title: HEK293T.Cascade_IL1RN_crRNA_26.antiFlag.rep2


title: HEK293T.Cascade_IL1RN_crRNA_26.antiFlag.rep1

status: Public on Jun 26 2019

type: SRA

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

country: USA

institute: Duke University

library_source: genomic

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned using Bowtie v1.0.0 (Langmead et al., 2009), reporting the best alignment with up to 2 mismatches (parameters --best --strata -v 2).
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
For the differential binding analysis, first, a union peakset was computed merging individual peak calls using bedtools2 v2.25.0 (Quinlan and Hall, 2010). Then, reads in peaks were estimated using featureCounts and the difference in binding was assessed with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: peaks in narrowPeak format
Supplementary_files_format_and_content: RPKM signal in bigWig format

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T Cells

growth_protocol: HEK293T cells were acquired from the ATCC and maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were plated into 15 cm dishes prior to transfection.

extract_protocol:
Cells were fixed with formaldehyde and lysed to isolate nuclei. Chromatin was sonicated and immunoprecipitated using an anti-FLAG antibody (M2, Sigma F3165).
Libraries were prepared using the Hyper Prep kit (Kapa Biosystems) and samples were barcoded with Illumina Truseq indexes.

treatment_protocol: HEK293T cells were transfected with 40 µg total plasmid in 15cm dishes and harvested 72 hours later for ChIP.

tag: cell line

tag: tissue

value: transformed human embryonic kidney cells

tag: chip antibody

value: FLAG (M2, Sigma F3165)


title: HEK293T.Cascade_IL1RN_crRNA_25.ctrl.rep3


title: HEK293T.Cascade_IL1RN_crRNA_25.ctrl.rep2


title: HEK293T.Cascade_IL1RN_crRNA_25.antiFlag.rep3


title: HEK293T.Cascade_IL1RN_crRNA_25.ctrl.rep1


title: hAECs+ RA 3

type: RNA

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description: Gene expression data from RA treated hAECs on 7th day

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top 3000 DEGs between T7 and D0 hAECs and for all DEGs between T7 and D7 hAECs to test whether a priori-defined groups of genes associated with neural differentiation were significantly related to the DEGs between RA-treated and control cells on day 0 and day 7
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HG-U219
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

molecule: total RNA

source_name: hAECs treated with RA for 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of RA every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture. Day 0 control samples were collected after the initial treatment.

tag: cell type

value: human amnion epithelial cells (hAECs)

tag: treatment

value: 20 μM RA for 7 days


title: VND7 Uninduced Root

city: Davis

first: Gina

middle: Marie

last: Turco

state: CA

address: University of California, Davis

institute: UC Davis

data_processing:
All Drop-seq data was pre-processed and aligned with STAR (Dobin et al., 2013) via the Drop-seq Tools v1.12 software.
Elbow plots where used to determine the best cut-offs for cell numbers
Gene expression matrices were further processed and normalized using the Seurat R package, with a cutoff of at least 500 genes/cell and for genes seen in at least 3 cells
When calculating variable genes cells with a high percentage of mitochondrial, chloroplast and protoplasting induced genes were regressed out variables for downstream clustering
Genome_build: Tair 10

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seeds were sterilized in a 50% bleach 10% tween solution and then stored at 4°C for 3 days. Sterilized seeds were germinated on nylon mesh (100 uM) filters on square MS petri dish plates and grown at 22° C, 74% humidity in a 12 hr light cycle chamber at a 100-120 light intensity.

extract_protocol:
For Drop-seq runs, plants were grown as described above and roots were harvested then protoplast as previously described (Benfey & Scheres, 2000; K. Birnbaum et al., 2003; Macosko et al., 2015). Individual cells were resuspended in Solution A containing: 600 mM Mannitol, 2mM MgCl2*6H20, 0.10% BSA, 2mM CaCl2*2H20, 2mM MES Hydrate, 10mM KCl and pH to 5.5 with 1M Tris.  Each sample of cells was filtered through a 40 μM Cell strainer (BD Falcon) into a 50 mL Falcon tube. Cells were then counted and diluted to 100-180 cells per μl immediately before Drop-seq (Supplemental Table 2).
All Drop-seq steps followed the standard protocol outlined by the McCarroll Lab. The droplet diameter ranged from 0.8 - 0.975 nl (Supplemental Table 2) and Drop-seq was run until 1 mL was collected according to standard Drop-seq protocol. cDNA was amplified to 13-17 cycles and double-purified in 6x volume of Agencourt AMPure XP beads. Tagmentation was carried out with 1200pg of DNA. Samples where ran on the Bioanalyzer  (Supplemental Figure 3)
DropSeq + Nextera

treatment_protocol: After 7 days of growth plants were transferred by mesh filters to either MS plates buffered to ph 5.8 with KOH or MS containing estradiol (0.01,0.05,0.075,0.1,0.13,0.15,0.175,0.2, 1,2,10, 20uM) plates and grown for an additional 24 hours (induction). All induction experiments were carried out at 7am and collected at 7am. Whole root samples were either imaged, frozen for RNA extraction and qRT-PCR or protoplasted for Drop-seq.

value: Root

tag: ecotype

tag: age

value: 7-Day Roots

tag: treament

value: control


title: HEK293T.Cascade_IL1RN_crRNA_25.antiFlag.rep2


title: MDS_BMSC_exo_UPN133

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

description:
test
MDS_BMSC_133_exo

data_processing: ath-miR-159 were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.

label: TaqMan probe (FAM-MGB)

source_name: AML patient (age of donor: 67 years)

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

growth_protocol: BMSCs were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2, and the adherent cells were collected after two or three passages for subsequent analysis.

extract_protocol: Total RNA was isolated with the miRNeasy mini kit (Qiagen).

treatment_protocol: The exosomes from culture medium of BMSCs were isolated by Total exosome isolation reagent (Invitrogen).

tag: diagnosis

value: myelodysplastic syndrome (MDS)

value: exosomal miRNAs of human bone marrow stromal cells

value: 67 years


title: HEK293T.Cascade_IL1RN_crRNA_25.antiFlag.rep1


title: genomic DNA from normal muscles [C5]

status: Public on Jun 27 2019

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina HumanMethylation850 BeadChip using standard Illumina protocol.

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

data_processing: Data was normalized using preprocessQuantile method using Biconductor package minfi.

label: Cy5 and Cy3

source_name: skeletal muscle

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.

tag: disease state

value: normal

tag: mutation

value: wild type SELENON and RYR1

tag: gender

value: male


title: VND7 Induced Root

value: induced with β-estradiol


title: MDS_BMSC_exo_UPN98

description:
test
MDS_BMSC_98_exo

source_name: AML patient (age of donor: 42 years)

value: 42 years


title: hAECs+ RA 1


title: MDS_BMSC_exo_UPN127

description:
test
MDS_BMSC_127_exo

source_name: AML patient (age of donor: 64 years)

value: 64 years


title: HEK293T.Cascade_HBE_crRNA.ctrl.rep3


title: H3K27ac_ChIPSeq CCF3069

city: La Jolla

first: Leo

last: Kim

address: 9500 Gilman Drive #0695

department: Medicine

institute: UC San Diego

data_processing:
Sequencing of H3K27ac  ChIP and an unenriched chromatin control library (input) was performed on a NextSeq, with read lengths of 50bp
Reads were aligned to hg19 using BWA (Li, et. al., 2009)
Identical ChIP-seq sequence reads were collapsed to a single read to avoid PCR duplicates.
Peaks were called using HOMER v4.6 (Heinz, et. al., 2010) using matched inputs with the following parameters : H3K27ac, –histone –tagThreshold 50
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file was generated for each sample by HOMER v4.6.

source_name: Primary glioblastoma tissue

extract_protocol:
For histone modification and transcription factor ChIP-Seq, tissue extracts were crosslinked in PBS + 1% fresh formaldehyde for 10 minutes at 37 C, quenched for 5 minutes with 125 mM glycine, washed twice in cold PBS with protease inhibitors (complete PI, Roche), and stored at -80 C. Pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g , resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes, sonicated to an average fragment size of 200-400 bp on a Branson sonifier, and cleared of debris by centrifugation. Samples were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 0.25% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4 C overnight with 2-5 ug of antibody towards H3K27ac (Active Motif, 39133) . Antigen-antibody complexes were collected with protein G Dynabeads (Life technologies) for 4 hours at 4 C, and sequentially washed with RIPA buffer (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 140 Mm NaCl), RIPA/High salt (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 360 mM NaCl), LiCl Wash Buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0), and TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Beads were resuspended in Low SDS ChIP elution buffer (10mM Tris-HCl pH 8.0, 0.5M EDTA, 300mM NaCl, 0.1% SDS, 5mM DTT) and incubated for 6 hours at 65 C to elute DNA and reverse crosslinking. Samples were treated with RNAase for 30 minutes and proteinase K for 2 hours at 37 C. ChIP DNA was then purified from supernatants with AMPure beads (Beckman-Coulter). Input DNA was prepared in parallel by adding unenriched, diluted chromatin directly into the elution / reverse crosslinking step.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated to barcoded illumina adaptors (Quick T4 DNA ligase, NEB). Each reaction was followed by clean-up with AMPure beads (Beckman-Coulter). Ligation products were amplified by PCR for 14-18 cycles with illumina primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection or gel purification (E-Gel SizeSelect 2%, Life technologies).

tag: individual

value: patient CCF3069

value: Primary glioblastoma tissue

value: H3K27ac (Active Motif, 39133)


title: MDS_BMSC_exo_UPN18

description:
test
MDS_BMSC_18_exo


title: HEK293T.Cascade_IL1RN_crRNA_26.ctrl.rep2

value: transformed human embryonic kidney cells


title: H3K27ac_ChIPSeq CCF3038

value: patient CCF3038


title: HEK293T.Cascade_HBE_crRNA.ctrl.rep1


title: hAECs+ RA 2

value: human amnion epithelial cells (hAECs)

value: 20 μM RA for 7 days


title: H3K27ac_ChIPSeq CCF3018

value: patient CCF3018


title: MDS_BMSC_exo_UPN13

description:
test
MDS_BMSC_13_exo

source_name: AML patient (age of donor: 61 years)

value: myelodysplastic syndrome (MDS)

value: 61 years


title: H3K27ac_ChIPSeq CCF3028

value: patient CCF3028


title: MDS_BMSC_exo_UPN30

description:
test
MDS_BMSC_30_exo

source_name: AML patient (age of donor: 72 years)

value: exosomal miRNAs of human bone marrow stromal cells

value: 72 years


title: HEK293T.Cascade_HBE_crRNA.antiFlag.rep3

value: FLAG (M2, Sigma F3165)


title: H3K27ac_ChIPSeq CCF2907

value: patient CCF2907


title: HEK293T.Cascade_HBE_crRNA.antiFlag.rep2


title: HEK293T.Cascade_HBE_crRNA.ctrl.rep2


title: MDS_BMSC_exo_UPN4

description:
test
MDS_BMSC_4_exo

source_name: AML patient (age of donor: 77 years)

value: 77 years


title: A549_72h_CAF_miRNA

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

description:
small RNA
expressed_miRNA_TPM_seq.txt
A62

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACTCTGAAC) trimmed with fastx_clipper
discovering novel miRNAs using miRDeep2,then predicting miRNA target gene using miRanda
mapped using bowtie -v 1
detecting different expression miRNA (TPM value) using Fisher exact test
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: human lung carcinoma cells

