title: Act_minus_Org-3

description:
Sample_W0094_Rn-885
Rn-885

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Mesonephric kidney organoid

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN).
Sequencing libraries were generated using KAPA Stranded mRNA Kit accoding to the manifacturer's instruction. The initial amount of total RNA was 500 ng.

treatment_protocol: For induction of metanephric NP-like cells, the medium was changed at Stage 4, to basal medium containing 3 μM CHIR99021, 100 ng/ml bFGF, 1 ng/ml BMP7, 10 ng/ml activin A and 30 μM Y-27632. At Stage 5, the medium was changed to basal medium containing 200 ng/ml FGF9, 0.1 μM RA and 25 ng/ml NOGGIN. At Stage 6, the medium was switched to basal medium containing 200 ng/ml FGF9 and 1 µM CHIR99021. Subsequently, the culture medium was refreshed every day. For induction of mesonephric NP-like cells, cells were cultured as the same protocol described above, but activin A was lacked in Stage 4 culture medium. Nephron organoid formation was performed as described previously (Li et al., 2016). Briefly, to form cellular aggregates, OSR1+SIX2+ progenitor cells were sorted by a FACS Aria II and plated in spindle-shaped bottom low adhesion 96-well plates at a density of 1.0 × 105 cells/well with basal medium supplemented with 10 μM Y-27632, 200 ng/ml FGF9 and 1 µM CHIR99021. After 24 h of incubation, the aggregates were transferred onto transwell inserts with KR5 medium (DMEM/F12 Glutamax containing 0.1 mM non-essential amino acids, 500 U/ml PS, 55 μM 2-mercaptoethanol and 5% KSR) in the presence of 4.5 μM CHIR99021 and 200 ng/ml FGF2. After 2 days of culture, the medium was refreshed with KR5 medium, and the aggregates were cultured for an additional 8 days.

value: iPSC-derived organoid


title: mutd14b

status: Public on Jul 15 2020

type: SRA

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

country: USA

institute: University of Arizona

library_source: transcriptomic

data_processing:
Alignment to mouse genome using Salmon (salmon-0.11.1-linux_x86_64) for single end reads.
Trim first column of Salmon output data to contain ENSMUST transcript identifiers. This was done using the Galaxy platform.
Created a file to convert ENSMUST identifiers to GeneID using Galaxy
Normalize count values and idnetify differentially expressed genes using DeSeq2. This was done using the Galaxy Platform.
Export Data and evaluate in R to create visuals.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Counts as computed from TPM values of all data in the experiment, done using Galaxy DeSeq2. File is CSV format.

molecule: total RNA

organism: Mus musculus

source_name: Dorsal Root Ganglia

growth_protocol: Embryonic neurons were cultured in Neurobasal with added B27, Pen/Strep, FDU (anti-mitotic) and NGF for 14 days, with media changes on Day 5 and Day 10.

extract_protocol:
Trizol (Invitrogen) was used to extract total RNA according to the manufacturer's instructions.
250-300bp insert library prepared according to Illumina instructions

treatment_protocol: A subset of mutant neurons received lentivirus that re-expressed Tmem184b (and a Venus fluorescent reporter) using a CMV promoter. Virus transduction efficiency was verified by Venus expression.

tag: strain

value: Tmem184b gene trap homozygous (C57BL/6 background)

tag: age

tag: cell type

value: DRG neurons

tag: days in culture

tag: transduced with virus


title: mutd14c


title: MUT_TMH


title: Act_minus_Org-2

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description:
Sample_W0094_Rn-884
Rn-884

organism: Homo sapiens

growth_protocol: hiPSC colonies grown on SNL feeder cells were first treated by an enzymatic method with CTK dissociation solution for 3 min to remove SNL cells, dissociated into single cells by gentle pipetting after treatment with Accutase for 6 min and seeded on Matrigel-coated 24-well plates at a density of 2.5 × 104 cells/cm2 with Primate Repro FF2 medium, 4 ng/ml bFGF, 10 µM Y-27632 and 500 U/ml Penicillin and Streptomycin (PS). On culture day 2, the cells were treated in serum-free differentiation medium consisting of DMEM/F12 Glutamax medium, B27 supplement minus vitamin A, and 500 U/ml PS (hereafter called basal medium) supplemented with 1 µM CHIR99021, 10 nM retinoic acid, 1 ng/ml BMP4 and 100 ng/ml bFGF to induce CDX1+ cells. For differentiation towards intermediate mesoderm (IM) and metanephric nephron progenitor (NP) cells, CDX1+ cells were cultured with 3 μM CHIR99021, 100 ng/ml bFGF and 1 ng/ml BMP7. After 12 h, the medium was switched to basal medium containing 3 μM CHIR99021, 100 ng/ml bFGF, 1 ng/ml BMP7 and 10 μM A83-01.

tag: cell line

value: 4A6 iPSC

tag: activin

value: minus


title: MUT_TMFG


title: Act_minus_NP-3

description:
Sample_W0094_Rn-877
Rn-877

source_name: Mesonephric nephron progenitor

value: iPSC-derived projenitor


title: OPSCC 39

type: RNA

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 39 -- ENT 88.1

data_processing:
Expression data were processed using Quant Studio Flex software qPCR Analysis Software (Applied Biosystems™, version 1.2.2). Fluorescence data was exported to CSV files by the software for use in R statistical software.
Data were analysed in R version 3.4.2. The relative expression of each miRNA was calculated as 2(40-Ct). All possible permutations of miRNA ratios were generated from the relative expression values using R version 3.4.2.
Nested cross validation and Lasso regression were used to select a panel of micrRNA ratios to build a logisitc regression model that could differentiate healthy controls and GORDs from OPSCCs.
Matrix normalized worksheet reports the miRNA ratio expression values generated by R version 3.0.2
Fold Change worksheet reports the fold difference of expression of the microRNA ratios between the indicated study groups

label: FAM

source_name: peripheral blood serum exosomes

label_protocol: PCR assays were performed by following the protocol for TaqMan@OpenArray Human MicroRNA Panel (4461104, Life technologies). For each sample, 3μl of RNA was reverse transcribed using pre-defined RT-primers (MegaplexTM Primer Human Pool A and Pool B) and the TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). Pre-amplifications were carried out with MegaplexTM PreAmp Pools and TaqMan PreAmp Master Mix on 7.5μl cDNA/ sample for each pool. The pre-amplified products (4μl per sample) were diluted at the recommended 1:40 dilution with 156μl of RNase-free ultra pure water before loading onto the 384-well TaqMan OpenArray loading plate.

extract_protocol: Exosomes were isolated from the serum samples using ExoquickTm (System Biosciences, EXOQ20A-1). Extraction of miRNA from exosomes was performed using a  miRNeasy Serum/Plasma kit (Qiagen, #217184) with a final elution volume of 24 microlitres ultra pure water

treatment_protocol: Peripheral blood was collected into serum clot activator tubes

tag: tissue

value: peripheral blood serum exosomes

tag: patient diagnosis

value: locally advanced oropharyngeal squamous cell carcinoma


title: Act_minus_Org-1

description:
Sample_W0073_Rn866
Rn-866


title: OPSCC 38

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 38 -- ENT 60.1


title: MUTD14H


title: MUT_TME


title: MUT_TMB


title: MUT_TMC


title: WTDAY04


title: mutd14e


title: Act_minus_NP-1

description:
Sample_W0094_Rn-875
Rn-875


title: WTDAY03


title: WTDAY02


title: Act_minus_NP-2

description:
Sample_W0094_Rn-876
Rn-876


title: WTDAY01


title: Act_plus_Org-3

description:
Sample_W0094_Rn-883
Rn-883

source_name: Metanephric kidney organoid

value: plus


title: OPSCC 36

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 36 -- ENT 473.1


title: OPSCC 35

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 35 -- ENT 459.1


title: Aorta, control, rep1

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

country: China

institute: Peking University

data_processing:
HCS2.2.58 and RTA v1.18 software was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, including those containing more than 10% of unknown nucleotides or more than 50% of low-quality (Q-value no larger than 20%) bases. Then they were filtered against rRNA database to remove potential rRNA contamination.
Reads that passed the above filtration and quality control were mapped to GRCm38 genome (Ensembl release 84), by using TopHat2 software (version 2.1.1) with custom parameters -g 1 -r 50 --mate-std-dev 80 --no-coverage-search --phred64-quals --keep-fasta-order
Gene abundances were quantified by RSEM software (version 1.2.19) with recommended command line parameters by Trpnell C, et al Nature protocol, 2012, 7(3): 562-578. The gene expression level was normalized by using Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method, where the number of fragments mapped to the specific gene was normalized by the total number of fragments that mapped to reference genes and the number of bases on this specific gene.
Genome_build: GRCm38 genome (Ensembl release 84)
Supplementary_files_format_and_content: Single tab-delimited text file that includes FPKM values (i.e. normalized gene expression levels) for all samples.

source_name: Aorta

growth_protocol: Male 14-week-old C57BL/6 mice were housed in standard cages in a temperature- and humidity-controlled environment, on a 12-h light/dark cycle, with regular feeding and free access to water. All animal care and experimental protocols complied with the Declaration of Helsinki, Animal Management Rules of the Ministry of Health of the People’s Republic of China and the guide for the Care and Use of the Laboratory Animals of Peking University. The protocol was approved by the Peking University Animal Ethics Committee.

extract_protocol:
Tissues were harvested, flash frozen on dry ice. Total RNA was extracted by using Qiagen RNeasy kit, prepared with Illumina TruSeq Stranded Total RNA Library Prep kit under the manufacturer's guideline.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For treatment group, the mice were treated with 300mg/kg (10mL/kg) metformin through gavage administration, for 30 days. For control group, the mice were treated with double distilled water through gavage administration, for 30 days.

