title: no manganese rep2

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were aligned to the Drosophila genome version dm6.24 with STAR version 2.5.2b
Counts were normalized to RPKM values with R
Differentially expressed genes were selected based on both fold change compared to the control and adjusted p-value as calculated using DESeq2
Genome_build: FlyBase release 6.24
Supplementary_files_format_and_content: text files with RPKM values and read counts of all samples for each gene of each sample

organism: Drosophila melanogaster

source_name: gut

growth_protocol: 10 females and 10 males of wild type of the Oregon R-C genotype, were mated and allowed to lay eggs for five days on two variants of chemical diet (no manganese added or 5 ppm manganese). Parents were removed and recently-eclosed females were transferred to fresh medium, respectively, for another five days.

extract_protocol:
RNA extraction and purification was performed using the Direct-zol RNAMicroPrepkit (Zymo Research) method.
RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced by Illumina NextSeq 500 instrument with a mid-output kit at the BPF Next-Gene Sequencing Core Facility at HMS.

treatment_protocol: two variants of chemical diet (no manganese added or 5 ppm manganese) for 5 days

value: maganese depletion

tag: replicate


title: added manganese rep2

status: Public on Aug 31 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: treatment

value: control


title: added manganese rep1


title: no manganese rep1


title: hSVP Exosomes-Donor 9

type: RNA

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

description: Exosomes isolated from hSVP

data_processing:
Immediately after a run,threshoulds were determined and data was analyzed using the QuantStudio™ 6 Flex Software. Spike-in control values were checked to determine the accuracy of RNA isolation and cDNA reaction. If a miRNA is expressed (i.e. Ct<40) in all donors of a group, it was considered as a valid miRNA for the comparison.
Different hSVP exosomes were compared to check whether they express a certain miRNA or not. If a miRNA had Ct value <40, it was considered as an epresseed miRNA in the hSVP exosomes..

label: SYBR Green

organism: Homo sapiens

source_name: Human saphenous vein pericytes

label_protocol: A synthetic analog of the non-human Caenorhabditis elegans microRNA-39 (cel-miR-39; Qiagen, Hilden, Germany) was spiked in (10 μl of a 5 fmol/μl stock) to normalize RNA extraction efficiency. cDNA synthesis and real-time qPCR was performed using the miRCURY LNA™ Universal RT microRNA PCR system (Exiqon, Denmark). The cDNA products were transferred to the microRNA PCR Human Panels (I + II; version 3) and run using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems, Foster City, CA, USA).

growth_protocol: Human saphenous vein pericytes (hSVPs) were cultured on 0.5% gelatin+20 µg/mL fibronectin coated plates in EGM-2 (Lonza). After the attachment of the cells, the medium was replaced by EGM-2 (without SingleQuot FBS; Lonza, Basel, Switzerland) containing 2% exosome-depleted FBS from Gibco (Waltham, MA, USA) and cells were put into hypoxia incubator (2% O2). The conditioned media were collected from the confluent pericyte cultures every 3 days and centrifuged at 300 × g for 10 minutes to remove cells. Then, supernatant was transferred into a new centrifuge tube and spun at 16,000 × g for 30 minutes to remove any remaining cell debris. The supernatant was transferred into a new falcon and kept at -80 °C until use. On the day of the isolation, supernatants were thawed on ice and then, exosome isolation was performed using Exo-SpinTM columns from Cell Guidance Systems (Cambridge, UK) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from isolated exosomes using the miRNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

treatment_protocol: Human saphenous vein pericytes were cultured under hypoxia (2% O2) and the exosomes were isolated from cell media using Exo-SpinTM columns from Cell Guidance Systems (Cambridge, UK).

tag: passage number


title: WT_CD8+CXCR5+PD1+_rep3

status: Public on Aug 30 2019

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

description:
Stat5CD8Cre.gct
M3493DP

data_processing:
Samples were demultiplexed using Illumina BaseSpace
Reads were aligned and quantified using STAR via basepairtech.com
Samples were normalized and differential expression analysis was conducted using DESeq via basepairtech.com
Genome_build: mm10
Supplementary_files_format_and_content: GCT files containing transcript abundances

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen cells

extract_protocol:
The CD8+ T cell subsets were FACS sorted from splenocytes of the indicated mice. The cells were lysed in TRIzol (LifeTechnologies) to isolate total RNA. The mRNA was purified using NEBNext poly(A) mRNA Magnetic Isolate Module (New England Biolabs) and processed as per manufacturer’s instructions.
The libraries were constructed using NEBNext Ultra RNA library Prep kit for Illumina (New England Biolabs), and quantified using QubitFluorometer (ThermoFisher) and Kapa Library Quantification Kit (KapaBiosystems). The average size of the libraries was measured using D1000 ScreenTape system (Agilent).

tag: strain

tag: genotype

value: LCMV(Armstrong), day8


title: Stat5KOIgHELsHEL_CD8+CXCR5+PD1-_rep3

description:
Stat5CD8CreIgHELsHEL.gct
M3545cxcr5


title: Stat5KOIgHELsHEL_CD8+CXCR5-PD1-_rep3

description:
Stat5CD8CreIgHELsHEL.gct
M3545DN


title: Stat5KOIgHELsHEL_CD8+CXCR5+PD1+_rep3

description:
Stat5CD8CreIgHELsHEL.gct
M3545DP


title: WT

data_processing:
Raw Illumina sequencing data was demultiplexed and fastq files were generated using 10X Genomics Cellranger mkfastq
Fastq files were aligned to the mm10 genome and unique UMI sums per gene were calculated using 10X Genomics Cellranger count
Genome_build: mm10
Supplementary_files_format_and_content: h5 format matrices containing the number of UMIs aligned to each gene, per cell.  Raw matrices contain all UMI data while filtered matrices exclude UMIs not associated with putative cells.

extract_protocol:
The cells were FACS sorted from splenocytes of the indicated mice.  10X Genomics single-cell 3’ RNA expression profiling, GEM (Gel bead-in-EMulsions) generation & barcoding, post GEM-RT cleanup & cDNA amplification and the library construction were done according to manufacture procedures using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell A Chip Kit (PN-1000009) and Chromium i7 Multiplex Kit (PN-120262) by 10x Genomics (Pleasanton, California, USA).
10X Genomics single-cell 3’ RNA expression profiling, GEM (Gel bead-in-EMulsions) generation & barcoding, post GEM-RT cleanup & cDNA amplification and the library construction were done according to manufacture procedures using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell A Chip Kit (PN-1000009) and Chromium i7 Multiplex Kit (PN-120262) by 10x Genomics (Pleasanton, California, USA).

tag: treatmen


title: Stat5KOIgHELsHEL


title: WTIgHELsHEL


title: PAX1-2_rep1

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

description:
2nd time point
SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: Hela cells cultured with EGF for three weeks and induced PAX1 expression by doxycycline at the last two weeks.

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: Hela cells were cultured in Dulbecco's modified Eagle's medium (DMEM) or RPMI 1640 medium containing 10% (w/v) fetal calf serum, penicillin at 100 U/ml, streptomycin at 100 g/ml, and L-glutamine at 2 mmol/l.

extract_protocol: The total RNA was harvested by using a Qiagen RNeasy kit. An additional DNase I digestion procedure was included in the isolation of RNA to remove contaminating DNA according to the manufacturer's protocol.  The mRNA quality has achieved the ratio of  28S/18S >1 and RNA quality indicator (RQI) > 7 by using Agilent 2100 620 Bioanalyzer to send to the core service unit (Health GeneTech Corp., Taoyuan, Taiwan) for whole genome expression analysis.

treatment_protocol: PAX1 (NM_006192) was constructed by inserting a full-length cDNA product into a pT-Rex-DEST31 vector. The construct was then transfected into HeLa cells with Lipofectamine 2000 in Opti-MEM I reduced-serum medium at 37 °C in a 5% CO2 atmosphere for 4–5 hours, after which the medium was removed and replaced with fresh culture medium. Cells were selected by the antibiotic (G418) after 2 days in culture. The stablelly transfected cells treated EGF (50ng/ml). The PAX1 expression was induced by using doxycycline.

tag: cell line

value: HeLa


title: PAX1-2_rep2

description:
2nd time point
SAMPLE 6


title: Stat5KO


title: PAX1-1_rep1

description:
1st time point
SAMPLE 3

source_name: Hela cells cultured with EGF for two weeks and induced PAX1 expression by doxycycline at the last week.


title: EGF_rep2

description:
control
SAMPLE 2

source_name: Hela cells cultured with EGF for a week and  transfected  pT-Rex-DEST31 vector contained full-length PAX1 cDNA, which was  not inducing to expression .


title: Stat5KO_CD8+CXCR5+PD1-_rep3

description:
Stat5CD8Cre.gct
M3488CXCR5


title: WT_CD8+CXCR5+PD1+_rep2

description:
Stat5CD8Cre.gct
M3469DP


title: PAX1-1_rep2

description:
1st time point
SAMPLE 4


title: Stat5KO_CD8+CXCR5+PD1+_rep3

description:
Stat5CD8Cre.gct
M3488DP


title: Stat5KO_CD8+CXCR5-PD1-_rep3

description:
Stat5CD8Cre.gct
M3488DN


title: Cyp27b1-knockout mpkDCT cells, 128_siCT_25D3_7_1

city: Itabashi-ku

first: Takao

last: Susa

state: Tokyo

department: Department of Biochemistry

country: Japan

institute: Teikyo University School of Medicine

description: 10-7M of 25(OH)2D3 treated Cyp27b1 knockout mpkDCT cells.

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Cyp27b1-knockout mpkDCT cells

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: CRISPR-Cas9 mediated Cyp27b1 knockout mpkDCT cells were cultured as previously reported (Diepens, et al., J Physiol Renal Physiol. 2004, 286, F483-9).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Twenty-four hours before 1,25(OH)2D3 or 25(OH)D3 administration to the cells, culture medium was changed to the phenol red-free medium containing 2 % charcoal stripped fetal bovine serum (FBS), then the cells were exposed to the indicated hormones for another 24 h with the same medium.

value: mpkDCT


title: Cyp27b1-knockout mpkDCT cells, 128_siCT_V_1

description: Vehicle treated Cyp27b1 knockout mpkDCT cells.


title: WT_CD8+CXCR5+PD1-_rep2

description:
Stat5CD8Cre.gct
M3469CXCR5


title: WT_CD8+CXCR5-PD1-_rep2

description:
Stat5CD8Cre.gct
M3469DN


title: Stat5KO_CD8+CXCR5+PD1+_rep2

description:
Stat5CD8Cre.gct
M3466DP


title: Cyp27b1-knockout mpkDCT cells, 128_siCT_1_25D3_7_1

description: 10-7M of 1,25(OH)2D3 treated Cyp27b1 knockout mpkDCT cells.


title: EGF_rep1

description:
control
SAMPLE 1


title: Stat5KO_CD8+CXCR5+PD1-_rep2

description:
Stat5CD8Cre.gct
M3466CXCR5


title: WT_CD8+CXCR5-PD1-_rep3

description:
Stat5CD8Cre.gct
M3493DN


title: Stat5KO_CD8+CXCR5+PD1+_rep1

description:
Stat5CD8Cre.gct
M3465DP


title: Stat5KO_CD8+CXCR5-PD1-_rep2

description:
Stat5CD8Cre.gct
M3466DN


title: WT_CD8+CXCR5-PD1-_rep1

description:
Stat5CD8Cre.gct
M3461DN


title: WT_CD8+CXCR5+PD1-_rep3

description:
Stat5CD8Cre.gct
M3493CXCR5


title: WT_CD8+CXCR5+PD1+_rep1

description:
Stat5CD8Cre.gct
M3461DP


title: Stat5KO_CD8+CXCR5+PD1-_rep1

description:
Stat5CD8Cre.gct
M3465CXCR5


title: Stat5KOIgHELsHEL_CD8+CXCR5-PD1-_rep2

description:
Stat5CD8CreIgHELsHEL.gct
M3456DN


title: Stat5KOIgHELsHEL_CD8+CXCR5+PD1+_rep1

description:
Stat5CD8CreIgHELsHEL.gct
M3450DP


title: Stat5KOIgHELsHEL_CD8+CXCR5+PD1-_rep1

description:
Stat5CD8CreIgHELsHEL.gct
M3450cxcr5


title: Stat5KOIgHELsHEL_CD8+CXCR5+PD1+_rep2

description:
Stat5CD8CreIgHELsHEL.gct
M3456DP


title: Stat5KOIgHELsHEL_CD8+CXCR5-PD1-_rep1

description:
Stat5CD8CreIgHELsHEL.gct
M3450DN


title: V5_input

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq using mm10 RefSeq as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using limma voom.  Low expressed genes were removed and genes with logCPM greater than 0.5 in at least 4 samples were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: logCPM

extract_protocol:
HA samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by tapestation.
Paired-end libraries for ultiplexed sequencing were generated from 100ng of IP or input RNA using Nugen Ovation RNA-Seq System V2 kit with mRNA enrichment.