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For RNA-seq, total RNA was extracted from each sample, 10 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo (dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95 degrees C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and applied to Illumina NextSeq 500 system 151 nt pair-end sequencing by ABlife, Inc. (Wuhan, China). For small RNA-seq, total RNA was extracted from each sample. 3μg of each RNA sample was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (GnomeGen, San Diego, CA, USA) based on manufacturer’s instruction. Briefly, RNAs were ligated to 3’ and 5’ adaptor sequentially, reverse transcribed to cDNA and PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to miRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified small RNA libraries were quantified with Qubit Fluorometer (Invitrogen, Carlsbad, CA, USA), used for cluster generation and applied to Illumina NextSeq 500 system 75 or 151 nt pair-end sequencing according to the manufacturer’s instructions. The small RNA libraries sequencing was perfomed in ABLife, Inc. (Wuhan, China).

value: CAF conditioned medium

tag: time


title: HEK293T.Cascade_HBE_crRNA.antiFlag.rep1


title: A549_72h_control_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A61

value: control


title: MDS_BMSC_exo_UPN108

description:
test
MDS_BMSC_108_exo

source_name: MDS patient (age of donor: 87 years)

value: 87 years


title: A549_48h_CAF_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A52


title: MDS_BMSC_exo_UPN175

description:
test
MDS_BMSC_175_exo

source_name: MDS patient (age of donor: 68 years)

value: 68 years


title: 64 genomic DNA from GBM xenograft

city: ROCHESTER

first: Shulan

last: Tian

state: Minnesota

address: 200 1st street SW

department: Health Science Research

institute: Mayo Clinic

description: xenograft sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: xenograft 64

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: M


title: 66 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 66

value: F


title: MDS_BMSC_exo_UPN120

description:
test
MDS_BMSC_120_exo


title: HEK293T.rnaseq.Cascade_p300_IL1RN_crRNA.rep1

data_processing:
Reads were aligned against the human reference genome using the aligner STAR v2.4.1a following the proposed 2-pass strategy to first identify a splice junction database to improve the overall mapping quality.
Gene counts were estimated with featureCounts from the subread package v1.4.6-p6, using gene annotations from Refseq and allowing for multimapping reads (-M and --fraction arguments).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file with raw gene counts

molecule: polyA RNA

growth_protocol: HEK293T cells were acquired from the ATCC and maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were plated into 6-well dishes prior to transfection.

extract_protocol:
Cells were lysed and total RNA was extracted using Qiagen RNeasy Plus mini kit (Qiagen cat. #74136).
mRNA sample preparation was performed with the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: HEK293T cells were transfected with 3 µg total plasmid in 6-well dishes and harvested 72 hours later for RNA-sequencing.

value: transformed human embryonic kidney cells


title: 85 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 85


title: HEK293T.rnaseq.Cascade_p300_IL1RN_crRNA.rep2

source_name: HEK293T Cells


title: 67 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 67


title: 43 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 43


title: A549_48h_control_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A51


title: 56 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 56


title: MDS_BMSC_exo_UPN38

description:
test
MDS_BMSC_38_exo

source_name: MDS patient (age of donor: 56 years)

value: 56 years


title: A549_24h_CAF_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A42


title: A549_24h_control_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A41


title: MDS_BMSC_exo_UPN44

description:
test
MDS_BMSC_44_exo

source_name: MDS patient (age of donor: 72 years)


title: 36 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 36


title: MDS_BMSC_exo_UPN58

description:
test
MDS_BMSC_58_exo

source_name: MDS patient (age of donor: 71 years)

value: 71 years


title: 91 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 91


title: HEK293T.rnaseq.Cascade_p300_IL1RN_crRNA.rep3


title: A549_12h_CAF_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A32


title: HEK293T.rnaseq.Cascade_p300_GFP_crRNA.rep2


title: MDS_BMSC_exo_UPN22

description:
test
MDS_BMSC_22_exo

source_name: MDS patient (age of donor: 66 years)

value: myelodysplastic syndrome (MDS)

value: 66 years


title: HEK293T.rnaseq.Cascade_p300_GFP_crRNA.rep1


title: A549_6h_CAF_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A22


title: A549_12h_control_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A31


title: MDS_BMSC_exo_UPN12

description:
test
MDS_BMSC_12_exo

source_name: MDS patient (age of donor: 38 years)

value: 38 years


title: 69 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 69


title: 6 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 6


title: HEK293T.rnaseq.Cascade_IL1RN_crRNA.rep2


title: MDS_BMSC_exo_UPN8

description:
test
MDS_BMSC_8_exo

value: exosomal miRNAs of human bone marrow stromal cells


title: HEK293T.rnaseq.Cascade_IL1RN_crRNA.rep3


title: 39 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 39


title: A549_6h_control_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A21

source_name: human lung carcinoma cells


title: HEK293T.rnaseq.Cascade_p300_GFP_crRNA.rep3


title: 3 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 3


title: 192 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 192


title: HEK293T.rnaseq.Cascade_IL1RN_crRNA.rep1

source_name: HEK293T Cells


title: MDS_BMSC_exo_UPN115

description:
test
MDS_BMSC_115_exo

source_name: MDS patient (age of donor: 50 years)

value: 50 years


title: MDS_BMSC_exo_UPN141

description:
test
MDS_BMSC_141_exo

source_name: MDS patient (age of donor: 84 years)

value: 84 years


title: A549_3h_control_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A11


title: MDS_BMSC_exo_UPN64

description:
test
MDS_BMSC_64_exo

source_name: MDS patient (age of donor: 46 years)

value: 46 years


title: A549_72h_CAF_mRNA

description:
expressed_gene_RPKM.txt
A62

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
mapped using tophat2 --microexon-search --no-coverage-search --b2-N 1
detecting different expression gene using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample


title: MDS_BMSC_exo_UPN107

description:
test
MDS_BMSC_107_exo

source_name: MDS patient (age of donor: 82 years)

value: 82 years


title: A549_3h_CAF_miRNA

description:
small RNA
expressed_miRNA_TPM_seq.txt
A12

value: CAF conditioned medium


title: 26 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 26


title: 28 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 28


title: 22 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 22


title: A549_72h_control_mRNA

description:
expressed_gene_RPKM.txt
A61

value: control


title: 181 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 181


title: TE1 cell line - siFOXM1 - replicate 2

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

hyb_protocol: AFFYMETRIX GENECHIP WT TERMINAL LABELING AND HYBRIDIZATION KIT

scan_protocol: Genechip Scanner 3000 7G

data_processing:
EXPRESSION CONSOLE AFFYMETRIX, RMA
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: TE1 cell line - siFOXM1

growth_protocol: RPMI 10%SFB 37ºC

extract_protocol: RNEAsy MINI KIT QIAGEN

treatment_protocol: siRNA treatment conducted with lipofectamine 2000

value: TE1 cell line derived of esophageal squamous cell carcinoma

value: siRNA against FOXM1


title: MDS_BMSC_exo_UPN103

description:
test
MDS_BMSC_103_exo

source_name: MDS patient (age of donor: 22 years)

value: 22 years


title: 195 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 195

value: M


title: A549_48h_CAF_mRNA

description:
expressed_gene_RPKM.txt
A52


title: 184 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 184


title: MDS_BMSC_exo_UPN102

description:
test
MDS_BMSC_102_exo

source_name: MDS patient (age of donor: 47 years)

value: 47 years


title: A549_48h_control_mRNA

description:
expressed_gene_RPKM.txt
A51

source_name: human lung carcinoma cells


title: 44 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 44

value: F


title: tumor sample 16

source_name: ESCC patient 16

label_protocol: AFFYMETRIX GENECHIP WT TERMINAL LABELING AND HYBRIDIZATION KIT

tag: patient

value: esophageal tumor

tag: tumor differentiation

value: poor


title: A549_24h_CAF_mRNA

description:
expressed_gene_RPKM.txt
A42


title: MDS_BMSC_exo_UPN101

description:
test
MDS_BMSC_101_exo

source_name: MDS patient (age of donor: 77 years)

value: myelodysplastic syndrome (MDS)

value: 77 years


title: TE1 cell line - SCR - replicate 2

source_name: TE1 cell line - SCR

value: siRNA SCR


title: nonmalignant sample 16

value: nonmalignant surrounding mucosa


title: TE1 cell line - SCR - replicate 1


title: 16 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 16


title: TE1 cell line - siFOXM1 - replicate 1


title: A549_24h_control_mRNA

description:
expressed_gene_RPKM.txt
A41


title: A549_12h_CAF_mRNA

description:
expressed_gene_RPKM.txt
A32


title: tumor sample 15

source_name: ESCC patient 15

value: moderate


title: 187 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 187


title: MDS_BMSC_exo_UPN82

description:
test
MDS_BMSC_82_exo

source_name: MDS patient (age of donor: 78 years)

value: exosomal miRNAs of human bone marrow stromal cells

value: 78 years


title: A549_12h_control_mRNA

description:
expressed_gene_RPKM.txt
A31


title: nonmalignant sample 15


title: MDS_BMSC_exo_UPN95

description:
test
MDS_BMSC_95_exo

source_name: MDS patient (age of donor: 68 years)

value: 68 years


title: tumor sample 14

source_name: ESCC patient 14


title: MDS_BMSC_exo_UPN59

description:
test
MDS_BMSC_59_exo

source_name: MDS patient (age of donor: 55 years)

value: 55 years


title: MDS_BMSC_exo_UPN93

description:
test
MDS_BMSC_93_exo

source_name: MDS patient (age of donor: 82 years)

value: 82 years


title: 196 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 196


title: MDS_BMSC_exo_UPN54

description:
test
MDS_BMSC_54_exo

source_name: MDS patient (age of donor: 58 years)

value: 58 years


title: nonmalignant sample 14


title: MDS_BMSC_exo_UPN33

description:
test
MDS_BMSC_33_exo

source_name: MDS patient (age of donor: 51 years)

value: 51 years


title: A549_3h_CAF_mRNA

description:
expressed_gene_RPKM.txt
A12

value: CAF conditioned medium


title: 174 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 174


title: tumor sample 12

source_name: ESCC patient 12


title: 146 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 146


title: A549_3h_control_mRNA

description:
expressed_gene_RPKM.txt
A11

source_name: human lung carcinoma cells

value: control


title: A549_6h_CAF_mRNA

description:
expressed_gene_RPKM.txt
A22


title: LONZA_BMSC_exo_old_1

description:
control
normal_BMSC_1_exo

source_name: elderly donors (age of donor: 68 years)

value: normal


title: 150 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 150

value: M


title: Kat6b-shRNA-3

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
name in processed data file:
Myst4-287544-BR4_GT19-05878_ATTGTGAA-GCAATGCA_S10

