title: TL-Om1_shCtrl_H3K27me3

source_name: H3K27me3 ChIP DNA from TL-Om1_shCtrl


title: TL-Om1_shEZH2_SUZ12

status: Public on Oct 03 2019

type: genomic

city: Minato-ku

first: Makoto

last: Yamagishi

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: The University of Tokyo

hyb_protocol: Hybridization was performed at 65°C for 40h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with Agilent Oligo aCGH/ChIP-on-chip Wash Buffer 1 for 5min and with Agilent Oligo aCGH/ChIP-on-chip Wash Buffer 2 for 5min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner C using the two color scan setting for 2x400K microarray slides (Scan Area: 61x21.6 mm, Scan resolution: 3 um, Dye channel: red and green, Tiff: 16bit, XDR ratio: NoXDR)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 using default parameters (protocol: ChIP_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: genomic DNA

organism: Homo sapiens

source_name: SUZ12 ChIP DNA from TL-Om1_shEZH2

label_protocol: Labeled DNA was prepared from 2.6 μg of amplified DNA using SureTag DNA Labeling Kit according to the manufacturer's instructions.

extract_protocol: 1×10E7 cells were cross-linked in fixing solution. After 15 min incubation at room temperature, cross-linking was stopped by adding 1.375 M glycine. The cells were centrifuged for 5 min, 1,400 × g at 4°C. The supernatant was discarded and the pellet was washed two times in PBS. After the washes, cell pellets were resuspended in LB1 (50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation for 5 min, 1,400 × g at 4°C, the pellet was resuspended in LB2 (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at room temperature. After centrifugation for 5 min, 1,400 × g at 4°C, the nuclei were resuspended in micrococcal nuclease digestion buffer and incubated in 37°C to digest chromatin to the appropriate size fragments. Digestion was stopped by adding 0.5 M EDTA. After centrifugation, nuclei pellets were resuspended in LB3 (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-Lauroylsarcosine) and sonicated for 10 min. After sonication and 10 min high-speed centrifugation, sheared chromatin was recovered in the supernatant.

tag: cell type

value: ATL cell line

source_name: Input DNA from TL-Om1_shEZH2


title: monocytes.CON-7

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
CD14+CD66bneg cells
CON-7

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

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

data_processing:
Rstudio
the normalization method: Average Beta

label: Cy3, Cy5

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from sorted monocytes using the ReliaPrep FFPE gDNA Miniprep System (Promega) according to standard instructions

tag: sofa

tag: Sex

value: M

tag: age

tag: donor

value: HD

tag: batch


title: monocytes.CON-6

description:
CD14+CD66bneg cells
CON-6


title: TL-Om1_shEZH1_SUZ12

source_name: SUZ12 ChIP DNA from TL-Om1_shEZH1

source_name: Input DNA from TL-Om1_shEZH1


title: Primary human fibroblasts  Fib_27_bsl_RNA

type: SRA

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

description:
Fib_27_bsl_RNA
poly(A) RNA

library_source: transcriptomic

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq V2.19.0.316 and the adaptors were trimmed using Trimmomatic45 V0.36, retaining reads longer than 20 nt post-clipping. RNA-seq reads were further clipped with FASTX Toolkit V0.0.14 to 29nt, to allow comparison directly with Ribo-seq reads. Reads were aligned using bowtie46 to known rRNA, tRNA and mt-rRNA sequences (RNACentral47, release 5.0), aligned reads were filtered out to obtain only RPFs. Alignment to the human genome (hg38) was done using STAR48. Gene expression was quantified on the CDS (coding sequence region) using uniquely mapped reads (Ensembl database release GRCh38 v86 combined with additional transcripts from RefSeq GRCh38, latest version downloaded January 2018) with feature counts49. Genes with mean transcripts per million mapped reads, TPM < 1 in either RNA-seq or Ribo-seq across all conditions were removed before downstream analysis. Ribotaper50 was used to obtain the in-frame reads around the start and stop codon. These p-sites were then visualized across samples and genes. Heatmap for the ribosome drop-off was generated using pheatmap 1.0.8 R package51. Data quality check was done using MultiQC52. Principal component analysis was carried out using prcomp function in R. Individual gene batch effect for ITGA7 was removed using limma package53 in R.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix file consisting of genes as rows and samples as columns

molecule: polyA RNA

source_name: Patient 2

extract_protocol:
Human atrial fibroblasts were prepared and cultured as described previously12. All the experiments were carried out at low cell passage (<P4). In all experiments, cells were starved in serum-free DMEM for 16 hours prior to TGFβ1 stimulation. Stimulated fibroblasts were compared to unstimulated fibroblasts that have been grown for the same duration under the same conditions (serum-free DMEM), but without the stimuli.
Ribosome profiling was performed as previously described16. Briefly, snap-frozen cell pellets or 50-100 mg of tissue, previously powdered under liquid nitrogen, were lysed in 1ml cold lysis buffer (formulation as in TruSeq Ribosome Profile, Illumina) supplemented with 0.1mg/ml cycloheximide (CHX) to stabilize ribosomal subunits and prevent post-lysis translocation. Homogenized and cleared lysates were then footprinted with Truseq Nuclease (Illumina) according to manufacturer’s instructions. Ribosomes were purified using Illustra Sephacryl S400 columns (GE Healthcare) and the protected RNA fragments were extracted with standard phenol:chloroform:isoamylalcohol technique. Following ribosomal RNA removal (Mammalian RiboZero Magnetic Gold, Illumina), sequencing libraries were prepared out of the footprinted RNA. Ribo-seq libraries were pooled to perform multiplex sequencing on Illumina Hiseq machines. To prepare polyA+ RNA-seq libraries from primary cardiac fibroblasts, total RNA was extracted with Trizol from one 10cm dish per condition. Following cleanup with RNeasy kit (Qiagen), ~500ng of each sample were further processed with the Truseq Stranded mRNA kit (Illumina). Barcoded RNA-seq libraries were pooled and sequenced on the Illumina HiSeq platform.
The RNAseq data for the heart tissue was derived from Henig et al24. To prepare polyA+ RNA-seq libraries from primary cardiac fibroblasts, total RNA was extracted with Trizol from one 10cm dish per condition. Following cleanup with RNeasy kit (Qiagen), ~500ng of each sample were further processed with the Truseq Stranded mRNA kit (Illumina). Barcoded RNA-seq libraries were pooled and sequenced on the Illumina HiSeq platform.

value: Cardiac fibroblasts

tag: sequencing

value: RNA-seq


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_34_2hr_RNA

description:
Fib_34_2hr_RNA
poly(A) RNA

source_name: Patient 3


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_27_2hr_RNA

description:
Fib_27_2hr_RNA
poly(A) RNA


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_27_24hr_RNA

description:
Fib_27_24hr_RNA
poly(A) RNA


title: TL-Om1_OR-S1_H3K27ac

source_name: H3K27ac ChIP DNA from TL-Om1_OR-S1

source_name: Input DNA from TL-Om1_OR-S1


title: monocytes.CON-5

description:
CD14+CD66bneg cells
CON-5


title: Primary human fibroblasts  Fib_24_bsl_RNA

description:
Fib_24_bsl_RNA
poly(A) RNA

source_name: Patient 1


title: TL-Om1_DMSO_H3K27ac

source_name: H3K27ac ChIP DNA from TL-Om1_DMSO

source_name: Input DNA from TL-Om1_DMSO


title: monocytes.SIRS-1

description:
CD14+CD66bneg cells
SIRS-1

value: SIRS


title: monocytes.CON-4

description:
CD14+CD66bneg cells
CON-4

value: F


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_24_24hr_RNA

description:
Fib_24_24hr_RNA
poly(A) RNA


title: TL-Om1_DMSO_RNApolII

source_name: RNApolII ChIP DNA from TL-Om1_DMSO


title: TL-Om1_OR-S1_RNApolII

source_name: RNApolII ChIP DNA from TL-Om1_OR-S1


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_24_2hr_RNA

description:
Fib_24_2hr_RNA
poly(A) RNA


title: monocytes.CON-3

description:
CD14+CD66bneg cells
CON-3


title: TL-Om1_OR-S1_H2AK119ub

source_name: H2AK119ub ChIP DNA from TL-Om1_OR-S1


title: Primary human fibroblasts  Fib_41_bsl

description:
Fib_41_bsl
Ribosome protected fragment

molecule: total RNA

source_name: Patient 4

value: Ribo-seq


title: monocytes.CON-2

description:
CD14+CD66bneg cells
CON-2


title: monocytes.CON-1

description:
CD14+CD66bneg cells
CON-1


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_41_24hr

description:
Fib_41_24hr
Ribosome protected fragment


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_41_2hr

description:
Fib_41_2hr
Ribosome protected fragment


title: TL-Om1_OR-S1_RelB

source_name: RelB ChIP DNA from TL-Om1_OR-S1


title: TL-Om1_OR-S1_RelA

source_name: RelA ChIP DNA from TL-Om1_OR-S1


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_34_24hr

description:
Fib_34_24hr
Ribosome protected fragment


title: TL-Om1_DMSO_RelA

source_name: RelA ChIP DNA from TL-Om1_DMSO


title: TL-Om1_DMSO_RelB

source_name: RelB ChIP DNA from TL-Om1_DMSO


title: Primary human fibroblasts  Fib_34_bsl

description:
Fib_34_bsl
Ribosome protected fragment


title: Primary human fibroblasts  Fib_27_bsl

description:
Fib_27_bsl
Ribosome protected fragment


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_34_2hr

description:
Fib_34_2hr
Ribosome protected fragment


title: Aged_V2

city: Beijing

first: Hao

last: Wang

address: No.49 Huayuan North Road

country: China

institute: Peking University Third Hosptial

description: miRNA

data_processing:
Base callings performed using Illumina softwares
Sequenced reads were trimmed for 3' adaptor sequence and masked low-quality sequence using Fastx-Toolkit to gain clean small RNA reads
Clean reads performed identical sequences merge, then compared with Rfam and miRBase to identify miRNAs
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The xls files summary the counts and TPM value of each miRNA in all 20 samples

organism: Rattus norvegicus

source_name: plasma

extract_protocol:
Plasma was isolated from EDTA-anticoagulant blood, and RNA was harvested using TRIzol reagent
RNA libraries were prepared for sequencing using TruseqTM Small RNA sample prep Kit

tag: tissue

value: plasma

value: aged (22-months)

tag: vascular origin

value: vein

tag: strain

value: Sprague-Dawley


title: Aged_V5

description: miRNA


title: Aged_V3

description: miRNA


title: HUT102_OR-S2_EZH2

source_name: EZH2 ChIP DNA from HUT102_OR-S2

value: HTLV-1 infected cell line

source_name: Input DNA from HUT102_OR-S2


title: Aged_V4

description: miRNA


title: Aged_V1

description: miRNA


title: HUT102_DMSO_EZH2

source_name: EZH2 ChIP DNA from HUT102_DMSO

source_name: Input DNA from HUT102_DMSO


title: TL-Om1_DMSO_H2AK119ub

source_name: H2AK119ub ChIP DNA from TL-Om1_DMSO


title: Aged_A5

description: miRNA

value: artery


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_27_2hr

description:
Fib_27_2hr
Ribosome protected fragment

source_name: Patient 2


title: Aged_A4

description: miRNA


title: HUT102_DMSO_EZH1

source_name: EZH1 ChIP DNA from HUT102_DMSO


title: HUT102_OR-S1_H3K27me3

source_name: H3K27me3 ChIP DNA from HUT102_OR-S1

source_name: Input DNA from HUT102_OR-S1


title: Primary human fibroblasts  Fib_24_bsl

description:
Fib_24_bsl
Ribosome protected fragment

source_name: Patient 1


title: Aged_A3

description: miRNA


title: Aged_A2

description: miRNA


title: DLCL2_OR-S2_EZH1

source_name: EZH1 ChIP DNA from DLCL2_OR-S2

value: DLBCL cell line

source_name: Input DNA from DLCL2_OR-S2


title: HUT102_DMSO_H3K27me3

source_name: H3K27me3 ChIP DNA from HUT102_DMSO


title: Ctrl_V5

description: miRNA

value: young (8-weeks)