tag: strain background

tag: genotype/variation

value: wild-type

tag: age

value: adult (P63)

tag: Sex

value: male

tag: injection

value: vehicle

tag: tissue

value: brain

tag: cell type

value: striatal astrocyte

tag: rna sample type

value: input


title: V4_IP

value: HA IP


title: V3_IP


title: V2_IP


title: V2_input


title: C5_IP

value: 1 mg/kg CNO


title: FVB4

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
For scRNA-Seq, the Cell Ranger Single Cell Software Suite, version 1.3 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome for FVB3 and FVB4 and to th Hg19 for the 3 Cell-line mixture
10xbulk and freash frozen mRNA-Seq libraries were aligned to the mouse mm10 and GRCh38 reference genome using the STAR aligner algorithm. Resulting BAM files were sorted and indexed using Samtools and QC was performed using Picard. Tran-script read counts were determined was performed using Salmon
Genome_build: mm10, hg19, GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Normal adult Mammary Gland

growth_protocol: All cell lines were maintained independently in culture medium DMEM (Gibco) supplemented with 10% FBS (Millipore) and 1% penicillin-streptomycin (Gibco) and grown in incubators maintained at 37°C with 5% CO2

extract_protocol:
The FVB/NJ mammary glands were placed in 10 ml of a digestion medium con-taining EpiCultTM-B Mouse Medium Kit (#05610, StemCell Technologies), Col-lagenase/Hyaluronidase (#07912, StemCell Technologies) and 1% penicillin streptomycin (Gibco). The mammary gland was digested overnight in a thermocycler maintained at 37 C with continuous rotation. RNA was isolated from the cell-lines and the mammary glands using the RNeasy Mini Kit (#74104, Qiagen) according to manufacturer protocol.
scRNA-Seq libraries were prepared following the Single Cell 30 Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A) using the following Single Cell 30 Reagent Kits v2: ChromiumTMSingle Cell 3' Library & Gel Bead Kit v2, PN-120237, Single Cell 3' Chip Kit v2 PN-120236, and i7 Multiplex Kit PN-120262 (10X Genomics). 10xBulk and Fresh frozen mRNA-Seq were made using total RNA and the Illu-mina TruSeq mRNA sample preparation kit.
scRNA-Seq Libraries were run on an Illumina HiSeq 4000 as 2 150 paired-end reads. 10x bulk andfresh frozen mRNA-Seq Paired end (2 50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer

tag: tag

value: 12 weeks old mouse mammary gland

value: FVB/NJ mouse/ female


title: C4_IP


title: FVB3


title: C5_input


title: C3_input


title: C3_IP


title: Stat5KO_CD8+CXCR5-PD1-_rep1

description:
Stat5CD8Cre.gct
M3465DN


title: C4_input


title: WT_CD8+CXCR5+PD1-_rep1

description:
Stat5CD8Cre.gct
M3461CXCR5


title: C2_IP


title: 3 Cell-line mixture

source_name: Human Cell-lines

value: MDA-MB-438, MCF7, Human dermal fibroblast (HF)

value: Ratios of mixing:MDA-MB-438:60%, MCF7:30%, HF:10%


title: C2_input


title: Stat5KOIgHELsHEL_CD8+CXCR5+PD1-_rep2

description:
Stat5CD8CreIgHELsHEL.gct
M3456cxcr5


title: V5_IP


title: V4_input


title: V3_input


title: Dnmt1KOd8.2.H11

city: Cambridge

first: Alex

last: Shalek

address: 45 Carleton Street

department: Chemistry

institute: MIT

description:
day 8 dox+ DNMT1 KO
Differentiation_Timecourse_TPM.txt

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Regression analysis was done as described in manuscript
Genome_build: hg38

source_name: ES cells

extract_protocol:
Smart-seq 2
Illumina Nextera XT

tag: time point

value: day 8

value: DNMT1 KO


title: Dnmt1KOd8.63.H09


title: Dnmt1KOd8.28.H12


title: Dnmt1KOd8.92.H10


title: Dnmt1KOd8.67.H08


title: Dnmt1KOd8.33.H06


title: Dnmt1KOd8.6.H07


title: Dnmt1KOd8.74.H03


title: Dnmt1KOd8.10.H05


title: Dnmt1KOd8.31.H02


title: Dnmt1KOd8.16.G10


title: Dnmt1KOd8.87.G11


title: Dnmt1KOd8.44.G08


title: Dnmt1KOd8.24.G07


title: Dnmt1KOd8.39.G05


title: Dnmt1KOd8.3.G04


title: Dnmt1KOd8.45.G02


title: Dnmt1KOd8.11.G03


title: Dnmt1KOd8.26.F10


title: Dnmt1KOd8.50.F11


title: Dnmt1KOd8.93.G06


title: Dnmt1KOd8.78.H04


title: Dnmt1KOd8.82.H01


title: Dnmt1KOd8.46.F06


title: Dnmt1KOd8.22.F05


title: Dnmt1KOd8.53.F08


title: Dnmt1KOd8.1.F07


title: Dnmt1KOd8.23.F09


title: Dnmt1KOd8.77.G12


title: Dnmt1KOd8.86.E11


title: Dnmt1KOd8.65.F01


title: Dnmt1KOd8.56.F03


title: Dnmt1KOd8.34.G09


title: Dnmt1KOd8.84.E12


title: Dnmt1KOd8.18.E10


title: Dnmt1KOd8.58.F02


title: Dnmt1KOd8.51.F12


title: Dnmt1KOd8.68.E09


title: Dnmt1KOd8.30.E08


title: Dnmt1KOd8.20.E07


title: Dnmt1KOd8.13.E06


title: Dnmt1KOd8.8.E05


title: Dnmt1KOd8.62.E02


title: Dnmt1KOd8.69.E03


title: Dnmt1KOd8.70.E04


title: Dnmt1KOd8.76.E01


title: Dnmt1KOd8.73.D10


title: Dnmt1KOd8.64.D08


title: Dnmt1KOd8.47.D09


title: Dnmt1KOd8.36.F04


title: Dnmt1KOd8.25.D06


title: Dnmt1KOd8.9.D01


title: Dnmt1KOd8.60.D03


title: Dnmt1KOd8.95.D02


title: Dnmt1KOd8.59.C10


title: Dnmt1KOd8.57.D05


title: Dnmt1KOd8.79.C11


title: Dnmt1KOd8.35.D11


title: Dnmt1KOd8.72.C12


title: Dnmt1KOd8.17.D04


title: Dnmt1KOd8.29.C09


title: Dnmt1KOd8.15.C06


title: Dnmt1KOd8.37.C04


title: Dnmt1KOd8.4.C03


title: Dnmt1KOd8.12.C08


title: Dnmt1KOd8.89.C02


title: Dnmt1KOd8.7.C01


title: Dnmt1KOd8.43.B11


title: Dnmt1KOd8.5.B12


title: Dnmt1KOd8.66.B10


title: Dnmt1KOd8.38.D12


title: Dnmt1KOd8.90.D07


title: Dnmt1KOd8.88.B07


title: Dnmt1KOd8.80.B09


title: Dnmt1KOd8.54.B04


title: Dnmt1KOd8.48.C07


title: Dnmt1KOd8.21.B06


title: Dnmt1KOd8.32.B02


title: Dnmt1KOd8.55.A11


title: Dnmt1KOd8.81.A09


title: Dnmt1KOd8.49.A08


title: Dnmt1KOd8.52.B05


title: Dnmt1KOd8.19.G01


title: Dnmt1KOd8.41.B01


title: Dnmt1KOd8.91.C05


title: Dnmt1KOd2.90.H12

description:
day 2 dox+ DNMT1 KO
Differentiation_Timecourse_TPM.txt

value: day 2


title: Dnmt1KOd8.42.A04


title: Dnmt1KOd8.85.A02


title: Dnmt1KOd2.36.H09


title: Dnmt1KOd2.52.H07


title: Dnmt1KOd8.75.A01


title: Dnmt1KOd2.54.H04


title: Dnmt1KOd2.67.H10


title: Dnmt1KOd2.51.H05


title: Dnmt1KOd2.92.H03


title: Dnmt1KOd2.89.H06


title: Dnmt1KOd8.83.B08


title: Dnmt1KOd2.45.H02


title: Dnmt1KOd2.75.H01


title: Dnmt1KOd8.96.A12


title: Dnmt1KOd8.61.A07


title: Dnmt1KOd2.40.G12


title: Dnmt1KOd2.27.G06


title: Dnmt1KOd2.5.G07


title: Dnmt1KOd2.23.G11


title: Dnmt1KOd2.71.G05


title: Dnmt1KOd2.64.G04


title: Dnmt1KOd2.28.G03


title: Dnmt1KOd2.77.F10


title: Dnmt1KOd2.44.G01


title: Dnmt1KOd2.60.F09


title: Dnmt1KOd2.18.F08


title: Dnmt1KOd2.74.F11


title: Dnmt1KOd2.32.G02


title: Dnmt1KOd2.7.F06


title: human lymphocyte- before activate-2

city: Fukuoka

first: Akiko

last: Fujimura

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Cancer Therapy and Research

institute: Graduate School of Medical Sciences Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: human lymphocyte before activate, healthy volunteer #2