data_processing:
Trimmed alignment files (with trimmed base quality value < 30, and 70% of read bases surpassing that threshold) were processed using the RSEM (v1.2.12; RNA-Seq by Expectation-Maximization) software and the Mus musculus reference GRCm38. This software estimates gene (and isoform) expression levels from RNA-Seq data with a statistical model that considers reads that map to multiple positions. Alignment was completed using Bowtie 2 (v2.2.0) and processed using SAMtools (v0.1.18). Fragment length mean was set to 280 and standard deviation to 50.
Expected read counts per gene produced by RSEM were rounded to integer values, filtered to include only genes that have at least two samples within a sample group having a cpm > 1.0, and were passed to edgeR (v3.5.3) for differential expression analysis. The negative binomial conditional common likelihood was maximized to estimate a common dispersion value across all genes. Exact tests were used to elucidate statistical differences between the two sample groups of negative-binomially distributed counts producing p-values per test. The Benjamini and Hochberg’s algorithm (p-value adjustment) was used to control the false discovery rate (FDR). Features with an FDR-adjusted p-value < 0.05 were declared significantly differentially expressed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text files containing RSEM counts

organism: Mus musculus

source_name: LT-HSCs

growth_protocol: LT-HSCs were resuspended in SFEMII (Stemcell Technologies) supplemented with growth factors described previously Holmfeldt et al., 2016; Stem cell factor (SCF; 10 ng/ml), thrombopoietin (TPO; 20 ng/ml), insulin-like growth factor 2 (IGF2; 20 ng/ml) and fibroblast growth factor (FGF; 10 ng/ml) (BioLegend or StemCell Technologies) along with 5ug/ml polybrene (Sigma) and viral supernatant. Lentiviral supernatant was added at concentration of 1000 MOI in a total volume of 200 ul in a 96-well U-bottom plate. The plate was spun at 2500 rpm for 60 min at room temperature. After this, cells were cultured at 37oC and 5% CO2 for 36 hours. Transduced cells (viable GFP+) were sorted on a FACSAria (BD Biosciences) directly into RLT buffer.

extract_protocol:
Transduced GFP+ LT-HSCs from 3 independent biological replicates were sorted directly into 350 ul of RLT buffer (Qiagen). Total RNA was isolated from cells using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. Sample concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico LabChip assay (Agilent Technologies).
Libraries were prepared by the Genome Technologies core facility at The Jackson Laboratory using the Ovation RNA-seq System V2 (Nugen) and Hyper Prep Kit (Kapa Biosystems). Briefly, the protocol entails first and second strand cDNA synthesis and cDNA amplification utilizing Nugen’s Ribo-SPIA technology, cDNA fragmentation, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. Libraries were checked for quality and concentration using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (Kapa Biosystems), according to the manufacturers’ instructions. Libraries were pooled and sequenced 75 bp single-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2.5 reagents (Illumina).

tag: strain

tag: Sex

value: Female

value: Bone marrow

tag: shRNA transduced

value: 2-4 month


title: 154 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 154


title: Kat6b-shRNA-2

description:
name in processed data file:
Myst4-287544-BR2_GT19-05876_CCTTCACC-GGAGCGTC_S13

tag: tissue


title: tumor sample 10

source_name: ESCC patient 10

value: esophageal tumor

value: poor


title: nonmalignant sample 11

source_name: ESCC patient 11

value: nonmalignant surrounding mucosa


title: LONZA_BMSC_exo_old_2

description:
control
normal_BMSC_2_exo

source_name: elderly donors (age of donor: 72 years)

value: exosomal miRNAs of human bone marrow stromal cells

value: 72 years


title: 155 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 155


title: 139 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 139

value: F


title: tumor sample 11

value: moderate


title: Kat6b-shRNA-1

description:
name in processed data file:
Myst4-287544-BR1_GT19-05874_GTGTCGGA-GCGCAAGC_S15


title: 147 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 147


title: NTC-3

description:
name in processed data file:
Sh202-BR4_GT19-05877_GCCACAGG-ATGGCATG_S4

value: NTC


title: A549_6h_control_mRNA

description:
expressed_gene_RPKM.txt
A21

tag: cell line


title: tumor sample 9

source_name: ESCC patient 9


title: nonmalignant sample 12


title: NTC-2

description:
name in processed data file:
Sh202-BR2_GT19-05875_TTCCTGTT-AAGATACT_S25


title: 156 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 156


title: 134 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 134


title: tumor sample 8

source_name: ESCC patient 8


title: nonmalignant sample 9


title: 137 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 137


title: RRBS_WT Replicate 2

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

description: bisulfite treated gDNA

data_processing:
Trim galore v0.5 was used to clip the first 6basepairs and to trim poor quality calls and adapters(--paired -q 20 --clip_r1 6 and --clip_r2 6)
Bismark v0.19.1 was used to to align the trimmed RRBS fastq
Differential methylation analysis was done in R package methyKitV1.9.0 and DMRs were reported at q-value <0.05 and percent methylation difference cutoff of 25.
Genome_build: MM9
Supplementary_files_format_and_content: spreadsheet contains the list of DMRs and their annotations

source_name: murine embryonic stem cells

growth_protocol: mESC were cultured on gelatin adapted tissue culture plates in normal culture conditions as previously described. Wang et al, Nature, 2006. PMID:17093407

extract_protocol:
gDNA was extracted using Puregene Blood Core Kit B (Qiagen)
RRBS libraries were made using Premium RRBS Kit (Diagenode Cat #C02030032)

tag: cell type

value: embryonic stem cells

value: 129 derived

tag: genotype

value: WT


title: tumor sample 7

source_name: ESCC patient 7


title: nonmalignant sample 7


title: RRBS_WT Replicate 1

description: bisulfite treated gDNA


title: nonmalignant sample 10


title: 123 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 123


title: 125 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 125


title: nonmalignant sample 8


title: RRBS_TKO Replicate 2

description: bisulfite treated gDNA

value: DKO


title: 132 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 132


title: RRBS_TKO Replicate 1

description: bisulfite treated gDNA


title: tumor sample 6

source_name: ESCC patient 6


title: RRBS_DKO Replicate 2

description: bisulfite treated gDNA


title: RRBS_WT Replicate 3

description: bisulfite treated gDNA


title: NTC-1

description:
name in processed data file:
Sh202-BR1_GT19-05873_ACACTAAG-ATATGGAT_S1

source_name: LT-HSCs

tag: age


title: tumor sample 5

source_name: ESCC patient 5


title: nonmalignant sample 5


title: 12 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 12


title: RRBS_DKO Replicate 1

description: bisulfite treated gDNA


title: nonmalignant sample 6


title: 129 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 129


title: RRBS_Tet2-/- Replicate 2

description: bisulfite treated gDNA


title: 117 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 117


title: tumor sample 4

source_name: ESCC patient 4


title: 126 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 126


title: nonmalignant sample 4


title: RRBS_Tet1-/- Replicate 3

description: bisulfite treated gDNA


title: RRBS_Tet1-/- Replicate 2

description: bisulfite treated gDNA


title: RRBS_Tet2-/- Replicate 1

description: bisulfite treated gDNA


title: nonmalignant sample 3

source_name: ESCC patient 3


title: RRBS_Tet1-/- Replicate 1

description: bisulfite treated gDNA


title: tumor sample 2

source_name: ESCC patient 2


title: tumor sample 3

value: well


title: 116 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 116


title: nonmalignant sample 2


title: WT_rep1 [D6]

data_processing:
The raw  fastq files were mapped to mouse referance genome ,MM9 and ERCC transcripts using STAR v2.5.1
Differential Expression Analysis was done using DESEQ2
Genome_build: MM9
Supplementary_files_format_and_content: TXT file contains the feature counts for genes across samples

extract_protocol:
RNA extracted using Trizol reagent and protocol, further purification was done by Qiagen Rneasy Plus Kit
ERCC Spike In Mix from Thermo Fisher was used prior to NEBNext Poly(A) mRNA Magnetic Isolation Module. NEBNext Ultra RNA Library Prep Kit for Illumina was used for library generation. A 1% PhiX spike in was added prior to sequencing.

treatment_protocol: mESC were plated at low density on gelating adapted tissue culture plates in normal ESC media. The following day the media was replaced with ESC media that contained no LIF. Media was changed each subsequent day and RNA was collected on day 6.

tag: genotype/variation

tag: time point

value: Day 6


title: 14 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 14

value: M


title: 102 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 102


title: WT_rep2 [D6]

source_name: murine embryonic stem cells


title: tumor sample 1

source_name: ESCC patient 1


title: 120 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 120


title: 177 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 177


title: WT_rep3 [D6]


title: FVB_MMTV_Wnt1_125285_aCGH_Perou

city: Chapel Hill

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

description: Agilent Feature Extractor Software

hyb_protocol: described in Herschkowitz et al., 2012, PNAS, 109:2778-2783

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: FVB WT DNA

extract_protocol: Genomic DNA was extracted from 11 Wnt1-EarlyEx and 10 Wnt1-LateEx tumors using a DNeasy blood and tissue kit (Qiagen #69504), labeled with a Sure Tag DNA kit (Agilent #5190-4240), and hybridized to 244K CGH microarrays (Agilent #G4415A) as previously described.

value: FVB DNA Reference

source_name: Tumor DNA 125285

value: FVB/n MMTV-Wnt1 mammary tumor


title: Tet2-/-_rep1 [D6]


title: FVB_MMTV_Wnt1_126355_aCGH_Perou

description: Agilent Feature Extractor Software

label_protocol: described in Herschkowitz et al., 2012, PNAS, 109:2778-2783

source_name: Tumor DNA 126355


title: nonmalignant sample 1


title: Tet2-/-_rep2 [D6]


title: 80 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 80


title: FVB_MMTV_Wnt1_124504_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 124504


title: Tet1-/-_rep1 [D6]


title: FVB_MMTV_Wnt1_123070_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 123070


title: Tet1-/-_rep2 [D6]


title: FVB_MMTV_Wnt1_125799_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 125799


title: 10 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 10


title: 63 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 63


title: Tet1-/-_rep3 [D6]


title: FVB_MMTV_Wnt1_123420_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 123420


title: 108 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 108


title: DKO_rep1 [D6]


title: FVB_MMTV_Wnt1_125673_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 125673


title: 110 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 110


title: 75 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 75


title: FVB_MMTV_Wnt1_124326_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 124326


title: DKO_rep2 [D6]

source_name: murine embryonic stem cells


title: FVB_MMTV_Wnt1_124607_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 124607


title: TKO_rep2 [D6]

value: TKO


title: TKO_rep1 [D6]


title: 76 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 76


title: 59 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 59


title: FVB_MMTV_Wnt1_122016_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: FVB WT DNA

source_name: Tumor DNA 122016


title: FVB_MMTV_Wnt1_124328_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 124328


title: WT_3 [D0]

value: Day 0


title: 34 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 34


title: FVB_MMTV_Wnt1_123738_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 123738


title: WT_1 [D0]


title: TKO_2 [D0]


title: FVB_MMTV_Wnt1_121993_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 121993


title: TKO_1 [D0]


title: 161 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 161


title: 157 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 157


title: 46 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 46


title: 164 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 164


title: FVB_MMTV_Wnt1_123114_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 123114


title: 118 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 118


title: WT_2 [D0]


title: 40 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 40


title: 38 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 38


title: Tet2_2 [D0]

source_name: murine embryonic stem cells


title: FVB_MMTV_Wnt1_134413_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 134413


title: Tet2_1 [D0]


title: d6diff_EpiLCEBd4_2nd

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

description:
BrdU-immunoprecipitated DNA.
Biological replicate 2 of 2.

hyb_protocol: Labeling early and late-replicating DNA samples after WGA with Cy3 and Cy5 or vice versa followed by overnight hybridization, washing and slide scanning, according to the manufacturer’s instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Microarray data sets were processed as described (Ryba et al., Nat. Protoc. 2011) to obtain genome-wide Repli-chip (RT) data profile (log2[Early-S/Late-S ratio]).

label_protocol: Randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: MEFs (mouse embryonic fibroblasts) were isolated from 12.5-day-old embryos from C57BL6 mice and cultured in D-MEM supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as described (Tesar et al. 2007).

extract_protocol: For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). Using a cell sorter, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a GenomePlex kit (Sigma, WGA2) for CGH microarray analysis.

