title: WT-24h

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Sample scan protocol provided and performed by NimbleGen.

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

organism: Tetrahymena thermophila SB210

source_name: Tetrahymena thermophila  SB210 Total mRNA

label_protocol: Sample labeling protocol provided and performed by NimbleGen.

growth_protocol: T. thermophila strain SB210 was cultured axenically at 30°C，in SPP medium (Gorovsky et al., 1975), which consists of 2% proteose peptone (Becton, Dickinson and Company, BD), 0.1% yeast extract (Oxoide), 0.2% glucose (Sinopharm Chemical Reagent Co., Ltd.) and 0.003% ferric citrate (Sigma).

extract_protocol: the total RNA was extracted using an RNeasy Protect Cell Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions

treatment_protocol: In the experiment, cells were inoculated at a final concentration of about 4000 cells/ml to 300 ml medium containing 30 μM sodium arsenate dodecahydrate, with plain medium as a negative control. Following 2, 6, 12, 24 h of exposure, appropriate amount of cells were harvested.

tag: agent

value: control


title: TFi1.E11

status: Public on Dec 01 2019

type: SRA

city: Yokoham

first: Joachim

middle: Felix

last: Luginbühl

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

molecule: total RNA

organism: Homo sapiens

source_name: Transcription factor induced fibroblasts

growth_protocol: Human dermal fibroblasts were purchased from Lonza (passages 4-8) and cultured in DMEM containing 10% FBS/L-glutamine/10% Penicilin&Streptomycin at 37°C 5% CO2 until virus infection. For TFi generation, a total of 6 MOI (~0.3 MOI per virus) were pooled into culture medium containing 8 mg*ml-1 Polybrene (SIGMA) to increase infection efficiency. The virus pool was infected and incubated overnight at 37°C 5% CO2. On the following day, virus-containing medium was removed and cells were incubated for an additional day in fresh culture medium at 37°C 5% CO2. For iN generation, infected cells were split onto Poly-d-lysine (100μg*ml-1) / Laminin (50μg*ml-1) (SIGMA)-coated culture plates and incubated overnight in culture medium at 37°C 5% CO2. On the following day, medium was changed to neuronal induction medium containing DMEM/F12 and Neurobasal-A (Thermo Fisher Scientific) mixed at a 1:1 ratio, 2% (vol/vol) B27 supplement and 0.5% N2 Supplement (GIBCO), 1x nonessential amino acids (Thermo Fisher Scientific), 1% GlutaMAX supplement, 10ng*ml-1 BDNF (GIBCO), 10ng*ml-1 NT3 (R&D Systems), 10ng*ml-1 GDNF (Thermo Fisher Scientific), VPA (0.5mM, WAKO), L-Ascorbic acid (200nM, SIGMA), Y-27632 (10μM, WAKO), dcAMP (0.5mM, SIGMA), 10% FBS and 10% Penicilin&Streptomycin (WAKO). The concentrations of small molecules used were as follows: CHIR99021 (2μM, Abcam), SB-431542 (10μM, SIGMA), LDN-193189 (0.5μM, Stemgent), Noggin (100ng*ml-1, SIGMA). Neuronal induction medium was changed every third day, during which the concentration of FBS was gradually reduced from 10% to 1%. After 2 weeks, neuronal induction medium was replaced with neuronal maturation medium without small molecules and 1% FBS and the medium was changed every third day until further analysis.

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

tag: cell type

tag: time

value: 9 days after induction

tag: passages

tag: treatment

value: Ectopic expression of transcription factors

tag: batch


title: TFi1.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: WT12h

type: RNA


title: HUVEC_mock_rep1

city: Münster

first: Dzmitry

last: Sinitski

address: Vesaliusweg 2-4

department: Anatomy and Vascular Biology

country: Germany

institute: University of Münster

description: replicate 1

hyb_protocol: Standard Illumina direct hybridization assay protocol

scan_protocol: Standard Illumina scanning protocol, BeadScan software, Illumina BeadArray Reader hardware

data_processing: The data were normalised using quantile normalisation with Genome Studio

label: biotin

source_name: Human umbilical cord

label_protocol: Biotinylated cRNA were prepared with the TargetAmp™-Nano Labeling Kit for Illumina arrays

growth_protocol: HUVEC were seeded in 6-well plates (30.000 cells/cm²) and were grown till confluence.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit, followed by clean-up and DNase I treatment with QIAGEN RNase-Free DNase Set in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HUVEC culture were infected with respective strain of Staphylococcus aureus (MOI=50) for 3 hours. Extracellular bacteria were washed with lysostaphin (20µg/ml) for 30 minutes. Cells were further incubated till 7 hours postinfection. Negative control - Mock infection. Positive control - 3,5 hours of TNF-alpha stimulation (100 ng/ml).

tag: donor

value: Mock treated

tag: tissue

value: Endothelium


title: WT-6h


title: AS-24h

value: arsenic


title: Thyroid tumor, TC120_S17_R1_001 (RNA-seq)

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts table generated by merging of STAR output. Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset

source_name: Thyroid gland, primary tumor

extract_protocol:
Tissue specimens were formalin fixed and embedded in paraffin.
RNA was extracted from the FFPE samples using RecoverAll™ Total Nucleic Acid Isolation  Kit. KAPA  RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for further depletion of ribosomal  RNA and library preparation. Different adaptors were used for multiplexing samples in one  sequencing run.
Illumina Library prep kit

tag: subtype

value: thyroid cancer

tag: Stage

value: Primary


title: AS-6h


title: cG13-treat_Subtel_2p_OICR

city: Haifa

first: Shir

last: Toubiana

address: 1 Efron st.

country: Israel

institute: Technion

library_source: genomic

data_processing:
BISMARK (v0.17.0): Adaptors and low quality bases were trimmed out. Reads were then aligned to the customized reference human genome GRCh38 by using the Bismark aligner.
Methylation scores were performed using Bismark methylation extractor script.
For 10qMultiple and 10q_2q+4q files the different subtelomeres were told apart based on single nucleotide differences compared to subtelomere 10q. We used a Perl homemade script.
Genome_build: hg38

molecule: genomic DNA

source_name: iPSCs

growth_protocol: IPSCs were cultured on plates coated with Cultrex® Reduced Growth Factor Basement Membrane Matrix (343300501, Trevigen, MD, USA), and grown in either mTeSR-1 media (85850, StemCell Technologies, Vancouver, Canada) or PepRoGrow™ hESC Media (hESC-100, PepRoTech, NJ, USA). Cells were passaged every 4–6 days. Cell were dissociated from plates with 0.5 mM EDTA and following each passage, 2mM Thiazovivin (14245, Cayman CHEMICAL, MI, USA was added to the media. FLs derived from iPSCs  were grown in fibroblast media (DMEM media supplemented with 20% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin) at standard conditions.

extract_protocol:
Genomic DNA was extracted according to standard procedures and was bisulfite-converted with the Methylamp DNA Modification kit (EPIGENTEK, NY, USA)
PCR products were purified by QIAquick PCR purification kit (28104, QIAGEN, MD, USA). Further amplicon processing, sequencing, and analysis were performed as described (Sagie, Toubiana, et al. 2017).

treatment_protocol: For drug treatment, iPSCs were treated with 1 μM of OICR-9429 (SML1209, MERCK) or 0.1% DMSO for 72 hours, replacing the medium every 24 hours.

tag: passage (p), population doubling (pd)

tag: genotype

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: AS-2h


title: Thyroid tumor, TC119_S16_R1_001 (RNA-seq)


title: Thyroid tumor, TC117_S15_R1_001 (RNA-seq)


title: WT-2h


title: NRCWE-049_D28 54µg Sample 45 Group 2

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

description: NRCWE-049_D28 54µg

scan_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm. Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

organism: Mus musculus

source_name: Lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via single intratracheal instillation of  18µg (medium,dose),and 54 µg (high dose) of NRCWE-046, NRCWE-047, NRCWE-048 or NRCWE-049 in a 40 µl suspension   Tissues were collected 28 days after instillation.

tag: gender

value: Female

tag: time point

value: C57BL/6 mice

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: cG13-treat_Subtel_4p_OICR


title: cG13-treat_Subtel_5p_OICR


title: TFi1.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: cG13-treat_Subtel_10q_2q+4q_OICR


title: Thyroid tumor, TC116_S14_R1_001 (RNA-seq)


title: AS-12h


title: TFi1.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: cG13-treat_Subtel_9p+Xq_OICR


title: Thyroid tumor, TC115_S13_R1_001 (RNA-seq)


title: cG13-untreat_Subtel_10p+18p_OICR


title: TFi1.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC114_S12_R1_001 (RNA-seq)


title: TFi1.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D28 54µg Sample 44 Group 2

description: NRCWE-049_D28 54µg

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.