value: Aorta

value: 14 weeks

tag: Sex

value: male

tag: treatment


title: MUTDAY0C


title: MUTDAY0B


title: OPSCC 34

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 34 -- ENT 439.1


title: Act_plus_Org-2

description:
Sample_W0094_Rn-882
Rn-882


title: mutd0h


title: mutd0fg


title: Act_plus_NP-3

description:
Sample_W0094_Rn-874
Rn-874

source_name: Metanephric nephron progenitor


title: Act_plus_Org-1

description:
Sample_W0073_Rn865
Rn-865


title: OPSCC 32

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 32 -- ENT 403.1


title: Dormant Tumor, 1105_S11

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description:
Tissues_fpkm.txt
S11

data_processing:
Mapping was carried out using Tophat.
Samtools and Cufflinks were used to generate FPKM values
To minimize the effects of dividing FPKM values by numbers close to 0 and stochastic nois, 0.1 was added to each FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: Dormant Tumor

growth_protocol: Tumors grown in genetically engineered melanoma tumor mouse

extract_protocol:
cell line RNA was  extracted using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dox treantment to turn off the Braf oncogene

value: tumor

tag: status

value: Dormant Tumor

tag: genotype

value: Dct::TVA; Cdkn2alox/lox; Ptenlox/lox Tet-Off, CRE and TRE-BRAFVE

value: BRAF-OFF dormant


title: OPSCC 37

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 37 -- ENT 553.1


title: OPSCC 31

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 31 -- ENT 385.1


title: Act_plus_NP-2

description:
Sample_W0094_Rn-873
Rn-873


title: OPSCC 30

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 30 -- ENT 36.1


title: Dormant Tumor, 1099_S8

description:
Tissues_fpkm.txt
S8


title: Dormant Tumor, 1096_S7

description:
Tissues_fpkm.txt
S7


title: Act_plus_NP-1

description:
Sample_W0094_Rn-872
Rn-872


title: Dormant Tumor, 1095_S6

description:
Tissues_fpkm.txt
S6


title: Dormant Tumor, 1102_S9

description:
Tissues_fpkm.txt
S9


title: OPSCC 29

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 29 -- ENT 358.1


title: Dormant Tumor, 1050T1_S13

description:
Tissues_fpkm.txt
S13


title: Dormant Tumor, 1045_S5

description:
Tissues_fpkm.txt
S5


title: OPSCC 28

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 28 -- ENT 339.2


title: Treated with miR-887-3

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: Human Pulmonary Microvascular Endothelial Cell

growth_protocol: HPEMCs (Lonza) were cultured in Endothelial Basal Media-2 supplemented with EBM-2 SingleQuots (Lonza) at 37 degrees untill 80-90% confluent and then serum starved overnight.

extract_protocol:
RNA was extracted using Rneasy plus mini kit (Qiagen) following the manufacturer's instructions.  RNA integrity and quantity were measured with NanoDrop One (Thermofisher).
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer. MiRNA libraries were prepaired using Illumina's TruSeq Small RNA Library Prep Kit following the manufactuer's protocol (San Diego, CA).

treatment_protocol: Cells were then transfected with miR-887-3p mimic (Qiagen) or all-stars negative control (Qiagen) using HiPerfect transfection reagent.  48 hours later, RNA was extracted.


title: Treated with miR-887-1


title: Dormant Tumor, 1106_S12

description:
Tissues_fpkm.txt
S12


title: OPSCC 27

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 27 -- ENT 336.1


title: Dormant Tumor, 1044_S4

description:
Tissues_fpkm.txt
S4


title: OPSCC 33

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 33 -- ENT 419.1


title: OPSCC 26

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 26 -- ENT 335.1


title: Control 3

value: Control


title: Dormant Tumor, 1038_S3

description:
Tissues_fpkm.txt
S3


title: Dormant Tumor, 0933_S1

description:
Tissues_fpkm.txt
S1


title: Control 2


title: Primary Tumor, 194_S46

description:
Tissues_fpkm.txt
S46

source_name: Primary Tumor

value: Primary Tumor

value: BRAF-ON


title: OPSCC 25

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 25 -- ENT 306.1


title: Primary Tumor, 193_S45

description:
Tissues_fpkm.txt
S45


title: OPSCC 24

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 24 -- ENT 305.1


title: Primary Tumor, 188_S43

description:
Tissues_fpkm.txt
S43


title: Control 1


title: Primary Tumor, 189_S44

description:
Tissues_fpkm.txt
S44


title: K562_NPAT_low_salt_2_(20191125_SH_Hs_NPAT_2_1h_1115)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: low salt CUT&Tag for NPAT in thawed crosslinked nuclei from 60,000 K562 cells

library_source: genomic

data_processing:
Library strategy:  CUT&TAG
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19.bed.gz).

molecule: genomic DNA

extract_protocol:
CnT_d2PCR_Protocols_io_v3beta.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: NPAT Thermo Invitrogen cat# PA5-66839 lot# SL2495022A

value: K562 human immortalised myelogenous leukemia cell line


title: Primary Tumor, 192_S41

description:
Tissues_fpkm.txt
S41


title: Treated with miR-887-2


title: OPSCC 23

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 23 -- ENT 302.1


title: Dormant Tumor, 0935_S2

description:
Tissues_fpkm.txt
S2


title: OPSCC 22

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 22 -- ENT 127.1


title: Primary Tumor, 187_S39

description:
Tissues_fpkm.txt
S39


title: Dormant Tumor, 1104_S10

description:
Tissues_fpkm.txt
S10


title: Recurrent tumor, 521_S38

description:
Tissues_fpkm.txt
S38

source_name: Recurrent tumor

value: Recurrent tumor

value: BRAF-OFF


title: Primary Tumor, 191_S40

description:
Tissues_fpkm.txt
S40


title: K562_NPAT_low_salt_0_5_(20191125_SH_Hs_NPAT_0_5_1_1115)

source_name: low salt CUT&Tag for NPAT in thawed crosslinked nuclei from 60,000 K562 cells


title: DU145 cells, mut_rep3

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

country: Italy

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

description:
DU145 cells treated with SPOP mutation
200796230064_I

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v4. Raw expression data were log2-transformed and normalized using the robust spline normalization method.

label: Biotin

source_name: DU145 cells

label_protocol: Biotinylated cRNA were prepared with Illumina RNA TotalPrep amplification kit (Ambion)

growth_protocol: 0.25 x 10e6 cells/ml of DU145 cells in 2 ml of RPMI 10% FBS medium without antibiotics per well (in a 6-well plate) so that they were 90% confluent at the time of transfection

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: DU145 cells were transfected with 50mg of plasmids expressing wt or mutated SPOP combined 1:1 with Lipofectamine 2000 and resuspended in a total of 500ml of Optimem Medium (amounts per well)

value: DU145 cells

value: SPOP mutation


title: OPSCC 20

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 20 -- VCB 17PM0037

value: peripheral blood serum exosomes

value: locally advanced oropharyngeal squamous cell carcinoma


title: Recurrent tumor, 447_S35

description:
Tissues_fpkm.txt
S35


title: Recurrent tumor, 519_S36

description:
Tissues_fpkm.txt
S36


title: OPSCC 21

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 21 -- ENT 100.1


title: K562_NPAT_300_salt_20_(20191209_SH_Hs_NPAT_20_1h_1126)

description: CUT&Tag for H3K4me3 in thawed crosslinked nuclei from 120,000 K562 cells


title: K562_Neg_control_XLink_(20200110_SH_Hs_K27ac_X_0107)

description: CUT&Tag for Control in 120000 K562 cross-linked cells Direct

extract_protocol:
CnT_Protocols_io_v2.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: H3K27ac Thermo cat# MA5-23516 (mouse) primary; Guinea pig anti-rabbit Antibodies-Online ABIN101961 secondary


title: Recurrent tumor, 520_S37

description:
Tissues_fpkm.txt
S37


title: Recurrent tumor, 419_S34

description:
Tissues_fpkm.txt
S34


title: Recurrent tumor, 417_S33

description:
Tissues_fpkm.txt
S33


title: K562_Neg_control_XLink_PCI_(20200110_SH_Hs_K27ac_Xpc_0107)

description: CUT&Tag for Control in 120000 K562 cross-linked nuclei PCI


title: OPSCC 18

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 18 -- ENT 558.1


title: K562_NPAT_low_salt_1_(20191125_SH_Hs_NPAT_1_1h_1115)


title: OPSCC 19

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 19 -- VCB 16MH1733


title: Recurrent tumor, 395_S31

description:
Tissues_fpkm.txt
S31


title: OPSCC 17

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 17 -- ENT 550.1


title: K562_Neg_control_Native_(20200110_SH_Hs_K27ac_N_0107)

description: CUT&Tag for Control in 120000 K562 cells Direct


title: Cdx2_ES_D5_Alkbh1OE_N6mA_MeDIP

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

data_processing:
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
After sequencing and filter, high quality raw reads were aligned to the mouse genome (UCSC, mm9) with bowtie (2.3.1, default)
To identify uniquely mapped N6-mA peaks prior to peak calling, multiple-alignment reads were filtered using Samtools to retain reads with map quality (MapQ) scores above 20 and with properly oriented read mates.
N6-mA enriched regions were called against ssDNA input with SICER  (version 1.1, FDR<0.01)
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: ES cell

growth_protocol: The Tet-inducible-Cdx2-Flag ES cell line (Cdx2 ES cells) was obtained from NIA mouse ES cell bank. Cdx2 ES cells were maintained on feeder cells in DMEM supplemented with 15% fetal bovine serum (Gibco, Thermo Fisher Scientific), 1% non-essential amino acids, 2 mM l-glutamine, 1,000 units of mLIF (EMD Millipore), 0.1 mM β-mercaptoethanol (Sigma), antibiotics and 2 µg/ml doxycycline (Sigma).

extract_protocol:
Cellular genomic DNA was purified using the DNeasy kit (QIAGEN, 69504) with minor modifications. In brief, the cell lysate was treated with RNAse A1/T mix at 37 °C for 30 min. Then Proteinase K was added to the lysate and treated at 56 °C for 3 hours or overnight. The remaining steps were performed as described in the kit, and the DNA was eluted with ddH2O.
In briefly, 5 μg extracted genomic DNA was sonicated to 200–500 bp with Bioruptor. Then, adaptors were ligated to genomic DNA fragments following the Illumina protocol. The ligated DNA fragments were denatured at 95 °C for 5 min. Then, the single-stranded DNA fragments were immunoprecipitated with N6-mA antibodies (5 μg for each reaction, 202-003, Synaptic Systems) overnight at 4 °C. N6-mA enriched DNA fragments were purified according to the Active Motif hMeDIP protocol. IP DNA and input DNA were PCR amplified with NEBNext Multiplex Oligos for Illumina indexing primers.

treatment_protocol: When starting differentiation, Cdx2 ES cells were selectively seeded on gelatin-coated plates after stepwise elimination of the feeder MEF, then Cdx2 overexpression was induced by removing doxycycline. The cells were split at day 1 after doxycycline withdrawal and cell samples were collected in the following days.