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cell

value: lymphocytes


title: Dnmt1KOd2.63.F04


title: Dnmt1KOd2.31.F02


title: Dnmt1KOd2.82.F05


title: Dnmt1KOd2.62.E11


title: Dnmt1KOd2.70.F03


title: Dnmt1KOd2.35.E10


title: Dnmt1KOd2.86.E08


title: Dnmt1KOd2.12.E09


title: Dnmt1KOd2.14.E07


title: Dnmt1KOd2.11.G09


title: Dnmt1KOd2.1.E05


title: Dnmt1KOd2.58.E03


title: Dnmt1KOd2.59.D12


title: Dnmt1KOd2.6.D09


title: Dnmt1KOd2.80.E01


title: Dnmt1KOd2.46.F07


title: Dnmt1KOd2.79.F12


title: Dnmt1KOd2.22.D10


title: Dnmt1KOd2.2.E02


title: Dnmt1KOd2.81.E06


title: Dnmt1KOd2.42.D02


title: Dnmt1KOd2.72.D03


title: Dnmt1KOd2.29.E04


title: Dnmt1KOd2.24.C11


title: Dnmt1KOd2.16.F01


title: Dnmt1KOd2.84.D06


title: Dnmt1KOd2.39.C08


title: Dnmt1KOd2.13.D08


title: Dnmt1KOd2.10.D04


title: Dnmt1KOd2.76.D01


title: Dnmt1KOd2.73.C12


title: Dnmt1KOd2.38.C09


title: Dnmt1KOd2.3.C06


title: Dnmt1KOd2.85.C05


title: Dnmt1KOd2.93.C04


title: Dnmt1KOd2.55.C01


title: Dnmt1KOd2.19.C10


title: Dnmt1KOd2.69.C02


title: Dnmt1KOd2.95.C03


title: Dnmt1KOd2.17.B11


title: Dnmt1KOd2.34.B12


title: Dnmt1KOd2.25.B08


title: Dnmt1KOd2.33.D05


title: Dnmt1KOd2.49.B06


title: Dnmt1KOd2.66.B07


title: Dnmt1KOd2.41.C07


title: Dnmt1KOd2.83.B05


title: Dnmt1KOd2.48.B10


title: Dnmt1KOd2.30.B04


title: Dnmt1KOd2.68.B03


title: Dnmt1KOd2.94.B01


title: Dnmt1KOd2.57.A12


title: Dnmt1KOd2.78.A08


title: Dnmt1KOd2.26.A11


title: Dnmt1KOd2.15.A10


title: Dnmt1KOd2.37.A05


title: Dnmt1KOd2.9.A04


title: Dnmt1KOd2.87.A09


title: Dnmt1KOd2.88.A06


title: Dnmt1KOd2.43.A07


title: Dnmt1KOd2.91.A03


title: Dnmt1KOd0.70.H06

description:
day 0 dox+ DNMT1 KO
Differentiation_Timecourse_TPM.txt

value: day 0


title: Dnmt1KOd2.4.A02


title: Dnmt1KOd0.22.H03


title: Dnmt1KOd2.65.B09


title: Dnmt1KOd0.1.H09


title: Dnmt1KOd2.8.A01


title: Dnmt1KOd0.63.H12


title: Dnmt1KOd0.74.G10


title: Dnmt1KOd0.10.G05


title: Dnmt1KOd0.25.G04


title: Dnmt1KOd0.30.G01


title: Dnmt1KOd0.43.G09


title: Dnmt1KOd0.58.H07


title: Dnmt1KOd0.77.G03


title: Dnmt1KOd0.9.H05


title: Dnmt1KOd0.50.H02


title: Dnmt1KOd0.45.G11


title: Dnmt1KOd0.17.G08


title: Dnmt1KOd0.24.G12


title: Dnmt1KOd0.93.F07


title: Dnmt1KOd0.80.H01


title: Dnmt1KOd2.53.B02


title: Dnmt1KOd0.6.G02


title: Dnmt1KOd0.49.G06


title: Dnmt1KOd0.3.G07


title: Dnmt1KOd0.84.F04


title: Dnmt1KOd0.19.F01


title: Dnmt1KOd0.31.F12


title: Dnmt1KOd0.13.F02


title: Dnmt1KOd0.38.E06


title: Dnmt1KOd0.41.F09


title: Dnmt1KOd0.54.E08


title: Dnmt1KOd0.14.F08


title: Dnmt1KOd0.8.F05


title: Dnmt1KOd0.78.F06


title: Dnmt1KOd0.5.F10


title: Dnmt1KOd0.81.E09


title: Dnmt1KOd0.65.E12


title: Dnmt1KOd0.2.E05


title: Dnmt1KOd0.85.E10


title: Dnmt1KOd0.56.E04


title: Dnmt1KOd0.52.E11


title: Dnmt1KOd0.28.F03


title: Dnmt1KOd0.71.E03


title: Dnmt1KOd0.15.D09


title: Dnmt1KOd0.96.E07


title: Dnmt1KOd0.44.E02


title: Dnmt1KOd0.29.E01


title: Dnmt1KOd0.47.F11


title: Dnmt1KOd0.4.D10


title: Dnmt1KOd0.90.D11


title: Dnmt1KOd0.42.D07


title: Dnmt1KOd0.20.D08


title: Dnmt1KOd0.92.D06


title: Dnmt1KOd0.69.D05


title: Dnmt1KOd0.88.D01


title: Dnmt1KOd0.83.C12


title: Dnmt1KOd0.40.C11


title: Dnmt1KOd0.82.C09


title: Dnmt1KOd0.51.C10


title: Dnmt1KOd0.21.D04


title: Dnmt1KOd0.48.C04


title: Dnmt1KOd0.32.C07


title: Dnmt1KOd0.12.C03


title: Dnmt1KOd0.89.C05


title: Dnmt1KOd0.53.B12


title: Dnmt1KOd0.33.C01


title: Dnmt1KOd0.62.B11


title: Dnmt1KOd0.7.D12


title: Dnmt1KOd0.18.B10


title: Dnmt1KOd0.95.B06


title: Dnmt1KOd0.57.B08


title: Dnmt1KOd0.11.B04


title: Dnmt1KOd0.36.B03


title: Dnmt1KOd0.61.B09


title: Dnmt1KOd0.72.D03


title: Dnmt1KOd0.91.D02


title: Dnmt1KOd0.68.B07


title: Dnmt1KOd0.75.C08


title: Dnmt1KOd0.86.A11


title: Dnmt1KOd0.23.A12


title: Dnmt1KOd0.55.B01


title: Dnmt1KOd0.67.B02


title: Dnmt1KOd0.76.A10


title: Dnmt1KOd0.94.A08


title: Dnmt1KOd0.26.A07


title: Dnmt1KOd0.46.C06


title: Dnmt1KOd0.37.A05


title: Dnmt1KOd0.60.A03


title: Dnmt1KOd0.27.A06


title: dMEd5.95.P22

description:
dME differentiation 5 day replicate 1
Differentiation_Timecourse_TPM.txt

value: day 5

value: WT


title: Dnmt1KOd0.59.A01


title: dMEd5.96.P22


title: Dnmt1KOd0.87.A04


title: Dnmt1KOd0.66.A02


title: dMEd5.94.P22


title: dMEd5.93.P22


title: dMEd5.92.P22


title: dMEd5.87.P22


title: dMEd5.91.P22


title: dMEd5.83.P22


title: dMEd5.89.P22


title: dMEd5.90.P22


title: dMEd5.82.P22


title: dMEd5.86.P22


title: dMEd5.84.P22


title: dMEd5.79.P22


title: Dnmt1KOd0.79.A09


title: dMEd5.81.P22


title: dMEd5.77.P22


title: dMEd5.80.P22


title: dMEd5.72.P22


title: dMEd5.73.P22


title: dMEd5.74.P22


title: dMEd5.70.P22


title: dMEd5.69.P22


title: dMEd5.68.P22


title: dMEd5.67.P22


title: dMEd5.65.P22


title: dMEd5.66.P22


title: dMEd5.63.P22


title: dMEd5.64.P22


title: dMEd5.88.P22


title: dMEd5.62.P22


title: dMEd5.61.P22


title: dMEd5.59.P22


title: dMEd5.78.P22


title: dMEd5.57.P22


title: dMEd5.58.P22


title: dMEd5.56.P22


title: dMEd5.55.P22


title: dMEd5.49.P22


title: dMEd5.54.P22


title: dMEd5.71.P22


title: dMEd5.51.P22


title: dMEd5.50.P22


title: dMEd5.53.P22


title: dMEd5.75.P22


title: dMEd5.46.P22


title: dMEd5.60.P22


title: dMEd5.47.P22


title: dMEd5.41.P22


title: dMEd5.48.P22


title: dMEd5.42.P22


title: dMEd5.43.P22


title: dMEd5.45.P22


title: dMEd5.37.P22


title: dMEd5.30.P22


title: dMEd5.39.P22


title: dMEd5.35.P22


title: dMEd5.34.P22


title: dMEd5.38.P22


title: dMEd5.32.P22


title: dMEd5.36.P22


title: dMEd5.31.P22


title: dMEd5.27.P22


title: dMEd5.26.P22


title: dMEd5.22.P22


title: dMEd5.40.P22


title: dMEd5.25.P22


title: dMEd5.28.P22


title: dMEd5.29.P22


title: dMEd5.44.P22


title: dMEd5.21.P22


title: dMEd5.24.P22


title: dMEd5.20.P22


title: dMEd5.16.P22


title: dMEd5.33.P22


title: dMEd5.18.P22


title: dMEd5.19.P22


title: dMEd5.13.P22


title: dMEd5.12.P22


title: dMEd5.14.P22


title: dMEd5.6.P22


title: dMEd5.15.P22


title: dMEd5.8.P22


title: dMEd5.11.P22


title: dMEd5.4.P22


title: dMEd5.23.P22


title: dMEd5.9.P22


title: dMEd5.7.P22


title: dMEd5.5.P22


title: dMEd5.2.P22


title: dECd5.96.P22

description:
dEC differentiation 5 day replicate 1
Differentiation_Timecourse_TPM.txt