title: NRCWE-048_D28 54µg Sample 43 Group 2

description: NRCWE-048_D28 54µg


title: Thyroid tumor, TC113_S11_R1_001 (RNA-seq)


title: NRCWE-048_D28 18µg Sample 41 Group 2

description: NRCWE-048_D28 18µg


title: cG13-untreat_Subtel_10q_2q+4q_OICR


title: NRCWE-049_D28 54µg Sample 42 Group 2

description: NRCWE-049_D28 54µg


title: TFi1.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-047_D28 54µg Sample 40 Group 2

description: NRCWE-047_D28 54µg


title: Thyroid tumor, TC112_S9_R1_001 (RNA-seq)


title: cG13-untreat_Subtel_2p_OICR


title: cG13-untreat_Subtel_4p_OICR


title: TFi1.D11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC-111_S15_R1_001 (RNA-seq)


title: cG13-untreat_Subtel_5p_OICR


title: TFi1.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.D10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D28 18µg Sample 39 Group 2

description: NRCWE-049_D28 18µg


title: Thyroid tumor, TC-105_S12_R1_001 (RNA-seq)


title: Thyroid tumor, TC-109_S13_R1_001 (RNA-seq)


title: cG13-untreat_Subtel_7q_OICR


title: cG13-untreat_Subtel_9p+Xq_OICR


title: Thyroid tumor, TC-104_S11_R1_001 (RNA-seq)


title: TFi1.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC-103_S10_R1_001 (RNA-seq)


title: NRCWE-046_D28 18µg Sample 37 Group 2

description: NRCWE-046_D28 18µg


title: pG-treat_Subtel_10q_2q+4q_OICR

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: TFi1.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.D06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC-101_S8_R1_001 (RNA-seq)


title: pG-treat_Subtel_2p_OICR


title: Thyroid tumor, TC-100_S7_R1_001 (RNA-seq)


title: TFi1.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: pG-treat_Subtel_5p_OICR


title: Thyroid tumor, TC-99_S6_R1_001 (RNA-seq)


title: pG-treat_Subtel_7q_OICR


title: NRCWE-047_D28 54µg Sample 35 Group 2

description: NRCWE-047_D28 54µg


title: Thyroid tumor, TC-102_S9_R1_001 (RNA-seq)


title: NRCWE-046_D28 54µg Sample 38 Group 2

description: NRCWE-046_D28 54µg


title: Control_D28 0µg Sample 33 Group 2

description: Control_D28 0µg

value: Control


title: Thyroid tumor, TC-97_S4_R1_001 (RNA-seq)


title: NRCWE-048_D28 18µg Sample 31 Group 2

description: NRCWE-048_D28 18µg


title: NRCWE-048_D28 18µg Sample 36 Group 2

description: NRCWE-048_D28 18µg


title: Thyroid tumor, TC-96_S3_R1_001 (RNA-seq)


title: pG-treat_Subtel_4p_OICR


title: TFi1.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: pG-untreat_Subtel_10p+18p_OICR


title: Thyroid tumor, TC-95_S2_R1_001 (RNA-seq)


title: pG-untreat_Subtel_10q_2q+4q_OICR


title: Thyroid tumor, TC-94_S1_R1_001 (RNA-seq)


title: TFi1.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: pG-treat_Subtel_9p+Xq_OICR


title: Thyroid tumor, TC_76_S4_L003_R1_001 (RNA-seq)


title: pG-untreat_Subtel_2p_OICR


title: cG13-treat_Subtel_7q_OICR


title: TFi1.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_75_S3_L003_R1_001 (RNA-seq)


title: pG-untreat_Subtel_5p_OICR


title: TFi1.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D28 18µg Sample 32 Group 2

description: NRCWE-049_D28 18µg


title: Thyroid tumor, TC_74_S2_L003_R1_001 (RNA-seq)


title: pG-untreat_Subtel_4p_OICR


title: TFi1.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: pG-untreat_Subtel_7q_OICR


title: NRCWE-046_D28 54µg Sample 29 Group 2

description: NRCWE-046_D28 54µg


title: Thyroid tumor, TC_73_S1_L003_R1_001 (RNA-seq)


title: NRCWE-047_D28 18µg Sample 34 Group 2

description: NRCWE-047_D28 18µg


title: NRCWE-048_D28 54µg Sample 30 Group 2

description: NRCWE-048_D28 54µg


title: NRCWE-047_D28 18µg Sample 28 Group 2

description: NRCWE-047_D28 18µg


title: NRCWE-046_D28 54µg Sample 27 Group 2

description: NRCWE-046_D28 54µg


title: TFi1.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: pG-treat_Subtel_10p+18p_OICR


title: TFi1.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Control_D28 0µg Sample 25 Group 2

description: Control_D28 0µg


title: NRCWE-048_D28 18µg Sample 23 Group 2

description: NRCWE-048_D28 18µg


title: NRCWE-049_D28 18µg Sample 26 Group 2

description: NRCWE-049_D28 18µg


title: NRCWE-047_D28 54µg Sample 24 Group 2

description: NRCWE-047_D28 54µg


title: NRCWE-049_D28 54µg Sample 21 Group 2

description: NRCWE-049_D28 54µg


title: NRCWE-046_D28 18µg Sample 22 Group 2

description: NRCWE-046_D28 18µg


title: TFi1.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_72_S20_L002_R1_001 (RNA-seq)


title: Thyroid tumor, TC_69_S18_L002_R1_001 (RNA-seq)


title: Fibroblast_pG_Subtel_10p+18p

source_name: Fibroblasts


title: pG-untreat_Subtel_9p+Xq_OICR


title: Fibroblast_pG_Subtel_2p


title: Thyroid tumor, TC_66_S15_L002_R1_001 (RNA-seq)


title: Fibroblast_pG_Subtel_4p


title: Thyroid tumor, TC_68_S17_L002_R1_001 (RNA-seq)


title: Thyroid tumor, TC_65_S14_L002_R1_001 (RNA-seq)


title: Fibroblast_pG_Subtel_5p


title: TFi1.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Fibroblast_pG_Subtel_7q


title: TFi1.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_64_S13_L002_R1_001 (RNA-seq)


title: Thyroid tumor, TC_63_S12_L002_R1_001 (RNA-seq)


title: NRCWE-049_D28 18µg Sample 17 Group 2

description: NRCWE-049_D28 18µg


title: TFi1.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Fibroblast_pG_Subtel_9p+Xq


title: Fibroblast_pR_Subtel_10p+18p

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: NRCWE-047_D28 18µg Sample 19 Group 2

description: NRCWE-047_D28 18µg


title: NRCWE-048_D28 54µg Sample 20 Group 2

description: NRCWE-048_D28 54µg


title: NRCWE-046_D28 18µg Sample 18 Group 2

description: NRCWE-046_D28 18µg


title: NRCWE-046_D28 54µg Sample 15 Group 2

description: NRCWE-046_D28 54µg


title: Control_D28 0µg Sample 16 Group 2

description: Control_D28 0µg


title: Thyroid tumor, TC_62_S11_L002_R1_001 (RNA-seq)


title: Control_D28 0µg Sample 14 Group 2

description: Control_D28 0µg


title: NRCWE-046_D28 54µg Sample 13 Group 2

description: NRCWE-046_D28 54µg


title: Thyroid tumor, TC_61_S10_L001_R1_001 (RNA-seq)


title: Fibroblast_pR_Subtel_2p


title: TFi1.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.B10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_58_S7_L001_R1_001 (RNA-seq)


title: Thyroid tumor, TC_60_S9_L001_R1_001 (RNA-seq)


title: Fibroblast_pR_Subtel_4p


title: Fibroblast_pR_Subtel_5p


title: TFi1.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_57_S6_L001_R1_001 (RNA-seq)


title: Fibroblast_pR_Subtel_7q


title: Fibroblast_pR_Subtel_9p+Xq


title: FL_cR35_Subtel_10p+18p

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: Thyroid tumor, TC_54_S3_L001_R1_001 (RNA-seq)


title: TFi1.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_56_S5_L001_R1_001 (RNA-seq)


title: TFi1.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-047_D28 18µg Sample 11 Group 2

description: NRCWE-047_D28 18µg


title: Thyroid tumor, TC-52_S25_L005_R1_001 (RNA-seq)


title: Thyroid tumor, TC-53_S26_L005_R1_001 (RNA-seq)


title: FL_cR35_Subtel_2p


title: TFi1.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC_51_S2_L001_R1_001 (RNA-seq)


title: NRCWE-046_D28 18µg Sample 9 Group 2

description: NRCWE-046_D28 18µg


title: NRCWE-047_D28 54µg Sample 7 Group 2

description: NRCWE-047_D28 54µg


title: TFi1.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D28 54µg Sample 10 Group 2

description: NRCWE-049_D28 54µg


title: FL_cR35_Subtel_4p


title: NRCWE-048_D28 18µg Sample 12 Group 2

description: NRCWE-048_D28 18µg


title: NRCWE-048_D28 54µg Sample 8 Group 2

description: NRCWE-048_D28 54µg


title: NRCWE-047_D28 54µg Sample 5 Group 2

description: NRCWE-047_D28 54µg


title: Control_D28 0µg Sample 3 Group 2

description: Control_D28 0µg


title: NRCWE-048_D28 54µg Sample 6 Group 2

description: NRCWE-048_D28 54µg


title: FL_cR35_Subtel_5p


title: Thyroid tumor, TC37_S19_R1_001 (RNA-seq)


title: TFi1.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_cR35_Subtel_7q


title: NRCWE-046_D28 18µg Sample 4 Group 2

description: NRCWE-046_D28 18µg


title: TFi1.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC35_S6_R1_001 (RNA-seq)


title: FL_cR35_Subtel_9p+Xq


title: TFi1.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_cR35_Subtel_10qMulti


title: Thyroid tumor, TC39_S20_R1_001 (RNA-seq)


title: Thyroid tumor, TC36_S13_R1_001 (RNA-seq)


title: NRCWE-047_D28 18µg Sample 1 Group 2

description: NRCWE-047_D28 18µg


title: TFi1.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC34_S12_R1_001 (RNA-seq)


title: Thyroid tumor, TC32_S11_R1_001 (RNA-seq)


title: FL_cR35_Subtel_2q+4q+10q


title: TFi1.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC-31_S7_R1_001 (RNA-seq)


title: TFi1.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_cR7_Subtel_2q+4q+10q


title: FL_cR7_Subtel_10qMulti


title: FL_cR7_Subtel_2p


title: NRCWE-049_D28 18µg Sample 2 Group 2

description: NRCWE-049_D28 18µg


title: TFi1.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_cR7_Subtel_4p


title: Thyroid tumor, TC-30_S6_R1_001 (RNA-seq)


title: NRCWE-043_D28 54µg Sample 32 Group 2

description: NRCWE-043_D28 54µg

scan_protocol: Scanned on an Agilent G2565AA scanner.

treatment_protocol: Mice were dosed via single intratracheal instillation of  18 µg (medium dose) and 54 µg (high dose) of NRCWE-043, NRCWE-044 and NRCWE-045 in a 40 µl suspension   Tissues were collected 28 days  after instillation.


