeq X Kit v2 using 2.5 nM and PE 150 bps and were sequenced on the Illumina HiSeqX using the HiSeq X Kit v2 (PE 150 cycle)

treatment_protocol: TILs were cultured in vitro  in the absence (ctrl) or presence of PD1-IL15 antibody fusion cytokine (m2) or the combined treatment of anti-PD1 antibody + IL-15 agonist (comb) for 9 days.

tag: cell type

tag: cancer type

value: Hepatocellular carcinoma

tag: treatment (days in vitro)

value: PD1-IL15 antibody fusion cytokine (9d)


title: HCC213L_ctrl_CD8

value: control, untreated (9d)


title: HCC213L_m2_CD8


title: ACHN_Input

tag: overexpression

tag: antibody


title: Normal sample patient M1-1

tag: surgical indication

tag: Sex


title: HCC213L_ctrl_CD4


title: HCC213L_comb_CD8

value: combined teatment anti-PD1 + IL-15 agonist (9d)


title: ACHN_Flag

value: FLAG


title: HCC189L_comb_CD8


title: HCC206L_ctrl_CD8


title: HCC206L_m2_CD8


title: HCC206L_ctrl_CD4


title: HCC213L_comb_CD4


title: HCC206L_comb_CD8


title: HCC189L_ctrl_CD4


title: HCC189L_m2_CD4


title: HCC189L_m2_CD8


title: HCC206L_m2_CD4


title: HCC189L_comb_CD4


title: HCC189L_ctrl_CD8


title: HCC206L_comb_CD4


title: Healthy control [CTRL99]

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description:
Healthy control
CTRL99
Controls_only.txt
miR_181_controls.csv

data_processing:
Data were aligned to the genome using the GeneGlobe pipeline (https://geneglobe.qiagen.com/us/)
Data were filtered using the following specifications: >50 UMIs in >60% of the samples for longitudinal analysis, >100 UMIs on average for other analyses
Data were corrected for batch using the ComBat function in R and then normalized by DESeq2
Supplementary_files_format_and_content: txt files contain raw UMI counts, after alignment
Supplementary_files_format_and_content: xls files contain batch and DESeq2 corrected UMIs, after filtration of low-abundance miRNAs. Related R code are in the same folder
Supplementary_files_format_and_content: csv files contain categorial values for miRNAs and other clinical features, to be run by an R code for calculation of hazard ratios by COX proportional hazard analysis. Related R codes are in the same folder

source_name: Blood plasma

extract_protocol:
Plasma were isolated from blood and total RNA was extracted using the Qiagen miRNeasy micro kit (Cat# 217184)
libraries were prepared from 7.5 ng of total RNA using the QIAseq miRNA library kit and QIAseq miRNA NGS 48 Index IL (Qiagen, Cat# 331505 and 331565), by an experimenter who was blinded to the identity of samples. Samples were randomly allocated to library preparation and sequencing in batches. Libraries with different indices were multiplexed and sequenced on NextSeq 500/550 v2 flow cell or Novaseq SP100 (Illumina), with 75bp single read and 6bp index read.

tag: condition

value: Healthy control


title: Healthy control [CTRL98]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL98
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL94]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL94
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL92]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL92
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL88]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL88
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL9]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL9
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL91]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL91
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL87]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL87
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL96]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL96
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL86]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL86
Controls_only.txt
miR_181_controls.csv


title: Normal3

city: Shanghai

first: Yu

last: Li

address: Minhang Dongchuan Road No.500

institute: East China Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
FPKM were calculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for differentially expressed genes in  each sample

source_name: Adipocytes

extract_protocol:
Fat tissues frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Inguinal white adipose tissues

tag: strain

tag: treatment

value: 22C for 7 days


title: Normal2


title: Healthy control [CTRL81]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL81
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL84]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL84
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL80]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL80
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL83]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL83
Controls_only.txt
miR_181_controls.csv


title: NSG_ATRX_30

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

institute: INSERM

description: Tum NSG shATRX 30

data_processing:
RNA reads were aligned to the mm10 genome assembly with STAR v2.6.0c.
Gene expression (FPKM values) was quantified with Cufflinks v2.2.1, using RefSeq genes (without miRNA and rRNA) from mm10 UCSC Table Browser fixed on 2019-01-28. FPKM values less than 1 were excluded and log2-transformed with an offset value of 1.
Differential gene expression was performed by R package DESeq, between ATRXKD and ATRXCT tumors extracted from Balb/c mice. Relationships between proteins overexpressed in ATRXKD and ATRXCT tumors were assessed by the STRING Database
Genome_build: mm10