title: dECd5.95.P22


title: dMEd5.1.P22


title: dECd5.93.P22


title: dECd5.94.P22


title: dECd5.92.P22


title: dECd5.90.P22


title: dECd5.89.P22


title: dECd5.87.P22


title: dECd5.88.P22


title: dMEd5.17.P22


title: dECd5.85.P22


title: dECd5.84.P22


title: dECd5.86.P22


title: dECd5.81.P22


title: dECd5.83.P22


title: dECd5.80.P22


title: dECd5.77.P22


title: dECd5.78.P22


title: dECd5.73.P22


title: dECd5.74.P22


title: dMEd5.3.P22


title: dECd5.75.P22


title: dECd5.70.P22


title: dECd5.68.P22


title: dECd5.76.P22


title: dECd5.65.P22


title: dECd5.67.P22


title: dECd5.66.P22


title: dECd5.64.P22


title: dECd5.61.P22


title: dECd5.60.P22


title: dECd5.63.P22


title: dECd5.59.P22


title: dECd5.58.P22


title: dECd5.56.P22


title: dECd5.52.P22


title: dECd5.55.P22


title: dECd5.82.P22


title: dECd5.50.P22


title: dECd5.72.P22


title: dECd5.51.P22


title: dECd5.71.P22


title: dECd5.46.P22


title: dECd5.44.P22


title: dECd5.47.P22


title: dECd5.45.P22


title: Dnmt1KOd0.64.C02


title: dECd5.41.P22


title: dECd5.39.P22


title: dECd5.49.P22


title: dECd5.42.P22


title: dECd5.38.P22


title: dECd5.37.P22


title: dECd5.35.P22


title: dECd5.62.P22


title: dECd5.36.P22


title: dECd5.34.P22


title: dECd5.33.P22


title: dECd5.32.P22


title: dECd5.54.P22


title: dECd5.31.P22


title: dECd5.28.P22


title: dECd5.29.P22


title: dECd5.26.P22


title: dECd5.25.P22


title: dECd5.22.P22


title: dECd5.48.P22


title: dECd5.24.P22


title: dECd5.20.P22


title: dECd5.40.P22


title: dECd5.19.P22


title: dECd5.17.P22


title: dECd5.13.P22


title: dECd5.14.P22


title: dECd5.12.P22


title: dECd5.11.P22


title: dECd5.15.P22


title: dECd5.10.P22


title: dECd5.8.P22


title: dECd5.9.P22


title: dECd5.5.P22


title: dECd5.6.P22


title: dECd5.4.P22


title: dECd5.3.P22


title: dECd5.1.P22


title: hu64_21.49.H11

description:
HUES64 DKO ES cells
Differentiation_Timecourse_TPM.txt

value: HUES64 DKO clone #21

value: DKO


title: dECd5.27.P22


title: hu64_21.13.H12


title: dECd5.2.P22


title: hu64_21.94.H10


title: hu64_21.17.H09


title: dECd5.21.P22


title: hu64_21.4.H07


title: hu64_21.57.H06


title: hu64_21.66.H08


title: hu64_21.18.H05


title: hu64_21.87.H04


title: dECd5.7.P22


title: hu64_21.28.G12


title: hu64_21.16.G11


title: hu64_21.34.G10


title: hu64_21.20.G09


title: hu64_21.61.G07


title: hu64_21.3.H03


title: hu64_21.37.G08


title: hu64_21.24.H02


title: hu64_21.77.G05


title: hu64_21.90.G03


title: hu64_21.39.G02


title: hu64_21.63.G01


title: hu64_21.2.H01


title: hu64_21.56.F12


title: hu64_21.10.F10


title: hu64_21.11.F08


title: hu64_21.14.F07


title: hu64_21.91.F06


title: hu64_21.44.F05


title: hu64_21.43.F09


title: hu64_21.88.F04


title: hu64_21.50.F03


title: hu64_21.69.F02


title: hu64_21.27.E12


title: hu64_21.40.E11


title: hu64_21.9.E10


title: hu64_21.81.F01


title: hu64_21.72.E08


title: hu64_21.48.E09


title: hu64_21.85.G06


title: hu64_21.31.E06


title: hu64_21.22.G04


title: hu64_21.68.E05


title: hu64_21.76.E04


title: hu64_21.70.D09


title: hu64_21.47.E01


title: hu64_21.73.D12


title: hu64_21.29.D10


title: hu64_21.26.E03


title: hu64_21.95.D07


title: hu64_21.65.D08


title: hu64_21.42.D06


title: hu64_21.51.D03


title: hu64_21.86.D05


title: hu64_21.78.D04


title: hu64_21.52.D02


title: hu64_21.45.C10


title: hu64_21.93.C07


title: hu64_21.80.C11


title: hu64_21.36.C12


title: hu64_21.19.C09


title: hu64_21.30.E07


title: hu64_21.6.C08


title: hu64_21.60.D01


title: hu64_21.46.C04


title: hu64_21.83.C06


title: hu64_21.38.C05


title: hu64_21.54.B12


title: hu64_21.64.C03


title: hu64_21.25.C01


title: hu64_21.41.C02


title: hu64_21.55.E02


title: hu64_21.7.B11


title: hu64_21.33.B09


title: hu64_21.92.B10


title: hu64_21.71.B08


title: hu64_21.74.B07


title: hu64_21.8.B05


title: hu64_21.84.B06


title: hu64_21.12.B04


title: hu64_21.82.B02


title: hu64_21.23.B03


title: hu64_21.75.B01


title: hu64_21.32.A10


title: hu64_21.59.A11


title: hu64_21.62.A12


title: hu64_21.79.A06


title: hu64_21.5.A07


title: hu64_21.1.A09


title: hu64.58.H09

description:
HUES64 ES cells replicate 1
Differentiation_Timecourse_TPM.txt


title: hu64.48.H07


title: hu64.62.H03


title: hu64.85.H10


title: hu64_21.21.A01


title: hu64_21.89.A04


title: hu64.75.H11


title: hu64.53.H12


title: hu64.24.H01


title: hu64.71.H02


title: hu64_21.15.A03


title: hu64_21.35.A05


title: hu64.16.H05


title: hu64.44.G10


title: hu64.7.G08


title: hu64.31.G05


title: hu64.90.G06


title: hu64.65.G07


title: hu64_21.67.A02


title: hu64.39.G04


title: hu64.49.G03


title: hu64.8.G01


title: hu64.51.F12


title: hu64.37.G02


title: hu64.6.F10


title: hu64.63.F11


title: hu64.55.F09


title: hu64.29.F02


title: hu64.11.F05


title: hu64.40.F08


title: hu64.2.F03


title: hu64.13.G09


title: hu64.21.E10


title: hu64.93.E11


title: hu64.80.F01


title: hu64.22.F06


title: hu64.88.F07


title: hu64.12.E07


title: hu64.57.E09


title: hu64.66.G11


title: hu64.82.E12


title: hu64.74.E06


title: hu64.33.E05


title: hu64.69.G12


title: hu64.81.E03


title: hu64.28.E02


title: hu64.59.D12


title: hu64.79.E01


title: hu64.1.E04


title: hu64.17.D11


title: hu64.25.D09


title: hu64.54.D10


title: hu64.94.D08


title: hu64.61.D07


title: hu64.3.E08


title: hu64.43.D05


title: hu64.89.D03


title: hu64.30.C11


title: hu64.87.D04


title: hu64.84.C12


title: hu64.19.C06


title: hu64.23.D02


title: hu64.41.C07


title: hu64.86.C08


title: hu64.56.C10


title: hu64.76.C03


title: hu64.46.C04


title: hu64.32.C02


title: hu64.68.B06


title: hu64.78.B08


title: hu64.77.B04


title: hu64.45.C01


title: hu64.9.B07


title: hu64.20.B12


title: hu64.73.B03


title: hu64.27.B11


title: hu64.42.B01


title: hu64.52.B05


title: hu64.70.D06


title: hu64.38.A11


title: hu64.91.A10


title: hu64.47.C09


title: hu64.60.A09


title: hu64.64.C05


title: hu64.95.A08


title: hu64.14.A07


title: hu64.10.A06


title: hu64.5.A05


title: hu64.50.A03


title: hu64.34.A04


title: hu64.83.A02


title: hu64_2.94.H07

description:
HUES64 ES cells replicate 2
Differentiation_Timecourse_TPM.txt


title: hu64_2.47.H08


title: hu64_2.41.H09


title: hu64_2.1.H02


title: hu64_2.31.H01


title: hu64.72.B02


title: hu64_2.28.H04


title: hu64_2.6.H06


title: hu64_2.24.G11


title: hu64_2.55.G09


title: hu64_2.70.G08


title: hu64_2.64.G12


title: hu64_2.43.G07


title: hu64.15.A12


title: hu64_2.67.G06


title: hu64_2.84.G05


title: hu64_2.75.G04


title: hu64_2.16.G02


title: hu64_2.37.G03


title: hu64_2.92.H12


title: hu64_2.18.G01


title: hu64_2.11.F12


title: hu64_2.30.F07


title: hu64_2.82.F10


title: hu64_2.17.F11


title: hu64_2.56.F08


title: hu64_2.44.F09


title: hu64_2.68.H03


title: hu64_2.63.F06


title: hu64_2.62.H05


title: hu64_2.33.F03


title: hu64_2.21.F04


title: hu64_2.29.F05


title: hu64_2.23.F02


title: hu64_2.58.E10


title: hu64_2.7.F01


title: hu64_2.40.E06


title: hu64_2.14.E08


title: hu64_2.50.E12


title: hu64_2.89.E05


title: hu64_2.69.E02


title: hu64_2.85.E03


title: hu64_2.60.E01


title: hu64_2.22.E07


title: hu64_2.4.D11


title: hu64_2.26.D10


title: hu64_2.19.D12


title: hu64_2.77.D08


title: hu64_2.71.D09


title: hu64_2.42.D05


title: hu64_2.51.D03


title: hu64_2.32.D06


title: hu64_2.61.D04


title: hu64_2.2.D07


title: hu64_2.13.D01


title: hu64_2.53.E11


title: hu64_2.46.C12


title: hu64_2.49.C09


title: hu64_2.54.C08


title: hu64_2.10.C10


title: hu64_2.80.C07


title: hu64_2.81.C11


title: hu64_2.74.C03


title: hu64_2.65.C04


title: hu64_2.25.C05


title: hu64_2.36.E04


title: hu64_2.95.C02


title: hu64_2.79.C01


title: hu64_2.20.B12


title: hu64_2.66.B11


title: hu64_2.88.B10


title: hu64_2.83.B09


title: hu64_2.12.B08


title: hu64_2.45.D02


title: hu64_2.52.B07


title: hu64_2.39.B04


title: hu64_2.34.B06


title: hu64_2.90.B05


title: hu64_2.93.B02


title: hu64_2.78.B01


title: hu64_2.72.A12


title: hu64_2.15.A10


title: hu64_2.9.A09


title: hu64_2.57.C06


title: hu64_2.3.A08


title: hu64_2.8.A07


title: hu64_2.59.A06


title: hu64_2.76.A04


title: hu64_2.38.A03


title: hu64_2.35.A05


title: hu64_2.5.A01


title: dECd5_21.15.H09

description:
dEC differentiation 5 day DKO
Differentiation_Timecourse_TPM.txt


title: dECd5_21.84.H08


title: dECd5_21.24.H06


title: dECd5_21.1.H03


title: dECd5_21.9.H05


title: dECd5_21.4.H02


title: hu64_2.91.B03


title: dECd5_21.83.G12


title: dECd5_21.5.H01


title: dECd5_21.93.G11


title: hu64_2.73.A11


title: dECd5_21.88.G09


title: dECd5_21.87.G10


title: dECd5_21.67.G08


title: dECd5_21.85.G04


title: dECd5_21.58.G07


title: dECd5_21.49.G06


title: dECd5_21.6.G05


title: dECd5_21.74.G03


title: dECd5_21.86.G02


title: dECd5_21.36.F12


title: hu64_2.87.A02


title: dECd5_21.77.F09


title: dECd5_21.43.H11


title: dECd5_21.45.H07


title: dECd5_21.78.F10


title: dECd5_21.19.F06


title: dECd5_21.34.F07


title: dECd5_21.71.G01


title: dECd5_21.51.F05


title: dECd5_21.13.F04


title: dECd5_21.7.H04


title: dECd5_21.20.F03


title: dECd5_21.33.F01


title: dECd5_21.64.E12


title: dECd5_21.37.E11


title: dECd5_21.54.E10


title: dECd5_21.91.E08


title: dECd5_21.70.E09


title: dECd5_21.69.E07


title: dECd5_21.29.E06


title: dECd5_21.59.F11


title: dECd5_21.16.E05


title: dECd5_21.25.E01


title: dECd5_21.65.E02


title: dECd5_21.81.F08


title: dECd5_21.95.D12


title: dECd5_21.94.D11


title: dECd5_21.27.D09


title: dECd5_21.47.E03


title: dECd5_21.80.D07


title: dECd5_21.53.D10


title: dECd5_21.90.D04


title: dECd5_21.76.D05


title: dECd5_21.50.D06


title: dECd5_21.2.D03


title: dECd5_21.92.D08


title: dECd5_21.40.D02


title: dECd5_21.38.D01


title: dECd5_21.39.C12


title: dECd5_21.32.C11


title: dECd5_21.30.F02


title: dECd5_21.72.C10


title: dECd5_21.82.C08


title: dECd5_21.41.C09


title: dECd5_21.42.C05


title: dECd5_21.28.C06


title: dECd5_21.52.E04


title: dECd5_21.22.C04


title: dECd5_21.17.C07


title: dECd5_21.66.C02


title: dECd5_21.46.C01


title: dECd5_21.61.B10


title: dECd5_21.11.B11


title: dECd5_21.62.B12


title: dECd5_21.73.B08


title: dECd5_21.79.B07


title: dECd5_21.35.B05


title: dECd5_21.23.B04


title: dECd5_21.12.B06


title: dECd5_21.31.B03


title: dECd5_21.44.B02


title: dECd5_21.89.A11