title: TFi1.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC-28_S4_R1_001 (RNA-seq)


title: NRCWE-044_D28 18µg Sample 34 Group 2

description: NRCWE-044_D28 18µg


title: FL_cR7_Subtel_7q


title: Thyroid tumor, TC-27_S3_R1_001 (RNA-seq)


title: FL_cR7_Subtel_10p+18p


title: FL_cR7_Subtel_9p+Xq


title: TFi1.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC26_S17_L006_R1_001 (RNA-seq)


title: TFi1.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_cR7_Subtel_5p


title: FL_pR_Subtel_10p+18p


title: Ci2.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Chemically induced fibroblasts

value: Chemically induced fibroblasts

value: 21 days after induction

value: Chemical cocktail of small molecules


title: Thyroid tumor, TC24_S16_L006_R1_001 (RNA-seq)


title: NRCWE-044_D28 18µg Sample 33 Group 2

description: NRCWE-044_D28 18µg


title: Thyroid tumor, TC23_S15_L006_R1_001 (RNA-seq)


title: FL_pR_Subtel_10qMulti


title: Thyroid tumor, TC22_S14_L006_R1_001 (RNA-seq)


title: Control_D28 0µg Sample 30 Group 2

description: Control_D28 0µg


title: NRCWE-044_D28 54µg Sample 28 Group 2

description: NRCWE-044_D28 54µg


title: FL_pR_Subtel_2q+4q+10q


title: FL_pR_Subtel_2p


title: Ci2.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_pR_Subtel_4p


title: Thyroid tumor, TC21_S13_L006_R1_001 (RNA-seq)


title: NRCWE-045_D28 54µg Sample 26 Group 2

description: NRCWE-045_D28 54µg


title: NRCWE-043_D28 18µg Sample 31 Group 2

description: NRCWE-043_D28 18µg


title: NRCWE-045_D28 18µg Sample 24 Group 2

description: NRCWE-045_D28 18µg


title: Thyroid tumor, TC-29_S5_R1_001 (RNA-seq)


title: NRCWE-045_D28 54µg Sample 29 Group 2

description: NRCWE-045_D28 54µg


title: Thyroid tumor, TC19_S9_L005_R1_001 (RNA-seq)


title: Ci2.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D28 18µg Sample 27 Group 2

description: NRCWE-044_D28 18µg


title: FL_pR_Subtel_5p


title: Thyroid tumor, TC20_S10_L005_R1_001 (RNA-seq)


title: FL_pR_Subtel_7q


title: Ci2.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D28 54µg Sample 23 Group 2

description: NRCWE-044_D28 54µg


title: NRCWE-044_D28 18µg Sample 25 Group 2

description: NRCWE-044_D28 18µg


title: Thyroid tumor, TC18_S8_L005_R1_001 (RNA-seq)


title: Control_D28 0µg Sample 20 Group 2

description: Control_D28 0µg


title: FL_pR_Subtel_9p+Xq


title: NRCWE-043_D28 54µg Sample 21 Group 2

description: NRCWE-043_D28 54µg


title: Ci2.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D28 18µg Sample 19 Group 2

description: NRCWE-043_D28 18µg


title: Ci2.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC17_S7_L005_R1_001 (RNA-seq)


title: FL_UN_Subtel_10p+18p

value: healthy control (DNMT3B wt/wt)


title: Thyroid tumor, TC16_S6_L005_R1_001 (RNA-seq)


title: Ci2.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_UN_Subtel_10qMulti


title: NRCWE-044_D28 54µg Sample 17 Group 2

description: NRCWE-044_D28 54µg


title: Ci2.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC15_S5_L005_R1_001 (RNA-seq)


title: FL_UN_Subtel_2p


title: Ci2.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC14_S4_L005_R1_001 (RNA-seq)


title: Thyroid tumor, TC13_S3_L005_R1_001 (RNA-seq)


title: NRCWE-043_D28 54µg Sample 22 Group 2

description: NRCWE-043_D28 54µg


title: Ci2.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_UN_Subtel_2q+4q+10q


title: Ci2.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC11_S1_L005_R1_001 (RNA-seq)


title: FL_UN_Subtel_5p


title: Thyroid tumor, TC12_S2_L005_R1_001 (RNA-seq)


title: FL_UN_Subtel_4p


title: Ci2.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FL_UN_Subtel_7q


title: FL_UN_Subtel_9p+Xq


title: Ci2.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D28 18µg Sample 15 Group 2

description: NRCWE-044_D28 18µg


title: iPS_cG13_+23p_satellite_2


title: Thyroid tumor, TC7_S7_L005_R1_001 (RNA-seq)


title: Ci2.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC6_S6_L005_R1_001 (RNA-seq)


title: NRCWE-043_D28 18µg Sample 13 Group 2

description: NRCWE-043_D28 18µg


title: Thyroid tumor, TC5_S5_L005_R1_001 (RNA-seq)


title: NRCWE-043_D28 0µg Sample 11 Group 2

description: NRCWE-043_D28 0µg


title: iPS_cG13_+23p_Subtel_10p+18p


title: Ci2.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D28 54µg Sample 16 Group 2

description: NRCWE-043_D28 54µg


title: NRCWE-045_D28 54µg Sample 18 Group 2

description: NRCWE-045_D28 54µg


title: NRCWE-044_D28 54µg Sample 14 Group 2

description: NRCWE-044_D28 54µg


title: Thyroid tumor, TC8_S8_L005_R1_001 (RNA-seq)


title: NRCWE-045_D28 18µg Sample 9 Group 2

description: NRCWE-045_D28 18µg


title: iPS_cG13_+23p_Subtel_10qMulti


title: Ci2.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D28 18µg Sample 10 Group 2

description: NRCWE-043_D28 18µg


title: Thyroid tumor, TC4_S4_L005_R1_001 (RNA-seq)


title: Control_D28 0µg Sample 8 Group 2

description: Control_D28 0µg


title: Thyroid tumor, TC3_S3_L005_R1_001 (RNA-seq)


title: Ci2.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-045_D28 54µg Sample 6 Group 2

description: NRCWE-045_D28 54µg


title: Ci2.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG13_+23p_Subtel_4p


title: Thyroid tumor, RAIR-14_S23_R1_001 (RNA-seq)


title: Ci2.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG13_+23p_Subtel_5p


title: NRCWE-043_D28 54µg Sample 4 Group 2

description: NRCWE-043_D28 54µg


title: iPS_cG13_+23p_Subtel_2p


title: NRCWE-044_D28 54µg Sample 5 Group 2

description: NRCWE-044_D28 54µg


title: NRCWE-045_D28 18µg Sample 7 Group 2

description: NRCWE-045_D28 18µg


title: NRCWE-043_D28 18µg Sample 3 Group 2

description: NRCWE-043_D28 18µg


title: Ci2.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, RAIR-12_S10_R1_001 (RNA-seq)


title: Ci2.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG13_+23p_Subtel_7q


title: iPS_cG13_+23p_Subtel_9p+Xq


title: Thyroid tumor, RAIR-11_S16_R1_001 (RNA-seq)


title: iPS_cG13_+23p_Subtel_2q+4q+10q


title: iPS_cG13_+3p_satellite_2


title: Ci2.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG13_+3p_Subtel_10p+18p


title: Thyroid tumor, RAIR-9_S17_R1_001 (RNA-seq)


title: Thyroid tumor, RAIR-13_S22_R1_001 (RNA-seq)


title: Ci2.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Control_D1 0µg Sample 45

description: Control_D1 0µg

hyb_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

scan_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

data_processing: Scanned on an Agilent G2565AA scanner.

label_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

extract_protocol: Mice were dosed via single intratracheal instillation of  18 µg (medium dose),and 54 µg (high dose) of NRCWE-046, NRCWE-047, NRCWE-048 or NRCWE-049 in a 40 µl suspension   Tissues were collected 24h   days after instillation.

treatment_protocol: Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.


title: iPS_cG13_+3p_Subtel_10qMulti


title: Thyroid tumor, RAIR-7_S15_R1_001 (RNA-seq)


title: Control_D28 0µg Sample 1 Group 2

description: Control_D28 0µg


title: Ci2.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG13_+3p_Subtel_2p


title: NRCWE-048_D1 54µg Sample 44

description: NRCWE-048_D1 54µg


title: Thyroid tumor, RAIR-6_S14_R1_001 (RNA-seq)


title: iPS_cG13_+3p_Subtel_2q+4q+10q


title: Ci2.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-046_D1 18µg Sample 42

description: NRCWE-046_D1 18µg


title: iPS_cG13_+3p_Subtel_4p


title: Thyroid tumor, RAIR-4_S12_R1_001 (RNA-seq)


title: Ci2.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, RAIR-3_S10_R1_001 (RNA-seq)


title: NRCWE-047_D1 18µg Sample 41

description: NRCWE-047_D1 18µg


title: Ci2.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG13_+3p_Subtel_7q


title: NRCWE-047_D1 54µg Sample 43

description: NRCWE-047_D1 54µg


title: iPS_cG13_+3p_Subtel_9p+Xq


title: Thyroid tumor, RAIR-5_S13_R1_001 (RNA-seq)


title: Thyroid tumor, RAIR-1_S8_R1_001 (RNA-seq)


title: NRCWE-049_D1 18µg Sample 39

description: NRCWE-049_D1 18µg


title: Thyroid tumor, RAIR-2_S9_R1_001 (RNA-seq)


title: NRCWE-049_D1 54µg Sample 40

description: NRCWE-049_D1 54µg


title: iPS_cG13_+3p_Subtel_5p


title: iPS_cG50_+23p_Subtel_2p


title: NRCWE-046_D1 54µg Sample 38

description: NRCWE-046_D1 54µg


title: iPS_cG50_+23p_Subtel_10p+18p


title: Ci2.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG50_+23p_satellite_2


title: Ci2.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-048_D1 18µg Sample 35

description: NRCWE-048_D1 18µg


title: Thyroid tumor, TC5 (miRNA-seq)