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain/background

value: CBA/MsM

value: day6 differentiated ESCs

tag: fraction

value: Early S phase

value: Late S phase


title: FVB_MMTV_Wnt1_121796_aCGH_Perou

description: Agilent Feature Extractor Software

source_name: Tumor DNA 121796


title: Tet1_3 [D0]


title: FVB_MMTV_Wnt1_2406-4R_CGH_Rosen

description: Agilent Feature Extractor Software

source_name: MRR


title: 84 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 84

tag: gender

value: F


title: 148 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 148


title: Tet1_1 [D0]


title: FVB_MMTV_Wnt1_3718-3R_CGH_Rosen

description: Agilent Feature Extractor Software


title: d4diff_EpiLCEBd2_2nd

value: day4 differentiated ESCs


title: FVB_MMTV_Wnt1_2543-4L_CGH_Rosen

description: Agilent Feature Extractor Software


title: DKO_2 [D0]


title: d5diff_EpiLCEBd3_2nd

value: day5 differentiated ESCs


title: 5 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 5


title: DKO_1 [D0]

value: 129 derived


title: 122 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 122


title: HA_vp160_allsites_stringent: HA VP16(10x) ERBS Rep 2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

data_processing:
Reads were aligned to hg19 using bowtie v1.1.2 with parameters - m 1 –t –best -q -S -l 32 -e 80 -n 2.
Sam alignments were converted to sorted bams using samtools.
Duplicates were removed from BAM files using samtools rmdup with modifier flag –s for single end reads.
Counts were generated using bedtools coverage.
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100.
Bedtools intersect was used to find all overlapping peaks between ChIP-seq experiments with the same antibody. Counts were then normalized by the average counts per overlapping peak, calculated by bedtools coverage.
Fold change in ChIP-seq signal was calculated as the ratio of a targeted region’s normalized counts vs the same region’s normalized counts in a non-targeted control.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files (from MACS2)
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: .txt Tab-separated Normalized Counts File

source_name: Ishikawa Cell Line (endometrial carcinoma)

growth_protocol: Ishikawa cells were cultured in RPMI (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco) and incubated at 37°C with 5% CO2. Cells were transferred to hormone depleted media (phenol red-free RPMI (Gibco) with 10% charcoal-dextran stripped fetal bovine serum (Sigma)), at least 5 days before transfection with gRNA and dCas9 fusion plasmids.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking. Crosslinked cells were then washed with cold PBS and scraped to harvest. ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009. The following antibodies were used: HA (Biolegend   16B12), H3K27ac (Active Motif pAb Cat #39133) and RNAPII (abcam ab5408)

treatment_protocol: dCas9 fusions (dCas9-VP16(10x) or dCas9-p300(core)) plasmids were transfected using fugene HD reagent. Guide RNAs were transfected in the following pools: Pool 1: MMP17-2, CISH-1, FHL2-2, HES2-3  Pool 2: MMP17-1, CISH-2, FHL2-3, HES2-1  Pool 3: MMP17-3, CISH-3, FHL2-1, HES2-2  ERBS: Pools 1, 2 and 3  Adjacent Pool: MMP17-A, MMP17-B, CISH-A, CISH-B, FHL2-A, FHL2-B

value: Ishikawa

value: endometrial carcinoma

tag: antibody target

value: HA

tag: activation construct

tag: targeted pools

value: ERBS (all)


title: ha_vp160_adjacent: HA VP16(10x) Adjacent Rep 2

value: Adjacent


title: d3diff_EpiLCEBd1_2nd

value: day3 differentiated ESCs


title: FVB_MMTV_Wnt1_2494-2L_CGH_Rosen

description: Agilent Feature Extractor Software

value: FVB DNA Reference

value: FVB/n MMTV-Wnt1 mammary tumor


title: 115 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 115


title: 61 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 61


title: ha_p300_allenhancers_r2: HA P300 ERBS Rep 2


title: EpiSC_p4_onMEF_1st

description:
BrdU-immunoprecipitated DNA.
Biological replicate 1 of 2.

source_name: EpiSC

value: epiblast stem cell


title: 170 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 170

value: M


title: EpiSC_p5_onMEF_2nd


title: MEF2_male_2nd

value: mouse embryonic fibroblast


title: ha_p300_allenhancers_r1: HA P300 ERBS Rep 1


title: 28B genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 28B


title: HA_offtarget_stringent: HA VP16(10x) Adjacent Rep 1


title: HA_IL1RN_stringent: HA IL1RN/Control


title: MEF1_female_2nd

value: Early S phase


title: HA_allSites_onTarget_stringent: HA VP16(10x) ERBS Rep 1


title: PolII_pool3_stringent: RNAPII VP16(10x) Pool3 rep2

value: RNAPII

value: Pool 3


title: MEF1_female_1st

value: Late S phase


title: Tet1_2 [D0]

value: Day 0


title: PolII_pool2_stringent: RNAPII VP16(10x) Pool2 rep2

value: Pool 2


title: MEF2_male_1st


title: d7diff_EpiLCEBd5_2nd

value: CBA/MsM

value: day7 differentiated ESCs


title: polii_vp160_pool3_stringent: RNAPII VP16(10x) Pool3 rep1

value: Ishikawa

value: endometrial carcinoma


title: MEF2_p2_150917

description:
Biological replicate 3 of 3.
Miura_FileName: RNA_MEF2_p2_150917
Miura_Project ID: P215_19_1
Miura_MEMO: RNA_MEF2_p2_150917
processed data file: gene_fpkm.xlsx

data_processing:
Before mapping, trimming the adaptor sequence and removing the low quality base reads were performed by Cutadapt version 1.4.1 (Martin, 2011) and Fastx_tool kit version 0.0.14 (https://github.com/agordon/fastx_toolkit). After this, fastq file was aligned to the mouse genome (UCSC mm9) by HISAT2 version 2.0.4 (Sirén et al., 2014). Mapped reads were quantified against the annotated UCSC transcriptome for mm9 to calculate FPKM (Fragments per kilobase per million mapped fragments) values using the Cuffdiff program of the Cufflinks package version 2.2.1 (Trapnell et al., 2012).
Genome_build: UCSC mm9 (MGSCv37)
Supplementary_files_format_and_content: gene_fpkm.xlsx: Excel file includes FPKM values.

source_name: MEF

extract_protocol:
Cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
Library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).


title: 143 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 143


title: FVB_MMTV_Wnt1_3065_CGH_Rosen

description: Agilent Feature Extractor Software


title: polii_vp160_pool2_stringent: RNAPII VP16(10x) Pool2 rep1


title: MEF1_p2_150917

description:
Biological replicate 3 of 3.
Miura_FileName: RNA_MEF1_p2_150917
Miura_Project ID: P215_18_1
Miura_MEMO: RNA_MEF1_p2_150917
processed data file: gene_fpkm.xlsx


title: d6diff_EpiLCEBd4_1st

value: day6 differentiated ESCs


title: 15 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 15


title: 5-ASA(1), biological rep4

city: Sunto-gun

first: Yoko

last: Ono

state: Shizuoka

address: 1188, Shimotogari, Nagaizumi-cho

institute: Kyowa Hakko Kirin Co., Ltd

description: Gene expression of colon of APC mice which were given drinking water supplemented with 1.5% (w/v) Dextran sulphate sodium (DSS) through day 0 to day 3, then allowed to recover by drinking water including 5-aminosalicylic acid (5-ASA) for 25 additional days.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray Kit(G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1010_Sep10  and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw signals were liner-shifted with 75 percentile value of each array as a reference, followed by the baseline transformation by Sham in each probe.

source_name: colorectal tissues of ApcMin/+ mice, which were given drinking water supplemented with 1.5 w/v% dextran sulphate sodium (DSS) for 3 days to induce colitis, and were intracolorectally administrated with 5-aminosalicylic acid (5-ASA) for 28 days.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick-Amp Labeling Kit 1color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All animal studies were performed in accordance with Standards for Proper Conduct of Animal Experiments at Kyowa Hakko Kirin Co., Ltd. under the approval of the company’s Institutional Animal Care and Use Committee. Fuji Research Park of Kyowa Hakko Kirin co., Ltd. is fully accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care.

extract_protocol: Total RNA extracted by Trizol reagents according to the manufacturer's instruction.

treatment_protocol: ApcMin/+ mice were given drinking water supplemented with 1.5 w/v% dextran sulphate sodium (DSS) for 3 days to induce colitis, and were intracolorectally administrated with 5-aminosalicylic acid (5-ASA) or Saline (Control) for 28 days.  ApcMin/+  mice (Sham) were given drinking water alone for 28 day.