source_name: xenograft tumor

extract_protocol:
RNA extraction was performed using standard TRIzol / chloroform extraction followed by 100% ethanol precipitation and RNA purification using the RNeasy Mini Kit with DNase treatment. Total RNA was quantified using a Nanodrop 1000 spectrophotometer and qualified with an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit according to the manufacturer’s instructions.
Libraries from total RNA were prepared using the TruSeq®Stranded Total RNA Gold Library Preparation Kit according to the manufacturer’s protocol. Briefly, 0.5 µg of total RNA was ribo-depleted using the Ribo-Zero Gold Kit. RNA fragmentation resulted in fragments of 80 – 450 nt, with a major peak at 160 nt. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by second-strand cDNA synthesis, performed in presence of dUTP instead of dTTP. Blunt-ended double-stranded cDNA was 3´adenylated and Illumina-indexed adapters were ligated. Resulting libraries were enriched with 15 PCR cycles.

tag: genotype/variation

value: shRNA against ATRX

value: NSG


title: Cold3

value: 4C for 7 days


title: Cold1


title: Cold2


title: Normal1


title: Healthy control [CTRL78]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL78
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL95]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL95
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL93]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL93
Controls_only.txt
miR_181_controls.csv


title: NSG_ATRX_29

description: Tum NSG shATRX 29


title: Healthy control [CTRL77]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL77
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL76]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL76
Controls_only.txt
miR_181_controls.csv


title: NSG_ATRX_28

description: Tum NSG shATRX 28


title: Healthy control [CTRL75]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL75
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL89]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL89
Controls_only.txt
miR_181_controls.csv


title: NSG_ATRX_27

description: Tum NSG shATRX 27


title: NSG_ATRX_26

description: Tum NSG shATRX 26


title: Healthy control [CTRL85]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL85
Controls_only.txt
miR_181_controls.csv


title: NSG_CT_5

description: Tum NSG shCT 5

value: shRNA control


title: Healthy control [CTRL79]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL79
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL73]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL73
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL82]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL82
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL72]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL72
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL71]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL71
Controls_only.txt
miR_181_controls.csv


title: NSG_CT_4

description: Tum NSG shCT 4


title: NSG_CT_3

description: Tum NSG shCT 3


title: NSG_CT_1

description: Tum NSG shCT 1


title: Healthy control [CTRL7]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL7
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL69]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL69
Controls_only.txt
miR_181_controls.csv


title: Balb_ATRX_60

description: Tum Balb/c shATRX 60

value: Balb/c


title: Healthy control [CTRL68]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL68
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL67]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL67
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL70]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL70
Controls_only.txt
miR_181_controls.csv


title: Balb_ATRX_56

description: Tum Balb/c shATRX 56


title: Healthy control [CTRL74]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL74
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL65]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL65
Controls_only.txt
miR_181_controls.csv


title: Balb_CT_45

description: Tum Balb/c shCT 45


title: Balb_ATRX_58

description: Tum Balb/c shATRX 58


title: Healthy control [CTRL63]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL63
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL61]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL61
Controls_only.txt
miR_181_controls.csv


title: Balb_CT_43

description: Tum Balb/c shCT 43


title: Healthy control [CTRL62]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL62
Controls_only.txt
miR_181_controls.csv


title: Balb_CT_41

description: Tum Balb/c shCT 41


title: Healthy control [CTRL60]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL60
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL6]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL6
Controls_only.txt
miR_181_controls.csv


title: Balb_ATRX_59

description: Tum Balb/c shATRX 59


title: Healthy control [CTRL59]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL59
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL58]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL58
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL57]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL57
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL66]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL66
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL56]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL56
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL55]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL55
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL54]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL54
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL52]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL52
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL53]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL53
Controls_only.txt
miR_181_controls.csv


title: HeLa

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

description:
not replicate
SAMPLE 18

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol in Illumina iScan Microarray scanner

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio 2.0

source_name: Cell line

label_protocol: Biotinylated cRNA were prepared with the Epicentre Target Amp Nano Labeling kit for Illumina arrays.