title: Control_D1 0µg Sample 37

description: Control_D1 0µg


title: Ci2.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, RAIR-8_S16_R1_001 (RNA-seq)


title: Thyroid tumor, TC36 (miRNA-seq)


title: Ci2.F02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.E11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D1 54µg Sample 36

description: NRCWE-049_D1 54µg


title: Thyroid tumor, TC35 (miRNA-seq)


title: Control_D1 0µg Sample 33

description: Control_D1 0µg


title: NRCWE-046_D1 18µg Sample 34

description: NRCWE-046_D1 18µg


title: iPS_cG50_+23p_Subtel_2q+4q+10q


title: Ci2.E10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC37 (miRNA-seq)


title: iPS_cG50_+23p_Subtel_4p


title: NRCWE-047_D1 18µg Sample 32

description: NRCWE-047_D1 18µg


title: Ci2.E09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG50_+23p_Subtel_5p


title: Thyroid tumor, TC34 (miRNA-seq)


title: Thyroid tumor, TC32 (miRNA-seq)


title: iPS_cG50_+23p_Subtel_10qMulti


title: Ci2.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC3 (miRNA-seq)


title: NRCWE-046_D1 18µg Sample 30

description: NRCWE-046_D1 18µg


title: Thyroid tumor, TC26 (miRNA-seq)


title: iPS_cG50_+23p_Subtel_9p+Xq


title: Ci2.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC24 (miRNA-seq)


title: iPS_cG50_+3p_satellite_2


title: iPS_cG50_+3p_Subtel_10p+18p


title: Control_D1 0µg Sample 29

description: Control_D1 0µg


title: NRCWE-047_D1 54µg Sample 28

description: NRCWE-047_D1 54µg


title: NRCWE-049_D1 18µg Sample 27

description: NRCWE-049_D1 18µg


title: NRCWE-048_D1 54µg Sample 31

description: NRCWE-048_D1 54µg


title: iPS_cG50_+3p_Subtel_10qMulti


title: Ci2.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D1 18µg Sample 26

description: NRCWE-049_D1 18µg


title: iPS_cG50_+23p_Subtel_7q


title: Ci2.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC22 (miRNA-seq)


title: Ci2.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG50_+3p_Subtel_2p


title: Thyroid tumor, TC21 (miRNA-seq)


title: NRCWE-046_D1 54µg Sample 25

description: NRCWE-046_D1 54µg


title: Ci2.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC20 (miRNA-seq)


title: Thyroid tumor, TC23 (miRNA-seq)


title: NRCWE-045_D28 54µg Sample 12 Group 2

description: NRCWE-045_D28 54µg


title: Ci2.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG50_+3p_Subtel_2q+4q+10q


title: iPS_cG50_+3p_Subtel_4p


title: NRCWE-048_D1 18µg Sample 24

description: NRCWE-048_D1 18µg


title: NRCWE-047_D1 18µg Sample 22

description: NRCWE-047_D1 18µg


title: Thyroid tumor, TC19 (miRNA-seq)


title: NRCWE-049_D1 54µg Sample 23

description: NRCWE-049_D1 54µg


title: Thyroid tumor, TC2_S2_L005_R1_001 (RNA-seq)


title: iPS_cG50_+3p_Subtel_5p


title: iPS_cG50_+3p_Subtel_7q


title: NRCWE-046_D1 18µg Sample 21

description: NRCWE-046_D1 18µg


title: Thyroid tumor, TC18 (miRNA-seq)


title: Ci2.D11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cG50_+3p_Subtel_9p+Xq


title: Thyroid tumor, TC16 (miRNA-seq)


title: Thyroid tumor, TC17 (miRNA-seq)


title: Ci2.D10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-048_D1 54µg Sample 20

description: NRCWE-048_D1 54µg


title: NRCWE-046_D1 54µg Sample 19

description: NRCWE-046_D1 54µg


title: iPS_cR35_+23p_satellite_2


title: Thyroid tumor, TC15 (miRNA-seq)


title: Ci2.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR35_+23p_Subtel_10p+18p


title: Thyroid tumor, TC14 (miRNA-seq)


title: NRCWE-044_D28 18µg Sample 2 Group 2

description: NRCWE-044_D28 18µg


title: Thyroid tumor, TC13 (miRNA-seq)


title: Ci2.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR35_+23p_Subtel_10qMulti


title: NRCWE-047_D1 54µg Sample 18

description: NRCWE-047_D1 54µg


title: Ci2.D06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR35_+23p_Subtel_2p


title: Thyroid tumor, TC12 (miRNA-seq)


title: Ci2.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC112 (miRNA-seq)


title: Ci2.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D1 18µg Sample 17

description: NRCWE-049_D1 18µg


title: Ci2.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC11 (miRNA-seq)


title: NRCWE-048_D1 54µg Sample 14

description: NRCWE-048_D1 54µg


title: NRCWE-048_D1 18µg Sample 16

description: NRCWE-048_D1 18µg


title: NRCWE-046_D1 54µg Sample 15

description: NRCWE-046_D1 54µg


title: iPS_cR35_+23p_Subtel_4p


title: iPS_cR35_+23p_Subtel_5p


title: Ci2.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: MCF7 Input

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

country: USA

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers.

growth_protocol: MCF7 cells were obtained from the American Type Culture Collection and cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum, as previously described (Tsai et al, Nature, 2010. PMID:21164480)

extract_protocol:
Chromatin immuoprecipitation (ChIP) experiments with MCF7 cells were performed as previously described (Tsai et al, Nature, 2010. PMID:21164480). Briefly, the fragmented chromatin lysate was immunoprecipitated overnight using TRIM24 antibody. The protein-DNA complexes were washed several times and the phenol-chloroform-extracted DNA was used for library construction and sequencing.
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

treatment_protocol: For hormone (Estrogen) depletion, cells were changed to charcoal-stripped hormone-free medium (Gibco, Grand Island, NY) supplemented with 10% charcoal dextran-treated fetal bovine serum (Thermal Scientific Hyclone, Logan, UT) for 72 hours. Estrogen induction was performed using 10 nM of 17β-estradiol (Sigma, St. Louis, MO) for 3 hours (E2pos), and Ethanol was used as a vehicle control (E2neg), as previously described (Tsai et al, Nature, 2010. PMID:21164480)

tag: cell line

value: Ethanol as vehicle control

tag: antibody


title: iPS_cR35_+23p_Subtel_7q


title: TRIM24 ChIP-seq in E2neg

source_name: MCF7 E2neg

value: TRIM24 (Novus Biologicals)


title: Ci2.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TRIM24 ChIP-seq in E2pos

source_name: MCF7 E2pos

value: Estrogen (10 nM) for 3 hours


title: Ci2.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-047_D1 18µg Sample 13

description: NRCWE-047_D1 18µg


title: iPS_cR35_+23p_Subtel_2q+4q+10q


title: iPS_cR35_+23p_Subtel_9p+Xq


title: NRCWE-047_D1 54µg Sample 11

description: NRCWE-047_D1 54µg


title: Control_D1 0µg Sample 12

description: Control_D1 0µg


title: Ci2.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Thyroid tumor, TC8 (miRNA-seq)

value: thyroid cancer


title: iPS_cR35_+3p_Subtel_10p+18p


title: Ci2.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR35_+3p_Subtel_10qMulti


title: Ci2.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D1 54µg Sample 10

description: NRCWE-049_D1 54µg


title: NRCWE-046_D1 18µg Sample 8

description: NRCWE-046_D1 18µg


title: Arabidopsis leaves_Wild-type_Dark-Submerged 4h_Replicate 3

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit; Chip hybridization with 130ul of hyb master mix => Incubate 48°C for 16 to 18 hours

scan_protocol: GeneChip Scanner 3000 7G

data_processing: RMA

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves_Wild-Type_Dark 12h_Replicate 3

label_protocol: FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: Arabidopsis plants grown in pots with soil

extract_protocol: RNA was extracted unsing the miRvana Kit Thermo Fisher Scientific

treatment_protocol: Plants were submerged in tanks with a water level of 10 cm above leaf level. The submergence treatment (12h) was carried out in the dark.

tag: organ

value: Leaves

tag: ecotype

tag: genotype/variation

value: wild type

tag: age

value: 4 weeks old

value: Dark + Submergence


title: Control_D1 0µg Sample 9

description: Control_D1 0µg

value: Female

value: C57BL/6 mice

tag: cell type

value: 11 mouse cell lines


title: iPS_cR35_+3p_Subtel_2p


title: NRCWE-048_D1 54µg Sample 7

description: NRCWE-048_D1 54µg

tag: treatment


title: Ci2.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: time

tag: passages

tag: batch


title: iPS_cR35_+3p_satellite_2


title: Ci2.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR35_+3p_Subtel_4p


title: Ci2.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT17_VZ

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_mulatta.MMUL_1(ftp://ftp.ensembl.org/pub/release-75/fasta/macaca_mulatta/dna/)whole genome using bowtie v0.12.2
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated. First step, align RNA seq reads to the genome by using  Hista2 ; and then Cufflinks2 will assemble transcripts and computed the FPKM vlues(http://cufflinks.cbcb.umd.edu/),following protocol from Pertea, M.et al  Nat Protoc 11, 1650-1667, (2016).
Genome_build: Macaca_mulatta.MMUL_8(ftp://ftp.ensembl.org/pub/release-92/fasta/macaca_mulatta/dna/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Macaca mulatta