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_24_2hr

description:
Fib_24_2hr
Ribosome protected fragment


title: DLCL2_OR-S1_EZH1

source_name: EZH1 ChIP DNA from DLCL2_OR-S1

source_name: Input DNA from DLCL2_OR-S1


title: SGI_9

type: RNA

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

hyb_protocol: (according to user manual GeneChip® 3' IVT PLUS Reagent Kit) 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: CEL files were analysed using the affy R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: biotin

source_name: ML-2 cells, treated with SGI-110 for 33 h

label_protocol: The Affymetrix Gene Chip 3´IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA. Label : Biotin

growth_protocol: ML-2 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum, 1% penicillin/streptomycin and 1% sodium pyruvate.

extract_protocol: RNA was isolated using the PeqGold Total RNA Kit and the PeqGOLD DNAase digest kit (Peqlab, Erlangen, Germany) following the manufacturer's protocol.

treatment_protocol: ML-2 cells were pre-treated with 2 µM SGI-110 or equal volume of solvent for 24 h, followed by addition of 5 µM ASTX660 or equal volumen of solvent for another 9 h.

tag: cell line


title: SGI_2


title: Kombi_9

source_name: ML-2 cells, pre-treated with SGI-110 for 24 h, followed by addition of ASTX660 for another 9 h


title: Ctrl_V4

description: miRNA

source_name: plasma


title: SGI_13


title: Kombi_2


title: ctrl_9

source_name: ML-2 cells,solvend-treated control


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_27_24hr

description:
Fib_27_24hr
Ribosome protected fragment


title: DLCL2_GSK126_EZH1

source_name: EZH1 ChIP DNA from DLCL2_GSK126

source_name: Input DNA from DLCL2_GSK126


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_24_24hr

description:
Fib_24_24hr
Ribosome protected fragment


title: HUT102_OR-S1_EZH1

source_name: EZH1 ChIP DNA from HUT102_OR-S1


title: DLCL2_DMSO_EZH1

source_name: EZH1 ChIP DNA from DLCL2_DMSO

source_name: Input DNA from DLCL2_DMSO


title: Ctrl_V3

description: miRNA


title: DLCL2_OR-S2_H3K27me3

source_name: H3K27me3 ChIP DNA from DLCL2_OR-S2


title: WIBR3 Naïve rep1

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

description: WIBR3 Naïve

data_processing:
STAR was used to map sequencing reads to human reference genome (Ensembl annotation of hg19 assembly).
Read counts over transcripts were calculated using HTSeq v.0.6.0 based on Ensembl annotation of hg19 genome.
Differential expression analysis was performed using EdgeR.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Tab-delimited tables of RPKM values

source_name: human embryonic stem cells

growth_protocol: Conventional primed human ESCs (WIBR3) and iPSCs (GEN1C) were maintained on Matrigel (Corning) coated dishes in mTeSR edium (Stem Cell Technologies) and passaged using gentle cell dissociation reagent (Stem Cell Technologies). For maintenance, cells were passaged every 4-5 days. Established naïve hESC lines were cultured on irradiated CF-1 MEFs (2.5x106 cells per 9.5 cm2) in 5i/LA medium and passaged every 6-7 days. Cells were feeded daily with fresh medium. 5i/LAF medium contained a 50:50 mixture of DMEM/F-12 (Life Technologies) and Neurobasal medium (Life Technologies) containing 1x N2 supplement (Life Technologies), 1x B27 supplement (Life Technologies), 10 ng/mL bFGF (Peprotech), 1% nonessential amino acids (Life Technologies), 1mM GlutaMAX (Life Technologies), penicillin-streptomycin (Life Technologies), 0.1 mM beta-mercaptoethanol (Life Technologies), 50 μg/mL BSA (Life Technologies), 0.5 μM IM-12 (Axon Medchem), 0.5 μM SB590885 (Axon Medchem), 1 μM WH-4-023 (Axon Medchem), 10 μM Y-27632 (Axon Medchem), 20 ng/mL Activin A (Peprotech), 20 ng/mL rhLIF (Peprotech), 0.5% KSR (Life Technologies) and 0.5 or 1 μM PD0325901 (Axon Medchem)

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen). RNA was eluted from the columns using RNase-free water and quantified using a Nanodrop ND-1000.
RNA sequencing libraries were prepared using Ribo-Zero rRNA Removal Kit (H/M/R) (Illumina Cat#: MRZH11124) and NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#: E7420).  The total RNA input amount for the RiboZero kit was 1 m total.  The rRNA input for library construction was 50 ng total.  Libraries were amplified for 14 cycles.  Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit.  Libraries were quantified using the Kapa Biosystems Library Quantification kit (Catalog Number KK4828) and the BioRad CFX96 instrument.

treatment_protocol: Cells were harvested following acutase treatment and processed for total RNA extraction

value: naive hESCs


title: Ctrl_V2

description: miRNA


title: Ctrl_V1

description: miRNA


title: DLCL2_OR-S1_H3K27me3

source_name: H3K27me3 ChIP DNA from DLCL2_OR-S1


title: Aged_A1

description: miRNA


title: MA9+EV_ChIPseq_H3K9me3_1

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

library_source: genomic

data_processing:
Quality control performed on fastq files using FastQC version 0.11.7
RNA-seq fastq files were trimmed for quality using Cutadapt version 1.18, parameters = -q20,20 --minimum-length 30; ATAC-seq and ChIP-seq fastq files were trimmed for quality, adapter removal, and polyG removal using AfterQC version 0.9.6, parameters = -q20 -u 19 -p19 -s 25
RNA-seq fastq files were aligned to the mouse genome using STAR version 2.6.0c, parameters = genomeGenerate: --sjdbOverhang 49, Alignment: --outSamtype BAM SortedByCoordinate; ATAC-seq and ChIP-seq files were aligned to the mouse genome using Bowtie2 version 2.3.4.3, parameters = --very-sensitive -X 2000
RNA-seq aligned BAM files were assigned to genes and features were counted using HTSeq 0.11.0, parameters= -s reverse -r pos
RNA-seq count files were analyzed for differential expression using DESeq2 version 3.8, parameters = alpha = 0.05 lfcThreshold = log2(1.5)
ChIP-seq and ATAC-seq aligned BAM files were sorted and filterd for quality using SAMtools version 1.9, parameters = view -b -q 25 -f 0x2
ChIP-seq and ATAC-seq filtered BAM files had duplicates removed using Picard version 2.18.19
ChIP-seq and ATAC-seq filtered and deduplicated BAM files were used for peak calling using MACS version 2.1.2; 10% input was used as control for ChIP-seq experiments; parameters varied for different conditions: for H3K9ac ChIP-seq =  -f BAMPE -g mm --keep-dup all; for H3K9me3 and H3K79me2 ChIP-seq = -f BAMPE -g mm --scale-to-large --braod --keep-dup all; for ATAC-seq = -f BAM -g mm --nomodel --shift -100 --extsize 200 --keep-dup all
ChIP-seq BAM files were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000
ATAC-seq pileup files from MACS peak calling were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --extendReads
Genome_build: GRCm38 (M20 build from GENCODE)
Supplementary_files_format_and_content: RNAseq counts files contain the HTSeq assigned genes and count from the aligned BAM files; ChIP-seq and ATAC-seq BAM files contain the filtered and deduplicated aligned reads to the mouse genome.

organism: Mus musculus

growth_protocol:
AML cell line generated from mouse bone marrow and grown in culture for 8-12 weeks
MLL-AF9+SETDB1 or MLL-AF9+MSCVpuroEmpty Vector (EV) control cells were generated by harvesting lin- mouse BM and spininfecting with MLL-AF9 and either SETDB1 or EV. Cells were selected for ~3-6 weeks using puromycin in IMDM supplemented with IL-3, SCF, and pen/strep.

extract_protocol:
Cells were fixed with 1%paraformaldehyde, the fixation was quenched with glycine, and the fixed cells were snap-frozen and stored at -80C. Cells were slow thawed on ice for 15 minutes, then lysed in 1% SDS lysis buffer. Chromatin was sheared on a water bath sonicator, and IPs were performed using the indicated antibodies and protein G magnetic beads. DNA was decrosslinked and purified using Qiagen PCR purification kit.
Libraries were prepped using 5ng DNA and the iDeal library prep kit. Amplification cycles of the library preps were optimized using qPCR.

tag: tissue source

value: bone marrow

tag: cell line background

value: MLL-AF9 (MA9) acute myeloid leukemia cell line

tag: retroviral transduction

value: MLL-AF9 + EV control

tag: chip antibody


title: GEN1C sgDDX6 TGFBi rep2

description: GEN1C sgDDX6 + TGFBi

source_name: human induced pluripotent stem cells

value: primed hiPSCs


title: Ctrl_A5

description: miRNA


title: DLCL2_GSK126_H3K27me3

source_name: H3K27me3 ChIP DNA from DLCL2_GSK126


title: GEN1C sgDDX6 TGFBi rep1

description: GEN1C sgDDX6 + TGFBi


title: WIBR3 Naïve rep2

description: WIBR3 Naïve


title: ctrl_13


title: ASTX_9

source_name: ML-2 cells, treated with ASTX660 for 9 h


title: ctrl_2


title: GEN1C sgCTRL TGFBi rep2

description: GEN1C sgCTRL + TGFBi


title: ASTX_2


title: Kombi_13


title: wild-type BMDM to osteoclast differentiation at day 5

city: Ann Arbor

first: Lingxin

last: Zhu

state: Michigan

address: 210 Washtenaw Ave, Life Sciences Institute, Room 5008

institute: Univeristy of Michigan in Ann Arbor

description: Gene expression data

hyb_protocol: Following labeling procedure, 2.75 ug of cDNA were hybridized at 48C on Mouse ST 2.1 Arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: RMA values were fit using the oligo package of bioconductor in R version 3.4.0

source_name: bone marrow-derived macrophages and osteoclasts

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico kit protocol (GeneChip® WT Pico Reagent Kit Manual P/N 703262 Rev. 1) from 5 ng total RNA

growth_protocol: Bone marrow cells were isolated from wild-type mice and cultured on plastic substrata for differentiation into osteoclasts with M-CSF and RANKL.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Bone marrow-derived macrophages were cultured with 20 ng/ml M-CSF and 30 ng/ml RANKL for 0-5 days

tag: genotype

value: wild-type

value: 10 weeks

tag: time

value: osteoclast differentiation at day 5

value: mature osteoclasts


title: TL-Om1_shYY1_GSK126_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shYY1_GSK126

tag: cell type

value: ATL cell line

source_name: Input DNA from TL-Om1_shYY1_GSK126


title: Ctrl_A3

description: miRNA

value: plasma


title: Ctrl_A2

description: miRNA


title: TL-Om1_shYY1_DMSO_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shYY1_DMSO

source_name: Input DNA from TL-Om1_shYY1_DMSO


title: ASTX_13


title: Ctrl_A1

description: miRNA

source_name: plasma


title: GEN1C sgCTRL TGFBi rep1

description: GEN1C sgCTRL + TGFBi


title: WIBR3 shDDX6 TGFBi rep2

description: WIBR3 shDDX6 + TGFBi

value: primed hESCs


title: Ctrl_A4

description: miRNA

value: Sprague-Dawley


title: wild-type BMDM to osteoclast differentiation at day 2

description: Gene expression data

value: osteoclast differentiation at day 2

value: BMDM-osteoclasts during differentiation


title: TL-Om1_shCtrl_GSK126_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shCtrl_GSK126

source_name: Input DNA from TL-Om1_shCtrl_GSK126


title: EC

city: Seattle

first: Quy

middle: Ha

last: Le

state: WA

address: 1100 Fairview Ave. N., D2-367

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: not in edgeR analysis (control)