value: Alkbh1 OE

tag: time point


title: Cdx2_ES_D13_N6mA_MeDIP_rep3

value: WT


title: OPSCC 16

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 16 -- ENT 467.1


title: Cdx2_ES_D13_N6mA_MeDIP_rep2


title: Cdx2_ES_D7_N6mA_MeDIP_rep2


title: Cdx2_ES_D7_N6mA_MeDIP_rep3


title: K562_K4me3_XLink_(20200110_SH_Hs_K4m3_X_0107)

description: CUT&Tag for K4me3 in 120000 K562 cross-linked cells

value: H3K4me3 Active Motif cat# 39159 lot# 22118006


title: OPSCC 15

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 15 -- ENT 440.1


title: Cdx2_ES_D5_N6mA_MeDIP_rep2


title: Cdx2_ES_D5_N6mA_MeDIP_rep3


title: K562_Neg_control_Native_PCI_(20200110_SH_Hs_K27ac_Npc_0107)

description: CUT&Tag for Control in 120000 K562 nuclei PCI


title: Cdx2_ES_D7_N6mA_MeDIP


title: Cdx2_ES_D3_N6mA_MeDIP_rep3


title: K562_K4me3n_rep2_(20190927_SH_Hs_K4m3n_0920)

description: CUT&Tag for H3K4me3 in nuclei from 500000 K562 cells


title: OPSCC 14

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 14 -- ENT 399.1


title: Cdx2_ES_D3_N6mA_MeDIP


title: OPSCC 13

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 13 -- ENT 394.1


title: OPSCC 12

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 12 -- ENT 376.1


title: Cdx2_ES_D0_N6mA_MeDIP_rep3


title: OPSCC 11

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 11 -- ENT 363.1


title: K562_K4me3nf_rep2_(20190927_SH_Hs_K4m3nf_0920)

description: CUT&Tag for H3K4me3 in crosslinked nuclei from 500000 K562 cells


title: Satb1_ChIP_D5_WT

data_processing:
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
After sequencing and filter, high quality raw reads were aligned to the mouse genome (UCSC, mm9) with bowtie (2.3.1, default)
Multiple alignments were removed by samtools to keep reads with quality score above 20 .
Peak calling was performed against input by Sicer V1.1, W200, G600, FDR0.01. Differential Satb1 deposition regions among two samples of interest were identified with the SICER-df setting.
Genome_build: mm9
Supplementary_files_format_and_content: bed

extract_protocol:
10^7 Cells were washed once with DPBS and then fixed in 5 mL DMEM medium with 1% formaldehyde for 10 min at RT with rotation.  Fixation was terminated with addition of 100 mM glycine followed by 5 min rotation at RT. Cells were then scraped and spun down at 4 °C at 1000 rpm for 5 min, followed by two washes of ice-cold PBS. Cell pellets were resuspended in 1 mL Lysis Buffer 1 (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, and 0.25% Triton X-100) followed by rotation at 4 °C for 10 min. Cell pellets were spun down at 1400g for 5 min and resuspended in 1 mL Lysis Buffer 2 buffer (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA). Following another 10 min incubation at 4 °C, cell pellets were again spun down at 1400g for 5 min and resuspended in 200 to 300 µL Lysis Buffer 3 (10 mM Tris-HCl, pH8.0, 100 mM NaCl, 1 mM EDTA,0.5 mM EGTA, 0.5% Na-Deoxycholate and 0.5% N-lauroylsarcosine).  Cells were then sonicated to about 500 bp DNA products using Covaris S200 machine with the following parameters: peak power=120, duty factor=2.0, cycle/burst=200, temperature=5°C and scale=10 min and a power output at 2.1.  The sonicated cell solution was then diluted with Lysis buffer 3 plus 1% Triton X-100, incubated for 15 min with rotation at 4 °C and spun down at 20,000g for 15 min. 10 µg anti-Stab1 antibodies (Abcam, Ab109122) were added into the supernatant with equivalent amount of Rabbit IgG antibody as controls.  After overnight incubation at 4 °C, antibodies were pulled down using anti-Rabbit dynabeads (10 µL per 1 µg antibody) after incubation with beads for 2 hr at 4 °C and dynabeads were extensively washed with RIPA buffer (50 mM Hepes-KOH, pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP40 and 0.7% Na-Deoxycholate) with rotation at 4°C for 3 times, 10 min each time.  After last RIPA wash, beads were washed once with 1×TE+50 mM NaCl buffer. DNA was then eluted in elution buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA and 1% SDS) twice at 65 °C for 20 min. Eluted DNA was then at 65 °C overnight for reverse cross-link. The solution was treated with RNase A1/T mix (thermo scientific) and incubated at 37 °C for 1 hr. This is followed by addition of 3 µL of proteinase K and incubation for 2 hr at 56 °C.  The solution was then phenol-chloroform extracted once followed by DNA extraction using MinElute PCR Purification Kit (28004, Qiagen).  DNA was eluted with EB buffer for downstream qPCR analysis or CHIP-seq library preparation.
NEB NEBNext Ultra DNA Library Prep Kit

tag: differentiation

tag: chip antibody

value: anti-Stab1 (Abcam, Ab109122)


title: K562_K4me3nf_rep1_(20190927_SH_Hs_K4m3_NX_0918)

description: CUT&Tag for H3K4me3 in crosslinked nuclei from 120000 K562 cells


title: OPSCC 10

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 10 -- ENT 292.1


title: Cdx2_ES_SATB1KO_clone1_D4_RNAseq

data_processing:
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
Transcriptome mapping was performed with STAR version 2.5.2b using mm9 Gencode vM1 release exon/spice-junction annotation.
Differential expression analysis was performed using cufflinks version 2.2.1 using UCSC gene annotation with fr-firststrand library type and the correction of sequencing bias and multiple reads mapping.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

molecule: polyA RNA

extract_protocol:
RNA was extracted with miRNeasy kit (QIAGEN, 217004)
RNA-seq libraries were constructed with Illumina Truseq stranded mRNA library prep kit


title: Cdx2_ES_SATB1KO_clone2_D0_RNAseq


title: Cdx2_ES_SATB1KO_clone2_D4_RNAseq


title: OPSCC 9

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 9 -- ENT 254.1


title: K562_K4me3_Native_(20200110_SH_Hs_K4m3_N_0107)

description: CUT&Tag for K4me3 in 120000 K562 cells

source_name: CUT&Tag for K4me3 in 120000 K562 cells


title: K562_K4me3_XLink_PCI_(20200110_SH_Hs_K4m3_Xpc_0107)

description: CUT&Tag for K4me3 in 120000 K562 cross-linked nuclei


title: OPSCC 8

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 8 -- ENT 195.1


title: Primary Tumor, 197_S42

description:
Tissues_fpkm.txt
S42

value: tumor

value: Dct::TVA; Cdkn2alox/lox; Ptenlox/lox Tet-Off, CRE and TRE-BRAFVE


title: Cdx2_ES_SATB1CTRL_D0_RNAseq


title: Cdx2_ES_SATB1KO_clone1_D0_RNAseq


title: Cdx2_ES_SATB1CTRL_D4_RNAseq


title: BTBPE_0.07_rep4

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: BTBPE treated 0.07 mg/kg R. norvegicus sample

hyb_protocol: The amplified RNA (aRNA) was fragmented then hybridized to Affymetrix Rat Genome 230 2.0 arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Affymetrix Scanner 3000 7G

data_processing:
Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized separately for each chemical.
RMA expression measures from R/affy package

label: biotin

organism: Rattus norvegicus

source_name: liver, BTBPE 0.07 mg/kg

label_protocol: Microarray expression analysis was performed using total RNA isolated from liver samples. RNA meeting the following acceptance criteria were used for microarray expression analysis: RNA samples with a concentration ≥ 35 ng/μL and purity between l.80 to 2.20 and an RNA integrity number (RIN) ≥ 7.0. The RNA was amplified through cDNA synthesis, in vitro transcription and biotin labeling using GeneChip® 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA). One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

growth_protocol: At the start of the study, the animals were 7 weeks of age. The animals were given NTP-2000 diet (Zeigler 117 Brothers, Gardners, PA) and tap water ad libitum. The animal studies were conducted according to the guidelines of the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC) and approved by the local Animal Care and Use Committee.

extract_protocol: Necropsy was conducted after five days of dosing (one day after the last dose). At necropsy, the remaining left lobe of the liver was processed for RNA isolation. Tissue was placed in a cryotube containing RNAlaterTM and stored at 2-8 °C overnight. After overnight storage the RNAlaterTM was removed and the samples stored at -60 °C to -80 °C until processed for RNA isolation for use in microarray analysis. RNA was extracted from frozen samples using a Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA) with a deoxyribonucleic acid (DNA) digestion step. The concentration and purity of each RNA sample was calculated from UV absorbance readings (A260 and A280) obtained using a NanoDrop Spectrophotometer (ND-1000, NanoDrop Products; Thermo Scientific, Wilmington, DE). All samples were also evaluated for RNA integrity using an Agilent RNA 6000 Nano Chip kit with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: BTBPE (Cerilliant, ER081208-02) were prepared for oral gavage administration in corn oil (Spectrum, New Brunswick, New Jersey) to deliver BTBPE at doses of 0, 0.07, 0.69, 6.88, 68 or 680 mg/kg for 5 consecutive days to male Harlan Sprague Dawley rats in a volume of 5-ml/kg body weight.

tag: strain

value: Sprague Dawley

tag: gender

value: male

value: liver


title: K562_K4me3n_rep1_(20190927_SH_Hs_K4m3_N_0918)

description: CUT&Tag for H3K4me3 in nuclei from 120000 K562 cells

value: K562 human immortalised myelogenous leukemia cell line


title: K562_K4me3_low_salt_2_(20200103_SH_Hs_K4m3_Ale_1224)

description: low salt CUT&Tag for H3K4me3 in thawed crosslinked nuclei from K562 cells


title: OPSCC 7

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 7 -- ENT 188.1


title: Cdx2_ES_D3_N6mA_MeDIP_rep2


title: Cdx2_ES_ALKBH1OE_D5_RNAseq


title: Cdx2_ES_ALKBH1OE_D4_RNAseq


title: Cdx2_ES_D0_N6mA_MeDIP_rep2


title: OPSCC 6

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 6 -- ENT 186.1


title: Recurrent tumor, 416_S32

description:
Tissues_fpkm.txt
S32

value: Recurrent tumor


title: Cdx2_ES_ALKBH1OE_D0_RNAseq


title: Cdx2_ES_ALKBH1CTRL_D6_RNAseq


title: K562_K4me3c_rep2_(20190927_SH_Hs_K4m3c_0920)

description: CUT&Tag for H3K4me3 in 500000 K562 cells


title: OPSCC 5

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 5 -- ENT 177.1


title: K562_K4me3c_rep1_(20190927_SH_Hs_K4m3_0918)

description: CUT&Tag for H3K4me3 in 120000 K562 cells


title: Cdx2_ES_ALKBH1CTRL_D5_RNAseq


title: Cdx2_ES_ALKBH1CTRL_D4_RNAseq


title: OPSCC 4

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 4 -- ENT 167.1


title: K562_K4me3cf_rep1_(20190927_SH_Hs_K4me3_X_0918)

description: CUT&Tag for H3K4me3 in 120000 crosslinked K562 cells


title: Cdx2_ES_ALKBH1OE_D6_RNAseq


title: K562_K4me3_Native_PCI_(20200110_SH_Hs_K4m3_Npc_0107)

description: CUT&Tag for K4me3 in 120000 K562 nuclei

source_name: CUT&Tag for K4me3 in 120000 K562 nuclei


title: OPSCC 3

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 3 -- ENT 163.1


title: OPSCC 2

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 2 -- ENT 154.1


title: K562_K36me3_XLink_(20200110_SH_Hs_K36m3_X_0107)