source_name: Ventricular Zone

extract_protocol:
The fetal monkey brain tissues were partitioned into several sections, after that, the specimens were embedded in OCT and then gradually frozen in an ethnol /dry ice, and stored at −80°C until processing. Frozen tissue was cryosectioned at 30μm onto polyethylene naphthalate (PEN) slides (Leica Microsystems) and place immediately into microslide box on dry ice, and stored at -80°C until use.     Taking the section slides from the -80°C freezer and put them on a blotting paper for 30s, and then transfer the slides into the 95% EtOH for 30s, 75% EtOH for 30s and 50% EtOH for 30s, place the slides on a blotting paper. Add 400ul Nissl stain solution on the slide, and incubate at room temperature for 40s. Proceed through the dehydration series (50%, 75% and 95% EtOH) till the two rounds of 100% EtOH, and leave the slides in the final xylene jar for 5 min. After air-drying in the fume hood for 5 min, proceed immediately with laser capture microdissection (LCM).    Laser microdissection was performed on a Leica LMD6000 (Leica Microsystems). Microdissected tissues including CP, OSVZ, SVZ and VZ were collected directly into QIAzol buffer from the miRNeasy Mini Kit (Qiagen) in a 0.2ml tubes, vortexed, centrifuged, and frozen at −80 °C. RNA was isolated following the manufacturer’s directions for the miRNeasy Mini Kit. RNA samples were run on the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Ventricular Zone

value: Embryonic 92days


title: Ci2.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts


title: WT17_SVZ

source_name: Subventricular Zone

value: Subventricular Zone


title: WT17_OSVZ

source_name: Outer Subventricular Zone

value: Outer Subventricular Zone


title: iPS_cR35_+3p_Subtel_5p

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: iPS_cR35_+3p_Subtel_7q


title: Ci2.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 21 days after induction

value: Chemical cocktail of small molecules


title: Arabidopsis leaves_Wild-type_Dark-Submerged 4h_Replicate 2

source_name: Arabidopsis leaves_Wild-Type_Dark 12h_Replicate 2


title: iPS_cR35_+3p_Subtel_9p+Xq


title: NRCWE-047_D1 18µg Sample 5

description: NRCWE-047_D1 18µg


title: Arabidopsis leaves_Wild-type_Dark-Aerobic 4h_Replicate 2

source_name: Arabidopsis leaves_Wild-type_Submerged 12h_Replicate 2

value: Dark


title: Arabidopsis leaves_Wild-type_Dark-Aerobic 4h_Replicate 1

source_name: Arabidopsis leaves_Wild-type_Submerged 12h_Replicate 1


title: Arabidopsis leaves_Wild-type_Dark-Submerged 4h_Replicate 1

source_name: Arabidopsis leaves_Wild-Type_Dark 12h_Replicate 1


title: NRCWE-049_D1 54µg Sample 3

description: NRCWE-049_D1 54µg


title: iPS_cR35_+3p_Subtel_2q+4q+10q


title: WT17_CP

source_name: Cortical plate

value: Cortical plate


title: NRCWE-048_D1 18µg Sample 6

description: NRCWE-048_D1 18µg


title: iPS_cR35_+44p_Subtel_10p+18p


title: NRCWE-048_D1 18µg Sample 2

description: NRCWE-048_D1 18µg


title: iPS_cR35_+44p_Subtel_10qMulti


title: WT16_SVZ


title: WT16_VZ


title: NRCWE-045_D1 54µg Sample 35 Group 1

description: NRCWE-045_D1 54µg

treatment_protocol: Mice were dosed via single intratracheal instillation of  18 µg (medium dose) and 54 µg (high dose) of NRCWE-043, NRCWE-044 and NRCWE-045 in a 40 µl suspension   Tissues were collected 24h  after instillation.


title: Ci2.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-049_D1 18µg Sample 1

description: NRCWE-049_D1 18µg


title: NRCWE-047_D1 54µg Sample 4

description: NRCWE-047_D1 54µg


title: WT16_OSVZ


title: NRCWE-044_D1 54µg Sample 34 Group 1

description: NRCWE-044_D1 54µg


title: Ci2.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D1 18µg Sample 33 Group 1

description: NRCWE-043_D1 18µg


title: iPS_cR35_+44p_Subtel_2q+4q+10q


title: Ci2.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT16_CP


title: Ci2.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR35_+44p_Subtel_4p


title: WT15_VZ


title: Ci2.B10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT15_SVZ


title: iPS_cR35_+44p_Subtel_2p


title: Ci2.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT15_OSVZ


title: WT15_CP


title: iPS_cR35_+44p_Subtel_9p+Xq


title: iPS_cR35_+44p_Subtel_7q


title: iPS_cR7_+23p_satellite_2


title: NRCWE-044_D1 54µg Sample 31 Group 1

description: NRCWE-044_D1 54µg


title: Control_D1 0µg Sample 30 Group 1

description: Control_D1 0µg

value: Control


title: NRCWE-045_D1 54µg Sample 32 Group 1

description: NRCWE-045_D1 54µg


title: Control_D1 0µg Sample 29 Group 1

description: Control_D1 0µg


title: NRCWE-045_D1 54µg Sample 28 Group 1

description: NRCWE-045_D1 54µg


title: iPS_cR7_+23p_Subtel_10p+18p


title: WT14_VZ

value: Embryonic 76days

value: wild type


title: Ci2.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT14_SVZ


title: Ci2.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR7_+23p_Subtel_2p


title: iPS_cR7_+23p_Subtel_10qMulti


title: WT14_CP


title: WT14_OSVZ


title: Ci2.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D1 18µg Sample 26 Group 1

description: NRCWE-043_D1 18µg


title: WT13_VZ


title: iPS_cR7_+23p_Subtel_2q+4q+10q


title: iPS_cR7_+23p_Subtel_4p


title: NRCWE-044_D1 54µg Sample 24 Group 1

description: NRCWE-044_D1 54µg


title: Ci2.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT13_OSVZ


title: WT13_SVZ


title: iPS_cR7_+23p_Subtel_5p


title: WT13_CP


title: Ci2.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D1 18µg Sample 23 Group 1

description: NRCWE-044_D1 18µg


title: NRCWE-045_D1 18µg Sample 27 Group 1

description: NRCWE-045_D1 18µg


title: NRCWE-045_D1 18µg Sample 25 Group 1

description: NRCWE-045_D1 18µg


title: iPS_cR7_+23p_Subtel_9p+Xq


title: iPS_cR7_+23p_Subtel_7q


title: NRCWE-043_D1 54µg Sample 22 Group 1

description: NRCWE-043_D1 54µg


title: NRCWE-044_D1 18µg Sample 21 Group 1

description: NRCWE-044_D1 18µg


title: Ci2.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D1 18µg Sample 20 Group 1

description: NRCWE-043_D1 18µg


title: Ci2.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D1 54µg Sample 18 Group 1

description: NRCWE-044_D1 54µg


title: NRCWE-043_D1 54µg Sample 19 Group 1

description: NRCWE-043_D1 54µg


title: TG11_SVZ

value: MCPH1 transgenic


title: iPS_cR7_+3p_satellite_2


title: TG11_VZ


title: TG11_OSVZ


title: Ci2.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D1 18µg Sample 17 Group 1

description: NRCWE-044_D1 18µg

value: Female


title: iPS_cR7_+3p_Subtel_10p+18p


title: iPS_cR7_+3p_Subtel_10qMulti


title: TG11_CP


title: Ci2.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TG10_VZ


title: Ci2.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR7_+3p_Subtel_2q+4q+10q


title: TG10_SVZ


title: Ci2.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR7_+3p_Subtel_4p


title: Control_D1 0µg Sample 15 Group 1

description: Control_D1 0µg

value: C57BL/6 mice


title: Ci2.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-043_D1 54µg Sample 16 Group 1

description: NRCWE-043_D1 54µg

value: 11 mouse cell lines


title: NRCWE-045_D1 54µg Sample 14 Group 1

description: NRCWE-045_D1 54µg


title: iPS_cR7_+3p_Subtel_5p


title: Ci2.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR7_+3p_Subtel_7q


title: TG10_CP


title: TG09_VZmd

value: Ventricular Zone

value: Embryonic 76 days


title: iPS_cR7_+3p_Subtel_2p


title: iPS_cR7_+3p_Subtel_9p+Xq


title: NRCWE-044_D1 18µg Sample 11 Group 1

description: NRCWE-044_D1 18µg


title: TG09_VZ


title: iPS_cR7_+54p_Subtel_10p+18p


title: NRCWE-045_D1 18µg Sample 12 Group 1

description: NRCWE-045_D1 18µg


title: TG09_SVZmd


title: iPS_cR7_+54p_Subtel_10qMulti


title: TG10_OSVZ

value: Embryonic 92days


title: Ci2.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts


title: NRCWE-045_D1 18µg Sample 13 Group 1

description: NRCWE-045_D1 18µg


title: TG09_SVZ

value: Subventricular Zone


title: Ci1.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: NRCWE-043_D1 18µg Sample 10 Group 1

description: NRCWE-043_D1 18µg


title: NRCWE-045_D1 54µg Sample 8 Group 1

description: NRCWE-045_D1 54µg


title: NRCWE-043_D1 54µg Sample 9 Group 1

description: NRCWE-043_D1 54µg


title: TG09_OSVZmd

value: Outer Subventricular Zone


title: iPS_cR7_+54p_Subtel_2p

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: NRCWE-044_D1 18µg Sample 6 Group 1

description: NRCWE-044_D1 18µg


title: TG09_OSVZ


title: Ci1.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: iPS_cR7_+54p_Subtel_4p


title: Ci1.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TG09_CPmd

value: Cortical plate


title: Control_D1 0µg Sample 7 Group 1

description: Control_D1 0µg

value: Control


title: Ci1.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_cR7_+54p_Subtel_5p


title: TG09_CP


title: WT_12_Muscle

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_mulatta.MMUL_1(ftp://ftp.ensembl.org/pub/release-75/fasta/macaca_mulatta/dna/)whole genome using bowtie v0.12.2
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated. First step, align RNA seq reads to the genome by using Bowtie; Second step TopHat uses Bowtie as an alignment ‘engine’ and breaks up reads; and then Cufflinks will assemble transcripts and computed the FPKM vlues(http://cufflinks.cbcb.umd.edu/),following protocol from Trapnellet al., Nature Protocol, 2012.
Genome_build: Macaca_mulatta.MMUL_1(ftp://ftp.ensembl.org/pub/release-75/fasta/macaca_mulatta/dna/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Muscle