title: dECd5_21.57.B01


title: dECd5_21.63.A12


title: dECd5_21.75.A10


title: dECd5_21.68.A09


title: dECd5_21.55.A07


title: dECd5_21.10.A05


title: dECd5_21.60.A08


title: dECd5_21.8.A03


title: dECd5_21.14.C03


title: dECd5_21.3.A04


title: dECd5_21.21.A06


title: dECd5_21.26.A01


title: dMEd5_21.95.ME

description:
dME differentiation 5 day DKO
Differentiation_Timecourse_TPM.txt


title: dMEd5_21.94.ME


title: dMEd5_21.96.ME


title: dMEd5_21.93.ME


title: dECd5_21.56.A02


title: dMEd5_21.92.ME


title: dMEd5_21.91.ME


title: dMEd5_21.89.ME


title: dECd5_21.48.B09


title: dMEd5_21.90.ME


title: dMEd5_21.86.ME


title: dMEd5_21.83.ME


title: dMEd5_21.82.ME


title: dMEd5_21.85.ME


title: dMEd5_21.84.ME


title: dMEd5_21.81.ME


title: dMEd5_21.80.ME


title: dMEd5_21.79.ME


title: dMEd5_21.76.ME


title: dMEd5_21.77.ME


title: dMEd5_21.78.ME


title: dMEd5_21.74.ME


title: dMEd5_21.69.ME


title: dMEd5_21.68.ME


title: dMEd5_21.72.ME


title: dMEd5_21.75.ME


title: dMEd5_21.66.ME


title: dMEd5_21.65.ME


title: dMEd5_21.71.ME


title: dMEd5_21.70.ME


title: dMEd5_21.67.ME


title: dMEd5_21.73.ME


title: dMEd5_21.64.ME


title: dMEd5_21.63.ME


title: dMEd5_21.87.ME


title: dMEd5_21.60.ME


title: dMEd5_21.58.ME


title: dMEd5_21.88.ME


title: dMEd5_21.61.ME


title: dMEd5_21.62.ME


title: dMEd5_21.54.ME


title: dMEd5_21.56.ME


title: dMEd5_21.53.ME


title: dMEd5_21.52.ME


title: dMEd5_21.51.ME


title: dMEd5_21.50.ME


title: dMEd5_21.49.ME


title: dMEd5_21.55.ME


title: dMEd5_21.46.ME


title: dMEd5_21.48.ME


title: dMEd5_21.45.ME


title: dMEd5_21.44.ME


title: dMEd5_21.42.ME


title: dMEd5_21.41.ME


title: dMEd5_21.43.ME


title: dMEd5_21.40.ME


title: dMEd5_21.37.ME


title: dMEd5_21.38.ME


title: dMEd5_21.39.ME


title: dMEd5_21.30.ME


title: dMEd5_21.32.ME


title: dMEd5_21.26.ME


title: dMEd5_21.36.ME


title: dMEd5_21.29.ME


title: dMEd5_21.31.ME


title: dMEd5_21.27.ME


title: dMEd5_21.33.ME


title: dMEd5_21.25.ME


title: dMEd5_21.24.ME


title: dMEd5_21.23.ME


title: dMEd5_21.22.ME


title: dMEd5_21.20.ME


title: dMEd5_21.19.ME


title: dMEd5_21.34.ME


title: dMEd5_21.28.ME


title: dMEd5_21.15.ME


title: dMEd5_21.13.ME


title: dMEd5_21.14.ME


title: dMEd5_21.17.ME


title: dMEd5_21.10.ME


title: dMEd5_21.8.ME


title: dMEd5_21.6.ME


title: dMEd5_21.5.ME


title: dMEd5_21.7.ME


title: dMEd5_21.21.ME


title: dMEd5_21.1.ME


title: hu64_139.15.H07

description:
HUES64 3AKO ES cells
Differentiation_Timecourse_TPM.txt

value: HUES64 3AKO clone #139


title: hu64_139.63.H05


title: hu64_139.91.H08


title: hu64_139.50.H03


title: dMEd5_21.18.ME


title: hu64_139.2.H11


title: dMEd5_21.3.ME


title: hu64_139.61.H06


title: dMEd5_21.16.ME


title: hu64_139.83.G12


title: hu64_139.25.H01


title: hu64_139.55.H09


title: hu64_139.74.G11


title: hu64_139.48.H10


title: hu64_139.62.G10


title: dMEd5_21.12.ME


title: hu64_139.32.H04


title: hu64_139.29.H02


title: hu64_139.7.G08


title: hu64_139.85.G06


title: hu64_139.16.G04


title: hu64_139.4.G05


title: hu64_139.84.G03


title: hu64_139.6.G02


title: hu64_139.65.G01


title: hu64_139.73.F09


title: hu64_139.49.F12


title: hu64_139.78.F07


title: hu64_139.76.F06


title: hu64_139.71.F11


title: hu64_139.24.F05


title: hu64_139.69.G09


title: hu64_139.39.F01


title: hu64_139.82.E10


title: hu64_139.20.E07


title: hu64_139.19.E12


title: hu64_139.90.F03


title: hu64_139.89.E08


title: hu64_139.72.E09


title: dMEd5_21.11.ME


title: hu64_139.70.F02


title: hu64_139.51.E06


title: hu64_139.88.E05


title: dMEd5_21.2.ME


title: hu64_139.44.E04


title: hu64_139.80.E02


title: hu64_139.8.E03


title: hu64_139.43.G07


title: hu64_139.28.E01


title: hu64_139.22.F10


title: hu64_139.27.D12


title: hu64_139.17.D10


title: hu64_139.45.H12


title: hu64_139.12.F04


title: hu64_139.35.D11


title: hu64_139.34.E11


title: hu64_139.9.D06


title: hu64_139.18.D08


title: hu64_139.54.D04


title: hu64_139.46.D05


title: hu64_139.68.D09


title: hu64_139.94.D03


title: hu64_139.21.C11


title: hu64_139.87.C12


title: hu64_139.93.D01


title: hu64_139.60.C10


title: hu64_139.33.C09


title: hu64_139.95.C08


title: hu64_139.86.C04


title: hu64_139.40.C03


title: hu64_139.23.C07


title: hu64_139.37.C02


title: hu64_139.53.C01


title: hu64_139.59.B11


title: hu64_139.38.B12


title: hu64_139.92.B09


title: hu64_139.81.B08


title: hu64_139.5.B07


title: hu64_139.31.B06


title: hu64_139.56.B10


title: hu64_139.66.B04


title: hu64_139.26.B03


title: hu64_139.67.B05


title: hu64_139.13.B01


title: hu64_139.77.A10


title: hu64_139.30.B02


title: hu64_139.79.A11


title: hu64_139.52.D02


title: hu64_139.11.C05


title: hu64_139.3.A05


title: hu64_139.75.C06


title: hu64_139.42.A04


title: hu64_139.36.A07


title: hu64_139.41.A09


title: hu64_139.1.A08


title: hu64_139.47.A12


title: hu64_139.64.A03


title: hu64_139.14.A01


title: dMEd5_139.96.ME2

description:
dME differentiation 5 day 3AKO
Differentiation_Timecourse_TPM.txt


title: dMEd5_139.95.ME2


title: dMEd5_139.93.ME2


title: dMEd5_139.94.ME2


title: dMEd5_139.92.ME2


title: dMEd5_139.91.ME2


title: dMEd5_139.88.ME2


title: dMEd5_139.85.ME2


title: hu64_139.10.A06


title: dMEd5_139.84.ME2


title: dMEd5_139.83.ME2


title: dMEd5_139.89.ME2


title: hu64_139.58.A02


title: dMEd5_139.82.ME2


title: dMEd5_139.80.ME2


title: dMEd5_139.78.ME2


title: dMEd5_139.76.ME2


title: dMEd5_139.79.ME2


title: dMEd5_139.81.ME2


title: dMEd5_139.74.ME2


title: dMEd5_139.71.ME2


title: dMEd5_139.73.ME2


title: dMEd5_139.77.ME2


title: dMEd5_139.72.ME2


title: dMEd5_139.69.ME2


title: dMEd5_139.70.ME2


title: dMEd5_139.66.ME2


title: dMEd5_139.65.ME2


title: dMEd5_139.68.ME2


title: dMEd5_139.64.ME2


title: dMEd5_139.90.ME2


title: dMEd5_139.87.ME2


title: dMEd5_139.63.ME2


title: dMEd5_139.86.ME2


title: dMEd5_139.62.ME2


title: dMEd5_139.61.ME2


title: dMEd5_139.59.ME2


title: dMEd5_139.58.ME2


title: dMEd5_139.60.ME2


title: dMEd5_139.56.ME2


title: dMEd5_139.54.ME2


title: dMEd5_139.47.ME2


title: dMEd5_139.49.ME2


title: dMEd5_139.50.ME2


title: dMEd5_139.51.ME2


title: dMEd5_139.67.ME2


title: dMEd5_139.44.ME2


title: dMEd5_139.46.ME2


title: dMEd5_139.45.ME2


title: dMEd5_139.41.ME2


title: dMEd5_139.39.ME2


title: dMEd5_139.75.ME2


title: dMEd5_139.38.ME2


title: dMEd5_139.37.ME2


title: dMEd5_139.35.ME2


title: dMEd5_139.36.ME2


title: dMEd5_139.34.ME2


title: dMEd5_139.33.ME2


title: dMEd5_139.57.ME2


title: dMEd5_139.43.ME2


title: dMEd5_139.53.ME2


title: dMEd5_139.30.ME2


title: dMEd5_139.48.ME2


title: dMEd5_139.32.ME2


title: dMEd5_139.29.ME2


title: dMEd5_139.31.ME2


title: dMEd5_139.28.ME2


title: dMEd5_139.26.ME2


title: dMEd5_139.42.ME2


title: dMEd5_139.24.ME2


title: dMEd5_139.23.ME2


title: dMEd5_139.40.ME2


title: dMEd5_139.25.ME2


title: dMEd5_139.21.ME2


title: dMEd5_139.20.ME2


title: dMEd5_139.17.ME2


title: dMEd5_139.22.ME2


title: dMEd5_139.19.ME2


title: dMEd5_139.52.ME2


title: dMEd5_139.16.ME2


title: dMEd5_139.18.ME2


title: dMEd5_139.14.ME2


title: dMEd5_139.13.ME2


title: dMEd5_139.12.ME2


title: dMEd5_139.11.ME2


title: dMEd5_139.10.ME2


title: dMEd5_139.9.ME2


title: dMEd5_139.27.ME2


title: dMEd5_139.7.ME2


title: dMEd5_139.5.ME2


title: dMEd5_139.6.ME2


title: dMEd5_139.2.ME2


title: dMEd5_139.4.ME2


title: dMEd5_139.3.ME2


title: dMEd5_139.1.ME2


title: dECd5_139.95.EC2

description:
dEC differentiation 5 day 3AKO
Differentiation_Timecourse_TPM.txt


title: dECd5_139.94.EC2


title: dECd5_139.96.EC2


title: dMEd5_139.15.ME2


title: dECd5_139.91.EC2


title: dECd5_139.92.EC2


title: dECd5_139.84.EC2


title: dECd5_139.88.EC2


title: dECd5_139.85.EC2


title: dECd5_139.86.EC2


title: dECd5_139.89.EC2


title: dECd5_139.93.EC2


title: dECd5_139.87.EC2


title: dECd5_139.83.EC2


title: dECd5_139.80.EC2


title: dECd5_139.79.EC2


title: dMEd5_139.8.ME2


title: dECd5_139.82.EC2


title: dECd5_139.77.EC2


title: dECd5_139.81.EC2


title: dECd5_139.76.EC2


title: dECd5_139.78.EC2


title: dECd5_139.75.EC2


title: dECd5_139.72.EC2


title: dECd5_139.74.EC2


title: dECd5_139.70.EC2


title: dECd5_139.71.EC2


title: dECd5_139.73.EC2


title: dECd5_139.69.EC2


title: dECd5_139.67.EC2


title: dECd5_139.65.EC2


title: dECd5_139.68.EC2


title: dECd5_139.64.EC2


title: dECd5_139.66.EC2


title: dECd5_139.62.EC2


title: dECd5_139.55.EC2


title: dECd5_139.59.EC2


title: dECd5_139.60.EC2


title: dECd5_139.58.EC2


title: dECd5_139.53.EC2


title: dECd5_139.52.EC2


title: dECd5_139.50.EC2


title: dECd5_139.46.EC2


title: dECd5_139.49.EC2


title: dECd5_139.61.EC2


title: dECd5_139.54.EC2


title: dECd5_139.57.EC2


title: dECd5_139.51.EC2


title: dECd5_139.47.EC2


title: dECd5_139.43.EC2


title: dECd5_139.45.EC2


title: dECd5_139.44.EC2


title: dECd5_139.42.EC2


title: dECd5_139.40.EC2


title: dECd5_139.38.EC2


title: dECd5_139.39.EC2


title: dECd5_139.41.EC2


title: dECd5_139.37.EC2


title: dECd5_139.63.EC2


title: dECd5_139.35.EC2


title: dECd5_139.34.EC2


title: dECd5_139.33.EC2


title: dECd5_139.48.EC2


title: dECd5_139.24.EC2


title: dECd5_139.14.EC2


title: dECd5_139.22.EC2


title: dECd5_139.26.EC2


title: dECd5_139.16.EC2


title: dECd5_139.27.EC2


title: dECd5_139.13.EC2


title: dECd5_139.31.EC2


title: dECd5_139.25.EC2


title: dECd5_139.28.EC2


title: dECd5_139.23.EC2


title: dECd5_139.30.EC2


title: dECd5_139.18.EC2


title: dECd5_139.7.EC2


title: dECd5_139.11.EC2


title: dECd5_139.17.EC2


title: dECd5_139.32.EC2


title: dECd5_139.15.EC2


title: dECd5_139.8.EC2


title: dECd5_139.9.EC2


title: dECd5_139.10.EC2


title: dECd5_139.29.EC2


title: dECd5_139.36.EC2


title: dECd5_139.6.EC2


title: dECd5_139.12.EC2


title: dECd5_139.4.EC2


title: dECd5_139.5.EC2


title: dECd5_139.20.EC2


title: dECd5_139.21.EC2


title: dECd5_139.3.EC2


title: dECd5_139.1.EC2


title: dECd5_139.2.EC2


title: IFN gamma treated rep1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Reads were trimmed using cutadapt, mapped using Hisat2 and reads were counted using featureCounts.
miRNA reads were trimmed using cutadapt, mapped  against miRBase v21 and reads were counted using a custom script.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for RNA-seq and normalized counts for miRNA-seq.