description: CUT&Tag for K36me3 in 120000 K562 cross-linked cells Direct


title: Cdx2_ES_ALKBH1CTRL_D0_RNAseq


title: dsWGAIP

description:
MeDIP from double-strand whole genome amplified DNA
ssDIP,dsDIP,ssWGAIP,dsWGAIP, ssIN, dsIN are control samples for N6-mA MeDIP to ensure the specificity of the experiment.
WGAIP refers to IP with the whole genome amplified DNA. After adapter ligation, single-stranded or double-stranded genomic DNA was amplified for 20 cycles to eliminate DNA modifications on the DNA.
processed data not produced for this sample


title: IgG

description:
IgG
processed data not produced for this sample


title: Cdx2_ES_ALKBH1OE_D2_RNAseq


title: OPSCC 1

description:
OPSCC
serum from patient with HPV-positive Oropharyngeal Squamous Cell Carcinoma
microRNA
OPSCC 1 -- ENT 110.1


title: ssWGAIP

description:
MeDIP from single-strand whole genome amplified DNA
ssDIP,dsDIP,ssWGAIP,dsWGAIP, ssIN, dsIN are control samples for N6-mA MeDIP to ensure the specificity of the experiment.
WGAIP refers to IP with the whole genome amplified DNA. After adapter ligation, single-stranded or double-stranded genomic DNA was amplified for 20 cycles to eliminate DNA modifications on the DNA.
processed data not produced for this sample


title: GORD 20

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 20 -- SAB 19344 SAB 19347

value: Gastro Oesophageal Reflux (GORD)


title: K562_K36me3_Native_(20200110_SH_Hs_K36m3_N_0107)

description: CUT&Tag for K36me3 in 120000 K562 cells Direct


title: K562_K36me3_XLink_PCI_(20200110_SH_Hs_K36m3_X_pc_0107)

description: CUT&Tag for K36me3 in 120000 K562 cross-linked nuclei PCI


title: K562_K4me3cf_rep2_(20190927_SH_Hs_K4m3cf_0920)

description: CUT&Tag for H3K4me3 in 500000 crosslinked K562 cells


title: ssIN

description:
single-strand input
used as input sample for peak calling
processed data not produced for this sample


title: ssDIP

description:
MeDIP from ssDNA
ssDIP,dsDIP,ssWGAIP,dsWGAIP, ssIN, dsIN are control samples for N6-mA MeDIP to ensure the specificity of the experiment.
processed data not produced for this sample


title: Cdx2_ES_ALKBH1CTRL_D2_RNAseq


title: dsIN

description:
double strand input
processed data not produced for this sample


title: GORD 19

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 19 -- SAB 19110


title: GORD 18

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 18 -- SAB 18893 SAB 18896


title: Cdx2_ES_D13_N6mA_MeDIP

description: processed data not produced for this sample


title: Cdx2_ES_D0_N6mA_MeDIP

description: N6mA_D5vsD0_W200-G600-increased-peaks-FDR0.01.bed.gz


title: K562_K4me3_300_salt_2_(20200103_SH_Hs_K4m3_Ahe_1224)

description: CUT&Tag for H3K4me3 in thawed crosslinked nuclei from K562 cells


title: Cdx2_ES_D5_N6mA_MeDIP


title: Input

data_processing:
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
After sequencing and filter, high quality raw reads were aligned to the mouse genome (UCSC, mm9) with bowtie (2.3.1, default)
Multiple alignments were removed by samtools to keep reads with quality score above 20 .
Peak calling was performed against input by Sicer V1.1, W200, G600, FDR0.01. Differential Satb1 deposition regions among two samples of interest were identified with the SICER-df setting.
Genome_build: mm9
Supplementary_files_format_and_content: bw, bed

extract_protocol:
10^7 Cells were washed once with DPBS and then fixed in 5 mL DMEM medium with 1% formaldehyde for 10 min at RT with rotation.  Fixation was terminated with addition of 100 mM glycine followed by 5 min rotation at RT. Cells were then scraped and spun down at 4 °C at 1000 rpm for 5 min, followed by two washes of ice-cold PBS. Cell pellets were resuspended in 1 mL Lysis Buffer 1 (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, and 0.25% Triton X-100) followed by rotation at 4 °C for 10 min. Cell pellets were spun down at 1400g for 5 min and resuspended in 1 mL Lysis Buffer 2 buffer (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA). Following another 10 min incubation at 4 °C, cell pellets were again spun down at 1400g for 5 min and resuspended in 200 to 300 µL Lysis Buffer 3 (10 mM Tris-HCl, pH8.0, 100 mM NaCl, 1 mM EDTA,0.5 mM EGTA, 0.5% Na-Deoxycholate and 0.5% N-lauroylsarcosine).  Cells were then sonicated to about 500 bp DNA products using Covaris S200 machine with the following parameters: peak power=120, duty factor=2.0, cycle/burst=200, temperature=5°C and scale=10 min and a power output at 2.1.  The sonicated cell solution was then diluted with Lysis buffer 3 plus 1% Triton X-100, incubated for 15 min with rotation at 4 °C and spun down at 20,000g for 15 min. 10 µg anti-Satb1 antibodies (Abcam, Ab109122) were added into the supernatant with equivalent amount of Rabbit IgG antibody as controls.  After overnight incubation at 4 °C, antibodies were pulled down using anti-Rabbit dynabeads (10 µL per 1 µg antibody) after incubation with beads for 2 hr at 4 °C and dynabeads were extensively washed with RIPA buffer (50 mM Hepes-KOH, pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP40 and 0.7% Na-Deoxycholate) with rotation at 4°C for 3 times, 10 min each time.  After last RIPA wash, beads were washed once with 1×TE+50 mM NaCl buffer. DNA was then eluted in elution buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA and 1% SDS) twice at 65 °C for 20 min. Eluted DNA was then at 65 °C overnight for reverse cross-link. The solution was treated with RNase A1/T mix (thermo scientific) and incubated at 37 °C for 1 hr. This is followed by addition of 3 µL of proteinase K and incubation for 2 hr at 56 °C.  The solution was then phenol-chloroform extracted once followed by DNA extraction using MinElute PCR Purification Kit (28004, Qiagen).  DNA was eluted with EB buffer for downstream qPCR analysis or CHIP-seq library preparation.
NEB NEBNext® Ultra™ DNA Library Prep Kit


title: K562_K27me3_XLink_(20200110_SH_Hs_K27m3_X_0107

description: CUT&Tag for K27me3 in 120000 K562 cross-linked cells Direct

value: H3K27me3 Cell Signaling Technology cat# 9733


title: Satb1_ChIP_ALKBH1_OE


title: GORD 17

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 17 -- SAB 18617 SAB 18620


title: K562_K27me3_XLink_PCI_(20200110_SH_Hs_K27m3_Xpc_0107)

description: CUT&Tag for K27me3 in 120000 K562 cross-linked nuclei PCI


title: dsDIP

description:
MeDIP from dsDNA
ssDIP,dsDIP,ssWGAIP,dsWGAIP, ssIN, dsIN are control samples for N6-mA MeDIP to ensure the specificity of the experiment.
processed data not produced for this sample


title: GORD 15

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 15 -- SAB 18109 SAB 18112


title: D5_OE_ATAC

data_processing:
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
After sequencing and filter, high quality raw reads were aligned to the mouse genome (UCSC, mm9) with bowtie2 (2.3.1, default).
After alignment, ATAC peaks were identified using MACS2 (2.1.1)10 with BAMPE mode. Reads with insertion size greater than 120bp were used to generate bigwig files by Deeptools
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig and NarrowPeak files

extract_protocol:
ATAC-seq was performed as described (Corces et al. 2017). In brief, 100,000 cells were collected after once DPBS wash. The cells were resuspended using ice-cold ATAC-RSB buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). After incubation on ice for 3 min, the cells were washed with ice-cold ATAC-RSB buffer without NP40. Then cells were resuspended in transposition mix composed of 0.33×DPBS, 0.01% Tween-20, 1×TD buffer (Nextera DNA Library Prep   Kit, Illumina) and Transposase (100 nM final concentration, Illumina). Transposition reaction was incubated at 37 ºC for 30 minutes in a thermomixer with mixing. Then transposed DNA was purified by MinElute PCR Purification Kit (28004, Qiagen).
Eluted DNA was amplified by using NEB Next UltraII Q5 Master Mix for 5 cycles. A real-time qPCR amplification was performed to determine additional cycles. The amplified DNA libraries were size-selected and purified by AMPure beads according to the manufacturer’s instructions.


title: GORD 16

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 16 -- SAB 18154 SAB 15157


title: D4_WT_ATAC


title: D4_OE_ATAC


title: K562_K27me3_Native_(20200110_SH_Hs_K27m3_N_0107)

description: CUT&Tag for K27me3 in 120000 K562 cells Direct


title: K562_K36me3_Native_PCI_(20200110_SH_Hs_K36m3_N_pc_0107)

description: CUT&Tag for K36me3 in 120000 K562 nuclei PCI


title: GORD 14

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 14 -- SAB 17838 SAB 17841


title: D3_OE_ATAC


title: K562_K27me3_low_salt_(20200103_SH_Hs_K27m_Ale_1224)

description: ;pw salt CUT&Tag for H3K27me3 in thawed crosslinked nuclei from K562 cells


title: D0_OE_ATAC


title: GORD 13

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 13 -- SAB 17166 SAB 17168


title: K562_K27me3_low_salt_50_(20191209_SH_Hs_K27m3_50l_1127)

description: low salt CUT&Tag for H3K27me3 in thawed crosslinked nuclei from 50,000 K562 cells


title: K562_K27me3_low_salt_25_(20191209_SH_Hs_K27m3_25l_1127)

description: low salt CUT&Tag for H3K27me3 in thawed crosslinked nuclei from 25,000 K562 cells


title: GORD 11

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 11 -- SAB 14470


title: WT_ST2

city: Cologne

first: Nirmal

last: Robinson

state: NRW

address: Joseph-Stelzmann-Str. 26

department: Institut für Medizinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: CECAD Forschungszentrum

data_processing:
Illumina Casava 1.8.2 software used for basecalling
RNA-Seq reads mapped with Tophat, version 2.0.10
FPKM calculated by Cufflinks, version 2.1.1
RNAseq reads were aligned mm10
Fragments Per Kilobase of exon per Million mapped fragments (FPKM) were calculated using a Cufflinks Version
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheets, FPKM

source_name: Macrophages

growth_protocol: Bone marrow from mice were differentiated into macrophages in medium supplemented with supernatant from L929 cells.