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Muscle

value: Embryonic 135days


title: iPS_cR7_+54p_Subtel_7q

source_name: iPSCs


title: Ci1.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NRCWE-044_D1 54µg Sample 4 Group 1

description: NRCWE-044_D1 54µg

source_name: Lung


title: iPS_cR7_+54p_Subtel_2q+4q+10q


title: NRCWE-043_D1 18µg Sample 5 Group 1

description: NRCWE-043_D1 18µg

source_name: Universal Mouse Reference RNA


title: iPS_cR35_+44p_Subtel_5p


title: WT_12_Liver

source_name: Liver

value: Liver

value: wild type


title: Ci2.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Chemically induced fibroblasts

value: 21 days after induction


title: iPS_pG_satellite_2

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: iPS_cR7_+54p_Subtel_9p+Xq


title: Ci1.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Nugen05

city: Oxford

first: Ling-Pei

last: Ho

address: Headley Way

department: MRC Human Immunology Unit

country: United Kingdom

institute: University of Oxford

data_processing:
Quality control analysis with the fastQC package (www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned using STAR against the hg19 human genome assembly.
Non-uniquely mapped reads and reads that were identified as PCR duplicates using SAMtools were discarded.
Gene expression levels were quantified as read counts using the featureCounts function from the Subread package with default parameters.
RPKM (reads per kilobase of transcript per million mapped reads) values were generated using the edgeR package.
Genome_build: Build 37 (GRCh37, UCSC hg19)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values for each Sample.

source_name: blood cells

extract_protocol:
TRIzol LS mRNA extraction was used for phase separation. The RNA-containing phase was then processed using Qiagen RNeasy Mini kit, and contaminating DNA was removed using Ambion Turbo DNase.
The total purified RNA was processed using a NuGEN Ovation RNA-Seq system V2 (Ultralow DR Multiplex kit). Samples were sequenced on an Illumina HiSeq 2000.

treatment_protocol: Skin blisters were created at house dust mite challenge sites.

value: Blood T cells


title: Nugen09

source_name: blister cells

value: Skin blister T cells


title: WT_12_Brain

source_name: Brain

value: Brain


title: NRCWE-043_D1 54µg Sample 3 Group 1

description: NRCWE-043_D1 54µg

value: Female

value: C57BL/6 mice

value: 11 mouse cell lines


title: Ci1.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts

value: 9 days after induction


title: iPS_pG_Subtel_10p+18p


title: NRCWE-045_D1 18µg Sample 1 Group 1

description: NRCWE-045_D1 18µg


title: Control_D1 0µg Sample 2 Group 1

description: Control_D1 0µg


title: Ci1.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: iPS_pG_Subtel_10qMulti


title: Vector-1# treatment

city: Hong Kong

first: HUANG

last: BIAO

address: Shatin, N. T, Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: hUC-MSCs

extract_protocol:
hUMMSCs were treated with siKDM3A, siKDM4C, siNC or overexpressing KDM3A, KDM4C, vector plasmids, and then collect treated cells, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: early passage hUC-MSCs

value: vector control


title: WT_11_Muscle

value: Muscle

value: Embryonic 145days


title: Ci1.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT_11_Brain


title: Ci1.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Vector-2# treatment


title: iPS_pG_Subtel_2p


title: iPS_pG_Subtel_2q+4q+10q


title: KDM4C OV-1# treatment

value: KDM4C overexpression


title: WT_10_Muscle

value: Embryonic 130days

value: wild type


title: Ci1.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pG_Subtel_4p

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: WT_10_Liver

value: Liver


title: KDM3A OV-2# treatment

value: KDM3A overexpression


title: Ci1.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pG_Subtel_5p


title: KDM3A OV-1# treatment


title: WT_10_Brain

value: Brain


title: iPS_pG_Subtel_7q


title: siRNA-NC treatment

value: negative siRNA control


title: WT_11_Liver


title: Ci1.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT_09_Muscle

value: Embryonic 140days


title: Ci1.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT_09_Liver


title: Ci1.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: siKDM4C 3# treatment

value: KDM4C knockdown


title: siKDM4C 1# treatment


title: WT_09_Brain


title: iPS_pR_old_Subtel_10p+18p

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: Ci1.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts

value: 9 days after induction


title: KDM4C OV-2# treatment

value: early passage hUC-MSCs


title: Ci1.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: TG04_Muscle

value: Muscle

value: Embryonic 136days

value: MCPH1 transgenic


title: siKDM3A 1# treatment

value: KDM3A knockdown


title: Ci1.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pR_old_Subtel_2p


title: iPS_pR_old_Subtel_10qMulti


title: TG04_Liver


title: iPS_pR_old_Subtel_2q+4q+10q


title: Ci1.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pR_old_Subtel_4p


title: Ci1.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pG_Subtel_9p+Xq


title: iPS_pR_old_Subtel_5p


title: shMYT1_3_neuroblastoma cell line

city: Shanghai

first: Kai

last: Chen

address: NO.1665, Kongjiang Road

institute: Xinhua hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: neuroblastoma cell line

growth_protocol: Human neuroblastoma cell line SK-N-BE(2) was kindly provided by Stem Cell Bank, Chinese Academy of Sciences and maintained in RPMI 1640 with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent.RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: To generate stable MYT1 knockdown cells, we used lentiviral particles to infect the neuroblastoma cells for 24h and the cells were selected and maintained in medium containing puromycin for 48h.

value: MYT1 knockout

value: SK-N-BE(2) neuroblastoma cell line

tag: replicate


title: TG03_Liver

value: Liver


title: shNC_1_neuroblastoma cell line

value: control


title: TG03_Brain

value: Brain


title: iPS_pR_old_Subtel_7q

tag: passage (p), population doubling (pd)


title: Ci1.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: shMYT1_2_neuroblastoma cell line

tag: genotype


title: WT_05_Muscle

description: Sample 9

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_mulatta.MMUL_1 (ftp://ftp.ensembl.org/pub/release-75/fasta/macaca_mulatta/dna/) whole genome using bowtie v0.12.2
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated. Firstly align RNA seq reads to the genome by using Bowtie; Secondly TopHat uses Bowtie as an alignment ‘engine’ and breaks up reads; and then Cufflinks will assemble transcripts and computed the FPKM vlues(http://cufflinks.cbcb.umd.edu/),following protocol from Trapnellet al., Nature Protocol, 2012.
Genome_build: Macaca_mulatta.MMUL_1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: wild type


title: shNC_3_neuroblastoma cell line


title: iPS_pR_young_satellite_2


title: iPS_pR_young_Subtel_10p+18p


title: WT_05_Liver

description: Sample 8


title: shMYT1_1_neuroblastoma cell line


title: siKDM3A 3# treatment


title: TG04_Brain


title: WT_05_Brain

description: Sample 7


title: Ci1.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci2.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 21 days after induction


title: Ci1.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HEK-TER_shMAP4K4_3

city: Cambridge

first: Jong Wook

last: Kim

state: MA

address: 45 Main Street

department: Cancer Program

institute: Broad Institute

data_processing:
ccal.count_transcripts_using_kallisto_quant (ccal version 0.6.25 [https://github.com/UCSD-CCAL/ccal]
kallisto version 0.44.0 [https://pachterlab.github.io/kallisto/]
Ensembl's Homo sapiens.GRCh38.cdna.all.fa.gz [ftp://ftp.ensembl.org/pub/release-93/fasta/homo sapiens/cds/Homo sapiens.GRCh38.cds.all.fa.gz]) function
transcript-to-gene mapping using Ensembl Biomart [http://uswest.ensembl.org/biomart/martview/25881b5fd2dcacc7162cbdcf10469f67]
merge duplicated genes using the max function.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM

source_name: HEK cells immortalized with hTERT, SV40 Large-T and H-RasG12V expressing shMAP4K4.

growth_protocol: Stable cell lines expressing shRNA targeting MAP4K4 or Luciferase control HEK-TER cells were generated by lentiviral infection followed by selection with 2 ug/ml puromycin for 7 days. These cells were cultured in MEM-alpha media supplemented with 10% FBS and passaged every 3 days.

extract_protocol:
Total RNA was extracted using an RNeasy Plus Kit (Qiagen).
RNA sequencing libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420).

tag: cell line background

value: HEK-TER

value: expressing shRNA targeting MAP4K4


title: iPS_pR_young_Subtel_10qMulti

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: TG03_Muscle


title: shNC_2_neuroblastoma cell line


title: Ci1.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts

value: 9 days after induction


title: WT_04_Muscle

description: Sample 6


title: iPS_pR_young_Subtel_2p


title: Ci1.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: HEK-TER_shMAP4K4_2


title: WT_04_Liver

description: Sample 5


title: HEK-TER_shMAP4K4_1


title: iPS_pR_old_Subtel_9p+Xq


title: Ci1.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pR_young_Subtel_2q+4q+10q


title: HEK-TER_shLuc3

source_name: HEK cells immortalized with hTERT, SV40 Large-T and H-RasG12V expressing shLuc.