growth_protocol: Primary uterine cervical lesions (n=11) and normal ectocervical tissue (n=5) were collected from the hospital section of Chittaranjan National Cancer Institute (CNCI), Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients. Normal ectocervical tissue was obtained from patients who underwent hysterectomy for benign reasons. SiHa (HPV16 positive), HeLa (HPV18 positive) and C33A (HPV negative) cell lines were obtained from NCCS, Pune and were grown and maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics and 10% fetal bovine serum and grown at 37 C, 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser/Denaturing RNA agarose gel electrophoresis.

tag: gender

value: Female

tag: tissue type

value: HPV18 positive cervical cancer cell line


title: Healthy control [CTRL51]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL51
Controls_only.txt
miR_181_controls.csv


title: Primary Tumor 10

description:
replicate 4
SAMPLE 15

source_name: Patient

value: hrHPV positive cervical squamous cell carcinoma


title: SiHa

description:
not replicate
SAMPLE 17

value: HPV16 positive cervical cancer cell line


title: C33A

description:
not replicate
SAMPLE 19

value: HPV negative cervical cancer cell line


title: Healthy control [CTRL5]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL5
Controls_only.txt
miR_181_controls.csv


title: Primary Tumor 6

description:
replicate 6
SAMPLE 11


title: Healthy control [CTRL48]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL48
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL47]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL47
Controls_only.txt
miR_181_controls.csv


title: Primary Tumor 8

description:
replicate 2
SAMPLE 13


title: Healthy control [CTRL49]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL49
Controls_only.txt
miR_181_controls.csv


title: Primary Tumor 11

description:
replicate 5
SAMPLE 16


title: Primary Tumor 7

description:
replicate 1
SAMPLE 12


title: Primary Tumor 5

description:
replicate 5
SAMPLE 10


title: Healthy control [CTRL46]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL46
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL50]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL50
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL45]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL45
Controls_only.txt
miR_181_controls.csv


title: Primary Tumor 3

description:
replicate 3
SAMPLE 8


title: Primary Tumor 4

description:
replicate 4
SAMPLE 9


title: Healthy control [CTRL44]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL44
Controls_only.txt
miR_181_controls.csv


title: Primary Tumor 1

description:
replicate 1
SAMPLE 6


title: Primary Tumor 2

description:
replicate 2
SAMPLE 7


title: Normal 5

description:
replicate 5
SAMPLE 5

value: HPV negative normal cervical epithelium


title: Healthy control [CTRL43]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL43
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL42]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL42
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL37]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL37
Controls_only.txt
miR_181_controls.csv


title: Normal 2

description:
replicate 2
SAMPLE 2


title: Normal 1

description:
replicate 1
SAMPLE 1


title: Normal 3

description:
replicate 3
SAMPLE 3


title: Healthy control [CTRL41]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL41
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL38]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL38
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL40]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL40
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL36]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL36
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL39]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL39
Controls_only.txt
miR_181_controls.csv


title: Normal sample patient M4-4

value: gastric tissue

value: advanced gastric cancer

value: f

tag: t stage

tag: n stage

tag: stage(tnm)

value: IIIa

tag: treatement after surgery

value: no

tag: recurrence

tag: disease free survival (months)

tag: death

tag: overall survial duration (months)


title: Normal 4

description:
replicate 4
SAMPLE 4


title: MM106-Eattss-24HPI-rep2_Cy5

city: Angers

first: Alexandre

last: Degrave

address: André Lenôtre

institute: Agrocampus Ouest

hyb_protocol: The hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple genotype MM106 (susceptible) leaf tissues, infiltrated with Ea 6023 mutant strain, sampled 24 hours after inoculation.