extract_protocol:
RNA was extracted using Qiagen All prep RNA extraction kit following manufacturer's instructions
Sequencing libraries were generated according to the Illumina protocol for total RNA library preparation and loaded onto Illumina flow cells (Illumina, San Diego, CA)

treatment_protocol: Macrophages were infected with S.Typhimurium (SL1344) for 2h

tag: age

value: 10 weeks

tag: cell type

value: Bone marrow derived macrophages

tag: infection

value: Salmonella typhimurium


title: WT_ST3


title: Satb1_ChIP_WT

tag: cell line


title: D3_WT_ATAC


title: WT3


title: WT_ST1

value: Bone marrow derived macrophage


title: D0_WT_ATAC


title: GORD 10

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 10 -- SAB 14092 SAB 14094

value: peripheral blood serum exosomes


title: WT2


title: K562_K27me3_low_salt_12_(20191209_SH_Hs_K27m3_12l_1127)

description: low salt CUT&Tag for H3K27me3 in thawed crosslinked nuclei from 12,500 K562 cells


title: WT1


title: GORD 12

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 12 -- SAB 14567 SAB 14569


title: D5_WT_ATAC

value: WT


title: JN16 - A3 - CI21

city: Tempe

first: Janet

middle: Leigh

last: Neisewander

address: 427 E. Tyler Mall Life Sciences E-Wing

department: School of Life Sciences

institute: Arizona State University

data_processing:
Fastq read files were uploaded to the public server at usegalaxy.org to analyze the data
Quality control analysis was performed for each file using FastQC, Galaxy Version 0.69 76 and aggregated using MultiQC, Galaxy Version 1.5.0
Reads were aligned using HISAT2, Galaxy Version 2.1.0, a splice-aware alignment program, and the Ensembl release 92 Rattus norvegicus reference genome
Transcript assembly and quantification were performed using StringTie, Galaxy Version 1.3.3.1, and an assembly reference guide acquired from Ensembl. Only alignments that matched reference transcripts were processed
All output files were then merged into a new reference transcript, keeping the original reference annotations from Ensembl, using the Stringtie merge function Galaxy Version 1.3.3 before reassembly and quantification of aligned reads with the new merged reference guide
Differential expression analysis was performed using the DESeq2 package in R, with additional contrasts probed using the “contrasts” feature, when necessary
Genome_build: Ensembl 92 Rattus norvegicus
Supplementary_files_format_and_content: tab-delimited files were generated using Stringtie's ability to prepare DESeq2 ready data output

source_name: nucleus accumbens shell

extract_protocol:
Animals were anesthetized with isoflurane, decapitated, and the brain was removed and flash-frozen in methylbutane before storage in a -70°C freezer. Brains were dissected using a brain matrix. Based on anatomical landmarks on the ventral surface of the brain, sections 2 mm thick containing the striatum were taken with guidance from a rat brain atlas. A 2.0 mm diameter punch (Harris Unicore™) of the NAcsh was then taken. RNA was isolated using standard Trizol® (Invitrogen, #15596026) extraction.
RNA was prepared using the Nugen Ovation RNA-seq system. cDNA was quantified using Nanodrop and sheared to approximately 300 base pair fragments. Libraries were generated using the Kapa Biosystem library preparation kit. Fragments were then end repaired and A-tailed. Sequencing was performed on a 1x75 flow cell using an Illumina NextSeq500 instrument.

value: Sprague-Dawley

tag: housing environment

value: isolation

tag: abstinence length

value: 21 days

value: nucleus accumbens shell


title: K562_K27me3_Native_PCI_(20200110_SH_Hs_K27m3_Npc_0107)

description: CUT&Tag for K27me3 in 120000 K562 nuclei PCI


title: GORD 9

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 9 -- SAB 13985 SAB 13987

tag: tissue

tag: patient diagnosis


title: K562_K27me3_hex_1_(20190404_SH_Hs_K27mB_2019029)

description: 1,6-hexanediol CUT&Tag for H3K27me3 in 500000 K562 cells

value: H3K4me3 Active Motif cat# 39159 lot# 22118006


title: K562_K27me3_con_1_(20190404_SH_Hs_K27mA_20190329)

description: CUT&Tag for H3K27me3 in 500000 K562 cells


title: JN14 - A27 - CE1

tag: Sex

value: male

value: enriched

value: 1 day


title: JN15 - A1 - CE21


title: GORD 8

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 8 -- SAB 13254


title: K562_K27me3_300_salt_(20200103_SH_Hs_K27m_Ahe_1224)

description: CUT&Tag for H3K27me3 in thawed crosslinked nuclei from K562 cells

value: K562 human immortalised myelogenous leukemia cell line


title: JN12 - A23 - CI1


title: GORD 7

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 7 -- SAB 12355

value: Gastro Oesophageal Reflux (GORD)


title: JN13 - A24 - CI21


title: K562_K27me3_300_salt_50_(20191209_SH_Hs_K27m3_50h_1127)

description: CUT&Tag for H3K27me3 in thawed crosslinked nuclei from 50,000 K562 cells

value: H3K27me3 Cell Signaling Technology cat# 9733


title: GORD 6

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 6 -- SAB 11473


title: GORD 5

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 5 -- SAB 10744


title: JN6 - A13 - CE21


title: JN10 - A20 - CI1


title: K562_K27me3_300_salt_25_(20191209_SH_Hs_K27m3_25h_1127)

description: CUT&Tag for H3K27me3 in thawed crosslinked nuclei from 25,000 K562 cells


title: JN5 - A12 - CE1


title: K562_K27me3_300_salt_12_(20191209_SH_Hs_K27m3_12h_1127)

description: CUT&Tag for H3K27me3 in thawed crosslinked nuclei from 12,500 K562 cells


title: GORD 3

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 3 -- SAB 09302


title: JN2 - A9 - CI21


title: JN7 - A14 - CE21


title: GORD 4

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 4 -- SAB 09560


title: GORD 2

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 2 -- SAB 08022


title: JN1 - A2 - CI1


title: H3K4me3_Dox_mut

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
polyA-RNA-Seq and FOXL2 ChIP-Seq read sequences were aligned to NCBI Build 37 (hg19) human reference genome using BWA-backtrack v0.5.7 and default parameters.
ribodepleted RNA-Seq and histone modifications ChIP-Seq read sequences were aligned to NCBI Build 37 (hg19) human reference genome using BWA mem v0.7.6 with option '-M '. For ribodepleted RNA-Seq read sequences, '-P' option was used. The transcriptome reference used to align polyA- and ribodepleted-RNA-Seq reads consists of the reference genome (hg19) extended by read-length-specific exon exon junction sequences (Ensembl v69).
Peak enrichment was computed using MACS v2.1.1 with a false discovery rate (FDR) value of 0.01. Input sample was used as control background.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with RPKM values where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: Bed files generated using MACS v2.1.1 (https://github.com/taoliu/MACS)

source_name: SVOG3e cells transduced with V5-FOXL2 C134W

growth_protocol: SVOG3e cells were grown in media 105/199 supplemented with 5% defined fetal bovine serum (Hyclone SH 30070.03) and with 0.5 μg/ml Puromycin (Sigma P8833) and 0.6 mg/ml Geneticin . Media 105/199 was prepared mixing equal volumes of media MCDB 105 (Sigma M6395) and media 199 (Sigma M5017) which were prepared according to manufacturer’s protocol.

extract_protocol:
Cells were trypsinized and collected by spin at 300g for 5 min. Then cell pellets were snap-freezed
We performed native chromatin immunoprecipitation (ChIP) as described previously (Lorzadeh et al., 2016). Libraries were constructed using an Agilent Bravo automated liquid handling platform. Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol: Cells were cultured without 0.5 μg/ml Puromycin (Sigma P8833) nor 0.6 mg/ml Geneticin. Then the induction of FOXL2 expression was done by the addition of media containing 12.5 ng/ml Doxycyclin.

value: SV40 large T antigen immortalized human granulosa cells

tag: genotype/variation

value: transduced with V5-FOXL2 C134W lentivirus

tag: induction

value: 12 hours Doxycycline induction

value: anti-H3K4me3, Cell Signaling Technology, Cat# 9751


title: H3K4me3_noDox_mut

value: non-induced

tag: antibody


title: mutd0

source_name: Dorsal Root Ganglia

extract_protocol:
Trizol (Invitrogen) was used to extract total RNA according to the manufacturer's instructions.
250-300bp insert library prepared according to Illumina instructions

value: Tmem184b gene trap homozygous (C57BL/6 background)

value: DRG neurons

tag: days in culture

tag: transduced with virus


title: GORD 1

description:
GORD
serum from patient with Gastro Oesophageal Reflux disease, without cancer
microRNA
GORD 1 -- SAB 07852

source_name: peripheral blood serum exosomes

extract_protocol: Exosomes were isolated from the serum samples using ExoquickTm (System Biosciences, EXOQ20A-1). Extraction of miRNA from exosomes was performed using a  miRNeasy Serum/Plasma kit (Qiagen, #217184) with a final elution volume of 24 microlitres ultra pure water

value: peripheral blood serum exosomes


title: H3K4me3_Dox_WT

source_name: SVOG3e cells transduced with V5-FOXL2 WT

value: transduced with V5-FOXL2 WT lentivirus


title: CONTROL 17

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 17 -- SAB 17927

value: healthy control


title: CONTROL 18

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 18 -- SAB 18680 SAB 18683


title: CONTROL 19

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 19 -- SAB 19382 SAB 19385


title: H3K4me3_noDox_V

source_name: SVOG3e cells empty vector control

value: empty vector control


title: H3K4me1_Dox_mut

value: anti-H3K4me1, Diagenode, C15410037


title: CONTROL 16

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 16 -- SAB 17883 SAB 17885


title: JN9 - A16 - CE1

value: Sprague-Dawley

value: male

value: enriched

value: nucleus accumbens shell


title: CONTROL 15

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 15 -- SAB 17793


title: H3K4me1_noDox_mut


title: H3K4me1_Dox_WT


title: CONTROL 13

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 13 -- SAB 17476 SAB 17478


title: CONTROL 14

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 14 -- SAB 17516 SAB 17519


title: H3K4me1_noDox_WT


title: CONTROL 11

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 11 -- SAB 17245


title: H3K4me1_Dox_V


title: CONTROL 10

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 10 -- SAB 15003 SAB 15005


title: CONTROL 12

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 12 -- SAB 17358 SAB 17361


title: H3K4me1_noDox_V


title: H3K27me3_noDox_mut

value: anti-H3K27me3, Diagenode, C15410195


title: CONTROL 8

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 8 -- SAB 11038


title: H3K27me3_Dox_WT

value: SV40 large T antigen immortalized human granulosa cells


title: CONTROL 7

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 7 -- SAB 09817


title: H3K27me3_noDox_WT


title: H3K27me3_Dox_mut

value: transduced with V5-FOXL2 C134W lentivirus


title: H3K4me3_noDox_WT


title: H3K4me3_Dox_V

value: 12 hours Doxycycline induction


title: CONTROL 9

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 9 -- SAB 12793


title: H3K27me3_noDox_V


title: CONTROL 4

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 4 -- SAB 08933


title: CONTROL 5

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 5 -- SAB 09604


title: H3K27ac_noDox_mut

value: anti-H3K27ac, Hiroshi Kimura, Kimura et al. 2008 PMID:18227620


title: CONTROL 3

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 3 -- SAB 08113


title: CONTROL 6

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 6 -- SAB 09782


title: CONTROL 2

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 2 -- SAB 08107


title: H3K27ac_noDox_WT

value: non-induced


title: H3K27ac_Dox_WT


title: CONTROL 1

description:
Control
serum from Healthy Control without GORD or cancer
microRNA
CONTROL 1 -- SAB 04927


title: Mammary tumor 995

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

description: Mammary tumor

data_processing:
Reads were aligned using Salmon V1.2.0 to mm9
Aligned reads were analyzed using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated file containing gene level expression values for each gene and each sample in the data

source_name: murine mammary gland tumor

growth_protocol: Both Cre- (control) and Cre+ mice were mated at 12 weeks of age to induce FBXW7 excision and monitored for tumor formation by weekly palpation. Mice were sacrificed upon tumor detection or at 40 weeks post pregnancy.