source_name: T98G_IFN gamma treated

growth_protocol: T98G cells (ATCC-CRL-1690) were grown in EMEM with 10% FBS. Cells were maintained at 37°C and 5% CO2.

extract_protocol:
RNA from T98G cells and primary tumor samples were extracted with TRIzol.
RNA-seq libraries were prepared using NEBNext small RNA library preparation kit (NEB E7330) .

treatment_protocol: For type I interferon treatment, cells were treated with universal type I IFN a (PBL assay science, 11200) at 100 U/ml final concentration for 6 hrs. For type II interferon treatment, cells were treated with IFN-γ (SRP3058) for 48 hr at 30 ng/ml final concentration.

tag: cancer type

value: Glioblastoma

tag: tissue source

value: Brain

tag: treatment

value: IFN gamma treatment


title: IFN gamma treated rep2


title: MOLM13 Daunorubicin KO_rep2

city: BOSTON

first: Benjamin

middle: Levine

last: Ebert

state: MASSACHUSETTS

address: 450 BROOKLINE AVENUE

department: Medical Oncology

institute: DANA-FARBER CANCER INSTITUTE

data_processing:
Fastq files were aligned to hg19 using STAR
Transcript counts per gene were quantified with STAR and RSEM
Normalized counts per million (CPM) and differential expression analysis was carried out by EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing the quantity of transcript reads per gene

source_name: Acute myeloid leukemia cell line

growth_protocol: K562 and MOLM13 cell lines were were cultured in RPMI, 100 U/ml penicillin and 100 mg/ml streptomycin with 10 or 20% FBS, respectively,

extract_protocol:
0.5x10e6 cells were collected, washed with ice-cold PBS followed by total RNA extraction using RNeasy kit (Qiagen, #74106). The quality of extracted RNA was determined using RNA ScreenTape (Agilent). RINe values were always >8.0. RNA was quantified by Qubit (ThermoFisher).
500 ng of RNA was used to prepare Illumina-compatible 3’-end sequencing libraries using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and then sequenced using a NextSeq™ 550 Sequencing System (Illumina) to obtain single-end reads.

treatment_protocol: K562 were treated with 100 nM daunorubicin for 24 hours. MOLM13 were treated with100 nM daunorubicin for 6 hours. Control K562 or MOLM13 cells were treated with DMSO.

value: Daunorubicin

value: KO


title: MOLM13 Daunorubicin WT_rep2


title: MOLM13 Daunorubicin KO_rep1


title: MOLM13 Daunorubicin KO_rep3


title: MOLM13 Daunorubicin R282W_rep2


title: MOLM13 Daunorubicin R273H_rep3


title: MOLM13 Daunorubicin R248Q_rep2


title: MOLM13 Daunorubicin WT_rep1


title: MOLM13 Daunorubicin M237I_rep3


title: MOLM13 Daunorubicin R248Q_rep1


title: MOLM13 Daunorubicin M237I_rep1


title: MOLM13 Daunorubicin M237I_rep2


title: MOLM13 Daunorubicin R273H_rep1


title: MOLM13 Daunorubicin Y220C_rep2


title: MOLM13 Daunorubicin R273H_rep2


title: MOLM13 Daunorubicin R248Q_rep3


title: MOLM13 Daunorubicin Y220C_rep3


title: MOLM13 Daunorubicin R175H_rep3


title: MOLM13 Daunorubicin Y220C_rep1


title: MOLM13 Daunorubicin R175H_rep2


title: MOLM13 Daunorubicin R282W_rep3


title: MOLM13 Daunorubicin R282W_rep1


title: MOLM13 Daunorubicin R175H_rep1


title: MOLM13 Daunorubicin WT_rep3


title: MOLM13 DMSO WT_rep2

value: DMSO


title: MOLM13 DMSO WT_rep1


title: MOLM13 DMSO WT_rep3


title: MOLM13 DMSO KO_rep3


title: MOLM13 DMSO KO_rep2


title: MOLM13 DMSO KO_rep1


title: MOLM13 DMSO R282W_rep3


title: MOLM13 DMSO R282W_rep2


title: MOLM13 DMSO R273H_rep3


title: MOLM13 DMSO R282W_rep1


title: MOLM13 DMSO R273H_rep1


title: MOLM13 DMSO M237I_rep3


title: MOLM13 DMSO R248Q_rep3


title: MOLM13 DMSO R248Q_rep2


title: MOLM13 DMSO R248Q_rep1


title: MOLM13 DMSO M237I_rep1


title: MOLM13 DMSO R175H_rep1


title: MOLM13 DMSO Y220C_rep1


title: MOLM13 DMSO Y220C_rep2


title: MOLM13 DMSO R175H_rep3


title: K562 Daunorubicin WT_rep2


title: K562 Daunorubicin KO_rep2


title: K562 Daunorubicin KO_rep3


title: MOLM13 DMSO R175H_rep2


title: MOLM13 DMSO M237I_rep2


title: K562 Daunorubicin WT_rep3


title: K562 Daunorubicin WT_rep1


title: K562 Daunorubicin KO_rep1


title: K562 Daunorubicin R282W_rep3


title: K562 Daunorubicin R282W_rep2


title: K562 Daunorubicin R273H_rep3


title: K562 Daunorubicin R282W_rep1


title: MOLM13 DMSO R273H_rep2


title: K562 Daunorubicin R248Q_rep3


title: K562 Daunorubicin R273H_rep1


title: K562 Daunorubicin R248Q_rep1


title: MOLM13 DMSO Y220C_rep3


title: K562 Daunorubicin M237I_rep3


title: K562 Daunorubicin Y220C_rep2


title: K562 Daunorubicin M237I_rep1


title: K562 Daunorubicin Y220C_rep3


title: K562 Daunorubicin M237I_rep2


title: K562 Daunorubicin R175H_rep3


title: K562 Daunorubicin R175H_rep1


title: K562 DMSO KO_rep1


title: K562 Daunorubicin R175H_rep2


title: K562 DMSO WT_rep2


title: K562 DMSO KO_rep2


title: K562 DMSO WT_rep1


title: K562 DMSO KO_rep3


title: K562 DMSO WT_rep3


title: K562 DMSO R273H_rep3


title: K562 DMSO R273H_rep1


title: K562 DMSO R248Q_rep3


title: K562 DMSO R273H_rep2


title: K562 Daunorubicin R273H_rep2


title: K562 DMSO R248Q_rep1


title: K562 Daunorubicin R248Q_rep2


title: K562 DMSO R248Q_rep2


title: K562 DMSO M237I_rep3


title: K562 DMSO M237I_rep2


title: K562 Daunorubicin Y220C_rep1


title: K562 DMSO M237I_rep1


title: K562 DMSO Y220C_rep2


title: K562 DMSO Y220C_rep3


title: K562 DMSO R175H_rep1


title: K562 DMSO R282W_rep2


title: K562 DMSO R282W_rep1


title: MOLM13 cells, WT, Daunorubicin

library_source: genomic

data_processing:
Fastq files were aligned to hg19 BWA
Duplicate reads marked and removed with picard MarkDuplicates
ChIP-seq peaks called and annotated using HOMER
Peaks filtered to those that had at least 30 normalized tag counts, those found in or 1kb upstream of the Transcriptional Start Site or found in intron 1 or exon 1 of the target gene
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph generated by HOMER, where scores represent normalized tag counts

molecule: genomic DNA

extract_protocol:
20x10e6 cells were crosslinked using 1% methanol-free formaldehyde (ThermoFisher, #28906) in PBS for 7 min at room temperature. Remaining formaldehyde was quenched with 100 mM Tris-HCl pH8.0 and 25 mM Glycine. Cytoplasm was stripped using 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1% SDS for 10 min at room temperature followed by precipitation of nuclei by centrifugation at 10,000g. The nuclei were then resuspended in 66 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1.7% Triton X-100, 0.5% SDS and sheared using an E220 sonicator (Covaris). Chromatin fragmentation was quality-controlled using ScreenTape D5000 (Agilent). Immunoprecipitation with anti-p53 antibodies (DO-1, abcam, #1101) and Protein G Dynabeads™ (ThermoFisher, #10003D) was performed overnight at 4 degree Celsius. Beads were washed and immunoprecipitated DNA was reverse-сrosslinked in 100 mM NaHCO3, 100 mM NaCl, 1% SDS, and quantified by ScreenTape HS D1000 (Agilent) and Qubit (ThermoFisher).
Illumina-compatible sequencing libraries were prepared using SMARTer® ThruPLEX® DNA-Seq Kit (Takara, #R400675) and sequenced using a NextSeq Sequencing System (Illumina) to obtain paired-end reads.

tag: disease state

value: AML

tag: genotype

tag: chip antibody

value: anti-p53 (mAB clone DO-1, abcam, #1101)


title: K562 DMSO Y220C_rep1

tag: cell line


title: MOLM13 cells, KO, Daunorubicin


title: MOLM13 cells, M237I, Daunorubicin


title: MOLM13 cells, R248Q, Daunorubicin


title: MOLM13 cells, R175H, Daunorubicin


title: MOLM13 cells, KO, DMSO


title: MOLM13 cells, Y220C, Daunorubicin


title: MOLM13 cells, WT, DMSO


title: K562 DMSO R175H_rep2

tag: genotype/variation


title: K562 DMSO R175H_rep3


title: K562 DMSO R282W_rep3


title: MOLM13 cells, R282W, Daunorubicin


title: MOLM13 cells, R175H, DMSO


title: MOLM13 cells, R282W, DMSO


title: MOLM13 cells, Y220C, DMSO


title: MOLM13 cells, R273H, DMSO


title: K562 cells, M237I, Daunorubicin


title: MOLM13 cells, R248Q, DMSO


title: K562 cells, Y220C, Daunorubicin


title: MOLM13 cells, R273H, Daunorubicin


title: K562 cells, R175H, Daunorubicin


title: K562 cells, WT, DMSO


title: MOLM13 cells, M237I, DMSO


title: K562 cells, KO, Daunorubicin


title: K562 cells, R282W, DMSO


title: K562 cells, WT, Daunorubicin


title: K562 cells, R282W, Daunorubicin


title: K562 cells, R175H, DMSO


title: K562 cells, R273H, Daunorubicin


title: K562 cells, KO, DMSO


title: K562 cells, R273H, DMSO


title: Control ChIP-seq from mammary epithelial cell (ENCLB481AJV)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000AMN/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on human mammary epithelial cell
experiment encode accession: ENCSR000AMN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB481AJV
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens mammary epithelial primary cell female (50 years)

extract_protocol: not provided

tag: antibody

value: Control

value: mammary epithelial cell

value: primary cell

tag: description

value: mammary epithelial cells

tag: biosample encode accession

tag: age

value: 50 year

tag: dev stage

value: unknown

value: female

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS091ENC at ENCODE; https://www.encodeproject.org/ENCBS091ENC/

value: Derived from ENCODE donor ENCDO830BUW; https://www.encodeproject.org/ENCDO830BUW/

value: ENCODE dbxrefs HMEC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HMEC


title: K562 cells, R248Q, Daunorubicin


title: Control ChIP-seq from mammary epithelial cell (ENCLB700EDY)

description:
https://www.encodeproject.org/experiments/ENCSR000AMN/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on human mammary epithelial cell
experiment encode accession: ENCSR000AMN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB700EDY
size range: 200-600

source_name: Homo sapiens female adult (50 years) mammary epithelial primary cell

value: HMEC Mammary Epithelial Primary Cells

tag: Sex

value: adult

tag: passage number

value: ENCBS045GHW at ENCODE; https://www.encodeproject.org/ENCBS045GHW/


title: Control ChIP-seq from mammary epithelial cell (ENCLB695AVX)

description:
https://www.encodeproject.org/experiments/ENCSR000AMN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human mammary epithelial cell
experiment encode accession: ENCSR000AMN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AVX
fragmentation methods: see document