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Malus × domestica MM106 or ME010 scions, grafted on MM106 rootstocks, were cultivated in greenhouse (semi-controlled conditions, natural photoperiod supplemented with artificial light if needed during a 16h photophase, 23-25 °C day, 17 °C night, watering every 2-4 days with tap water) in standard potting soil. Bacterial strains were grown overnight at 26°C on solid King’s B medium.

extract_protocol: Each sample corresponds to a pool of the youngest expanded leaf from 3 replicate plants per condition. Samples were snap-frozen in liquid nitrogen and further ground to a fine powder in liquid nitrogen using a tissue lyser (Retsch, Haan, Germany) and total RNA were extracted using the Nucleospin® RNA Plant Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s procedure. Purity and concentration of samples were assayed with a NanoDrop® One.

treatment_protocol: Bacterial suspensions were prepared in reverse osmotic water supplemented by 0.01 % of wetting agent Silwet L-77 from an exponential growth phase culture cultivated on solid King’s B medium overnight at 26 °C. The bacterial titer was adjusted 107 CFU mL-1 and used to inoculate young apple leaves by vacuum infiltration (3 min beyond -0.9 MPa).

tag: tissue

value: Leaf

tag: genotype

tag: resistance to ea

value: Susceptible

tag: inoculated

value: Inoculated

tag: bacterial strain

value: Mutant

tag: sampling time


title: MM106-EaWT-24HPI-rep2_Cy3

source_name: Apple genotype MM106 (susceptible) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 24 hours after inoculation.

value: Wild type


title: Healthy control [CTRL35]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL35
Controls_only.txt
miR_181_controls.csv

tag: condition

value: Healthy control


title: Healthy control [CTRL34]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL34
Controls_only.txt
miR_181_controls.csv


title: MM106-EaWT-24HPI-rep1_Cy5


title: MM106-Eattss-24HPI-rep1_Cy3


title: MM106-Eattss-6HPI-rep2_Cy3

source_name: Apple genotype MM106 (susceptible) leaf tissues, infiltrated with Ea 6023 mutant strain, sampled 6 hours after inoculation.


title: Healthy control [CTRL31]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL31
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL30]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL30
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL3]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL3
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL29]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL29
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL33]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL33
Controls_only.txt
miR_181_controls.csv


title: MM106-EaWT-6HPI-rep2_Cy3

source_name: Apple genotype MM106 (susceptible) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 6 hours after inoculation.


title: MM106-EaWT-6HPI-rep2_Cy5


title: Healthy control [CTRL28]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL28
Controls_only.txt
miR_181_controls.csv


title: Balb_CT_44

description: Tum Balb/c shCT 44

tag: cell line

tag: genotype/variation

value: shRNA control

tag: strain

value: Balb/c


title: Healthy control [CTRL27]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL27
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL24]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL24
Controls_only.txt
miR_181_controls.csv


title: MM106-Eattss-6HPI-rep1_Cy5


title: Healthy control [CTRL23]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL23
Controls_only.txt
miR_181_controls.csv


title: NSG_CT_2

description: Tum NSG shCT 2

value: NSG


title: Healthy control [CTRL26]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL26
Controls_only.txt
miR_181_controls.csv


title: ME010-EaWT-24HPI-rep2_Cy3

source_name: Apple genotype ME010 (resistant) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 24 hours after inoculation.

value: Resistant


title: ME010-Eattss-6HPI-rep2_Cy5

source_name: Apple genotype ME010 (resistant) leaf tissues, infiltrated with Ea 6023 mutant strain, sampled 6 hours after inoculation.


title: ME010-EaWT-6HPI-rep2_Cy5

source_name: Apple genotype ME010 (resistant) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 6 hours after inoculation.


title: MM106-EaWT-24HPI-rep2_Cy5


title: ME010-Eattss-24HPI-rep1_Cy3

source_name: Apple genotype ME010 (resistant) leaf tissues, infiltrated with Ea 6023 mutant strain, sampled 24 hours after inoculation.


title: ME010-EaWT-24HPI-rep2_Cy5


title: Healthy control [CTRL21]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL21
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL2]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL2
Controls_only.txt
miR_181_controls.csv


title: ME010-Eattss-24HPI-rep2_Cy5


title: ME010-Eattss-6HPI-rep1_Cy3


title: Healthy control [CTRL19]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL19
Controls_only.txt
miR_181_controls.csv


title: ME010-EaWT-24HPI-rep1_Cy3


title: ME010-EaWT-6HPI-rep2_Cy3


title: ME010-EaWT-24HPI-rep1_Cy5


title: Healthy control [CTRL20]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL20
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL22]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL22
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL18]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL18
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL16]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL16
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL13]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL13
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL12]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL12
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL15]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL15
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL120]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL120
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL32]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL32
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL112]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL112
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL111]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL111
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL11]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL11
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL108]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL108
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL109]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL109
Controls_only.txt
miR_181_controls.csv