extract_protocol:
RNA was extracted using Trizol, processed through the Qiagen RNAeasy Mini Plus Kit
RNA-seq libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Epithelial cells were extracted from homogenized glands and purified with mouse epithelial enrichement kit while whole glands and tissues were dissected and homogenized in TriZol.

tag: tissue type

value: mammary tumor tissue

value: 25 weeks

tag: cre status (pos or neg)

value: pos


title: H3K27ac_Dox_V


title: Mammary tumor 914

description: Mammary tumor

value: 53 weeks


title: H3K27ac_noDox_V


title: histoneMods_ChIPseq_input_noDox_mut


title: Mammary tumor 655

description: Mammary tumor

value: 19 weeks


title: histoneMods_ChIPseq_input_Dox_mut


title: histoneMods_ChIPseq_input_Dox_WT

value: transduced with V5-FOXL2 WT lentivirus


title: H3K27me3_Dox_V

value: empty vector control


title: histoneMods_ChIPseq_input_noDox_WT


title: WT mammary gland 981

description: WT mammary gland

source_name: murine mammary gland tissue

value: whole mammary gland tissue

value: 40 weeks

value: neg


title: WT mammary gland WTmam3

description: WT mammary gland

value: 20 weeks


title: histoneMods_ChIPseq_input_noDox_V

extract_protocol:
Cells were trypsinized and collected by spin at 300g for 5 min. Then cell pellets were snap-freezed.
We performed native chromatin immunoprecipitation (ChIP) as described previously (Lorzadeh et al., 2016). Libraries were constructed using an Agilent Bravo automated liquid handling platform. Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.


title: histoneMods_ChIPseq_input_Dox_V


title: H3K27ac_Dox_mut


title: WT mammary gland WTmam2

description: WT mammary gland


title: Mammary tumor 70

description: Mammary tumor


title: FOXL2_ChIPseq_Dox_mut_24

extract_protocol:
Crosslinked cells were quenched with one-tenth volume of 1.25 M Glycine (Sigma G7126) for 5 minutes and washed twice with dPBS before harvesting the cells. Cells were pelleted at 3,000 rpm, the supernatant removed and the cell pellet frozen at -80oC. Additionally, the control cell line, SVOG3e/rtTA/V5 that does not express V5-FOXL2, was seeded and treated as above for one time point at T=12 hours for  non- induced and Doxycycline-induced cells. Cell lysis, chromatin preparation, immunoprecipitation using anti-V5 antibody (Invitrogen, R960CUS) and recovery was performed as described previously (Pon et al. 2015), with the following modifications; the chromatin pellet was resuspended in 400 μl of ChIP IP buffer and sonicated (Duty Cycle 20%, Intensity 8,Cycles/burst 200, Time: 60 seconds) in a Covaris Cov-3 Sonicator. Pre-cleared chromatin (150 μg) was incubated with 4 μl (2 μg) of monoclonal mouse anti-V5 antibody (Invitrogen R960-25) for 1 hr at 4oC with rocking, followed by the addition of 40 μl of Protein G Dynabeads (Invitrogen) that was blocked with salmon sperm DNA and bovine serum albumin as previously described (3). Chromatin/antibody/Dynabead mixture was incubated overnight at 4oC on a nutator. The Dynabead bound proteins and associated chromatin was washed and eluted as previously described (3) and DNA was submitted for library construction and sequencing.
ChIP-seq library construction was performed according to standard operating procedures available at http://www.epigenomes.ca/protocols-and-standards.

value: 24 hours Doxycycline induction

value: anti-V5, Invitrogen R960CUS


title: Fbw7-/- epithelials, nontumor 042_epithelial

description: Fbw7-/- epithelials, nontumor

source_name: murine mammary epithelials

value: purified epithelials late PG Fbw7-/- mouse

value: 16 weeks


title: Fbw7-/- epithelials, nontumor 016_epithelial

description: Fbw7-/- epithelials, nontumor


title: WT mammary gland WTmam1

description: WT mammary gland


title: R-TEn-p1-Ebox_Mut_DP_Smc3

first: Kazuko

last: Miyazaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Institute for Life and Medical Sciences, Kyoto University

data_processing:
Illumina bcl2fastq software used for basecalling (HiSeq 2500, NovaSeq 6000,Illumina HiSeq X Ten).
ATAC-seq and ChIP-seq trimmed reads were mapped to the mm9 reference genome using Bowtie2 (version 1.2.7). Hi-C reads were trimmed from the 3’ end of sequences to GATC (MboI restriction enzyme site) and aligned to the mouse reference genome mm9 using bowtie2.
Tags mapped to unique DNA sequences of ATAC-seq, ChIP-seq and Hi-C were analyzed using HOMER (Lin et al., 2012, Heinz et al., 2018)
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq : Tab-delimited BED files containing peak positions for each ATAC-seq or ChIP-seq experiment. Hi-C: Tab-delimited Text files containing PC1 values for each experiment.

source_name: DP cells purified by MACS (CD4+CD8+CD69–TCRb– )

growth_protocol: For proB cell culture, B cells were enriched by B220-MACS column from total bone marrow cells. Then, B cells were cultured in PRMI 1640 with 10% fetal bovine serum, 2mg/ml sodium bicarbonate, 1 mM sodium pyruvate, 0.1mM nonessential amino acid solution, 5x10-5M 2-Mercaptoethanol, 100µg/ml streptomycine and 100U/ml penicillin in the presence of IL-7 and stem cell factor.

extract_protocol: ATAC-seq : ATAC-seq was performed as described (Buenrostro et al., 2013) with modifications. Cells were lysed, then treated with Tn5 transposase (Nextera DNA Sample Preparation Kit). After the treatment, the tagmentated DNA was cleaned up and purified with DNA Clean & Concentrator kit (Zymo Research).  The purified DNA were amplified with determined cycles of PCR based on the amplification curve, then were size-selected using Ampure XP beads. Hi-C : in situ Hi-C was performed as described (Rao et al., 2014).  DP and cultured proB cells from control and deletion mutant mice were fixed with 1% formaldehyde/FACS buffer for 10 minutes at room temperature. Cells were lysed and chromatin was digested overnight using MboI. The fragment overhangs generated by the restriction enzyme were filled in with biotin-14-dATP by Klenow fragment, then proximity ligation was performed.  Biotinylated DNA was sonicated to 300-500 bp on a Covaris M220. The biotinylated DNA was captured on Dynabeads MyOne Streptavidin T1 beads. After washing the beads, ends of sheared DNA were repaired and added A-tail according to the protocol. NEBNext Multiplex Oligos for Illumina (NEB) were ligated and the beads were washed.  Libraries were amplified by PCR and size selected using ProNex (Promega). As to CD4SP cells, Tethered Conformation Capture (TCC) was performed as described (Kalhor et al. 2012).  CD4SP cells were fixed with 1% formaldehyde/FACS buffer for 10 minutes at room temperature. Cells were lysed and chromatin was digested overnight using MboI.  ChIP-seq : Cells were fixed in 1% formaldehyde/PBS . The reactions were quenched by 1.5M glycine and cells were washed with PBS and pelleted. Pelleted cells were lysed and chromatin was sonicated by Covaris M220.  Diluted sheared chromatin was immunoprecipitated with each antibody which is pre-bound to Dynabead Protein G magnetic microbeads overnight at 4 °C. Samples were washed, eluted and reverse cross-linked  65°C overnight. Samples were next treated with RNase A and proteinase K and purified using DNA Clean & Concentrator kit (Zymo Research). Samples were ligated to NEBNext Multiplex Oligos for Illumina (NEB) and multiplex amplified by PCR. Amplified ChIP DNA was selected by size.

tag: strain

tag: cell

value: DP cells purified by MACS

tag: genotype

value: Thymus

tag: chip antibody

value: anti-SMC3 (abcam:# ab9263)


title: FOXL2_ChIPseq_Dox_WT_12

tag: cell type

value: SV40 large T antigen immortalized human granulosa cells

value: 12 hours Doxycycline induction


title: FOXL2_ChIPseq_Dox_WT_24


title: FOXL2_ChIPseq_Dox_mut_12

value: transduced with V5-FOXL2 C134W lentivirus


title: FOXL2_ChIPseq_noDox_mut_12

value: non-induced


title: Mammary tumor 569

description: Mammary tumor

value: mammary tumor tissue

tag: age

value: 39 weeks

value: pos


title: FOXL2_ChIPseq_noDox_WT_12

value: transduced with V5-FOXL2 WT lentivirus


title: FOXL2_ChIPseq_Dox_V_12

value: empty vector control


title: WT_DP_Smc3

value: Wild type


title: GXA_3095 Type: Patient derived Xenograft Passage: 4

type: genomic

city: Freiburg

first: Vincent

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

institute: 4HF Biotec

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Affymetrix Genome wide SNP6.0 CEL files were loaded into the Affymetrix Genotyping Console 4.1 Software (Affymetrix). After scanning, arrays were checked for quality using the Affymetrix Genotyping Console. In accordance with Affymetrix guidelines, SNP6.0 arrays with a Contrast QC value above 0.4 and MAPD below 0.35 were excluded from further analysis. Copy number variations were calculated using Affymetrix GTC v4.1 and PICNIC software provided by the Cancer Genome Project from the Welcome Trust Sanger Institute.   The PICNIC algorithm  (PICNIC - Predicting Integral Copy Numbers In Cancer) includes improved normalisation of the data together with determination of underlying copy numbers for each segment by genome wide analysis of allele ratio and signal strength data. The data was subsequently rescaled and plotted onto its predicted underlying integer value and segmentation was applied. This data analysis procedure also allowed for assignment of a genotype to each SNP. The PICNIC segment files were further compiled to generate a simplified gene matrix. A gene was assigned a deletion (CNV=0) if a deletion segment overlaps with the gene, otherwise the copy number of the most amplified segment overlapping with the gene was assigned.
PICNIC integer copy number score (0 is considered as a gene deletion, values between 1 and 7 are considered as a moderate gene copy alteration, values equal or greater than 8 are considered as a gene amplification)

source_name: patient-derived tumor xenograft

label_protocol: standard Affymetrix protocol

growth_protocol: PDX were passaged from mouse to mouse until DNA extraction

extract_protocol: DNA was extracted from snap frozen tumor xenografts, patient tumors or normal tissues. Samples were digested with proteinase K at 55°C overnight and the lysate was digested with DNAse-free RNAse (Qiagen). DNA was extracted with a mix of phenol:chloroform:isoamylalcohol and precipitated with ethanol. DNA pellets were washed and resuspended in Tris-EDTA buffer. Each DNA preparation was subjected to quality control using a 1.3% agarose gel and using NanoDrop 2000 to control for purity. Only DNA samples with no sign of degradation (a clearly defined high molecular weight band on the agarose gel) and the DNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.