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f10bdd36-e370-4777-a7f3-83091c115749/@@download/attachment/wgEncodeBroadHistone.html.pdf


title: K562 cells, M237I, DMSO

value: DMSO


title: Control ChIP-seq from mammary epithelial cell (ENCLB695AVW)

description:
https://www.encodeproject.org/experiments/ENCSR000AMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human mammary epithelial cell
experiment encode accession: ENCSR000AMN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AVW
fragmentation methods: see document


title: K562 cells, Y220C, DMSO

value: AML


title: Control ChIP-seq from HepG2 (ENCLB160HSF)

description:
https://www.encodeproject.org/experiments/ENCSR975KJI/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR975KJI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB160HSF
size range: 200-400

source_name: Homo sapiens HepG2 cell line

tag: line

value: cell line

value: Control ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

tag: health state

value: hepatocellular carcinoma

value: ENCBS623YQT at ENCODE; https://www.encodeproject.org/ENCBS623YQT/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: K562 cells, R248Q, DMSO

tag: treatment

value: anti-p53 (mAB clone DO-1, abcam, #1101)


title: Control ChIP-seq from K562 (ENCLB577DLO)

description:
https://www.encodeproject.org/experiments/ENCSR483GYO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR483GYO
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB577DLO
size range: 200-400

source_name: Homo sapiens K562 cell line

value: Control

value: Control ChIP-seq in K562

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS317FST at ENCODE; https://www.encodeproject.org/ENCBS317FST/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from K562 (ENCLB403RJU)

description:
https://www.encodeproject.org/experiments/ENCSR483GYO/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR483GYO
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB403RJU
size range: 200-400

value: cell line

value: adult

value: ENCBS145BAM at ENCODE; https://www.encodeproject.org/ENCBS145BAM/


title: HA-DNMT3B_ChIPseq_mESC_Parental

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We filtered CpGs with less than 5x coverage, overlapping with SNPs from dbSNPs (build 137) or located within the ENCODE DAC blacklisted regions or Duke excluded regions.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF.

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA Hyper Prep Kit

value: HA (ThermoFisher, #88836)

value: ESC line V6.5 1A

tag: cell type

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

value: Parental line stably expressing FLAG-HA tagged DNMT3B WT


title: Control ChIP-seq from K562 (ENCLB711UGZ)

description:
https://www.encodeproject.org/experiments/ENCSR625UIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF395 tagged K562 cell line.
experiment encode accession: ENCSR625UIZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB711UGZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-ZNF395

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF395

value: Kevin White, UChicago

value: ENCBS343LRB at ENCODE; https://www.encodeproject.org/ENCBS343LRB/


title: Control ChIP-seq from HepG2 (ENCLB610NUB)

description:
https://www.encodeproject.org/experiments/ENCSR975KJI/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR975KJI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB610NUB
size range: 200-400

value: Control

value: Control ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: ENCBS540MOP at ENCODE; https://www.encodeproject.org/ENCBS540MOP/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Control ChIP-seq from HepG2 (ENCLB242FBS)

description:
https://www.encodeproject.org/experiments/ENCSR352VNP/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR352VNP
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB242FBS
size range: 200-400

value: cell line

value: ENCBS158MMF at ENCODE; https://www.encodeproject.org/ENCBS158MMF/


title: Control ChIP-seq from K562 (ENCLB387XIP)

description:
https://www.encodeproject.org/experiments/ENCSR464FDA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR464FDA
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-15
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB387XIP
size range: 200-400

value: Control ChIP-seq in K562

value: female

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS441EZC at ENCODE; https://www.encodeproject.org/ENCBS441EZC/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: HA-DNMT3B_ChIPseq_SETD2_KO

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. The bigWig files were generated similarly as ChIP-seq.
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA HyperPrep Kit

value: HA (ThermoFisher, #88836)

value: C3H embryo-derived mesenchymal progenitor cells

tag: genotype

value: sgSETD2 #1 cells stably expressing FLAG-HA tagged DNMT3B WT


title: Control ChIP-seq from K562 (ENCLB749CPZ)

description:
https://www.encodeproject.org/experiments/ENCSR464FDA/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR464FDA
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-15
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB749CPZ
size range: 200-400

value: Control

value: ENCBS401NIV at ENCODE; https://www.encodeproject.org/ENCBS401NIV/


title: Control ChIP-seq from HepG2 (ENCLB650BNO)

description:
https://www.encodeproject.org/experiments/ENCSR254UDV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR254UDV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB650BNO
size range: 200-400

value: Control ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: ENCBS732PJR at ENCODE; https://www.encodeproject.org/ENCBS732PJR/


title: HA-DNMT3B_ChIPseq_NSD1_2_DKO

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA HTP Library Preparation Kit

tag: chip antibody

value: sgNSD1/2 #1 cells stably expressing FLAG-HA tagged DNMT3B WT


title: HA-DNMT3A_ChIPseq_NSD1_2_DKO

tag: cell line

value: sgNSD1/2 #1 cells stably expressing FLAG-HA tagged DNMT3A WT


title: HA-DNMT3A_ChIPseq_Parental

value: Parental line stably expressing FLAG-HA tagged DNMT3A WT


title: Control ChIP-seq from HepG2 (ENCLB810FPW)

description:
https://www.encodeproject.org/experiments/ENCSR352VNP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR352VNP
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB810FPW
size range: 200-400

value: cell line

value: ENCBS749JUQ at ENCODE; https://www.encodeproject.org/ENCBS749JUQ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: HA-DNMT3A_I310N_ChIPseq_Parental

value: HA (ThermoFisher, #88836)

value: C3H embryo-derived mesenchymal progenitor cells

value: Parental line stably expressing FLAG-HA tagged DNMT3A I310N


title: HA-DNMT3A_ChIPseq_SETD2_KO

value: sgSETD2 #1 cells stably expressing FLAG-HA tagged DNMT3A WT


title: HA-DNMT3B_ChIPseq_Parental

value: Parental line stably expressing FLAG-HA tagged DNMT3B WT


title: TF ChIP-seq from K562 (ENCLB085TGX)

description:
https://www.encodeproject.org/experiments/ENCSR189YMA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-VEZF1 ChIP-seq on human K562
experiment encode accession: ENCSR189YMA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR529YPZ
encode release date: 2017-11-08
lab: Kevin White, UChicago
library encode accession: ENCLB085TGX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-VEZF1

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to VEZF1

value: female

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS595PGN at ENCODE; https://www.encodeproject.org/ENCBS595PGN/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from ES-E14 (ENCLB074ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on mouse ES-E14 produced by the Snyder lab
experiment encode accession: ENCSR000ADJ
assay title: Control ChIP-seq
assembly: mm9, mm10
encode release date: 2012-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB074ZZZ
fragmentation methods: sonication (generic)
size range: 150-350

source_name: Mus musculus strain 129/Ola ES-E14 stem cell male embryo

extract_protocol:
general protocol: https://www.encodeproject.org/documents/302689be-b110-40b6-8912-cc9d934b002e/@@download/attachment/mouse.wgEncodeSydhHist.txt
extraction method: see document
general protocol: https://www.encodeproject.org/documents/302689be-b110-40b6-8912-cc9d934b002e/@@download/attachment/mouse.wgEncodeSydhHist.txt

value: Control

value: mouse embryonic stem cell line E14

value: embryonic

value: male

value: unknown

value: Michael Snyder, Stanford

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: TF ChIP-seq from K562 (ENCLB234VZX)

description:
https://www.encodeproject.org/experiments/ENCSR189YMA/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-VEZF1 ChIP-seq on human K562
experiment encode accession: ENCSR189YMA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR529YPZ
encode release date: 2017-11-08
lab: Kevin White, UChicago
library encode accession: ENCLB234VZX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to VEZF1

value: female

value: ENCBS641OVL at ENCODE; https://www.encodeproject.org/ENCBS641OVL/


title: Control ChIP-seq from HepG2 (ENCLB169IFQ)

description:
https://www.encodeproject.org/experiments/ENCSR254UDV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR254UDV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB169IFQ
size range: 200-400

value: Control ChIP-seq on HepG2 cells

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: ENCBS856PWK at ENCODE; https://www.encodeproject.org/ENCBS856PWK/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: TF ChIP-seq from K562 (ENCLB133JTF)

description:
https://www.encodeproject.org/experiments/ENCSR018MSO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF148 ChIP-seq on human K562
experiment encode accession: ENCSR018MSO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR745QMZ
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB133JTF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line stably expressing C-terminal eGFP-tagged eGFP-ZNF148

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF148

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS915LIT at ENCODE; https://www.encodeproject.org/ENCBS915LIT/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: WT_NC11_R3_B2_L2

city: Princeton

first: Amanda

last: Amodeo

state: NJ

address: Carl Ichan Laboratory, Washington Rd

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: Single end 75bp reads

data_processing:
Raw sequencing reads were filtered by Illumina HiSeq Control Software and only the Pass-Filter reads were used for further analysis.
Sequenced raw reads were demultiplexed using fastq-multx (v 1.3.1) and trimmed using Trim Galore (v 0.5.0) default parameters.
Trimmed reads were mapped to the Drosophila melanogaster transcriptome (r6.19) and quantified using default parameters in Salmon (0.10.2).
Normalization and differnetial gene expression analysis were performed using DESeq2 (v 1.20.0) after collapsing the technical replicates (same library sequenced in different batches/ lanes).
Genome_build: Drosophila melanogaster Trranscriptome r6.19
Supplementary_files_format_and_content: Tab-delimited raw quantfication output from Salmon. Tab-delimited files for DESeq2 normalized gene counts as well as DE analysis outputs for each of the Slbp, abo pooled and abo timecourse experiments.

source_name: Single Embryo

growth_protocol: Drosophila stocks grown and embryos collected in 18°C (Slbp experiment) or 25°C  (abo experiment). Embryos staged and imaged at 22°C.