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Adapter trimming and filtering with cutadapt version 1.9.1 (using -a AGATCGGAAGAGC -A AGATCGGAAGAGC -m 25)
Reads of low quality were excluded prior to alignment against against hg38 with tophat2 2.1.0 (using fr-secondstrand)
Quantitation with HTSeq count 0.6.1p1 (with -s yes -m intersection-strict)
Genome_build: hg38
Supplementary_files_format_and_content: results from edgeR analysis in tab-delimited text format

source_name: HUVEC

growth_protocol: Primary AML cells were cultured on endothelium in Stem Span media supplemented with human stem cell factor (50ng/mL).

extract_protocol:
Total RNA and genomic DNA were then purified using RNeasy Micro Kit (Qiagen, Cat#74004).
SMARTer Stranded Total RNA- Seq Kit-Pico Input Mammalian

treatment_protocol: Cultures were treated with AC220 (a FLT3 inhibitor) at 100nM or DMSO control for 2 days prior to RNA extraction and sequencing.

value: Endothelium

tag: tumor stage

value: normal


title: DERNAB03E16

description: edgeR analysis

source_name: primary AML

value: hematopoietic

value: AML


title: NL-iPSC2-GFP Hi

city: Tokyo

first: Kenzaburo

last: Tani

address: 4-6-1, Shirokanedai, Minato-ku

department: Project Division of ALA Advanced Medical Research

institute: The Institute of Medical Science, The University of Tokyo

description: iPSCs from CD34+ cord blood cells

data_processing:
A read quality analysis of the raw data was performed using FastQC (version 0.11.7, http://bioinformatics.babraham.ac.uk/projects/fastqc/).
Quality trimming and adapter clipping were performed using Trimmomatic version 0.38 (Bolger et al., 2014), trimming trailing bases below the average quality 15, minimum length 36 and clipping Illumina adapters.
Trimmed reads were mapped to transcripts in the reference human genome (hg19) using Bowtie2 aligner within RSEM (Robinson et al., 2009). RSEM performed the estimation of the abundance of genes and isoforms and  generated raw counts.
The EdgeR software program (Li et al., 2011) was used to normalize and detect the differentially expressed genes (DEGs).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalized CPM values for each sample.

source_name: NL-iPSC2-GFP Hi

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (ThermoFisher, MA, USA) and purified using SV Total RNA Isolation System (Promega, WI, USA) according to the manufacturer's instructions. RNA samples were quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was confirmed with a Tapestation (Agilent, CA, USA).
The sequencing libraries were prepared from 1 ug of total RNA with NEBNext Ultra II Directional RNA Library Prep kit (New England Biolab, MA, USA) according to the manufacturer's instructions.

tag: cells

value: iPSCs

tag: origin

value: CD34+ cord blood cells


title: wild-type BMDM to osteoclast differentiation at day 0

description: Gene expression data

tag: age

value: osteoclast differentiation at day 0

value: BMDMs


title: DLCL2_DMSO_H3K27me3

source_name: H3K27me3 ChIP DNA from DLCL2_DMSO

value: DLBCL cell line

source_name: Input DNA from DLCL2_DMSO


title: wild-type BMDM to osteoclast differentiation at day 3

description: Gene expression data

value: wild-type

value: 10 weeks

value: osteoclast differentiation at day 3


title: WIBR3 shCTRL TGFBi rep2

description: WIBR3 shCTRL + TGFBi

source_name: human embryonic stem cells


title: AERNAB03E16

description: edgeR analysis


title: NL-iPSC2-GFP Low

description: iPSCs from CD34+ cord blood cells

source_name: NL-iPSC2-GFP Low


title: WIBR3 shCTRL TGFBi rep1

description: WIBR3 shCTRL + TGFBi


title: GEN1C sgDDX6 rep2

description: GEN1C sgDDX6

source_name: human induced pluripotent stem cells

value: primed hiPSCs


title: A59733_DE

description: edgeR analysis


title: TL-Om1_shEZH2_2_EZH2

source_name: EZH2 ChIP DNA from TL-Om1_shEZH2

value: ATL cell line

source_name: Input DNA from TL-Om1_shEZH2


title: TL-Om1_shEZH2_1_EZH2


title: WIBR3 shDDX6 TGFBi rep1

description: WIBR3 shDDX6 + TGFBi

value: primed hESCs


title: TMP-iPSC4-GFP Hi

description: iPSCs from CD3+ cord blood cells

source_name: TMP-iPSC4-GFP Hi

value: CD3+ cord blood cells


title: wild-type BMDM to osteoclast differentiation at day 1

description: Gene expression data

source_name: bone marrow-derived macrophages and osteoclasts

value: osteoclast differentiation at day 1

value: BMDM-osteoclasts during differentiation


title: A59733_AE

description: edgeR analysis


title: GEN1C sgDDX6 rep1

description: GEN1C sgDDX6


title: GEN1C sgCTRL rep2

description: GEN1C sgCTRL


title: TMP-iPSC4-GFP Neg

description: iPSCs from CD3+ cord blood cells

source_name: TMP-iPSC4-GFP Neg


title: GEN1C sgCTRL rep1

description: GEN1C sgCTRL


title: A37927_AE

description: edgeR analysis


title: TL-Om1_shEZH1_1_EZH2

source_name: EZH2 ChIP DNA from TL-Om1_shEZH1

source_name: Input DNA from TL-Om1_shEZH1


title: TMP-iPSC4-GFP Low

description: iPSCs from CD3+ cord blood cells

source_name: TMP-iPSC4-GFP Low


title: TL-Om1_shCtrl_EZH2

source_name: EZH2 ChIP DNA from TL-Om1_shCtrl

source_name: Input DNA from TL-Om1_shCtrl


title: A37927_DE

description: edgeR analysis

source_name: primary AML


title: TL-Om1_shEZH2_2_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shEZH2


title: Egg-ChIP-siWde-2

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

description:
4 days knockdown
Egg-ChIP

data_processing:
adaptors were trimmed
mapped to dm6 transcriptome by bowtie2 v2.2.4
converted to bedGraph normalized by RPM
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: bedGraph normalized by RPM

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: OSCs were grown at 26°C in culture medium prepared from Shields and Sang M3 Insect Medium (Sigma) supplemented with 0.6 mg/mL glutathione, 10% FBS, 10 mU/mL insulin, and 10% fly extract (Saito et al. 2009).

extract_protocol: ChIP libraries were raised using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions

treatment_protocol: OSCs were crosslinked with 1% Formaldehyde (Wako) added directly to the medium. IP was performed using anti-Egg antibody.

value: Drosophila ovarian somatic cell

tag: knockdown

value: wde 4 days


title: TL-Om1_shCtrl_DMSO_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shCtrl_DMSO

source_name: Input DNA from TL-Om1_shCtrl_DMSO


title: WIBR3 shDDX6 rep2

description: WIBR3 shDDX6

source_name: human embryonic stem cells


title: AK49_CDK12-2

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

data_processing:
TopHat V2
FeatureCounts
edgeR
hypergeometric gene set enrichment test on the gene ontology + KEGG pathway
Genome_build: hg19
Supplementary_files_format_and_content: expression

source_name: ovarian cancer

growth_protocol: The OVCAR-8 cells were cultured in RPMI-1640 medium (Corning) supplemented with 8% fetal bovine serum (Millipore).

extract_protocol: Total RNA was extracted from frozen cells using the miRNeasy mini kit (Qiagen) following the supplier’s instructions. Libraries were prepared using Illumina TruSeq mRNA v2.

treatment_protocol: RNA-seq was performed  48 h after siRNA transfection.

value: ovarian cancer cell

tag: sirna

value: CDK12-2 siRNA


title: Egg-ChIP-siPiwi-2

description:
4 days knockdown
Egg-ChIP

value: piwi 4 days


title: NL-iPSC2-GFP Neg

description: iPSCs from CD34+ cord blood cells

source_name: NL-iPSC2-GFP Neg

value: iPSCs

value: CD34+ cord blood cells


title: AK49_CDK12-6

value: CDK12-6 siRNA


title: AK41_CDK12-6


title: WIBR3 shDDX6 rep1

description: WIBR3 shDDX6


title: TL-Om1_shEZH2_1_EZH1

source_name: Input DNA from TL-Om1_shEZH2


title: WIBR3 shCTRL rep2

description: WIBR3 shCTRL


title: Egg-ChIP-siEgg-2

description:
4 days knockdown
Egg-ChIP

value: egg 4 days


title: TL-Om1_shEZH1_2_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shEZH1


title: TL-Om1_shEZH1_2_EZH2


title: Egg-ChIP-siEGFP-2

description:
4 days knockdown
Egg-ChIP

value: egfp 4 days


title: WIBR3 shCTRL rep1

description: WIBR3 shCTRL


title: AK41_CDK12-2


title: AK39_CDK12-6


title: Input-siWde-2

description:
4 days knockdown
Egg-ChIP


title: TL-Om1_shCtrl_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_shCtrl


title: TL-Om1_shEZH1_1_EZH1


title: AK39_CDK12-2


title: Input-siPiwi-2

description:
4 days knockdown
Egg-ChIP


title: Input-siEgg-2

description:
4 days knockdown
Egg-ChIP


title: TL-Om1_OR-S2_H3K4me3

source_name: H3K4me3 ChIP DNA from TL-Om1_OR-S2

source_name: Input DNA from TL-Om1_OR-S2


title: TL-Om1_OR-S1_H3K4me3

source_name: H3K4me3 ChIP DNA from TL-Om1_OR-S1

source_name: Input DNA from TL-Om1_OR-S1


title: AK41_control luciferase

value: control luciferase siRNA


title: Input-siEGFP-2

description:
4 days knockdown
Egg-ChIP


title: TL-Om1_DMSO_H3K4me3

source_name: H3K4me3 ChIP DNA from TL-Om1_DMSO

source_name: Input DNA from TL-Om1_DMSO


title: TL-Om1_GSK126_H3K4me3

source_name: H3K4me3 ChIP DNA from TL-Om1_GSK126

source_name: Input DNA from TL-Om1_GSK126


title: AK39_control luciferase


title: RNAseq-PGPC1_73

city: Toronto

last: Ellis

state: ON

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

data_processing: Raw RNAseq fastq files were uploaded to http://pluritest.org for induced pluripotent stem cell pluripotency analysis. All processing and analysis were performed by their automated pipeline. No additional expression analysis was performed with the raw files.