value: colorectal tissues

tag: diarrhea score at day28


title: PolII_pool1_stringent: RNAPII VP16(10x) Pool1 rep2

value: Pool 1


title: 114 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 114


title: polii_vp160_pool1_stringent: RNAPII VP16(10x) Pool1 rep1


title: MEF1_p1_150916

description:
Biological replicate 2 of 3.
Miura_FileName: RNA_MEF1_p1_150916
Miura_Project ID: P215_16_1
Miura_MEMO: RNA_MEF1_p1_150916
processed data file: gene_fpkm.xlsx


title: 5-ASA(1), biological rep3


title: 5-ASA(1), biological rep6


title: d4diff_EpiLCEBd2_1st

value: day4 differentiated ESCs


title: polii_vp160_il1rn_r2_stringent: RNAPII VP16(10x) Control/IL1RN rep2


title: MEF2_p1_150916

description:
Biological replicate 2 of 3.
Miura_FileName: RNA_MEF2_p1_150916
Miura_Project ID: P215_17_1
Miura_MEMO: RNA_MEF2_p1_150916
processed data file: gene_fpkm.xlsx


title: 5-ASA(1), biological rep5


title: d2diff_EpiLCd2_2nd

value: day2 differentiated ESCs


title: 182 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 182

value: M


title: d3diff_EpiLCEBd1_1st

value: day3 differentiated ESCs


title: d5diff_EpiLCEBd3_1st

value: day5 differentiated ESCs

value: Early S phase


title: CBMS1ESC_2nd

value: embryonic stem cell


title: MEF2_p0_150914

description:
Biological replicate 1 of 3.
Miura_FileName: RNA_MEF2_p0_150914
Miura_Project ID: P215_15_1
Miura_MEMO: RNA_MEF2_p0_150914
processed data file: gene_fpkm.xlsx

value: mouse embryonic fibroblast


title: CBMS1ESC_1st

value: Late S phase


title: polii_vp160_il1rn_r1_stringent: RNAPII VP16(10x) Control/IL1RN rep1

value: RNAPII


title: 5-ASA(1), biological rep2


title: MEF1_p0_150914

description:
Biological replicate 1 of 3.
Miura_FileName: RNA_MEF1_p0_150914
Miura_Project ID: P215_14_1
Miura_MEMO: RNA_MEF1_p0_150914
processed data file: gene_fpkm.xlsx


title: 5-ASA(1), biological rep1


title: polii_vp160_adjacent_r2_stringent: RNAPII VP16(10x) Adjacent rep2

value: Adjacent


title: EpiSC7_p6-2_onMEF160310

description:
Biological replicate 3 of 3.
Miura_FileName: EpiSC7_p6-2_onMEF160310
Miura_Project ID: P242_15_1
Miura_MEMO: RNA_EpiSC7_p6-2_onMEF160310
processed data file: gene_fpkm.xlsx

value: epiblast stem cell


title: EpiSC7_p7_onMEF_160309

description:
Biological replicate 2 of 3.
Miura_FileName: EpiSC7_p7_onMEF_160309
Miura_Project ID: P242_14_1
Miura_MEMO: RNA_EpiSC7_p7_onMEF160309
processed data file: gene_fpkm.xlsx


title: polii_p300_pool3_r1: RNAPII P300 Pool3 rep2

value: Ishikawa

value: Pool 3


title: polii_p300_pool3_backup: RNAPII P300 Pool3 rep1

value: endometrial carcinoma


title: CBMS1_d7_EpiL-CEBd5_160129

description:
Biological replicate 5 of 5.
Miura_FileName: CBMS1_d7_EpiL-CEBd5_160129
Miura_Project ID: P242_12_1
Miura_MEMO: RNA_CBMS1_d7diff_EpiLCEBd5_160129
processed data file: gene_fpkm.xlsx

value: CBA/MsM

value: day7 differentiated ESCs


title: MYB83 Uninduced Root

data_processing:
All Drop-seq data was pre-processed and aligned with STAR (Dobin et al., 2013) via the Drop-seq Tools v1.12 software.
Elbow plots where used to determine the best cut-offs for cell numbers
Gene expression matrices were further processed and normalized using the Seurat R package, with a cutoff of at least 500 genes/cell and for genes seen in at least 3 cells
When calculating variable genes cells with a high percentage of mitochondrial, chloroplast and protoplasting induced genes were regressed out variables for downstream clustering
Genome_build: Tair 10

source_name: Root

value: Root

tag: ecotype

value: 7-Day Roots

tag: treament

value: control


title: EpiSC7_p6_onMEF_160309

description:
Biological replicate 1 of 3.
Miura_FileName: EpiSC7_p6_onMEF_160309
Miura_Project ID: P242_13_1
Miura_MEMO: RNA_EpiSC7_p6_onMEF160309
processed data file: gene_fpkm.xlsx


title: d2diff_EpiLCd2_1st

value: day2 differentiated ESCs


title: polii_vp160_adjacent_r1_stringent: RNAPII VP16(10x) Adjacent rep1


title: polii_p300_pool2_r2: RNAPII P300 Pool2 rep2

value: Pool 2


title: Control, biological rep6

description: Gene expression of colon of APC mice which were given drinking water supplemented with 1.5% (w/v) Dextran sulphate sodium (DSS) through day 0 to day 3, then allowed to recover by drinking water alone(Control) for 25 additional days.

source_name: colorectal tissues of ApcMin/+ mice, which were given drinking water supplemented with 1.5 w/v% dextran sulphate sodium (DSS) for 3 days to induce colitis, and were intracolorectally administrated with Saline (Control) for 28 days.

value: colorectal tissues


title: MYB83 Induced Root

value: induced with β-estradiol


title: CBMS1_d6_EpiL-CEBd4_160128

description:
Biological replicate 3 of 3.
Miura_FileName: CBMS1_d6_EpiL-CEBd4_160128
Miura_Project ID: P242_11_1
Miura_MEMO: RNA_CBMS1_d6diff_EpiLCEBd4_160128
processed data file: gene_fpkm.xlsx

value: day6 differentiated ESCs


title: Control, biological rep4


title: 9 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 9

value: F


title: polii_p300_pool2_r1: RNAPII P300 Pool2 rep1

value: RNAPII


title: CBMS1_d5_EpiL-CEBd3_160127

description:
Biological replicate 3 of 3.
Miura_FileName: CBMS1_d5_EpiL-CEBd3_160127
Miura_Project ID: P242_10_1
Miura_MEMO: RNA_CBMS1_d5diff_EpiLCEBd3_160127
processed data file: gene_fpkm.xlsx

value: day5 differentiated ESCs


title: MYB46 Uninduced Root


title: MYB46 Induced Root


title: polii_p300_pool1_r2: RNAPII P300 Pool1 rep2

value: Pool 1


title: Sham, biological rep4

description: Gene expression of colon of APC mice which were given drinking water alone through day 0 to day 28.

source_name: colorectal tissues of ApcMin/+ mice


title: Control, biological rep3


title: Control, biological rep2


title: Control, biological rep1


title: Control, biological rep5


title: CBMS1_d4_EpiL-CEBd2_160126

description:
Biological replicate 3 of 3.
Miura_FileName: CBMS1_d4_EpiL-CEBd2_160126
Miura_Project ID: P242_09_1
Miura_MEMO: RNA_CBMS1_d4diff_EpiLCEBd2_160126
processed data file: gene_fpkm.xlsx

value: day4 differentiated ESCs


title: polii_p300_pool1_r1: RNAPII P300 Pool1 rep1

value: Ishikawa


title: Sham, biological rep3


title: CBMS1_d3_EpiL-CEBd1_160125

description:
Biological replicate 3 of 3.
Miura_FileName: CBMS1_d3_EpiL-CEBd1_160125
Miura_Project ID: P242_08_1
Miura_MEMO: RNA_CBMS1_d3diff_EpiLCEBd1_160125
processed data file: gene_fpkm.xlsx

value: day3 differentiated ESCs


title: Naïve 3

city: Montréal

first: Brian

last: Hsu

state: QC

address: 1160 Pine Avenue West

country: Canada

institute: McGill University

data_processing:
Base calling was performed with Illumina RTA 1.17.21.3.  Base calls were then demultiplexed and converted to FASTQ using Illumina Casava 1.8.2.
Read trimmer was done by Trimmomatic
Alignment was performed by using STAR
Read counter was analyzed using STAR counts
Differential gene expression was analyzed using DESeq2 (version 1.16.1)
Genome_build: h19 genome

source_name: Neutrophils isolated from bone marrow

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

tag: strain

value: Balb/c

value: Female

value: 8 weeks


title: Naïve 4


title: CBMS1_d2_EpiL-Cd2_160124

description:
Biological replicate 5 of 5.
Miura_FileName: CBMS1_d2_EpiL-Cd2_160124
Miura_Project ID: P242_07_1
Miura_MEMO: RNA_CBMS1_d2diff_EpiLCd2_160124
processed data file: gene_fpkm.xlsx

value: CBA/MsM


title: Sham, biological rep2

tag: tissue


title: Input_polII_polII_CTD_S5ph_siRNA_KMT9a_PC-3M

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

data_processing:
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using STAR
peak finding algorithm MACS
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle files. The wig files include the read data mapped to the hg19 genome.

source_name: PC-3M cells

extract_protocol:
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008).
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using STAR

treatment_protocol: Human PC-3M cells were maintained in RPMI medium supplemented with 10 % FBS and glutamine

tag: differentiation stage

value: prostate cancer cells

value: AR-independent

tag: passages

tag: chip antibody

tag: sirna


title: Naïve 2

tag: age


title: polii_p300_il1rn_backup: RNAPII P300 Control/IL1RN rep1

source_name: Ishikawa Cell Line (endometrial carcinoma)

tag: cell line

tag: cell type

value: endometrial carcinoma


title: d7diff_EpiLCEBd5_1st

description:
BrdU-immunoprecipitated DNA.
Biological replicate 1 of 2.

tag: strain/background

value: day7 differentiated ESCs

tag: fraction

value: Early S phase

value: Late S phase


title: polii_p300_adjacent_r2: RNAPII P300 Adjacent rep2

tag: antibody target

value: Adjacent


title: Naïve 1

tag: gender


title: ChIP_polII_CTD_S5ph_siRNA_Ctrl_PC-3M

tag: genotype

value: anti-Pol II CTD S5ph, #C15200007, lot 001-12, Diagenode

value: Ctrl


title: LDN 7

source_name: Neutrophils isolated from peripheral blood


title: polii_p300_il1rn_r2: RNAPII P300 Control/IL1RN rep2

value: RNAPII

tag: activation construct

tag: targeted pools


title: CBMS1_d6_EpiL-CEBd4_160125

description:
Biological replicate 2 of 3.
Miura_FileName: CBMS1_d6_EpiL-CEBd4_160125
Miura_Project ID: P242_05_1
Miura_MEMO: RNA_CBMS1_d6diff_EpiLCEBd4_160125
processed data file: gene_fpkm.xlsx

value: day6 differentiated ESCs


title: 167 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 167

value: M


title: LDN 5


title: CBMS1_d7_EpiL-CEBd5_160126

description:
Biological replicate 4 of 5.
Miura_FileName: CBMS1_d7_EpiL-CEBd5_160126
Miura_Project ID: P242_06_1
Miura_MEMO: RNA_CBMS1_d7diff_EpiLCEBd5_160126
processed data file: gene_fpkm.xlsx


title: 7v3_stringent: H3K27ac VP16(10x) Pool3 rep2

value: Ishikawa

value: Pool 3


title: polii_p300_adjacent_r1: RNAPII P300 Adjacent rep1


title: Sham, biological rep1

value: colorectal tissues

tag: diarrhea score at day28


title: Input_polII_polII_CTD_S5ph_siRNA_Ctrl_PC-3M


title: CBMS1_d5_EpiL-CEBd3_160124

description:
Biological replicate 2 of 3.
Miura_FileName: CBMS1_d5_EpiL-CEBd3_160124
Miura_Project ID: P242_04_1
Miura_MEMO: RNA_CBMS1_d5diff_EpiLCEBd3_160124
processed data file: gene_fpkm.xlsx