tag: passages


title: R-TEn-p1-Ebox_Mut_DP_CTCF

tag: tissue

value: anti-CTCF (Milipore:# 07-729)


title: GXA_3096 Type: Patient derived Xenograft Passage: 4


title: GXA_3087 Type: Patient derived Xenograft Passage: 4


title: WT_DP_CTCF

value: anti-CTCF (Milipore:#07-729)


title: GXA_3084 Type: Patient derived Xenograft Passage: 6


title: FOXL2_ChIPseq_noDox_V_12

value: anti-V5, Invitrogen R960CUS


title: GXA_3083 Type: Patient derived Xenograft Passage: 5


title: GXA_3080 Type: Patient derived Xenograft Passage: 5


title: FOXL2_ChIPseq_Dox_WT_8

value: 8 hours Doxycycline induction


title: Adrb2cko_S33: HFSCs_Adrb2cko_Rep2

city: cambridge

first: Ya-Chieh

last: Hsu

state: MA

address: 7 Divinity Avenue, SF 312

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using Salmon (Patro et al., 2017).
Differential expression analysis was performed using DESeq2 (Love et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: cvs file includes normalized counts and TPM values for each sample

source_name: Hair follicle stem cells

extract_protocol:
Mouse back skin was dissected, and the fat layer was scraped using surgical scalpel. The skin was incubated in trypsin-EDTA at 37°C for 35-45 minutes on an orbital shaker. Single cell suspension was obtained by scraping the epidermal side and filtering through 70 µm and 40 µm filters. Single cell suspensions were then centrifuged for 8 minutes at 350g at 4°C, re-suspended in 5% FBS and stained for 30-45 minutes. The following antibodies were used: CD49f-PE-Integrin alpha 6 (eBioscience 12-0495-82, 1:500); CD34-eF660 (eBioscience 50-0341-82, 1:100); Ly-6A/E (Sca-1)-PerCp-Cy5.5 (eBioscience 45-5981-82, 1:1000); and, CD45-eF450 (eBioscience 48-0451-82, 1:250). DAPI was used to exclude dead cells. HFSCs were isolated as CD45 negative, Integrin alpha 6 +, CD34+, Sca-1 negative cells. Cell isolation was performed with BD-Aria sorters.
RNA-sequencing libraries were prepared using 1 ng of total RNA as input. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) was used for cDNA synthesis, with a 10 cycle PCR enrichment. Sequencing libraries were then made using Illumina's Nextera XT Library Prep kit. Modifid quarter-volume reaction protocol was used for both kits. The indexed libraries were sequenced over two flow cells on a NextSeq High-Output platform using the unpaired, 75-bp read-length sequencing protocol to obtain a total of at least 10 million reads per sample.

treatment_protocol: Control and mutant mice were treated 10x with 4% RU486

value: FACS sorted hair follicle stem cells

tag: hair cycle stage

value: telogen

value: K15-CrePGR; Adrb2 fl/fl


title: Adrb2cko_S34: HFSCs_Adrb2cko_Rep3


title: Adrb2cko_S32: HFSCs_Adrb2cko_Rep1


title: FOXL2_ChIPseq_Dox_mut_8

value: SV40 large T antigen immortalized human granulosa cells


title: Fbw7+/+ epithelials, nontumor 076_epithelial

description: Fbw7+/+ epithelials, nontumor

value: purified epithelials late PG Fbw7+/+ mouse

value: 16 weeks

value: neg


title: FOXL2_ChIPseq_Dox_mut_6

value: transduced with V5-FOXL2 C134W lentivirus

value: 6 hours Doxycycline induction


title: GXA_3079 Type: Patient derived Xenograft Passage: 3


title: Control_S31: HFSCs_Control_Rep2

value: control


title: FOXL2_ChIPseq_Dox_mut_3

value: 3 hours Doxycycline induction


title: GXA_3069 Type: Patient derived Xenograft Passage: 6


title: FOXL2_ChIPseq_Dox_WT_3

value: transduced with V5-FOXL2 WT lentivirus


title: Nfe2 KO CD41pos cells from embyonic day 13.5 liver

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

description: lineageMetaAllCell.txt

data_processing:
Read alignment and count summarization were performed using CellRanger v2.0 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

source_name: e13.5 fetal liver

extract_protocol:
A 10X Genomics Chromium machine was used for 3,900-6,900 single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of  about 750,000 barcodes to separately index each cell’s transcriptome. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina Nextseq 500 to achieve paired-end 75 bp reads.

treatment_protocol: preparation protocol: Fetal livers from 8X E13.5 wildtype and 6X Nf2-/- mutant embryos were mechanically dissociated, pooled by genotype and stained for CD41, CD42d, LIN (Ter119,B220). LIN- CD41high CD42d+ Cells were sorted on an Aria Cell Sorter (Becton Dickinson), centrifuged and counted.

value: embryonic day 13.5

tag: cell source

value: e13.5 fetal liver

tag: cell surface phenotype

value: LIN (Ter119,B220)- CD41high CD42d+

tag: number of cells


title: FOXL2_ChIPseq_noDox_WT_0

tag: genotype/variation

tag: induction

value: non-induced

tag: antibody

value: anti-V5, Invitrogen R960CUS


title: FOXL2_ChIPseq_input_V

value: empty vector control


title: GXA_3063 Type: Patient derived Xenograft Passage: 3


title: FOXL2_ChIPseq_input_mut


title: wildtype CD41pos cells from embyonic day 13.5 liver

description: lineageMetaAllCell.txt


title: FOXL2_ChIPseq_noDox_mut_0


title: GXA_3057 Type: Patient derived Xenograft Passage: 3


title: GXA_3054 Type: Patient derived Xenograft Passage: 4


title: GXA_3052 Type: Patient derived Xenograft Passage: 4


title: wildtype CD41pos cells from adult bone marrow

description: lineageMetaAllCell.txt

source_name: Bone marrow

treatment_protocol: preparation protocol: Fetal livers of 5X E13 wildtype or Nf2-/- embryos were prepared as above and transplanted into UBC-GFP+ recipients subjected to 2X 550cGrays irradiations (0.37 embryonic equivalent/recipient). Mice were screened at 4 weeks for blood platelet content and their GFP status. Bone marrow from the femurs, tibias, hips and humeri of 4 transplanted mice (2X WT donor, 2X Nf2-/- donor) was dissociated, pooled by genotype, filtered and stained for CD41, CD42d, LIN (Ter119, B220). GFP- LIN- CD41high CD42d+ Cells were sorted on an Aria Cell Sorter (Becton Dickinson), centrifuged and counted

value: Adult

value: bone marrow

value: LIN (Ter119,B220)- CD41high CD42d+GFP+


title: Nfe2 KO CD41pos cells from adult bone marrow

description: lineageMetaAllCell.txt


title: FOXL2_ChIPseq_Dox_WT_6

value: SV40 large T antigen immortalized human granulosa cells


title: ribodep_RNAseq_Dox_mut_12

extract_protocol:
Cells were trypsinized and collected by spin at 300g for 5 min. Then cell pellets were snap-freezed .  Total RNA was extracted using a combination of mirVana miRNA Isolation kit (Thermofisher, AM1560) and All prep DNA/RNA Mini Kit (Qiagen, 80204) and then assessed for quality and quantified using Agilent Bioanalyzer (Life Technologies).
First strand cDNA was generated using Maxima H minus First Strand cDNA Synthesis Kit (Thermo Scientific, K1652) with the addition of 1ug of Actinomycin D (Sigma, A9415). The product was purified using in-house prepared 20% PEG, 1M NaCL Sera-Mag bead solution at 1.8X ratio and eluted in 35uL of Qiagen EB buffer.  Second Strand cDNA was synthesized in a 50uL volume using SuperScript Choice System for cDNA Synthesis (Life Technologies, 18090-019) with 12.5mM GeneAmp dNTP Blend with dUTP.  Double stranded cDNA was then purified with 20% PEG, 1M NaCL Sera-Mag bead solution at 1.8X ratio, eluted in 40uL of Qiagen EB buffer, and fragmented using Covaris E220 (55 seconds, 20% duty factor, 200 cycles per burst).  Sheared cDNA was End Repaired/Phosphorylated, single A-tailed, and Adapter Ligated using custom reagent formulations (New England BioLabs, E6000B-10) and in-house prepared Illumina forked small adapter.  20% PEG, 1M NaCl Sera-Mag bead solution was used to purify the template in-between each of the enzymatic steps.  To complete the process of generating strand directionality, adapter-ligated template was digested with 5U of AmpErase Uracil N-Glycosylase (Life Technologies, N8080096).  Libraries were then PCR amplified and indexed using Phusion Hot Start II High Fidelity Polymerase (Thermo Scientific, F 549-L).  An equal molar pool of each library was sequenced on HiSeq2500 (Illumina) PE75.

value: 12 hours Doxycycline induction


title: GXA_3044 Type: Patient derived Xenograft Passage: 4


title: WT CD34 positive umbilical cord blood cells_WGBS

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: WGBS of WT CD34 positive umbilical cord blood cells

data_processing:
Fastq files were algined to the hg19 genome using walt form the methpipe pipeline version 3.4.3.
Aligned files were sorted using 'sort' 8.31 and duplicate reads were removed using duplicate-remover.
Methylation levels were determined using 'methcounts' and hypomethylated regions were identified using 'hmr.'
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in a tab-delimited .meth file format and contain CpG positions and methylations levels genomewide

source_name: Control umbilical cord CD34+

growth_protocol: CD34+ were isolated and expanded for 48 hours following DNMT3A was deleted using CRISPR-Cas9

extract_protocol:
We extracted DNA from cell pellets using DNeasy kit (Qiagen 69504).
WGBS libraries were made with the TruSeq DNA methylation kit according to the manufacturer’s instruction (Illumina). Libraries were sequenced using an IlluminaNextseq 500 sequencer

treatment_protocol: Deletion with  dual guides

value: Control

tag: time

value: 3 months following transplant

value: umbilical cord

value: CD34+ HSPCs


title: ribodep_RNAseq_Dox_WT_12


title: GXA_3044 Type: Patient derived Xenograft Passage: 3


title: CL1-0 FUT4 vector

city: Taipei

first: Hsing-Chen

last: Tsai

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan 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 hg19 whole genome using bowtie v2.2.6 with parameters --forward-prob 0 --output-genome-bam for both cell ine and clinical samples
Each cell line bam files were splig to two files using Python
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library using DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: normalized_count.txt: normalized count of clinical samples using DESeq2 of 81 tumor and 19 adjacent tissues
Supplementary_files_format_and_content: FPKM_A549_CL10.csv: FPKM of FUT4 overexpressed cell lines

source_name: cell line

growth_protocol: Lung cancer cell lines were cultured in RPMI-1640 medium with 10% FBS and 1% antibiotics.