source_name: induced pluripotent stem cells

growth_protocol: All iPSC lines were maintained on Matrigel (Corning) coated dishes using mTeSR1. Daily media changes were performed except for the day following passaging. ReLeSR (STEMCELL Technologies) was used to lift clumps of iPSCs for routine passaging.

extract_protocol:
RNA was collected from single wells of 6-well plates using RNA PureLink RNA mini kit (Life Technologies) as per supplied protocol.
RNA libraries were prepared using NEBNext Ultra RNA Library Preparation kit for Illumina, and total RNA was used for poly(A) mRNA enrichment

value: iPSC

tag: passages

tag: tissue

value: induced pluripotent stem cells


title: Egg-ChIP-siEGFP-1

data_processing:
adaptors were trimmed
mapped to dm6 transcriptome by bowtie2 v2.2.4
culculating FPKM
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: egg-chip.csv (file includes FPKM values for each sample)

source_name: OSC

value: ovarian somatic cell


title: Egg-ChIP-siEgg-1


title: TL-Om1_OR-S2_YY1

source_name: YY1 ChIP DNA from TL-Om1_OR-S2

value: ATL cell line


title: RNAseq-PGPC17_11

data_processing: Raw RNAseq fastq files were uploaded to http://pluritest.org for induced pluripotent stem cell pluripotency analysis. All processing and analysis were performed by their automated pipeline. No additional expression analysis was performed with the raw files.


title: RNAseq-PGPC14_26


title: Input-siEgg-1


title: Input-siEGFP-1


title: Kidney_Pkd1 knockout_Salsalate_rep10

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

institute: University of Toronto

description: Tamoxifen-inducible, kidney-specific, Pkd1 (iKsp-Pkd1del) conditional knock-out kidney

hyb_protocol: Following fragmentation, 5.5 μg of biotin-labelled ss-cDNAs were hybridized to GeneChip mouse Gene 2.0 ST Arrays for 16 hours at 45°C. Hybridized arrays were then stained and washed in the Affymetrix Fluidics Station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The (.DAT) image files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software to generate cell intensity (.CEL) files. The (.CEL) files were uploaded to the Transcriptome Analysis Console (TAC) 4.0 (Thermo Fisher Scientific) for further processing and quality control. The probe set's signal intensities were then extracted and normalized using the robust multi-array average (RMA) algorithm embedded in TAC4.0 software. The differentially expressed genes between different groups were determined by the Limma Bioconductor package implemented in TAC 4.0. Enrichr was used as the primary tool to identify potential gene pathways or key regulatory factors altered by Salsalate treatment.

source_name: kidney from Salsalate treated Pkd1 KO mouse at 113 days of age

label_protocol: Biotin-labelled ss-cDNAs were prepared by using the GeneChip WT PLUS Kit according to the standard Affymetrix protocol for 300 ng of total RNA.

growth_protocol: Pkd1-cKO mice have a homozygously bred kidney–specific, tamoxifen–inducible Cre and two LoxP sites that flank exons 2–11 of the Pkd1 gene. The mice received Tamoxifen (150 mg/kg) by oral gavage on days PN18 and PN19 to induce adult onset PKD. At PN30 the PKD mutant mice started on normal chow and randomly allocated to different groups. At PN40, the untreated PKD mice continued on the normal chow and the treated PKD mice were switched to the chow supplemented with 2.5 g/kg salsalate. Blood Urea (BU) levels were monitored weekly and the mice with end stage renal disease (ESRD, BU >20 mmol/L) were sacrificed. The experiment continued until 50% of the untreated mutant mice reached ESRD. For the whole gene expression study, KO and Sasalate-treated KO kidneys were selected around the median of the cystic indices, and the kidneys from mice not receiving Tamoxifen were used as wild type controls.

extract_protocol: The total RNA was extracted using miRNeasy Mini Kit (Qiagen) following the manufacturer’s protocol with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA sample was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the RNA integrity number (RIN) was greater than 9.

treatment_protocol: All kidney samples were snapped frozen in liquid nitrogen, and stored in a -80°C freezer.

tag: Sex

value: male

tag: strain

tag: genotype/variation

value: Pkd1 KO

tag: treatment

value: Salsalate


title: AK49_control luciferase

source_name: ovarian cancer

tag: cell line


title: TL-Om1_OR-S1_YY1

source_name: YY1 ChIP DNA from TL-Om1_OR-S1


title: Kidney_Pkd1 knockout_Salsalate_rep9

source_name: kidney from Salsalate treated Pkd1 KO mouse at 114 days of age


title: TL-Om1_GSK126_YY1

source_name: YY1 ChIP DNA from TL-Om1_GSK126


title: RNAseq-PGPC3_75


title: Kidney_Pkd1 knockout_Salsalate_rep8


title: TL-Om1_DMSO_YY1

source_name: YY1 ChIP DNA from TL-Om1_DMSO


title: Kidney_Pkd1 knockout_Salsalate_rep6


title: T15

city: Ningbo,

first: ZHENBIAO

last: LI

state: Zhejiang

address: No.818 Fenghua Road

institute: Ningbo University

description: treated with the two characteristic components in combination.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the B. cinerea genome (https://www.ncbi.nlm.nih.gov/genome/?term=Botrytis+cinerea) using Tophat2.
Gene expression levels were estimated using FPKM values (fragments per kilobase of exon per million fragments mapped) using Cufflinks.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Botrytis cinerea

source_name: Mycelia

growth_protocol: Botrytis cinerea cultured at 25 °C on potato dextrose agar medium. Spores were harvested by flooding a plate with 10 mL 0.9 % sterile NaCl solution. The spore suspension was adjusted to 5×106 spores/mL using a hemocytometer. One milliliter of the suspension was inoculated into 250 mL flasks containing 150 mL sterile potato dextrose broth medium and cultured at 25 °C on a rotary shaker at 150 revolutions per minute (rpm) for 3 d, and then mycelia were harvested.

extract_protocol:
The extraction protocol followed the instructions accompanying the Trizol Reagent (Life Technologies, California, USA).
The cDNA library was constructed using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500), following the manufacturer’s instructions.

treatment_protocol: Equal amounts (wet weight) of mycelia were resuspended in the same volume of PDB medium to which TTO, 1,8-cineole, terpinen-4-ol, or combined components had been added to a final concentration of 0.5 µL/mL. Samples resuspended in PDB alone (no TTO or components) were used as controls. Mixtures were incubated for 2 h at 25 °C with shaking at 150 rpm. Mycelia were harvested and rinsed three times with 0.1 M PBS (pH 7.4).

tag: developmental stage

value: Mycelia

value: post incubation day 3

tag: agent

value: 1,8-cineole and terpinen-4-ol


title: Kidney_Pkd1 knockout_Salsalate_rep11


title: Kidney_Pkd1 knockout_Salsalate_rep5


title: T14


title: T12

description: treated with terpinen-4-ol, another characteristic components of tea tree oil.


title: Cx17

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

description:
20170427B_N708_15w_Glo_L001
snDrop-seq data

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
First, paired-end reads were filtered out if read 1 had more than 4 non-T bases in the last 10 bases (to remove all non poly T-captured contaminated reads), or had one or more bases with poor quality score (less than 10). And cell barcode and UMI information were then inferred from the first 12 bases and the next 8 bases of read 1 respectively. The right mate of each read pair was trimmed to remove any portion of the SMART adaptor sequence or large stretches of polyA tails (6 consecutive bp or greater).
The trimmed reads were then aligned to the human genome (GENCODE GRCH38) using STAR v2.5 with the default parameter settings
Reads mapping to intronic or exonic regions of genes as per the GENCODE gene annotation were both recorded. One further correction step to fix barcode synthesis errors was performed by inserting N at last base of the cell barcode for reads which had identical first 11 bases of the cell barcode and same last T base of UMI.
Digital expression matrix was then generated with genes as rows and cells as columns. UMI counts were assigned for each gene of each cell by collapsing UMI reads which had only 1 edit distance
Genome_build: GENCODE GRCH38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each sample passing QC filtering

source_name: 15 Weeks_Kidney Cortex

extract_protocol:
Cells or tissue were treated with nuclear extraction buffer, isolated nuclei was stained with DAPI and FACS purified
Nuclei were loaded at the concentration of 100 nuclei/ml, and co-encapsulated in droplets with barcoded beads purchased from ChemGenes Corporation, Wilmington MA (Cat. # Macosko201110). When encapsulation was complete, droplets were heated to lyze the nuclei membrane, and were then broken by perfluorooctanol, following which beads were harvested, and hybridized RNA was reverse transcribed. Beads hybridized with RNA from individual nuclei was harvested, pooled and reverse transcribed. cDNA was then PCR amplified for 16 cycles with primer, buffer and cycle conditions identical to original Dropseq protocol and libraries were prepared by Nextera XT tagmentation according to Illumina's instructions and indexed with different Nextera index 1 primers
snDrop-seq and Nextera

value: 15 Weeks

tag: region

value: Glomeruli

tag: histology

value: Not specified

tag: experiment


title: Cx16

description:
20170427A_N707_13w_Glo_L001
snDrop-seq data

source_name: 13 Weeks_Kidney Cortex

value: 13 Weeks

value: Glomeruli + Biopsy Punch


title: TL-Om1_OR-S2_EZH2

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 using default parameters (protocol: ChIP_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: EZH2 ChIP DNA from TL-Om1_OR-S2

tag: cell type

source_name: Input DNA from TL-Om1_OR-S2


title: T13


title: T11


title: Kidney_Pkd1 knockout_Salsalate_rep3


title: TL-Om1_GSK126_EZH2

source_name: EZH2 ChIP DNA from TL-Om1_GSK126


title: TL-Om1_OR-S1_EZH2

source_name: EZH2 ChIP DNA from TL-Om1_OR-S1

source_name: Input DNA from TL-Om1_OR-S1


title: Kidney_Pkd1 knockout_Salsalate_rep7


title: T10


title: Kidney_Pkd1 knockout_Salsalate_rep1


title: Cx14

description:
20170425A_N702_14.4w_Cortex_L001
snDrop-seq data

source_name: 14.4 Weeks_Kidney Cortex

value: 14.4 Weeks

value: Renal Cortex


title: T09

description: treated with 1,8-cineole, a characteristic components of tea tree oil.