value: day5 differentiated ESCs


title: LDN 4

tag: strain

value: Balb/c

value: Female

value: 8 weeks


title: ChIP_polII_siRNA_Ctrl_PC-3M

value: prostate cancer cells

value: AR-independent

value: anti-Pol II, #C15200004, lot 001-12, Diagenode


title: CBMS1_d3_EpiL-CEBd1_160122

description:
Biological replicate 2 of 3.
Miura_FileName: CBMS1_d3_EpiL-CEBd1_160122
Miura_Project ID: P242_02_1
Miura_MEMO: RNA_CBMS1_d3diff_EpiLCEBd1_160122
processed data file: gene_fpkm.xlsx

value: CBA/MsM

value: day3 differentiated ESCs


title: LDN 3


title: 8 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 8

value: F


title: CBMS1_d2_EpiL-Cd2_160121

description:
Biological replicate 4 of 5.
Miura_FileName: CBMS1_d2_EpiL-Cd2_160121
Miura_Project ID: P242_01_1
Miura_MEMO: RNA_CBMS1_d2diff_EpiLCd2_160121
processed data file: gene_fpkm.xlsx

value: day2 differentiated ESCs


title: 6v2_stringent: H3K27ac VP16(10x) Pool2 rep2

value: endometrial carcinoma

value: Pool 2


title: ChIP_polII_siRNA_KMT9a_PC-3M


title: 168 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 168


title: PC-3M cells siRNA_KMT9a treated, biological replicate 3

description:
4c_PC-3M_plus_siRNA_KMT9a
Processed data file: CountsTable_PC3M.xlsx
Column header in processed data file: PC3M_siKMT9a_3_TagDir/

data_processing:
We aligned these reads to the hg19 build of the human genome using STAR
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files include the overall read count for a specific transcript (indicated by the NM accession number)

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

value: Prostate Cancer Cells

tag: treatment


title: PC-3M cells siRNA_KMT9a treated, biological replicate 2

description:
4b_PC-3M_plus_siRNA_KMT9a
Processed data file: CountsTable_PC3M.xlsx
Column header in processed data file: PC3M_siKMT9a_2_TagDir/


title: CBMS1_d7_EpiL-CEBd5_150817

description:
Biological replicate 3 of 5.
Miura_FileName: CBMS1_d7_EpiL-CEBd5_150817
Miura_Project ID: P215_13_1
Miura_MEMO: RNA_CBMS1_d7diff_EpiLCEBd5_150817
processed data file: gene_fpkm.xlsx

value: day7 differentiated ESCs


title: PC-3M cells siRNA_KMT9a treated, biological replicate 1

description:
4a_PC-3M_plus_siRNA_KMT9a
Processed data file: CountsTable_PC3M.xlsx
Column header in processed data file: PC3M_siKMT9a_1_TagDir/


title: CBMS1_d4_EpiL-CEBd2_160123

description:
Biological replicate 2 of 3.
Miura_FileName: CBMS1_d4_EpiL-CEBd2_160123
Miura_Project ID: P242_03_1
Miura_MEMO: RNA_CBMS1_d4diff_EpiLCEBd2_160123
processed data file: gene_fpkm.xlsx

value: day4 differentiated ESCs


title: CBMS1_d2_EpiL-Cd2_150812

description:
Biological replicate 3 of 5.
Miura_FileName: CBMS1_d2_EpiL-Cd2_150812
Miura_Project ID: P215_12_1
Miura_MEMO: RNA_CBMS1_d2diff_EpiLCd2_150812
processed data file: gene_fpkm.xlsx

value: embryonic stem cell


title: h3k27ac_vp160_pool3: H3K27ac VP16(10x) Pool3 rep1

value: Ishikawa

value: Pool 3


title: 159 genomic DNA from GBM xenograft

description: xenograft sample

source_name: xenograft 159

value: M


title: 5v1_stringent: H3K27ac VP16(10x) Pool1 rep2

value: Pool 1


title: HDN 4

value: Balb/c

value: Female

value: 8 weeks


title: PC-3M cells siRNA_Control, biological replicate 3

description:
3c_PC-3M_plus_siRNA_Control
Processed data file: CountsTable_PC3M.xlsx
Column header in processed data file: PC3M_sictr_3_TagDir/

value: control


title: 8vI_stringent: H3K27ac VP16(10x) Control/IL1RN rep2


title: ChIP_polII_CTD_S5ph_siRNA_KMT9a_PC-3M

tag: differentiation stage

value: prostate cancer cells

value: AR-independent

value: anti-Pol II CTD S5ph, #C15200007, lot 001-12, Diagenode


title: PC-3M cells siRNA_Control, biological replicate 2

description:
3b_PC-3M_plus_siRNA_Control
Processed data file: CountsTable_PC3M.xlsx
Column header in processed data file: PC3M_sictr_2_TagDir/

tag: passages


title: CBMS1_d2_EpiL-Cd2_150930

description:
Biological replicate 2 of 5.
Miura_FileName: CBMS1_d2_EpiL-Cd2_150930
Miura_Project ID: P215_10_1
Miura_MEMO: RNA_CBMS1_d2diff_EpiLCd2_150930
processed data file: gene_fpkm.xlsx

value: CBA/MsM

value: day2 differentiated ESCs


title: CBMS1_d0_ESC_p7_150813

description:
Biological replicate 3 of 3.
Miura_FileName: CBMS1_d0_ESC_p7_150813
Miura_Project ID: P215_11_1
Miura_MEMO: RNA_CBMS1_d0diff_ESC_p7_150813
processed data file: gene_fpkm.xlsx


title: h3k27ac_vp160_il1rn: H3K27ac VP16(10x) Control/IL1RN rep1

value: endometrial carcinoma


title: h3k27ac_vp160_pool2: H3K27ac VP16(10x) Pool2 rep1

value: Pool 2


title: CBMS1_d7_EpiL-CEBd5_150702

description:
Biological replicate 2 of 5.
Miura_FileName: CBMS1_d7_EpiL-CEBd5_150702
Miura_Project ID: P215_09_1
Miura_MEMO: RNA_CBMS1_d7diff_EpiLCEBd5_150702
processed data file: gene_fpkm.xlsx

value: day7 differentiated ESCs


title: MCF10A cells siRNA_KMT9a treated, biological replicate 3

description:
2c_MCF10A_plus_siRNA_KMT9a
Processed data file: CountsTable_MCF10A.xlsx
Column header in processed data file: 24_MCF10_A_siN6AMT1_out_TagDir/

source_name: MCF10A cells

value: Breast epithelial Cells


title: CP-1217: FVB_MMTV_Wnt1_125285_Perou

data_processing:
Reads were mapped to the Mm9 reference sequence. Hras, Kras, and Nras mutations were identified using the Integrative Genomics Viewer (IGV) from the Broad Institute.
Supplementary_files_format_and_content: no processed/abundance data was generated

source_name: mammary tumors

extract_protocol: RNAseq libraries were prepared from 26 MMTV-Wnt1 tumors using a TruSeq RNA kit (Illumina #RS-122-2001) before being submitted to the Lineberger Comprehensive Cancer Center Genomics Core to be run on the Illumina HiSeq 2000. Reads were mapped to the Mm9 reference sequence. Hras, Kras, and Nras mutations were identified using the Integrative Genomics Viewer (IGV) from the Broad Institute.

tag: tissue

value: mammary tumors


title: HDN 7


title: CP-1206: FVB_MMTV_Wnt1_183984_Perou


title: CBMS1_d7_EpiL-CEBd5_150905

description:
Biological replicate 1 of 5.
Miura_FileName: CBMS1_d7_EpiL-CEBd5_150905
Miura_Project ID: P215_08_1
Miura_MEMO: RNA_CBMS1_d7diff_EpiLCEBd5_150905
processed data file: gene_fpkm.xlsx

value: day6 differentiated ESCs


title: HDN 5


title: CBMS1_d6_EpiL-DEBd4_150904

description:
Biological replicate 1 of 3.
Miura_FileName: CBMS1_d6_EpiL-DEBd4_150904
Miura_Project ID: P215_07_1
Miura_MEMO: RNA_CBMS1_d6diff_EpiLCEBd4_150904
processed data file: gene_fpkm.xlsx

value: day5 differentiated ESCs


title: H3k27ac_off_il1rn_stringent: H3K27ac VP16(10x) Adjacent rep1

value: Ishikawa

value: Adjacent + IL1RN


title: MCF10A cells siRNA_KMT9a treated, biological replicate 2

description:
2b_MCF10A_plus_siRNA_KMT9a
Processed data file: CountsTable_MCF10A.xlsx
Column header in processed data file: 23_MCF10_A_siN6AMT1_out_TagDir/


title: CP-1211: FVB_MMTV_Wnt1_126355_Perou


title: h3k27ac_vp160_pool1: H3K27ac VP16(10x) Pool1 rep1

value: Pool 1


title: 3p3_stringent: H3K27ac P300 Pool3 rep2

value: Pool 3


title: MCF10A cells siRNA_KMT9a treated, biological replicate 1

description:
2a_MCF10A_plus_siRNA_KMT9a
Processed data file: CountsTable_MCF10A.xlsx
Column header in processed data file: 22_MCF10_A_siN6AMT1_out_TagDir/


title: CP-1210: FVB_MMTV_Wnt1_182281_Perou


title: HDN 3

value: Balb/c

value: Female

value: 8 weeks


title: h3k27ac_p300_pool3: H3K27ac P300 Pool3 rep1


title: CBMS1_d5_EpiL-CEBd3_150903

description:
Biological replicate 1 of 3.
Miura_FileName: CBMS1_d5_EpiL-CEBd3_150903
Miura_Project ID: P215_06_1
Miura_MEMO: RNA_CBMS1_d5diff_EpiLCEBd3_150903
processed data file: gene_fpkm.xlsx

value: day4 differentiated ESCs


title: CBMS1_d4_EpiL-CEBd2_150902

description:
Biological replicate 1 of 3.
Miura_FileName: CBMS1_d4_EpiL-CEBd2_150902
Miura_Project ID: P215_05_1
Miura_MEMO: RNA_CBMS1_d4diff_EpiLCEBd2_150902
processed data file: gene_fpkm.xlsx

value: CBA/MsM

value: day3 differentiated ESCs


title: CP-1209: FVB_MMTV_Wnt1_124328_Perou


title: CBMS1_d3_EpiL-CEBd1_150901

description:
Biological replicate 1 of 3.
Miura_FileName: CBMS1_d3_EpiL-CEBd1_150901
Miura_Project ID: P215_04_1
Miura_MEMO: RNA_CBMS1_d3diff_EpiLCEBd1_150901
processed data file: gene_fpkm.xlsx

value: day2 differentiated ESCs


title: MCF10A cells siRNA_Control, biological replicate 2

description:
1b_MCF10A_plus_siRNA_Control
Processed data file: CountsTable_MCF10A.xlsx
Column header in processed data file: 20_MCF10_A_sictrl_out_TagDir/

value: control


title: CP-1212: FVB_MMTV_Wnt1_172215_Perou


title: PC-3M cells siRNA_Control, biological replicate 1

description:
3a_PC-3M_plus_siRNA_Control
Processed data file: CountsTable_PC3M.xlsx
Column header in processed data file: PC3M_sictr_1_TagDir/

value: Prostate Cancer Cells


title: CP-1218: FVB_MMTV_Wnt1_123114_Perou


title: h3k27ac_p300_pool2: H3K27ac P300 Pool2 rep1

value: endometrial carcinoma

value: Pool 2


title: h3k27ac_vp160_adjacent: H3K27ac VP16(10x) Adjacent rep2

value: Adjacent


title: MCF10A cells siRNA_Control, biological replicate 1

description:
1a_MCF10A_plus_siRNA_Control
Processed data file: CountsTable_MCF10A.xlsx
Column header in processed data file: 19_MCF10_A_sictrl_out_TagDir/

value: Breast epithelial Cells


title: Input_KMT9b_siRNA_KMT9b_PC-3M

data_processing:
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using STAR
peak finding algorithm MACS
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle and bed files. The wig files include the read data mapped to the hg19 genome. The bed files contain the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input.