extract_protocol:
Lung cancer cell lines, frozen tumor or adjacent tissue were harvested for RNA  using Trizol reagent. Invitrogen PureLink RNA Mini Kit (Cat#12183018A) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lung cancer cell lines were transfected with FUT4 overexpression plasmid using Lipofectamine3000 reagent.

value: cell line

tag: cell line

value: FUT4 vector


title: GXA_3044 Type: Patient derived Xenograft Passage: 2


title: DNMT3A KO CD34 positive umbilical cord blood cells_WGBS

description: WGBS of DNMT3A KO CD34 positive umbilical cord blood cells

source_name: DNMT3A KO umbilical cord CD34+

value: DNMT3A KO


title: GXA_3067 Type: Patient derived Xenograft Passage: 6


title: ribodep_RNAseq_Dox_V_12


title: CL1-0 FUT4 over-expressed

value: FUT4 over-expressed


title: Control_S30: HFSCs_Control_Rep1

value: FACS sorted hair follicle stem cells

value: telogen

value: control


title: GXA_3044 Type: Patient derived Xenograft Passage: 1


title: ribodep_RNAseq_noDox_mut

value: transduced with V5-FOXL2 C134W lentivirus

value: non-induced


title: ribodep_RNAseq_noDox_WT

value: transduced with V5-FOXL2 WT lentivirus


title: A549 FUT4 over-expressed


title: ribodep_RNAseq_noDox_V

value: empty vector control


title: FOXL2_ChIPseq_input_WT

value: SV40 large T antigen immortalized human granulosa cells


title: GXA_3044 Type: Patient Normal Passage: 0

source_name: normal tissue


title: polyA_RNAseq_Dox_mut_24

source_name: SVOG3e cells transduced with V5-FOXL2 C134W

extract_protocol:
Cells were harvested in dPBS by scraping, transferred to an Eppendorf tube and spun down at 900 x g for 5 minutes. The supernatant was discarded and the cell pellet was resuspended in Qiazol Lysis reagent (Qiagen 79306). Total RNA was isolated using RNeasy kit (Qiagen 74106) as per the manufacturer’s protocol.
RNA-seq library construction was performed according to standard operating procedures available at http://www.epigenomes.ca/protocols-and-standards.

value: 24 hours Doxycycline induction


title: RH30 shSNAIL rep3 (SS3)

city: Krakow

first: Klaudia

last: Skrzypek

address: Wielicka 265

department: Department of Transplantation

country: Poland

institute: Jagiellonian University Medical College

data_processing:
Analysis of data were performed at Exiqon Services, Denmark. Expression levels are measured as Tags Per Million (“TPM”).
TPM is a unit used to measure expression levels in NGS experiments and can be used for any non-fragmenting library protocol. The number of reads that map to a particular RNA species is divided by the total number of mapped reads in the sample and subsequently multiplied by one million. This is a simple normalization procedure that corrects for the sequencing depth and provides a very transparent measure of quantity for each RNA species
For the statistical analyses presented in the manuscript the trimmed mean of M-values normalization method (TMM normalization) is used (Robinson and Oshlack, 2010).
The differential expression analysis is done using TMM in the EdgeR statistical software package (Bioconductor, http://www.bioconductor.org/). Differential expression analysis on TMMs investigates the relative change in expression (i.e. counts) between different samples.
As standard, Exiqon Services also perform TPM (tags per million) normalization as this normalization procedure is easier to interpret to an actual expression level for a microRNA in a given sample. The TPM normalized data is provided in the data tables accompanying this report.
Genome_build: Organism: Homo sapiens. Annotation reference: miRbase 20 (http://www.mirbase.org/).
Supplementary_files_format_and_content: MiRNA_tpm.tsv file shows table of TPM counts across samples per miRNA. De_result_with_tmm shows table of differential expression results with group TMM averages and sample TMM values.

source_name: RH30 shSNAIL

growth_protocol: RH30 cells were cultured in DMEM high-glucose medium  supplemented with 10% fetal bovine serum  and 50 ug/ml gentamicin (Lonza) at 37°C, 5% CO2 and 95% humidity.

extract_protocol:
Total RNA was isolated using the mirVana miRNA Isolation Kit (Ambion).
Library preparation, next generation sequencing and analysis of data were performed at Exiqon Services, Denmark. A total of 1 ug of total RNA was converted into microRNA NGS libraries using NEBNEXT library generation kit (New England Biolabs Inc) according to the manufacturer’s instructions. Each individual RNA sample had adaptors ligated to its 3’ and 5’ ends and converted into cDNA. Then the cDNA was pre-amplified with specific primers containing sample specific indexes. After 15 cycle pre-PCR the libraries were purified on QiaQuick columns and the insert efficiency eavaluated by Bioanalyzer 2100 instrument on high sensitivity DNA chip (Agilent Inc.) The microRNA cDNA libraries were size fractionated on a LabChip XT (Caliper Inc.) and a band representing adaptors and 15-40 bp insert excised using manufacturer’s instructions. Samples were then quantified using qPCR and concentration standards. Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar concentrations (all concentrations of libraries to be pooled are of the same concentration). The library pools were finally quantified again with qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing using v2 sequencing methodology according to the manufacturer instructions (Illumina Inc.).
MicroRNA sequencing. Samples were sequenced on the Illumina NextSeq 500 system. The system uses quality score binning enabling a more compact storage of raw sequences. Using only 8 levels (Levels: No call, 6, 15, 22, 27, 33, 37, 50) of quality method has been tested and found to virtually loss-less. Average number of reads per sample was 7.5mio. Number of sequencing cycles (read length) was 50 nt , single-end read.

treatment_protocol: Total RNA from three different cell types (RH30 WT, shCTRL, shSNAIL) was isolated at three independent time points (three independent experiments / treatments).

value: shSNAIL

tag: treatment time point

value: treatment 3

value: rhabdomyosarcoma (RMS) cell line RH30


title: GXA_3040 Type: Patient derived Xenograft Passage: 6


title: GXA_3040 Type: Patient derived Xenograft Passage: 2


title: GXA_3040 Type: Patient derived Xenograft Passage: 3


title: RH30 shSNAIL rep1 (SS1)

value: treatment 1


title: RH30 shCTRL rep3 (SC3)

source_name: RH30 shCTRL

value: shCTRL


title: polyA_RNAseq_Dox_mut_12

value: 12 hours Doxycycline induction


title: RH30 shSNAIL rep2 (SS2)

value: treatment 2


title: polyA_RNAseq_Dox_WT_12

source_name: SVOG3e cells transduced with V5-FOXL2 WT


title: GXA_3040 Type: Patient Tumor Passage: 0

source_name: patient tumor


title: A549 FUT4 vector

value: cell line

value: FUT4 vector


title: polyA_RNAseq_noDox_mut_12


title: GXA_3040 Type: Patient Normal Passage: 0


title: GXA_3040 Type: Patient derived Xenograft Passage: 1


title: polyA_RNAseq_Dox_V_12

source_name: SVOG3e cells empty vector control


title: GXA_3039 Type: Patient derived Xenograft Passage: 5


title: RH30 shCTRL rep1 (SC1)


title: RH30 WT rep2 (WT2)

source_name: RH30 WT

value: WT


title: GXA_3044 Type: Patient Tumor Passage: 0


title: RH30 WT rep3 (WT3)


title: polyA_RNAseq_noDox_V_12


title: polyA_RNAseq_noDox_WT_12


title: GXA_3039 Type: Patient derived Xenograft Passage: 3


title: polyA_RNAseq_Dox_WT_24


title: GXA_3039 Type: Patient derived Xenograft Passage: 2


title: RH30 WT rep1 (WT1)


title: GXA_3039 Type: Patient derived Xenograft Passage: 1


title: CPC5 rep25

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to miRbase 20
Expression levels are measured as Tags Per Million (TPM). The number of reads for a particular microRNA is divided by the total number of mapped reads and multiplied by 1 million (Tags Per Million). The differential expression analysis is done using the EdgeR statistical software package
Genome_build: miRbase 20
Supplementary_files_format_and_content: tsv (tab-separated values) text files contain counts and TPM of microRNAs for each sample

source_name: plasma

extract_protocol:
RNA was extracted from a total of 400 μl of plasma, then 6ul of total RNA was use to prepare short RNA NGS library using NEBNEXT library generation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma

tag: cerebral performance category score


title: RH30 shCTRL rep2 (SC2)

tag: genotype


title: polyA_RNAseq_Dox_mut_8

value: transduced with V5-FOXL2 C134W lentivirus

value: 8 hours Doxycycline induction


title: polyA_RNAseq_Dox_WT_8

value: transduced with V5-FOXL2 WT lentivirus


title: CPC5 rep24


title: CPC5 rep23


title: polyA_RNAseq_Dox_mut_6

value: 6 hours Doxycycline induction


title: GXA_3037 Type: Patient derived Xenograft Passage: 7


title: CPC5 rep21


title: GXA_3038 Type: Patient derived Xenograft Passage: 3


title: GXA_3039 Type: Patient Normal Passage: 0


title: polyA_RNAseq_Dox_WT_3

value: SV40 large T antigen immortalized human granulosa cells

value: 3 hours Doxycycline induction


title: polyA_RNAseq_Dox_WT_6


title: polyA_RNAseq_Dox_mut_3


title: GXA_3037 Type: Patient derived Xenograft Passage: 2


title: polyA_RNAseq_noDox_mut_0

value: non-induced


title: CPC5 rep19


title: CPC5 rep20


title: CPC5 rep22


title: GXA_3037 Type: Patient derived Xenograft Passage: 3


title: GXA_3037 Type: Patient derived Xenograft Passage: 1


title: CPC5 rep18


title: polyA_RNAseq_noDox_WT_0


title: GXA_3037 Type: Patient Tumor Passage: 0


title: CPC5 rep17


title: GXA_3037 Type: Patient Normal Passage: 0


title: GXA_3039 Type: Patient Tumor Passage: 0