title: Kidney_Pkd1 knockout_Salsalate_rep2


title: Cx11

description:
20161220_N707_14.4w_Cortex
snDrop-seq data


title: Cx13

description:
20170425A_N701_14.4w_Cortex_L001
snDrop-seq data


title: Cx12

description:
20161220_N708_14.4w_Cortex
snDrop-seq data


title: Cx15

description:
20170427A_N706_13w_Glo_L001
snDrop-seq data


title: Kidney_Pkd1 knockout_Salsalate_rep4


title: T08


title: Kidney_Pkd1 knockout_rep12

source_name: kidney from untreated Pkd1 KO mouse at 99 days of age

value: untreated


title: T07


title: Kidney_Pkd1 knockout_rep11

source_name: kidney from untreated Pkd1 KO mouse at 106 days of age


title: TL-Om1_DMSO_EZH2

source_name: EZH2 ChIP DNA from TL-Om1_DMSO

source_name: Input DNA from TL-Om1_DMSO


title: TL-Om1_GSK126_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_GSK126

source_name: Input DNA from TL-Om1_GSK126


title: TL-Om1_DMSO_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_DMSO


title: T06

description: treated with tea tree oil.

value: tea tree oil


title: TL-Om1_OR-S2_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_OR-S2


title: T05

description: treated with tea tree oil.

source_name: Mycelia


title: Cx10

description:
20161220_N706_14.4w_Cortex
snDrop-seq data


title: ATL3_EZH1

source_name: EZH1 ChIP DNA from ATL3

value: ATL patient PBMC

source_name: Input DNA from ATL3


title: TL-Om1_OR-S1_EZH1

source_name: EZH1 ChIP DNA from TL-Om1_OR-S1

value: ATL cell line


title: Kidney_Pkd1 knockout_rep9

value: male


title: Cx8

description:
20161114A_N708_16.5w_Cortex
snDrop-seq data

source_name: 16.5 Weeks_Kidney Cortex

value: 16.5 Weeks


title: Cx9

description:
20161220_N705_14.4w_Cortex
snDrop-seq data


title: Kidney_Pkd1 knockout_rep8

source_name: kidney from untreated Pkd1 KO mouse at 113 days of age

value: Pkd1 KO


title: Kidney_Pkd1 knockout_rep7


title: Kidney_Pkd1 knockout_rep10

source_name: kidney from untreated Pkd1 KO mouse at 114 days of age


title: T04

description: treated with tea tree oil.

value: Mycelia


title: ATL3_controlIgG

source_name: controlIgG ChIP DNA from ATL3


title: Cx6

description:
20161114A_N706_16.5w_Cortex
snDrop-seq data


title: Kidney_Pkd1 knockout_rep6

source_name: kidney from untreated Pkd1 KO mouse at 93 days of age


title: T03

description: treated without tea tree oil (TTO) as a control.

value: post incubation day 3


title: ATL2_EZH2

source_name: EZH2 ChIP DNA from ATL2

source_name: Input DNA from ATL2


title: Kidney_Pkd1 knockout_rep5

source_name: kidney from untreated Pkd1 KO mouse at 109 days of age


title: Cx5

description:
20161114A_N705_16.5w_Cortex
snDrop-seq data


title: ATL2_EZH1

source_name: EZH1 ChIP DNA from ATL2


title: ATL3_EZH2

source_name: EZH2 ChIP DNA from ATL3


title: Cx3

description:
20161114A_N703_16.5w_Cortex
snDrop-seq data


title: Cx4

description:
20161114A_N704_16.5w_Cortex
snDrop-seq data


title: ATL2_controlIgG

source_name: controlIgG ChIP DNA from ATL2


title: Kidney_Pkd1 knockout_rep4

description: Tamoxifen-inducible, kidney-specific, Pkd1 (iKsp-Pkd1del) conditional knock-out kidney


title: Kidney_Pkd1 knockout_rep3


title: NL-iPSC1

description: iPSCs from CD34+ cord blood cells

tag: cells

value: iPSCs

tag: origin

value: CD34+ cord blood cells


title: Cx2

description:
20161114A_N702_16.5w_Cortex
snDrop-seq data

tag: age


title: ATL1_EZH1

source_name: EZH1 ChIP DNA from ATL1

source_name: Input DNA from ATL1


title: NL-iPSC1-primed

description: iPSCs from CD34+ cord blood cells


title: ATL1_EZH2

source_name: EZH2 ChIP DNA from ATL1


title: Cx7

description:
20161114A_N707_16.5w_Cortex
snDrop-seq data


title: Cx1

description:
20161114A_N701_16.5w_Cortex
snDrop-seq data


title: T-2-Dpol

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

description:
HI.4318.001.Index_6.18-T-2-DPol
processed data file: organoids_expression_data.txt

data_processing:
Alignment using HISAT2 default settings.
Sorting bam files using samtools.
Indexing bam files using samtools.
Counting read counts using RPKMforGenes.py script settings : -fulltranscript, -onlycoding, -readcounts -mrnanorm
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: organoids_expression_data.txt: Tab-delimited text file includes RPKM values and reads counts for all samples. RPKM and gene counts values were output by the RPKMforGenes.py script.

source_name: pancreatic ductal adenocarcinoma mouse organoid

extract_protocol:
RNA was extracted using TRIzol (Invitrogen Cat# 15596018) according to the manufacturer’s instructions.
TruSeq

value: Pancreatic ductal adenocarcinoma organoid

value: Control

value: Polysome-associated mRNA

tag: replicate


title: N6_201105980146_R08C01

city: Tarragona

first: Carolina

last: Serena

state: Tarragona

address: C/Dr. Mallafre Guasch, 4

department: Research Unit

institute: Health Institute Pere Virgili

description:
Final Integration of 6 No-Crohn Disease (control) samples
This sample failed quality control thus no processed data are provided.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: DNA methylation data were processed using GenomeStudio software (Illumina) by applying the default settings

data_processing: All computations and statistical analyses were performed with the R statistical programming environment [version 3.5.3; R core team, 2019]. DNA methylation raw data [IDAT files, Illumina iScan system direct output storing probe intensities] were read using the Bioconductor package minfi [version 1.28.3]20,21 and the annotation packages IlluminaHumanMethylationEPICmanifest version 3.0 and IlluminaHumanMethylationEPICanno.ilm10b2.hg19 version 6.0. Initial pre-processing and quality control were performed with minfi. The CpG methylation level was calculated as M values [M = log2[M/U]. Differentially methylated positions [DMPs] were located through linear regression using dmpFinder, a minfi wraparound lmFit function of the limma software package. Based on Illumina’s manifest, DMPs were assigned to genes and candidate genes were identified based on a nominal p-value cut-off < 1×10-2 and ten or more DMPs per gene.  Differentially methylated regions [DMRs] were located using the minfi function bumphunter, with default settings and the smoothing option. In brief, bumphunter searches for DMRs by searching for CpGs with a mean difference above a certain threshold. We set the inclusion threshold to 0.2. To remove non-biologically significant DMRs, we filtered for at least three consecutive CpGs. Again, significant DMRs were assigned to genes based on Illumina’s manifest, and candidate genes were selected based on the number of DMRs per gene and their relation to the gene structure

label: Cy3 and Cy5

source_name: No Crohn - N

label_protocol: Standard Illumina protocol for Human Methylation850k DNA Analysis bead chip (Cy3, Cy5)

growth_protocol: DMEM/F12 media with 10% FBS and 1% ab/am

extract_protocol: NucleoSpin® Tissue Kit (Macherery-Nagal GmbH) gDNA extraction

treatment_protocol: No treatment, just ASCs from different origins, patients with Crohn's Diseases and no-Crohn's Disease individuals (control group)

value: Adipose derived stem cells (ASCs)

tag: patient diagnosis

value: No Crohn's Disease


title: T01

source_name: Mycelia


title: ATL1_controlIgG

first: Makoto

last: Yamagishi

address: 4-6-1, Shirokanedai

institute: The University of Tokyo

source_name: controlIgG ChIP DNA from ATL1

extract_protocol: 1×10E7 cells were cross-linked in fixing solution. After 15 min incubation at room temperature, cross-linking was stopped by adding 1.375 M glycine. The cells were centrifuged for 5 min, 1,400 × g at 4°C. The supernatant was discarded and the pellet was washed two times in PBS. After the washes, cell pellets were resuspended in LB1 (50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation for 5 min, 1,400 × g at 4°C, the pellet was resuspended in LB2 (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at room temperature. After centrifugation for 5 min, 1,400 × g at 4°C, the nuclei were resuspended in micrococcal nuclease digestion buffer and incubated in 37°C to digest chromatin to the appropriate size fragments. Digestion was stopped by adding 0.5 M EDTA. After centrifugation, nuclei pellets were resuspended in LB3 (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-Lauroylsarcosine) and sonicated for 10 min. After sonication and 10 min high-speed centrifugation, sheared chromatin was recovered in the supernatant.


title: Normal3_EZH1

source_name: EZH1 ChIP DNA from Normal3

value: Normal CD4+ T-cell

source_name: Input DNA from Normal3


title: Kidney_wild type_rep5

description: Wild type kidney

source_name: kidney from wild type mouse at 84 days of age

value: wild type

value: untreated


title: Normal3_EZH2

source_name: EZH2 ChIP DNA from Normal3


title: T-1-CRTotal

description:
HI.4318.001.Index_27.15-T-1-CRTotal
processed data file: organoids_expression_data.txt

tag: tissue

value: Total mRNA


title: Kidney_Pkd1 knockout_rep1

source_name: kidney from untreated Pkd1 KO mouse at 113 days of age

tag: Sex


title: T-1-Dpol

description:
HI.4318.001.Index_23.14-T-1-DPol
processed data file: organoids_expression_data.txt


title: Kidney_wild type_rep7

description: Wild type kidney

tag: strain


title: Normal3_controlIgG

source_name: controlIgG ChIP DNA from Normal3


title: T-1-CRPol

description:
HI.4318.001.Index_2.16-T-1-CRPol
processed data file: organoids_expression_data.txt


title: Kidney_wild type_rep6

description: Wild type kidney

tag: genotype/variation


title: Normal2_EZH2

source_name: EZH2 ChIP DNA from Normal2

source_name: Input DNA from Normal2


title: T-1-Dtotal

description:
HI.4318.001.Index_21.13-T-1-DTotal
processed data file: organoids_expression_data.txt

tag: treatment


title: T-2-Dtotal

description:
HI.4318.001.Index_13.17-T-2-DTotal
processed data file: organoids_expression_data.txt


title: Normal2_EZH1

source_name: EZH1 ChIP DNA from Normal2


title: Kidney_Pkd1 knockout_rep2

source_name: kidney from untreated Pkd1 KO mouse at 114 days of age


title: Normal2_controlIgG

source_name: controlIgG ChIP DNA from Normal2


title: MA9+SETDB1_RNAseq_2

extract_protocol:
RNA was harvested using Qiagen Rneasy Mini plus kit.
Strand specific polyA selected libraries were constructed by the University of Michigan sequencing core.