growth_protocol: Human PC-3M cells were maintained in RPMI medium supplemented with 10 % FBS and glutamine

value: prostate cancer cells

tag: phenotype

value: AR-independent

tag: chip antibody


title: h3k27ac_p300_pool1: H3K27ac P300 Pool1 rep1

tag: cell line

value: Ishikawa

value: Pool 1


title: CBMS1_d0_ESC_p7_150901

description:
Biological replicate 2 of 3.
Miura_FileName: CBMS1_d0_ESC_p7_150901
Miura_Project ID: P215_02_1
Miura_MEMO: RNA_CBMS1_d0diff_ESC_p7_150901
processed data file: gene_fpkm.xlsx

tag: cell type


title: 1p1_stringent: H3K27ac P300 Pool1 rep2


title: CP-1205: FVB_MMTV_Wnt1_183983_Perou

value: mammary tumors


title: Input_KMT9b_siRNA_Ctrl_PC-3M


title: CP-1213: FVB_MMTV_Wnt1_174861_Perou


title: CP-1215: FVB_MMTV_Wnt1_124326_Perou


title: MCF10A cells siRNA_Control, biological replicate 3

description:
1c_MCF10A_plus_siRNA_Control
Processed data file: CountsTable_MCF10A.xlsx
Column header in processed data file: 21_MCF10_A_sictrl_out_TagDir/


title: CBMS1_d0_ESC_p9_150901

description:
Biological replicate 1 of 3.
Miura_FileName: CBMS1_d0_ESC_p9_150901
Miura_Project ID: P215_01_1
Miura_MEMO: RNA_CBMS1_d0diff_ESC_p9_150901
processed data file: gene_fpkm.xlsx

tag: strain/background

value: embryonic stem cell


title: 4pI_stringent: H3K27ac P300 Control/IL1RN rep2


title: 2p2_stringent: H3K27ac P300 Pool2 rep2


title: CP-1207: FVB_MMTV_Wnt1_123070_Perou


title: EpiSC7_rep2_female

description: Biological replicate 2 of 2.

data_processing:
Read pairs were individually mapped to the mouse genome (UCSC mm9) using the hiclib pipeline (Imakaev et al., 2012) with iterative mapping method.
After read mapping, each side of the mapped reads was also applied to the hiclib pipeline. First, uniquely mapped paired-reads were assigned to HindIII fragments. Only those with correct orientations were considered valid pairs, and non-ligated and self-ligated read pairs were filtered out. Fragment-level filters were next applied to remove invalid reads: reads that started within 5 bp from the restriction sites, duplicated read pairs, extremely large and small restriction fragments (> 100 kbp and < 100 bp, respectively), and extremely high and low count restriction fragments (top 0.5% of all counts and zero counts, respectively).
Biological replicates were merged, and Hi-C contact heatmaps were generated in 200-kb or 40-kb non-overlapping genomic bins for both merged samples (mainly used for visualization) and for single biological replicates.
To correct the bias of the contact heatmaps, iterative correction was performed with the following steps: diagonal removal was applied to only the first diagonal (“removeDiagonal(0)”), bin removal was done by the sequence fraction (0.5), and finally high trans contacts (the fraction of the top 0.05% trans contacts) were removed. The bias-corrected contact heatmaps were used to generate the A/B compartment profiles (200-kb bins or 200-kb sliding windows at 40-kb interval) in each chromosome as previously described (Lieberman-Aiden et al., 2009) by the hiclib pipeline with a small modification in the ∆“doCisPCADomains(domaidunction=”lieverman-”)” function including observed / expected analysis, covariance matrix generation from the Pearson correlation matrix and principal component analysis. The first eigenvalues were used to identify A/B compartments (i.e. Hi-C PC1). Because positive and negative eigenvalues are arbitrary, correlation with the GC content was used to assign positive eigenvalues as ‘A compartment’ and negative eigenvalues as ‘B compartment’. After obtaining A/B compartment profile, quantile normalization was performed using the limma package (Ritchie et al., 2015).
Genome_build: UCSC mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph

source_name: EpiSC

extract_protocol:
Hi-C experiments were performed as previously reported with some modifications (Sofueva et al., 2013). Cells were fixed with 1% formaldehyde for 10 min at room temperature. Glycine was added to 0.125 M final concentration and incubated for 5 min at room temperature. Tubes were placed on ice for 15 min. Cells were washed in ice-cold PBS by centrifuging at 400 g at 4°C. Then, 1–2 x 10^6 fixed cell pellets were used for the following steps. Cell pellets were resuspended in 500 µl of 3C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40) with 1x protease inhibitor cocktail (Roche, 1873580), transferred to 1.5 ml Protein LoBind Tubes (Eppendorf) and incubated on ice for 20 min. The samples were spun down for 5 min at 1000 g at 4℃. After removing the supernatants carefully, pellets were resuspended in 212.5 µl of 1.2x NEBuffer 2 with 0.3% SDS and incubated for 1 h at 37°C in the Thermomixer C3 at 950 rpm (Eppendorf). Then, 25.5 µl of 20% Triton X-100 were added to 2% final concentration and the samples were incubated for 1 h at 37°C. Next, 400 U of HindIII (NEB, R0104S) was added and the samples were incubated overnight at 37°C in the Thermomixer C3 at 950 rpm. The next day, the samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 200 µl of 1x NEBuffer 2 with 300 U of HindIII and incubated for at least 8 h at 37°C in the ThermoMixer C3 at 950 rpm. The samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 200 µl of “Fill-in Mix” (1 x NEBuffer 2, 15 µM each of dATP, dGTP, dTTP and 15 µM of Biotin-14-dCTP (Invitrogen, 19518018), 25 U of Klenow (NEB, M0210S)) and incubated for 45 min at 37°C. After spinning down for 5 min at 4°C and removing the supernatants carefully, the pellets were resuspended in 100 µl of “Ligation Mix” (1x T4 DNA ligase buffer (NEB), 6 µl of T4 DNA ligase (1 U/µl, Invitrogen, 15224017)) and incubated overnight at 16°C. The sample volumes were brought up to ~300 µl by adding 10 mM Tris-HCl (pH 7.5) and RNaseA-treated for 30 min at 37°C by adding 3 µl of 10 mg/ml RNaseA. Reverse-crosslinking and proteinase K treatment were performed overnight at 65°C by adding 6.25 µl of 20 mg/ml Proteinase K. The next day, 6.25 µl of 20 mg/ml Proteinase K was added and incubated for 2 h at 65°C. Samples were then extracted twice with phenol/chloroform and once with chloroform. After this, 30 µl of 3 M sodium acetate (pH 5.2) was added and 825 µl of ice-cold EtOH was added. The samples were incubated overnight at –80°C and spun down for 30 min at 20,000 g at 4°C for DNA precipitation. After two 70% EtOH washes (add 1 ml, cfg for 20 min at 20,000 g at 4°C), the DNA pellets were resuspended in 30 µl of 10 mM Tris-HCl (pH 7.5).
For generating next-generation sequencing libraries, 2.5 µg of Hi-C DNA was used per library. To remove biotin from unligated ends, Hi-C DNA was mixed with 50 µl of “T4 DNA pol mix” (1x NEBuffer 2, 1x BSA, 100 µM dATP, 100 µM dGTP, 2.5 U of T4 DNA polymerase (NEB, M0203S)) and incubated for 2 h at 12°C. The sample volumes were brought up to 100 µl by adding 10 mM Tris-HCl (pH 7.5). Samples were extracted once each with phenol/chloroform and chloroform. After EtOH precipitation, the DNA pellets were resuspended in 130 µl of nuclease-free water. DNA samples were sheared (300–500 bp) using the following settings in Covaris S220 (Duty Factor: 5.0, Peak incident power: 175 W, Cycles per burst: 200, Treatment time: 120 sec) using microTUBE with snap cap (Covaris, 520045). After DNA shearing, DNA size selection was performed using AMPure XP beads (Beckman Coulter). Using the size-selected DNA samples, biotin pull-down and sequencing library preparations were performed using 30 µl of Dynabeads MyOne Streptavidin C1 (Invitrogen, 65001) and a part of Nextera Mate Pair Sample Preparation kit (Illumina, FC-132-1001) following the kit’s protocol at half scale. For library amplification, KAPA Real-Time Amplification Kits (KAPA BIOSYSTEMS, KK2701) were used to determine the optimal PCR cycles (9–12 cycles) and the final PCR products were purified by AMPure XP beads.

value: epiblast stem cell

value: female


title: h3k27ac_p300_adjacent_r2: H3K27ac P300 Adjacent rep2


title: Input_KMT9a_siRNA_Ctrl_PC-3M


title: CP-1204: FVB_MMTV_Wnt1_182352_Perou


title: h3k27ac_p300_il1rn: H3K27ac P300 Control/IL1RN rep1


title: EpiSC7_rep1_female

description: Biological replicate 1 of 2.


title: Input_KMT9a_siRNA_KMT9a_PC-3M


title: MEF2_rep2_male

description: Biological replicate 2 of 2.

source_name: MEF

value: mouse embryonic fibroblast

value: male


title: CP-1216: FVB_MMTV_Wnt1_125673_Perou


title: h3k27ac_p300_adjacent_r1: H3K27ac P300 Adjacent rep1


title: Input_H4K20me3_siRNA_Ctrl_PC-3M


title: CBMS1_d2_EpiL-Cd2_150831

description:
Biological replicate 1 of 5.
Miura_FileName: CBMS1_d2_EpiL-Cd2_150831
Miura_Project ID: P215_03_1
Miura_MEMO: RNA_CBMS1_d2diff_EpiLCd2_150831
processed data file: gene_fpkm.xlsx

value: CBA/MsM

value: day3 differentiated ESCs


title: Input_H4K20me3_siRNA_KMT9a_PC-3M


title: CP-1208: FVB_MMTV_Wnt1_123738_Perou


title: MEF1_rep2_female

description: Biological replicate 2 of 2.