extract_protocol:
The appropriately staged embryos were placed into an RNase free tube, lysed with a sterile needle. Then 100 μl of lysis buffer (Applied Biosystems, KIT0214) was added, and embryos were flash-frozen in liquid nitrogen, then stored at -80°C
For the Slbp comparison: rRNA depletion was performed using the Ribo-Zero rRNA Removal (Human, Mouse, Rat) Kit (Illumina, MRZH11124) followed by converting the poly-A containing RNA transcripts to cDNA using oligo-dT adaptor and further amplified by PCR following the Smart-seq2 method (Picelli et al, 2014). Illumina sequencing libraries were made from the amplified cDNA samples using the Nextera DNA library prep kit (Illumina, FC-121-1031). For the abo single time point comparison: poly-A containing RNA transcripts were enriched using oligo-dT bead and further converted to cDNA and Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324 NGS Library Prep System (Wafergen Biosystems) following the manufacturer's protocol. For the abo timecourse comparison: poly-A containing RNA transcripts were converted to cDNA using oligo-dT adaptor and further amplified by PCR following the Smart-seq2 method (Picelli et al, 2014). Illumina sequencing libraries were made from the amplified cDNA samples using the Nextera DNA library prep kit (Illumina, FC-121-1031). The RNA-seq libraries were sequenced on Illumina HiSeq 2500 Rapid flow-cells as single-end 75nt reads, following the standard Illumina protocol.

value: Wild-type

tag: developmental stage

tag: embryo/ biological replicate

value: Replicate 3

tag: sequencing batch/ lane/ technical replicate

value: abo timecourse experiment:Batch 2 Lane 2


title: WT_NC12_R2_B2_L2

description: Single end 75bp reads

value: Replicate 2


title: WT_NC13_R3_B2_L2

description: Single end 75bp reads


title: WT_NC12_R3_B2_L2

description: Single end 75bp reads


title: WT_NC12_R1_B2_L2

description: Single end 75bp reads

value: Replicate 1


title: WT_NC13_R2_B2_L2

description: Single end 75bp reads


title: WT_NC11_R1_B2_L2

description: Single end 75bp reads


title: WT_NC14_R3_B2_L2

description: Single end 75bp reads


title: WT_NC11_R2_B2_L2

description: Single end 75bp reads


title: WT_NC14_R1_B2_L2

description: Single end 75bp reads


title: WT_NC13_R1_B2_L2

description: Single end 75bp reads


title: WT_NC10_R3_B2_L2

description: Single end 75bp reads


title: WT_NC0_R1_B2_L2

description: Single end 75bp reads

value: Unfertilized


title: ABO_NC14_R2_B2_L2

description: Single end 75bp reads

value: abo mutation; Histone overexpression


title: WT_NC14_R2_B2_L2

description: Single end 75bp reads


title: WT_NC10_R2_B2_L2

description: Single end 75bp reads


title: WT_NC0_R2_B2_L2

description: Single end 75bp reads


title: ABO_NC14_R3_B2_L2

description: Single end 75bp reads


title: ABO_NC14_R1_B2_L2

description: Single end 75bp reads


title: ABO_NC13_R2_B2_L2

description: Single end 75bp reads


title: TF ChIP-seq from K562 (ENCLB252FKQ)

description:
https://www.encodeproject.org/experiments/ENCSR158RYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB40 ChIP-seq on human K562
experiment encode accession: ENCSR158RYZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR861LKS
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB252FKQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-ZBTB40

tag: antibody

value: cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB40

tag: biosample encode accession

value: female

value: ENCBS307VCX at ENCODE; https://www.encodeproject.org/ENCBS307VCX/


title: ABO_NC13_R3_B2_L2

description: Single end 75bp reads


title: ABO_NC13_R1_B2_L2

description: Single end 75bp reads


title: TF ChIP-seq from K562 (ENCLB257OJH)

description:
https://www.encodeproject.org/experiments/ENCSR018MSO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF148 ChIP-seq on human K562
experiment encode accession: ENCSR018MSO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR745QMZ
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB257OJH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF148

tag: dev stage

value: adult

tag: age

tag: lab

value: ENCBS061XWL at ENCODE; https://www.encodeproject.org/ENCBS061XWL/


title: ABO_NC12_R3_B2_L2

description: Single end 75bp reads


title: WT_NC0_R3_B2_L2

description: Single end 75bp reads


title: ABO_NC12_R1_B2_L2

description: Single end 75bp reads


title: WT_NC10_R1_B2_L2

description: Single end 75bp reads


title: ABO_NC11_R2_B2_L2

description: Single end 75bp reads


title: ABO_NC0_R2_B2_L2

description: Single end 75bp reads


title: WT_NC14_R3_B2_L1

description: Single end 75bp reads

value: abo timecourse experiment:Batch 2 Lane 1


title: ABO_NC0_R1_B2_L2

description: Single end 75bp reads


title: ABO_NC11_R1_B2_L2

description: Single end 75bp reads


title: WT_NC13_R3_B2_L1

description: Single end 75bp reads


title: WT_NC13_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC10_R3_B2_L2

description: Single end 75bp reads


title: ABO_NC10_R2_B2_L2

description: Single end 75bp reads


title: WT_NC11_R3_B2_L1

description: Single end 75bp reads


title: WT_NC12_R2_B2_L1

description: Single end 75bp reads


title: WT_NC12_R1_B2_L1

description: Single end 75bp reads


title: WT_NC12_R3_B2_L1

description: Single end 75bp reads


title: ABO_NC10_R1_B2_L2

description: Single end 75bp reads


title: WT_NC14_R2_B2_L1

description: Single end 75bp reads


title: WT_NC11_R2_B2_L1

description: Single end 75bp reads


title: WT_NC13_R2_B2_L1

description: Single end 75bp reads


title: WT_NC11_R1_B2_L1

description: Single end 75bp reads


title: WT_NC10_R3_B2_L1

description: Single end 75bp reads


title: WT_NC10_R2_B2_L1

description: Single end 75bp reads


title: ABO_NC12_R2_B2_L2

description: Single end 75bp reads


title: WT_NC10_R1_B2_L1

description: Single end 75bp reads


title: WT_NC0_R3_B2_L1

description: Single end 75bp reads


title: WT_NC0_R2_B2_L1

description: Single end 75bp reads


title: WT_NC0_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC11_R3_B2_L2

description: Single end 75bp reads


title: WT_NC14_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC14_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC14_R2_B2_L1

description: Single end 75bp reads


title: ABO_NC14_R3_B2_L1

description: Single end 75bp reads


title: ABO_NC13_R3_B2_L1

description: Single end 75bp reads


title: ABO_NC13_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC12_R3_B2_L1

description: Single end 75bp reads


title: ABO_NC11_R2_B2_L1

description: Single end 75bp reads


title: ABO_NC10_R2_B2_L1

description: Single end 75bp reads


title: ABO_NC10_R3_B2_L1

description: Single end 75bp reads


title: WT_NC14_R3_B1_L2

description: Single end 75bp reads

value: abo timecourse experiment:Batch 1 Lane 2


title: ABO_NC0_R2_B2_L1

description: Single end 75bp reads


title: ABO_NC11_R1_B2_L1

description: Single end 75bp reads


title: WT_NC14_R1_B1_L2

description: Single end 75bp reads


title: ABO_NC11_R3_B2_L1

description: Single end 75bp reads


title: ABO_NC10_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC12_R2_B2_L1

description: Single end 75bp reads


title: WT_NC13_R3_B1_L2

description: Single end 75bp reads


title: WT_NC14_R2_B1_L2

description: Single end 75bp reads


title: WT_NC12_R3_B1_L2

description: Single end 75bp reads


title: ABO_NC0_R1_B2_L1

description: Single end 75bp reads


title: WT_NC13_R1_B1_L2

description: Single end 75bp reads


title: WT_NC11_R3_B1_L2

description: Single end 75bp reads


title: WT_NC11_R2_B1_L2

description: Single end 75bp reads


title: WT_NC12_R1_B1_L2

description: Single end 75bp reads


title: WT_NC13_R2_B1_L2

description: Single end 75bp reads


title: WT_NC11_R1_B1_L2

description: Single end 75bp reads


title: WT_NC10_R2_B1_L2

description: Single end 75bp reads


title: WT_NC0_R3_B1_L2

description: Single end 75bp reads


title: WT_NC10_R3_B1_L2

description: Single end 75bp reads


title: WT_NC10_R1_B1_L2

description: Single end 75bp reads


title: ABO_NC12_R1_B2_L1

description: Single end 75bp reads


title: ABO_NC13_R2_B2_L1

description: Single end 75bp reads


title: WT_NC0_R1_B1_L2

description: Single end 75bp reads


title: ABO_NC14_R2_B1_L2

description: Single end 75bp reads


title: WT_NC0_R2_B1_L2

description: Single end 75bp reads


title: ABO_NC14_R1_B1_L2

description: Single end 75bp reads


title: MCFDCIS tumor treated with vehicle, recovery response (2VR-709R)

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

description: 2wk Vehicle + Recovery

data_processing:
Casava v1.8 basecalling
cutadapt adapter removal, demux
STAR RNAseq alignment to GRCh38, GRCm38, params: --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 –outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 –quantMode GeneCounts --twopassMode Basic --twopassMode Basic
Normalization, differential expression in R with edgeR
Genome_build: GRCh38, GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample ([ENSG|ENSMUSG]\tCOUNT)

source_name: MCFDCIS Hsapiens cell line

growth_protocol: 1 Million MCFDCIS cells were injected subcutaneously into Athymic Nude Mice and given 2 weeks to establish DCIS tumors in the animals prior to treatment initiation

extract_protocol:
Qiagen RNeasy extraction following tumor homogenization using the Roche MagNA Lyser
TruSeq RNA Library Prep

treatment_protocol: Animals were treated daily with 50mg/kg Palbociclib by oral gavage

value: MCFDCIS

value: Vehicle

tag: Stage

value: recovery


title: ABO_NC13_R1_B1_L2

description: Single end 75bp reads


title: ABO_NC13_R2_B1_L2

description: Single end 75bp reads


title: ABO_NC12_R3_B1_L2

description: Single end 75bp reads

value: Replicate 3


title: ABO_NC13_R3_B1_L2

description: Single end 75bp reads


title: MCFDCIS tumor treated with vehicle, recovery response (2VR-1092L)

description: 2wk Vehicle + Recovery


title: WT_NC12_R2_B1_L2

description: Single end 75bp reads

value: Wild-type

value: Replicate 2


title: MCFDCIS tumor treated with vehicle, recovery response (2VR-1081L)

description: 2wk Vehicle + Recovery


title: ABO_NC12_R1_B1_L2

description: Single end 75bp reads

value: Replicate 1


title: ABO_NC12_R2_B1_L2

description: Single end 75bp reads

value: abo mutation; Histone overexpression


title: MCFDCIS tumor treated with vehicle, initial response (2V-717L)

description: 2wk Vehicle

value: initial


title: ABO_NC11_R3_B1_L2

description: Single end 75bp reads


title: MCFDCIS tumor treated with vehicle, initial response (2V-096L)

description: 2wk Vehicle


title: MCFDCIS tumor treated with palbociclib, recovery response (2TR-705L)

description: 2wk Palbociclib + Recovery

value: Palbo


title: MCFDCIS tumor treated with vehicle, initial response (2V-720R)

description: 2wk Vehicle


title: ABO_NC11_R2_B1_L2

description: Single end 75bp reads


title: MCFDCIS tumor treated with palbociclib, recovery response (2TR-703R)

description: 2wk Palbociclib + Recovery


title: MCFDCIS tumor treated with palbociclib, recovery response (2TR-701R)

description: 2wk Palbociclib + Recovery


title: ABO_NC10_R3_B1_L2

description: Single end 75bp reads


title: MCFDCIS tumor treated with palbociclib, initial response (2T-714R)

description: 2wk Palbociclib


title: ABO_NC11_R1_B1_L2

description: Single end 75bp reads


title: MCFDCIS tumor treated with palbociclib, initial response (2T-712R)

description: 2wk Palbociclib


title: MCFDCIS tumor treated with palbociclib, initial response (2T-711L)

description: 2wk Palbociclib


title: ABO_NC10_R1_B1_L2

description: Single end 75bp reads


title: ABO_NC10_R2_B1_L2

description: Single end 75bp reads


title: ABO_NC14_R3_B1_L2

description: Single end 75bp reads


title: ABO_NC0_R2_B1_L2

description: Single end 75bp reads

value: Unfertilized


title: ABO_NC0_R1_B1_L2

description: Single end 75bp reads