tag: tissue source

value: bone marrow

tag: cell line background

value: MLL-AF9 (MA9) acute myeloid leukemia cell line

tag: retroviral transduction

value: MLL-AF9 + SETDB1


title: Kidney_wild type_rep4

description: Wild type kidney

value: male


title: Normal2_2_EZH2


title: MA9+SETDB1_RNAseq_1


title: T-3-CRPol

description:
HI.4292.002.Index_4.24-T-3-CRPol
processed data file: organoids_expression_data.txt


title: MA9+EV_RNAseq_3

value: MLL-AF9 + EV control


title: Kidney_wild type_rep3

description: Wild type kidney


title: Normal2_2_controlIgG


title: Kidney_wild type_rep1

description: Wild type kidney

source_name: kidney from wild type mouse at 83 days of age


title: MA9+EV_RNAseq_2


title: Normal1_EZH1

source_name: EZH1 ChIP DNA from Normal1

source_name: Input DNA from Normal1


title: T-3-Dtotal

description:
HI.4292.002.Index_18.21-T-3-DTotal
processed data file: organoids_expression_data.txt

source_name: pancreatic ductal adenocarcinoma mouse organoid


title: T-2-CRPol

description:
HI.4292.002.Index_7.20-T-2-CRPol
processed data file: organoids_expression_data.txt


title: T-3-CRTotal

description:
HI.4292.002.Index_16.23-T-3-CRTotal
processed data file: organoids_expression_data.txt


title: MA9+EV_RNAseq_1

extract_protocol:
RNA was harvestedK21:K56 using Qiagen Rneasy Mini plus kit.
Strand specific polyA selected libraries were constructed by the University of Michigan sequencing core.


title: Normal1_controlIgG

source_name: controlIgG ChIP DNA from Normal1


title: GG_scRNAseq

city: New York

first: Jin

state: NY

address: 3227 Broadway

institute: Columbia University

description: Each cell is marked with experiment number "JC04-JC12", the adapter number RPI "1-12", and the cell number "1-40" (using CELSeq multiplexing primers).

data_processing:
Paired-end reads were trimmed and aligned to GRCm38 (mm10) using STAR
Reads per million (RPM) counts for each gene were computed using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Reads per million (RPM) counts for each gene

source_name: sensory neurons

extract_protocol:
Geniculate ganglia from P2rx3-tdTomato animals were isolated and placed in a micro-dish containing 200µl of collagenase/dispase (Roche) solution (4mg/ml in HBSS) at 37oC for 15min. The collagenase/dispase solution was carefully removed without disturbing the tissue, and 200µl papain (Worthington) solution was added to the dish and incubated at 37oC for 15min.  Dissociated ganglion cells were spun down, re-suspended in 500 µl HBSS and placed in a collagen-coated micro-dish. To pick single tdTomato+ ganglion neuron, the cell suspension was monitored with an Olympus IX70 inverted fluorescence microscope through the entire picking process.
Cells were extracted from tongues of Pkd2l1-tdTomato mice. After isolation, cells were fractionated using a fluorescence activated cell sorter (MoFlo Astrios, Beckman Coulter). The tdTomato+ (sour TRCs) and tdTomato- (non-sour TRCs and supporting cells) were sorted (50-100 for cell pools, or single cells) into 96-well plates containing cDNA synthesis buffer.
The single-cell sequencing libraries were prepared using the CEL-Seq method as previously described (Hashimshony et al., 2016; Hashimshony et al., 2012).
The cDNA libraries from TRCs for bulk and single cell sequencing were prepared using the SMART-Seq Ultra Low Input RNA kit (TaKaRa) and the Nextera XT DNA Sample Kit (Illumina) using custom indexed adapters.

tag: genotype

value: P2rx3-tdTomato animals

tag: strain background

value: geniculate ganglia


title: T02

description: treated without tea tree oil (TTO) as a control.

source_name: Mycelia

tag: developmental stage

value: Mycelia

value: post incubation day 3

tag: agent


title: MT_si-NC_RNA-seq

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

description: poly A+ RNA

data_processing:
Illumina Casava1.8 software was used for basecalling.
RNA-seq reads were mapped to mm9 genome using TopHat2. If multiple reads aligned to the same genomic position, only one read per position was kept for downstream analyses.
Gene expression level was quantified by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are plain text files. Each entry represents expression level (RPKM) of all genes in mm9.

growth_protocol: C2C12 myoblasts were grown in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 μg of streptomycin (growth medium, GM) in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
For total RNA-seq, total RNAs were extracted from MB or MT C2C12 cells using TRIzol reagent (Invitogen) and then delivered to BGI HK for rRNA depletion; for poly A+ RNA-seq, RNA-seq was performed following the procedures described before (Chen et al., 2017; Zhou et al., 2015). Total RNAs were extracted from C2C12 cells using TRIzol reagent (Invitogen) following the manufacturer’s instructions and then subjected to poly(A) selection (Ambion, 61006).
For total RNA-seq, RNAs were submitted to Beijing Genomic Center, Hong Kong. The libraries were prepared following strand specific RNA-seq library preparation procedures and sequenced on the HiSeq2000 platform; for polyA+ RNA-seq, we prepared the libraries using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB, E7770S) and barcoded libraries were pooled at equal concentration and sequenced on the HiSeq1500 platform.

treatment_protocol: C2C12 myoblasts were induced to differentiation by switching to  DMEM supplemented with 2% horse serum, 100 U/ml penicillin and 100 μg of streptomycin  (differentiation medium, DM) when cell confluence reached 80%-90%. The cells were then cultured in DM for 48 h or 72 h.

tag: cell type

value: C2C12 myoblasts

tag: cell line

tag: culture conditions

value: DM 48 hours


title: T-2-CRTotal

description:
HI.4292.002.Index_15.19-T-2-CRTotal
processed data file: organoids_expression_data.txt

value: Pancreatic ductal adenocarcinoma organoid

tag: replicate


title: T-3-Dpol

description:
HI.4292.002.Index_14.22-T-3-DPol
processed data file: organoids_expression_data.txt

value: Control

value: Polysome-associated mRNA


title: N-3-CRPol

description:
HI.4287.006.Index_25.12-N-3-CRPol
processed data file: organoids_expression_data.txt

source_name: normal mouse organoid

value: Normal organoid


title: N-2-CRTotal

description:
HI.4287.006.Index_8.7-N-2-CRTotal
processed data file: organoids_expression_data.txt


title: MT_si-hnRNPL_RNA-seq

description: poly A+ RNA


title: N-3-Dpol

description:
HI.4287.006.Index_20.10-N-3-DPol
processed data file: organoids_expression_data.txt


title: MT_WT_GRO_rep2

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Illumina Casava1.8 software was used for basecalling.
GRO-seq reads were mapped to mm9 genome using Bowtie2. If multiple reads aligned to the same genomic position, only one read per position was kept for downstream analyses.
Transcript units were idenfitied and GRO-seq signal tracks were generated using HOMER (v4.4).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are bigWigs. Each entry represents the number of reads at each base.

growth_protocol: WT or MyoD KO C2C12 myoblasts were grown in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 μg of streptomycin (growth medium, GM) in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
GRO-seq experiments were carried out as previously described (Core et al., 2008; Mahat et al., 2016). Five million cells (WT or MyoD KO C2C12 cells at MB and MT stages) were resuspended in cold swelling buffer (10 mM Tris-HCl pH7.5, 2 mM MgCl2, 3 mM CaCl2) on ice for 5 minutes and then lysed in lysis buffer (swelling buffer + 0.5% IGEPAL + 10% glycerol + 2 units/ml SUPERase In, and cOmplete protease inhibitors) followed by gently pipetting up and down for 20 times. After centrifuge, nuclei were sequentially washed with lysis buffer and freezing buffer (50 mM Tris-HCl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA) and finally resuspended in 100 µl of freezing buffer and stored at -80 °C. Nuclear run-on (NRO) assays were performed with biotin-11-UTP as previously reported. In brief, 2× NRO master mix (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 1% Sarkosyl, 250 µM ATP, GTP, CTP, 50 µM biotin-11-UTP, and 0.8 u/µl SUPERase In) was pre-equilibrated at 37 °C for 10 minutes. Then, 5×106 cells / 100 µl nuclei were added to the same volume 100 µl of 2×NRO master mix and incubated at 37 °C for 5 minutes. The run-on RNA (NRO-RNA) was extracted with 2 ml of TRIzol reagent (Invitogen) following the manufacturer’s instructions.
The NRO-RNAs were then fragmented with 5 μl of ice-cold 1 N NaOH for 10 minutes on ice. The reaction was neutralized by mixing with 25 μl of 1 M Tris-HCl pH 6.8 and fragmented biotinylated RNA was purified through incubation with 30 µl of Dynabeads™ M-280 Streptavidin beads (Thermo Fisher Scientific) in binding buffer (10 mM Tris-HCl pH 7.4, 300 mM NaCl and 0.1% Triton X-100) for 20 minutes at room temperature while rotating. Then, the beads were sequentially washed two times with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl and 0.5% Triton X-100), two times with binding buffer, and one timer with low-salt wash buffer (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). After elution from beads, biotinylated RNA was subject to 3’ RNA adaptor ligation and incubated in a 10 µl reaction volume containing 50 pmol of 3’ RNA adaptor (5'p-rGrArUrCrGrUrCrGrGrArCrUrGrUrArGrArArCrUrCrUrGrArArC-/3’InvdT/) (Integrated DNA Technologies, IDT), 10 nmol of ATP, 10 unites of T4 RNA ligase I (NEB), 40 unites SUPERase In and 10% PEG 8000 at 20 ̊C for 6 hours. Ligated RNA was enriched by Streptavidin beads and RNA extraction with TRIzol. The 5’ ends of biotinylated RNA were then repaired with RNA 5´ Pyrophosphohydrolase (RppH) (NEB) and T4 polynucleotide kinase (PNK) (NEB) followed by Trizol extraction. Subsequently, the purified RNA was ligated to 5’ RNA adaptor (5'-rCrCrUrUrGrGrCrArCrCrCrGrArGrArArUrUrCrCrA-3’) (IDT) in a 10 µl reaction volume containing 50 pmol of 5’ RNA adaptor, 10 nmol of ATP, 10 unites of T4 RNA ligase I (NEB), 40 unites SUPERase In and 10% PEG 8000 at 20 ̊C for 6 hours. Following the ligation, ligated RNA was purified by the third round Streptavidin bead enrichment and TRIzol extraction. The resultant RNA was reverse transcribed with RP1 primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’) (IDT) using Superscript III RT enzyme (Thermo Fisher Scientific). A small portion of cDNA was serial diluted and subjected to test PCR amplification to determine optical PCR cycle. The full-scale PCR amplification was performed using Q5® High-Fidelity 2× Master Mix (NEB) with 12.5 pmol of RP1 primer and RPI-index primers (5’ -CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’, in which 'NNNNNN' is an index sequence) (IDT). The optimal PCR cycle for full-scale amplification is 14. PCR products were PAGE separated and DNA from 140 bp to 350 bp was eluted from PAGE gel. The library was quantified and sequenced in the Illumina HiSeq 1500.

treatment_protocol: WT or MyoD KO C2C12 myoblasts were induced to differentiation by switching to  DMEM supplemented with 2% horse serum, 100 U/ml penicillin and 100 μg of streptomycin  (differentiation medium, DM) when cell confluence reached 80%-90%. The cells were then cultured in DM for 48 h.