value: Luciferase control


title: WT_04_Brain

description: Sample 4


title: HEK-TER_shLuc2


title: TG_02_Muscle

description: Sample 3

value: Muscle


title: iPS_pR_young_Subtel_4p


title: Ci1.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_pR_young_Subtel_5p


title: Ci1.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TG_02_Brain

description: Sample 1

value: MCPH1 transgenic


title: siControl_rep1

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Basecalling
RNA-Seq paired reads were aligned to the human reference genome (UCSC Hg19) and transcript models (gencode release 19) using ‘STAR Aligner’ (v2.5.1b) with default parameters.
Aligned RNA-Seq reads were counted onto genes (gencode release 19) using ‘FeatureCounts’ from ‘Rsubread’ (v1.24) with the parameter strandSpecific set to 1, the rest of the parameters was set to default
The gene counts were subsequently normalized and transformed using the Variance Stabilizing Transformation from ‘DESeq2’ (v1.14.1).
Genome_build: hg19
Supplementary_files_format_and_content: CSV (matrix of normalized counts)

source_name: MCF10A cells (ATCC CRL-10317TM)

growth_protocol: MCF10A cells (ATCC CRL-10317TM) were cultured in Dulbecco’s modified eagle’s media (DMEM)/F12 (1:1) media (Gibco, Cat. No. 11330-032) with 5% horse serum (Gibco, Cat.No. 16050-122), 1% penicillin streptomycin (Gibco Cat. No. 15140-122), 20 ng/ml epithelial growth factor (Peprotech, Cat. No.AF-100-15), 0.5 mg/ml hydrocortisone (Sigma-Aldrich, Cat. No. H-0888), 100 ng/ml cholera toxin (Sigma-Aldrich, Cat. No. C-8052) and 10 μg/ml insulin (Sigma-Aldrich, Cat. No. I-1882).Cell cultures were incubated at 37ºC with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNAs targeting Control or TIP60 were transfected  using Lipofectamine RNAiMax reagent from Invitrogen/Life Technologies (Cat. No. 56532). The siRNA mixture used contained 15 l LipofectamineRNAiMax, 2 ml optimum media (Gibco, Cat. No. 31985-070) and 20 nM siRNA. The transfection mixture was incubated for 20 min at room temperature and then 8×10^5 cells were seeded in a 10-cm plate together with the siRNA mixture. After 6 h, the transfection mixture was replaced by growth media. Cells were harvested 72 h after siRNA transfection.

value: siControl


title: Ci1.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HEK-TER_shLuc1


title: iPS_pR_young_Subtel_9p+Xq


title: iPS_pR_young_Subtel_7q


title: HL60_TPA_treated_2

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
phorbol ester (TPA) treated HL60 Cell line
4D5E_HL60_Raw_500MB_blasts.txt

data_processing:
Genome-wide Hi-C analysis and contact maps were generated for each of the three cell types.
bowtie - alignment
HiCup (v0.5.826) - filtered set of mapped chromosome interactions
HOMER (v4.7, 8-25-2014) - identify significant structural interactions
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C Raw Counts

extract_protocol: 15x107 cells were crosslinked with Formaldehyde (2% FC, 10 min, RT), quenched with Glycine (125mM, 5 min, RT) and scraped from the plate. Cells were lysed on ice in lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40 and 50 μl protease inhibitors, 15 min) and disrupted using a Dounce homogenizer (10X, 1 min on ice, 10X). Lysed cells were pelleted (4°C, 5,000rpm, 3 min), wash twice in 1X restriction enzyme buffer, suspend in 1X buffer and divided into five tubes with a final volume of 362μl. SDS was added (1% FC), incubated (65°C, 10 min), place back on ice and Quenched with Triton X-100 (10% FC). Chromatin was digested with HindIII (400U, 37OC, 16 h with rotation). Restriction site overhangs were filled in with biotin labeled Cytosine (1.5 μl 10 mM dATP, 1.5 μl 10 mM dGTP, 1.5 μl 10 mM dTTP, 37.5 μl 0.4 mM biotin-14-dCTP, and 50U Klenow), mixed carefully and incubated (45 min, 37°C). Tubes were placed on ice and the enzyme inactivated by SDS (10%), incubated (65°C, exactly 30 min) and placed back on ice immediately. Biotinylated fragments were ligated by adding 7.61 ml ligation mix (745 μl 10% Triton X-100, 745 μl 10x ligation buffer [500 mM Tris-HCl pH 7.5, 100 mM MgCl2, 100 mM DTT], 80 μl 10 mg/ml BSA, 80 μl 100 mM ATP and 5.96 ml water), T4 DNA ligase (50U), mixed and incubated (4 h, 16°C). Crosslinks were reversed and protein degraded by Proteinase K (25 μl, 12 mg/ml) and incubation (16 h, 65°C). After 16 h, additional Proteinase K (25 μl 20 mg/ml) was added and further incubated (2 h, 65°C). The reactions were cooled to RT and DNA was purified by phenol (1X) and phenol:chloroform (1:1, 1X) extraction. The aqueous phase was transferred to high-speed centrifugation tubes (oakridge). The DNA was ethanol precipitated (2.5 volumes 100% Ethanol and 1/10th volume 3M Sodium Acetate), mixed by inversion, chilled (>30 min, -80°C), centrifuged (20 min, 10,000g, 4°C) and the DNA pellet dissolved in 450 μl 1x TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The DNA was phenol:chloroform (1:1) extracted twice more with centrifugation (5 min, 14,000rpm, RT). The DNA was ethanol precipitated (2.5 volumes 100% Ethanol and 1/10th volume 3M Sodium Acetate), mixed by inversion, chilled (>30 min, -80°C) and centrifuged (20 min, 10,000g, 4°C). The DNA pellet was washed with ice-cold 70% ethanol, centrifuged (10 min, >10,000g, 4°C), dried (~10 min) and suspended in 25 μl 1x TE. RNA was degraded by the addition of RNase A (1 μl 1 mg/ml), incubation (30 min, 37°C) and then the Hi-C libraries were pooled. Biotin was removed from unligated ends using T4 DNA polymerase. Mixed ~5μg of Hi-C library with T4 DNA polymerase reaction buffer (1 μl 10 mg/ml BSA, 10 μl 10x NEBuffer 2, 1 μl 10mM dATP, 1 μl 10mM dGTP) and T4 DNA polymerase (5U) in a total volume of 100 μl. Incubated the mixture (2 h, 12°C). Multiple 5 μg reactions were performed. Reactions were stopped by the addition of EDTA (2 μl 0.5M EDTA pH 8.0). Multiple 5 μg reactions were pooled and the DNA purified by three phenol pH 8.0:chloroform (1:1) extractions with centrifugation (5 min, 14,000 rpm, RT). The DNA was Ethanol precipitated (2.5 volumes 100% Ethanol and 1/10th volume 3M Sodium Acetate), mixed by inversion, chilled (>30 min, -80°C) and centrifuged (20 min, 10,000g, 4°C). The DNA pellet was washed with 70% Ethanol, dried, suspended and pooled in a total volume of 100 μl H2O. The DNA was sheared to a size of 300-500bp using a Covaris S2 instrument (duty cycle 5, intensity 5, cycles/burst 200, time 60 secs for 4 cycles). The sheared DNA ends were repaired (14 μl 10x ligation buffer, 14 μl 2.5 mM dNTP mix, 5 μl T4 DNA polymerase, 5 μl T4 polynucleotide kinase, 1 μl Klenow DNA polymerase and 1μl H2O) and incubated (30 min, RT). DNA was purified using a Qiagen MinElute column according to manufacturer's recommendations and the DNA eluted twice with Tris-Low-EDTA (TLE: 15 μl 1x [10 mM Tris pH 8.0, 0.1 mM EDTA]). An ‘A’ tail was added to the DNA fragments using Klenow (5 μl [10x NEBuffer2, 10 μl 1 mM dATP, 2 μl H2O and 3 μl Klenow (exo-)]) and incubation (30 min, 37°C). The Klenow was inactivated (20 min, 65°C) and the reaction was cooled on ice. The reaction volume was reduced to 20 μl using a speedvac, the DNA loaded on a 1.5% agarose gel with 1X TAE, run for 3 hours at 80V and DNA fragments between 300 and 500 bp were excised. The DNA was purified using a Qiagen gel extraction kit according to manufacturers recommendations and the DNA eluted with 50 μl 1x TLE. Combined the purified DNA in a final volume of 300 μl 1x TLE and determined the DNA concentration by QuBit. To enrich for biotin-labeled fragments magnetic streptavidin beads (100 μl) were washed twice with Tween Buffer (TB: 400 μl [5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween]) and suspended in a volume of 2x No Tween Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl) equivalent to the remaining Hi-C library volume. All subsequent steps were performed in DNA LoBind tubes. Combined the beads with Hi-C DNA and incubated (15 min, RT, slow rotation). Placed the tubes on a magnetic particle concentrator, removed the supernatant, washed the beads in NTB (NTB: 400 μl [5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl]) and then with ligation buffer (100 μl 1x). Suspend the beads in ligation buffer (30 μl 1x) and transferred to a new tube. The DNA bound to the streptavidin beads (~100 ng) was used for sequencing library preparation according to Illumina instructions. Resuspention buffer (2.5 µl), DNA adaptor index (2.5 µl) and Ligation Mix 2 (2.5 µl) were added to the tube, and incubated (30°C, 2 h). To stop the reaction Stop Ligation buffer (5 µl) was added to the tube. Removed non-ligated adapters by placing the tube on a magnetic particle concentrator and washing the beads twice with TB (400 μl 1x), once with NTB (200 μl 1x) and twice with NEBuffer 2 (200 μl and 50 μl 1x). Suspended the beads in 50 μl 1x NEBuffer 2 and transfered to a new tube. Determined the number of PCR cycles necessary to generate enough product for sequencing; set up four PCR reactions with 6, 9, 12 or 15 cycles (9 µl of sample [8 µl 1x NEBuffer2 + 1 µl DNA bound beads], 9 µl Enhancer PCR mix and 2 µl PCR cocktail. Run PCR: 95°C – 3 min, {98°C – 20 sec, 60°C – 15 sec, 6-15 cycles 72°C – 30 sec} 6-15 cycles, 72°C – 5 min, 4°C – forever. Determined the optimal cycle number by running the PCR reactions on a 5% polyacrylamide gel (60 min, 80 V). Amplified the remainder of the Hi-C-library-bound streptavidin beads in a large-scale PCR with the optimal number of PCR cycles. Pooled the PCR products from the separate wells and reclaimed the beads. Kept 1% of the large-scale PCR product separate to run on a gel and purify the remainder of the PCR product with Ampure beads (1.8x volume) according to the manufacturer's recommendations. Eluted the DNA with TLE (50 μl 1x) and compared 1% of the Ampure bead purified PCR product to the 1% aliquot of original PCR product on a 5% polyacrylamide gel to insure the successful removal of the PCR primers. Sequenced the Hi-C library with Illumina paired end sequencing (50 bp).