title: Input_H4K12me1_siRNA_KMT9a_PC-3M


title: CP-1214: FVB_MMTV_Wnt1_175317_Perou


title: MEF2_rep1_male

description: Biological replicate 1 of 2.


title: Input_H4K12me1_siRNA_Ctrl_PC-3M

value: control


title: CP-1219: FVB_MMTV_Wnt1_123420_Perou


title: ChIP_KMT9b_siRNA_KMT9b_PC-3M

value: anti-KMT9b, #28358, lot 27022018, Schüle Lab


title: CP-1031: FVB_MMTV_Wnt1_168512_Perou


title: CBMS1_rep3_d7_EpiLC_EB_d5

description: Biological replicate 3 of 3.

value: day7 differentiated ESCs


title: CBMS1_rep2_d6_EpiLC_EB_d4

description: Biological replicate 2 of 2.

value: day6 differentiated ESCs


title: CP-1030: FVB_MMTV_Wnt1_172499_Perou


title: A549 Erlotinib repeact 2

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

description:
A549 cells treated with Erlotinib repeat 2
Gene_Exp_Erlotinib.diff

data_processing:
tophat2 with default parameters
samtools to sort and convert the file format
cufflinks with default parameters
cuffmerge with default parameters
cuffdiff with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene_Exp_Compound_4a.diff, normalized expression values for compound 4a
Supplementary_files_format_and_content: Gene_Exp_Compound_4b.diff, normalized expression values for compound 4d
Supplementary_files_format_and_content: Gene_Exp_Erlotinib.diff, normalized expression values for Erlotinib

source_name: lung cancer

growth_protocol: density 1.6e6 A549 cells in 15cm dish, 24 hours, to 70% confluentence

extract_protocol:
2100 Bioanalyzer for quality check, DNaseI (Takara, Japan) for digestion at 37 C and 30 mins
100ng purified RNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: treatment with compounds or DMSO, after 24 hours

value: lung cancer


title: A549 Erlotinib repeact 1

description:
A549 cells treated with Erlotinib repeat 1
Gene_Exp_Erlotinib.diff


title: ChIP_KMT9b_siRNA_Ctrl_PC-3M

value: prostate cancer cells


title: A549 Compound 4d repeat 1

description:
A549 cells treated with Compound 4d repeat 1
Gene_Exp_Compound_4d.diff


title: ChIP_KMT9a_siRNA_KMT9a_PC-3M

value: AR-independent

value: anti-KMT9a, #27630, lot 20062017, Schüle Lab


title: A549 Compound 4a repeat 1

description:
A549 cells treated with Compound 4a repeat 1
Gene_Exp_Compound_4a.diff


title: ChIP_KMT9a_siRNA_Ctrl_PC-3M


title: CP-1033: FVB_MMTV_Wnt1_167209_Perou

first: Charles


title: A549 DMSO repeat 2

description:
A549 cells treated with DMSO repeat 2
Gene_Exp_Compound_4a.diff


title: ChIP_H4K20me3_siRNA_KMT9a_PC-3M

value: anti-H4K20me3, #C15410207, lot A2730P, Diagenode


title: CBMS1_rep3_d0_Undiff_P7

description: Biological replicate 3 of 3.


title: A549 DMSO repeat 1

description:
A549 cells treated with DMSO repeat 1
Gene_Exp_Compound_4a.diff


title: CBMS1_rep2_d7_EpiLC_EB_d5

description: Biological replicate 2 of 3.


title: CP-1032: FVB_MMTV_Wnt1_168508_Perou

value: mammary tumors


title: CBMS1_rep2_d4_EpiLC_EB_d2

description: Biological replicate 2 of 2.

value: day4 differentiated ESCs


title: ChIP_H4K20me3_siRNA_Ctrl_PC-3M


title: CP-1034: FVB_MMTV_Wnt1_169918_Perou


title: A549 Compound 4d repeat 2

description:
A549 cells treated with Compound 4d repeat 2
Gene_Exp_Compound_4d.diff


title: MEF1_rep1_female

description: Biological replicate 1 of 2.


title: SB.DOX_rep2

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: Riken

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using BWA
mapped CAGE tags were counted with respect to the FANTOM5-CAT TSSs (Hon et al., Nature 2017) to give a unit of CAGE tag start site (CTSS).
Genome_build: hg38
Supplementary_files_format_and_content: DEG_summary.txt contains result from edgeR.

growth_protocol: MCF10A cells were grown in DMEM/F12(1:1) medium with 5% horse serum, epidermal growth factor (10 ng/mL), cholera toxin (100 ng/mL) and insulin (0.023 IU/mL)

extract_protocol:
Total RNA was extracted by Qiagen miRNeasy Mini Kit (QIAGEN Inc.) according to the manufacturer’s instructions.
CAGE libraries were prepared as previously described (Murata et al., Methods Mol Biol 2014). Briefly, 3 μg of total RNA from each sample was subjected to reverse transcription using SuperScript III Reverse Transcriptase (Life Technologies, Carlsbad, CA, USA) with random primers. The 5-end cap structure were biotinylated by sequential oxidation with NaIO4 and biotinylation with biotin hydrazide (Vector Laboratories, Burlingame, CA, USA). After RNase I treatment (Promega, Madison, WI, USA), the biotinylated cap structure was captured with streptavidin-coated magnetic beads (Life Technologies). After ligation of 5’ and 3’ adaptors, second-strand cDNAs were synthesized with DeepVent (exo−) DNA polymerase (New England BioLabs, Ipswich, MA, USA). The double-stranded cDNAs were treated with exonuclease I (New England BioLabs) and purified.

treatment_protocol: MCF10A cells were treated by combinations of perturbations as follows: recombinant TGF-beta (200 nM) for 4 weeks, CRISPR/Cas9-mediated ZEB1 knockout, doxycycline-inducible expression of exogenous ZEB1, and TGF-beta type1 receptor inhibiotr (SB-431542, 10microM) treatment

value: mammary epithelial cells

tag: transgene

value: inducible ZEB1

value: TGF-beta type1 receptor inhibitor (SB-431542) + DOX


title: ChIP_H4K12me1_siRNA_KMT9a_PC-3M


title: CBMS1_rep1_d6_EpiLC_EB_d4

description: Biological replicate 1 of 2.


title: CP-1035: FVB_MMTV_Wnt1_171984_Perou


title: CP-1036: FVB_MMTV_Wnt1_171979_Perou


title: CBMS1_rep2_d5_EpiLC_EB_d3

description: Biological replicate 2 of 2.

value: day5 differentiated ESCs


title: ChIP_H4K12me1_siRNA_Ctrl_PC-3M


title: CBMS1_rep1_d5_EpiLC_EB_d3

description: Biological replicate 1 of 2.

value: CBA/MsM


title: SB.DOX_rep1


title: CP-907: FVB_MMTV_Wnt1_171053_Perou


title: SB_rep2

value: TGF-beta type1 receptor inhibitor (SB-431542)


title: FBs RNA-Seq JR101414

city: Cleveland

first: Emina

last: Huang

state: OH

address: 9500 Euclid Ave

department: Stem Cell

institute: Lerner Research Institute/Cleveland Clinic

data_processing:
FastQC (version 0.9.5) was used to check the quality of reads (*.Fastq) --> no need of trimming
TopHat (version 2.0.10) was used to align (*.bam) files
Cufflinks to generate assembled transcripts (*.gtf)
Cuffmerge to merge (*.gtf)+ (*.bam) files
Cuffdiff to generate differentially expressed genes(*.diff)
produce edgeR files
Supplementary_files_format_and_content: CPM

source_name: Primary adult intestinal FBs

growth_protocol: Carpentino JE et al Cancer Research 2009 10.1158/0008-5472.CAN-09-1132

extract_protocol:
Isolated fibrobllasts in passages 3-5 (NL n=5 CT n=8 and CA n=5) were isolated/propagated and harvested prior to RNA extraction and standard sequencing/processing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: tissue origin

value: FBs cultivated from patient-derived cancerous colon mucosa

value: 3-5 passages


title: A549 Compound 4a repeat 2

description:
A549 cells treated with Compound 4a repeat 2
Gene_Exp_Compound_4a.diff


title: DMSO.DOX_rep2

value: DMSO + DOX


title: CP-905: FVB_MMTV_Wnt1_169927.1_Perou


title: SB_rep1


title: CP-906: FVB_MMTV_Wnt1_169927.2_Perou


title: DMSO.DOX_rep1


title: FBs RNA-Seq JW82514


title: FBs RNA-Seq CR8614

value: Colorectal cancer fibroblast cell line


title: CBMS1_rep1_d4_EpiLC_EB_d2

description: Biological replicate 1 of 2.


title: CBMS1_rep2_d2_EpiLC

description: Biological replicate 2 of 2.

value: day2 differentiated ESCs


title: FBs RNA-Seq JA11214


title: CBMS1_rep2_d3_EpiLC_EB_d1

description: Biological replicate 2 of 2.

value: day3 differentiated ESCs


title: ILC3-a-DR3-rep-2

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Reads were mapped to Mouse Genome Assembly GRCm38.p5 by STAR v2.5.
Gene and isoform expression quantification was called by RSEM v1.2 with default parameters on GENCODE mouse M16 gene annotation file.
Differential expression analysis was performed by Bioconductor package edgeR v3.18.1.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Csv file indicates ratios of differential gene expression in a-DR3 treated versus wild-type group.

source_name: lamina proprial lymphocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen).Total RNA sample is digested by DNaseІ (NEB), and purified by oligo-dT beads (Dynabeads   mRNA purification kit, Invitrogen)
Poly (A)-containing mRNA were fragmented into 130bp   with First Strand buffer. First-strand cDNA is generated by N6 primer, First Strand Master Mix and   Super Script II reverse transcription(Invitrogen) (Reaction condition：25℃ for 10 min；42℃ for 40   min；70℃for 15 min). Then add Second Strand Master Mix to synthesize the second-strand cDNA   (16℃ for 1h). Purified the cDNA with Ampure XP Beads (AGENCOURT), then combine with End   Repair Mix, incubate at 20℃for 30min. Purified and add A-Tailing Mix, incubate at 37℃ for 30   min. Then combine the Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligate   reaction at 20℃for 20 min. Several rounds of PCR amplification with PCR Primer Cocktail and   PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products are   purified with Ampure XP Beads (AGENCOURT).

tag: genotype/variation


title: CBMS1_rep2_d0_Undiff

description: Biological replicate 2 of 3.

value: embryonic stem cell


title: DMSO_rep2

value: DMSO


title: FBs RNA-Seq CR7914

value: Colorectal adenocarcinoma fibroblast cell line


title: CBMS1_rep1_d7_EpiLC_EB_d5

description: Biological replicate 1 of 3.

value: day7 differentiated ESCs


title: ILC3-a-DR3-rep-1


title: FBs RNA-Seq RM10114

value: FBs cultivated from patient-derived colitic colon mucosa


title: ILC3-PBS-rep-2

value: PBS