value: wild type


title: N-3-Dtotal

description:
HI.4287.006.Index_11.9-N-3-DTotal
processed data file: organoids_expression_data.txt

value: Total mRNA


title: Nestin-Cre (Foxp1-/-) striatum at E18.5, biological rep6

city: Heidelberg

first: Henning

last: Froehlich

address: Im Neuenheimer Feld 366

institute: Institute of Human Genetics

hyb_protocol: The hybridization on the chip was performed on a GeneChip Hybridization oven, 640, then dyed in the GeneChip Fluidics Station 450

scan_protocol: Scanning was performed with a GeneChip Scanner 3000 from the Affymetrix-Company (Affymetrix, High Wycombe, UK).

data_processing:
A Custom CDF Version 21 with ENTREZ based gene definitions was used to annotate the arrays (Dai et. al, 2005). OneWay-ANOVA was performed to identify differential expressed genes using a commercial software package SAS JMP10 Genomics, version 6, from SAS (SAS Institute, Cary, NC, USA). A false positive rate of a=0.05 with FDR correction was taken as the level of significance. Plots (3D Scatterplots and Venndiagrams) are made with JMP.
The raw fluorescence intensity values were normalized applying quantile normalization and RMA background correction and log 2-transformed.

source_name: Nestin-Cre (Foxp1-/-) striatum at E18.5

label_protocol: standard label protocol

growth_protocol: Embryonic stage was calculated by vaginal plug check and by controlling the morphological parameters which accord to the respective Theiler stage.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The brain was removed and the striata from both hemispheres dissected in ice cold PBS.

value: Nestin-Cre (Foxp1-/-)

tag: age

value: striatum


title: Nestin-Cre (Foxp1-/-) striatum at E18.5, biological rep4

tag: tissue


title: N-2-Dpol

description:
HI.4287.005.Index_9.6-N-2-DPol
processed data file: organoids_expression_data.txt


title: Nestin-Cre (Foxp1-/-) striatum at E18.5, biological rep5


title: MT_MYOD_KO_GRO_rep2

description: nascent RNA

value: MyoD KO


title: MA9+SETDB1_RNAseq_3

data_processing:
Quality control performed on fastq files using FastQC version 0.11.7
RNA-seq fastq files were trimmed for quality using Cutadapt version 1.18, parameters = -q20,20 --minimum-length 30; ATAC-seq and ChIP-seq fastq files were trimmed for quality, adapter removal, and polyG removal using AfterQC version 0.9.6, parameters = -q20 -u 19 -p19 -s 25
RNA-seq fastq files were aligned to the mouse genome using STAR version 2.6.0c, parameters = genomeGenerate: --sjdbOverhang 49, Alignment: --outSamtype BAM SortedByCoordinate; ATAC-seq and ChIP-seq files were aligned to the mouse genome using Bowtie2 version 2.3.4.3, parameters = --very-sensitive -X 2000
RNA-seq aligned BAM files were assigned to genes and features were counted using HTSeq 0.11.0, parameters= -s reverse -r pos
RNA-seq count files were analyzed for differential expression using DESeq2 version 3.8, parameters = alpha = 0.05 lfcThreshold = log2(1.5)
ChIP-seq and ATAC-seq aligned BAM files were sorted and filterd for quality using SAMtools version 1.9, parameters = view -b -q 25 -f 0x2
ChIP-seq and ATAC-seq filtered BAM files had duplicates removed using Picard version 2.18.19
ChIP-seq and ATAC-seq filtered and deduplicated BAM files were used for peak calling using MACS version 2.1.2; 10% input was used as control for ChIP-seq experiments; parameters varied for different conditions: for H3K9ac ChIP-seq =  -f BAMPE -g mm --keep-dup all; for H3K9me3 and H3K79me2 ChIP-seq = -f BAMPE -g mm --scale-to-large --braod --keep-dup all; for ATAC-seq = -f BAM -g mm --nomodel --shift -100 --extsize 200 --keep-dup all
ChIP-seq BAM files were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000
ATAC-seq pileup files from MACS peak calling were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --extendReads
Genome_build: GRCm38 (M20 build from GENCODE)
Supplementary_files_format_and_content: RNAseq counts files contain the HTSeq assigned genes and count from the aligned BAM files; ChIP-seq and ATAC-seq BAM files contain the filtered and deduplicated aligned reads to the mouse genome.

value: bone marrow

value: MLL-AF9 (MA9) acute myeloid leukemia cell line

value: MLL-AF9 + SETDB1


title: Nestin-Cre (Foxp1-/-) striatum at E18.5, biological rep1


title: N-3-CRTotal

description:
HI.4287.006.Index_22.11-N-3-CRTotal
processed data file: organoids_expression_data.txt


title: Kidney_wild type_rep2

description: Wild type kidney

source_name: kidney from wild type mouse at 84 days of age

tag: Sex

value: male

value: untreated


title: N5_201105980146_R07C01

description: Final Integration of 6 No-Crohn Disease (control) samples

source_name: No Crohn - N

value: Adipose derived stem cells (ASCs)

tag: patient diagnosis

value: No Crohn's Disease


title: WT striatum at E18.5, biological rep5

source_name: WT striatum at E18.5

tag: genotype/variation


title: MB_WT_GRO_rep2

description: nascent RNA

value: C2C12 myoblasts

value: DM -24 hours


title: CD6_201105980146_R01C01

description: Final Integration of 7 Crohn Disease samples

source_name: Crohn - CD

value: Crohn's Disease


title: hnRNPL_CLIP

data_processing:
Library strategy: CLIP-seq
Illumina Casava1.8 software was used for basecalling.
CLIP-seq reads were mapped to mm9 genome using Bowtie2. If multiple reads aligned to the same genomic position, only one read per position was kept for downstream analyses.
hnRNPL binding sites were identified by CIMS analysis pipeline (MJ Moore, et. al. 2014); then the binding sites were annotated against RefSeq using Homer (v4.4).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file is bed file. Each entry represents a hnRNPL binding site.

extract_protocol:
hnRNPL CLIP-seq was performed following the procedures described before with minor modifications (Bao et al., 2018; Licatalosi et al., 2008; Moore et al., 2014; Van Nostrand et al., 2016). Differentiating C2C12 cells (2×107) were washed with PBS and crosslinked by irradiation one time at 254 nm for 400 mJ/cm2 in Stratalinker UV crosslinker (Stratagene). The cells were then collected and flash-frozen in liquid nitrogen and stored at - 80°C. Cells were lysed in 1ml Lysis Buffer (100mM KCl, 5mM MgCl2, 10mM HEPES-KOH pH 7.0, 0.5% NP-40) supplemented with 1mM DTT, 40 U/ml SUPERase In and Complete EDTA free cOmplete protease inhibitors for 15 min on ice with pipetting up and down for several times at intervals. Then, 2 µl of Turbo DNase (AM2238, Thermo Fisher Scientific) was added and the reaction was incubated at 37° for 5 min with rotating at 1000 rpm. Subsequently, 10 µl of diluted RNase A (5 µg/ml, 12091021, Thermo Fisher Scientific) was applied and the reaction was further incubated at 37° for 5 min with rotating at 1000 rpm. Cell lysate was cleared by centrifugation at 15,000 g for 20 min. Save 6 µl of cleared samples as Input sample to later determine immunoprecipitation efficiency and divide the remaining samples into three aliquots. To prepare IP buffer, 2550 μl of ice-cold lysis buffer was supplemented with 600 units SUPERase In, 30 μl of 100 mM DTT and EDTA to 20 mM and 300 μl of cleared cell lysate were then added to the IP buffer. Immunopreciptations were then performed using 10 µg anti-hnRNPL antibody (sc-28726, Santa Cruz), normal IgG control (sc-2027, Santa Cruz) and anti-HA tag (sc-805, Santa Cruz) respectively for overnight at 4°C with rotation. On the next day, 125 µl washed Dynabeads Protein G was added to each reaction and incubated for another 4 hours with rotation. After incubation, 1/10 volume of beads were saved to determine immunoprecipitation efficiency. Beads were collected and washed twice with high salt wash buffer (300mM KCl, 5mM MgCl2, 10mM HEPES-KOH pH 7.0, 0.5% NP-40) then PNK buffer (50 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.5% NP-40). Cross-linked RNA complexes were dephosphorylated by incubating with Alkaline Phosphatase (NEB) for 20 min at 37°C, followed by treatment with T4 PNK enzyme in acid PNK buffer (70 mM Tris-HCl pH 6.5, 10 mM MgCl2) for 20 min at 37°C. Beads were washed with high salt wash buffer and PNK buffer. Protein-RNA complexes were then divided into two portions. 1/10 volume was subjected to RNA 3’ end biotinylation (20160, Thermo Fisher Scientific) following the provider’s procedure. Remaining 9/10 volume was used for on-bead 3’ RNA linker ligation and incubated in a 30 µl reaction volume containing 50 pmol of 3’ RNA adaptor (5'p-rGrArUrCrGrUrCrGrGrArCrUrGrUrArGrArArCrUrCrUrGrArArC-/3’InvdT/) (IDT), 30 nmol of ATP, 30 unites of T4 RNA ligase I (NEB, Ipswich, MA), 20 unites RNase inhibitor and 10% PEG 8000 at 20 ̊C for overnight, shaking at 1200 rpm. After extensive wash, beads (3’ RNA adaptor ligated) were 5’ ends phosphorylated with T4 polynucleotide kinase (PNK) followed by wash steps. The beads (biotin labeled or 3’ RNA adaptor ligated) were then denatured in loading buffer and resolved on a Novex NuPAGE 10% Bis-Tris gel and then transferred to 0.45 µm nitrocellulose membranes for 2h at 60V. The biotin reaction group was then subjected to biotin detection using chemiluminescent nucleic acid detection Module (89880, Thermo Fihser Scientific) to indicate labeled RNA complexes. For western blot analysis to evaluate the IP efficiency, CLIP membranes were probed with anti-hnRNPL antibody for 16h overnight. For sequencing, labeled hnRNPL-RNA bands were excised from the membrane (50-20 kDa above the MW of hnRNPL) and eluted by incubating with PK buffer (100mM Tris-HCl pH 7.4, 50mM NaCl, 10mM EDTA) and Proteinase K at 4mg/ml (Thermo Fisher Scientific) for 30 min at 37°C, then for another 30 min at 37°C with PK buffer, 3.5M Urea and Proteinase K. RNA was subsequently purified using acidic phenol:chloroform (ThermoFisher) and ethanol precipitation.
The CLIP RNA was ligated to 5’ RNA adaptor (5'-rCrCrUrUrGrGrCrArCrCrCrGrArGrArArUrUrCrCrA-3’) (IDT) in a 10 µl reaction volume containing 50 pmol of 5’ RNA adaptor, 10 nmol of ATP, 10 unites of T4 RNA ligase I (NEB, Ipswich, MA), 40 unites RNase inhibitor and 10% PEG 8000 at 20 ̊C for 6 hours. Following the ligation, ligated RNA was purified by the acidic phenol:chloroform (ThermoFisher) and ethanol precipitation. The resultant RNA was reverse transcribed with RP1 primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’) using Superscript III RT enzyme (Thermo Fisher Scientific). A small portion of cDNA was serial diluted and subjected to test PCR amplification to determine optical PCR cycle. The full-scale PCR amplification was performed using Q5® High-Fidelity 2× Master Mix (NEB) with 12.5 pmol of RP1 primer and RPI-index primers (5’ -CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’, in which 'NNNNNN' is an index sequence). The optimal PCR cycle for full-scale amplification is 17. PCR products were PAGE separated and DNA from 140 bp to 350 bp was eluted from PAGR gel. The library was quantified and sequenced in the Illumina HiSeq 1500.