title: Ci1.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control


title: HL60_TPA_treated_1

source_name: phorbol ester (TPA) treated HL60 Cell line


title: iPS_UN_Subtel_10p+18p

value: healthy control (DNMT3B wt/wt)


title: Ci1.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_UN_satellite_2


title: Ci1.F02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HL60_untreated_2

description:
untreated HL60 Cell line
2B3C_HL60_Raw_500MB_blasts.txt

source_name: untreated HL60 Cell line


title: iPS_UN_Subtel_10qMulti


title: Ci1.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HL60_untreated_1


title: TG_02_Liver

description: Sample 2


title: iPS_UN_Subtel_2p


title: HL60_RA_treated

description:
retinoic acid (ATRA) treated HL60 Cell line
1A_HL60_Raw_500MB_blasts.txt


title: Ci1.E11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.E10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: RNA_LinxP-del_d1.5_rep1

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: tablecounts_raw.csv; ; D030T7

data_processing:
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Capture-C sequencing reads were trimmed using the Trim Galore! pipeline (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and then processed using the HiC-Pro pipeline 72 (v2.8.0).
RNA sequencing reads were aligned on the mouse genome using the STAR mapper. Raw counts have been generated from the STAR mapper using the GENCODE annotation database vM1.
ATAC-seq paired-end reads were trimmed of the adaptor sequences and aligned to the NCBIm37 genome using STAR v2.4.2a.  Duplicate fragments were removed using PICARD tools v1.90, only unique mapped fragments between 38bp and 1500bp in length were retained.  ATAC-seq peaks were called on the 1bp transposase cut-sites using MACS2 (with shift size 100 and extension size 200). Only the peaks considered reproducible by IDR (version 2), with an IDR threshold of 0.05, were kept.
Genome_build: mm9 / NCBIm37

source_name: mouse ESC (E14)

growth_protocol: Feeder-independent male mouse ESC (E14) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Feeder-independent female mouse ESC (Pgk12.1) were grown on gelatin-coated flasks in DMEM supplemented with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma) and 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged when needed. Medium was changed daily. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates or flasks and scraped off. For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate. For ATAC-seq, cells were washed once with PBS and directly incubated in the transposition reaction.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using KAPA Hyper Prep Kit (KK8500, Kapa Biosystems); RNA-seq libraries were generated using the TruSeq Stranded Total RNA kit (Illumina); ATAC-seq libraries were generated based on a Nextseq-compatible protocol (Buenrostro et al 2013).

value: mouse ESC (E14)

tag: strain

value: XY, 129/Ola

value: LinxP deletion

tag: differentiation stage

value: day 1.5

tag: capture-c viewpoint


title: RNA_LinxP-del_d1.5_rep2

description: tablecounts_raw.csv; ; D030T8


title: Hec1A TH63, FoxA1 ChIP

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

description: Peak file from HOMER: Peaks_Hec_3C_vrs_inp_TH48_TH126.txt

data_processing:
Reads were mapped to the human reference genome using bowtie version 1.1.2
Filtering of alignment files to identify uniquely mapping, non-duplicate reads, was performed using samtools version 1.3.1
Peak calling was performed by HOMER 4.7.2
Genome_build: hg19
Supplementary_files_format_and_content: peak files from HOMER, text format

source_name: Hec1A cell line, FOXA1-CHIP

extract_protocol:
Libraries from ChIP samples were made with two different kits. With Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation this modifications were used: ligation with of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA. Supplied by Diagenode) library preparatiopn the manufacturer’s instructions were followed.
ThruPLEX, Rubicon Genomics

tag: cell line

tag: chip antibody

value: FoxA1 rabbit ab23738 (lot GR292351-2)


title: iPS_UN_Subtel_5p

data_processing:
BISMARK (v0.17.0): Adaptors and low quality bases were trimmed out. Reads were then aligned to the customized reference human genome GRCh38 by using the Bismark aligner.
Methylation scores were performed using Bismark methylation extractor script.
For 10qMultiple and 10q_2q+4q files the different subtelomeres were told apart based on single nucleotide differences compared to subtelomere 10q. We used a Perl homemade script.
Genome_build: hg38

source_name: iPSCs


title: Control-2

city: Beijing

first: shuai

last: chen

state: Beijing

address: No. 22, Zhongguancun South Street, Haidian District,

department: Department of Oral Pathology

institute: Peking University School and Hospital of Stomatology

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hours at 45℃ on GeneChip Human Gene 1.0.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

source_name: SCC-15 cells transfected with miR-NC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetix protocol from 2 ug total RNA.

growth_protocol: 3*10^5 of SCC-15 cells were seeded in 6-well plate and transfected with mimics (30nM) 24 hours later.

extract_protocol: RNA was extracted by Qiangen RNA Isolation Kit according to the manufacturer' instructions

treatment_protocol: 36 hours after transfection,cells were collected for further total RNA extracion.

value: Tongue squamous cell carcinoma cell line

tag: genotype/variation

value: transfected with miR-NC


title: Hec1A TH61, FoxA1 ChIP


title: Hec1A TH46, FoxA1 ChIP

extract_protocol:
Libraries from ChIP samples were made with two different kits. With Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation this modifications were used: ligation with of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA. Supplied by Diagenode) library preparatiopn the manufacturer’s instructions were followed.
Illumina TruSeq™ DNA Sample Preparation


title: Ci1.E09

city: Yokoham

first: Joachim

last: Luginbühl

address: 1-7-22 Suehiro-cho

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).


title: Mimics-1

source_name: SCC-15 cells transfected with miR-611 mimics

value: transfected with miR-611 mimics


title: Ci1.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Hec1A TH126, input

source_name: Hec1A cell line, INPUT


title: RNA_LinxP-del_d0_rep1

description: tablecounts_raw.csv; ; D030T3

value: day 0 (undifferentiated)


title: iPS_UN_Subtel_9p+Xq

extract_protocol:
Genomic DNA was extracted according to standard procedures and was bisulfite-converted with the Methylamp DNA Modification kit (EPIGENTEK, NY, USA)
PCR products were purified by QIAquick PCR purification kit (28104, QIAGEN, MD, USA). Further amplicon processing, sequencing, and analysis were performed as described (Sagie, Toubiana, et al. 2017).


title: RNA_E14_d1.5_rep2

description: tablecounts_raw.csv; ; D030T6

value: wild type


title: Ci1.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Chemically induced fibroblasts

value: Chemically induced fibroblasts

value: 9 days after induction


title: RNA_E14_d1.5_rep1

description: tablecounts_raw.csv; ; D030T5


title: Ci1.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: iPS_UN_Subtel_2q+4q+10q


title: RNA_E14_d0_rep2

description: tablecounts_raw.csv; ; D030T2


title: Ci1.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: iPS_UN_Subtel_4p


title: RNA_LinxP-del_d0_rep2

description: tablecounts_raw.csv; ; D030T4


title: Mimics-2


title: Control-1


title: Ishikawa TH75, FoxA1 ChIP

description: Peak file from HOMER: Peaks_Ish_6C_inpTH1TH131.txt

source_name: Ishikawa cell line, FOXA1-CHIP

value: Ishikawa


title: iPS_UN_Subtel_7q


title: Ishikawa TH73, FoxA1 ChIP


title: RNA_E14_d0_rep1

description: tablecounts_raw.csv; ; D030T1


title: Ci1.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ishikawa TH59, FoxA1 ChIP


title: Hec1A TH48, input


title: Ci1.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ishikawa TH41, FoxA1 ChIP


title: Ci1.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ishikawa TH3, FoxA1 ChIP


title: SAFB-K9me3-HiChip-Rep1-plus

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

data_processing:
Library strategy: HiChIP
Hi-Chip paired-end reads were aligned to mm9 reference genome using the HiC-Pro pipeline (Servant et al., 2015) with default set- tings. We converted .all ValidPairs files to .hic files by the script hicpro2juicebox.sh from HiC-Pro utilities. To detect the differences between experiments, we normalized the interaction matrices for each chromosome separately according to the total contacts in each chromosome. This normalization led to the sum of contacts in each chromosome to 1e8.
Genome_build: mm9

source_name: AML12 shSafb

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol:
The HiChIP of H3K9me3 was performed as described (Mumbach et al., 2016), started with 2.5 millions of AML12 cells for each sam- ple. Briefly, 2.5 millions of cells were digested by 100U of MboI overnight at 37  C. After biotin filling and DNA ligating, the nuclear were resuspended by sonication buffer (1%SDS, 10mM EDTA, 50mM Tris-HCl, 20mM NaBu, 1 3 Proteinase Inhibitor), and chromatin was sheared into 300-700bp using Bioruptor followed by incubating with antibody overnight at 4 C. 25 mL beads were washed once with cold 0.5% BSA, and added into the sheared chromatin-protein supernatant for 2 hours at 4 C. Washed with high salt wash buffer (50mM HEPEs, 500mM NaCl, 1mM EDTA, 0.1%DOC, 1%Triton X-100) three times; low wash buffer (10mM Tris-HCl, 250mM LiCl, 1mM EDTA, 0.5%NP40, 0.5%DOC) twice; TE once. Chromatin-protein complex were eluted for 15min at 65 C in 50 mL elution buffer (1% SDS in TE). After reverse-crosslinking, DNA was extracted using ultrapure phenol/chloroform. Chromatin fragments con- taining biotin were captured by MyOne Streptatvidin beads (ThermoFished 65601), and libraries were prepared on beads using Tn5 from DNA Library Prep Kit V2 (Vazyme TD503) for 30min at 37 C, followed by amplification.
Illumina sequencing library were prepared according to the standard Illumina protocol.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.

tag: lentivirus

value: shSafb

tag: antibody


title: SAFB-K9me3-HiChip-Rep2


title: SAFB-K9me3-HiChip-Rep2-plus


title: Ci1.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: cell type

tag: treatment