treatment_protocol: C2C12 myoblasts were induced to differentiation by switching to  DMEM supplemented with 2% horse serum, 100 U/ml penicillin and 100 μg of streptomycin  (differentiation medium, DM) when cell confluence reached 80%-90%. The cells were then cultured in DM for 48 h.

value: DM 48 hours

tag: antibody

value: anti-hnRNPL (sc-28726, Santa Cruz)


title: N2_201105980146_R04C01


title: N-1-CRTotal

description:
HI.4287.005.Index_19.3-N-1-CRTotal
processed data file: organoids_expression_data.txt

value: Normal organoid

tag: treatment


title: N4_201105980146_R06C01


title: N1_201105980146_R03C01


title: N3_201105980146_R05C01


title: MB_MYOD_KO_GRO_rep2

description: nascent RNA


title: CD4_201105980145_R07C01

description: Final Integration of7 Crohn Disease samples


title: N-1-CRPol

description:
HI.4287.005.Index_1.4-N-1-CRPol
processed data file: organoids_expression_data.txt

value: Polysome-associated mRNA


title: N-2-CRPol

description:
HI.4287.006.Index_10.8-N-2-CRPol
processed data file: organoids_expression_data.txt


title: Nestin-Cre (Foxp1-/-) striatum at E18.5, biological rep2

value: Nestin-Cre (Foxp1-/-)


title: LT-HSCs , Ccp3_WT

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Basecalls performed using BGISEQ-500.
Mapping clean reads to mm9 whole genome using HISAT2. HISAT parameters for SE reads:-p8--phred64--sensitive-I1-X 1000.
RSEM was used to calculate Fragments Per Kilobase Million (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: LT-HSC

extract_protocol:
LT-HSCs were sorted by flow cytometry. Total RNAs were extracted with an RNA Miniprep Kit (Tiangen, Beijing, China) according to the manufacturer’s protocol. 0.5 ug of total RNA were qualified using Agilent 2100 for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: hematopoietic stem cell

value: wild type


title: Nestin-Cre (Foxp1-/-) striatum at E18.5, biological rep3

value: striatum


title: CD2_201105980145_R05C01


title: MB_MYOD_KO_GRO_rep1

description: nascent RNA

value: MyoD KO


title: CD1_201105980145_R04C01


title: MT_MYOD_KO_GRO_rep1

description: nascent RNA


title: CD5_201105980145_R08C01


title: CD3_201105980145_R06C01


title: N-2-Dtotal

description:
HI.4287.005.Index_3.5-N-2-DTotal
processed data file: organoids_expression_data.txt

value: Control

value: Total mRNA


title: MT_WT_GRO_rep1

description: nascent RNA


title: N-1-Dtotal

description:
HI.4287.005.Index_5.1-N-1-DTotal
processed data file: organoids_expression_data.txt


title: WT striatum at E18.5, biological rep6


title: iRFA_rep2

status: Public on Oct 02 2019

city: Changsha

first: Liangrong

last: Shi

state: Hunan

address: No. 87 Xiangya Rd.

department: Interventional Radilology Center

institute: Xiangya Hospital, Central South University

data_processing:
FastQC softwae was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Genome_build: Mus_musculus.GRCm38.92.gtf
Supplementary_files_format_and_content: fpkm

source_name: Implanted CT26 colon cancer

growth_protocol: A density of 1x106 CT26 cells were injected i.d. into male BALB/C mice on the right flank. The treatments were initiated when the longest diameter reached about 0.8 cm.

extract_protocol:
The totla RNA was extracted  for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The tip of the electrode reaches the middle point of the tumor's long axis. The treatments were administered for 1.5-2.0 min at the target temperature of 70 °C for partial necrosis of the target tumors.

value: Balb/c

value: CT26 colon cancer

value: iRFA

tag: time point

value: 3 days


title: Ctr_ rep3

tag: genotype

value: No treatment


title: iRFA_rep1


title: Ctr_ rep1


title: MB_WT_GRO_rep1

description: nascent RNA

value: C2C12 myoblasts

value: DM -24 hours


title: GDC_3: GDC_ notirradiated_rep3

city: Toulouse

first: Solene

middle: Marie

last: Evrard

address: 1 avenue Irène Joliot Curie

country: France

institute: CHU toulouse IUCT

description: Gene expression data of GDC obtained from non-irradiated SRC3 GSC

hyb_protocol: All subsequent sample handling, labeling, and GeneChip (Human Gene 2.0 ST arrays, Affymetrix) processing was performed at the Genotoul Get laboratory (Toulouse, France; http://www.get.genotoul.fr).

data_processing: The affymetrix chips were standardized by the RMA method (R software version 3.3.2, Bioconductor version 3.4). The differences between the different conditions were tested using an ANOVA (R software version 3.3.2) corrected for multiple tests using the Benjamini & Hochberg method. The gene lists were compared to different databases GeneOntology C5, Reactome ) using the ZE Autocompare software based on an exact Zelen test.

source_name: GDC obtained from non irradiated SRC3 GSC

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

growth_protocol: The GBM samples were processed in order to obtain the corresponding primary neurospheres (NS) cell lines shown by other groups to be enriched in Glioblastoma stem-like cells, neurospheres GSLC lines were maintained in DMEM-F12 (Lonza, Levallois-Perret, France) supplemented with B27 and N2, 25â€‰ng/ml of FGF-2 and EGF at 37â€‰Â°C in 5% CO2 humidified incubators.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen), and eluted with nuclease-free water.

value: brain

value: Glioblastoma differentiated cells obtained from Glioblastoma stem cell

tag: irradiation of gsc

value: no


title: TDEC_3: TDEC_notirradiated_rep3

description: Gene expression data of TDEC obtained from non-irradiated SRC3 GSC

scan_protocol: All subsequent sample handling, labeling, and GeneChip (Human Gene 2.0 ST arrays, Affymetrix) processing was performed at the Genotoul Get laboratory (Toulouse, France; http://www.get.genotoul.fr).

source_name: TDEC obtained from non irradiated SRC3 GSC

value: Tumor derived endothelial cells obtained from Glioblastoma stem cell


title: TDEC_1: TDEC_notirradiated_rep1


title: GSC_3: GSC_ notirradiated_rep3

description: Gene expression data of  non-irradiated SRC3 GSC

source_name: non irradiated SRC3 GSC

value: Glioblastoma stem cells


title: Adult-3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description: circRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.83 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38.83

source_name: ovaries

growth_protocol: Six-week-old and 5-day-old C57BL/6 mice ovaries samples  were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Ovaries were removed, flash frozen on dry ice, and RNA was harvested using TRIzol reagent (Life Technologies, CA, USA), total RNA (5μg) was incubated for 15 min at 37°C with 3U/μg of RNase R (Epicentre Biotechnologies)  was used with 1 ug of total RNA for the construction of sequencing libraries.
Then the rRNA depleted RNA samples or circRNAs samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with an Agilent 2100 Bioanalyzer and sequenced by HiSeq 2500 (Illumina, San Diego, CA) on a 150 bp paired-end (PE) run.

value: ovaries

value: 6 week-old


title: GDC_1: GDC_ notirradiated_rep1


title: TDEC_IR_3: TDEC_Irradiated_rep3

description: Gene expression data of TDEC obtained from irradiated SRC3 GSC

source_name: TDEC obtained from irradiated SRC3 GSC

value: yes


title: Adult-2

description: circRNA


title: WT striatum at E18.5, biological rep4

tag: strain background

value: wild type

value: striatum


title: LT-HSCs , Ccp3_KO

city: Beijing

value: hematopoietic stem cell


title: Adult-1

description: circRNA


title: Neonatal-1

description: circRNA

value: post natal day 5


title: PCB209_RNA

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

data_processing:
Raw reads aligned to GRCh38 human reference genome using STAR.
Aligned transcripts were quantified using RSEM.
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: *.txt: Result files are in tabular format. These files have quantified TPM data with additional information.

source_name: tumor

growth_protocol: No growth conditions.

extract_protocol:
RNA was isolated from preserved clinical tissue stored as cryopreserved tissue or FFPE tissue. RNA isolation was performed at OHSU Genomic Profiling Shared Resource.
Library construction was performed at OHSU Sequencing Core.
Paired-end RNA sequencing

treatment_protocol: No treatment conditions.

tag: tumor type

value: Undifferentiated pleomorphic sarcoma

tag: sample type

value: Primary tissue


title: N-1-Dpol

description:
HI.4287.005.Index_12.2-N-1-Dpol
processed data file: organoids_expression_data.txt

value: Normal organoid

value: Control

value: Polysome-associated mRNA


title: WT striatum at E18.5, biological rep3


title: CLR32 LVM

first: Norihiro

last: Yamaguchi

state: Ny

address: 1230 York Avenue, Box 16

department: Systems Cancer Biology

institute: The Rockefeller University

data_processing:
The sequencing data was cleaned of low quality base pairs and trimmed of linker sequences using cutadapt (v1.2) and aligned to the reference transcriptome (Hg19) using TopHat (v2). Cufflinks (v2) was used to estimate transcript abundances. Upon merging assemblies (Cuffmerge), comparison of samples was made using Cuffdiff (v2) to determine genes that were differentially expressed between parental and liver-metastatic derivative xenografts.    Fisher’s method was used to determine genes that were differentially expressed across all analyzed gene sets
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM in .txt file format and logFC in excel format

source_name: patient derived xenograft

growth_protocol: 20-30mm^3 PDX fragments were surgically sutured to subcutaneous tissue of NSG mice and harvest grown tumors. 1million single cell suspension of the corresponding parental PDXs were intra-splenically injected and liver metastatic tumor foci were harvested

extract_protocol:
To ensure minimal contamination from mouse stromal or blood cells during RNA sequencing, we performed flow cytometric cell sorting of the PDX cell suspension after it had been processed through the magnetic-based mouse cell depletion kit (130-104-694, Miltenyi).  Single cells that bound an APC-conjugated anti-human CD326 antibody (324208, BioLegend) and did not bind to a FITC-conjugated anti-mouse H-2Kd antibody (116606, BioLegend) were positively selected and considered to be PDX colorectal cancer cells.  RNA was isolated from these double-sorted CRC PDX cells (37500, Norgen),
ribosomal RNA was removed (MRZH11124, illumina), and the samples were prepared for RNA-sequencing using script-seq V2 (SSV21124, illumina).

tag: xenograft

value: CLR32 LVM

tag: passages

value: 5 passage

tag: mouse strain

value: NSG


title: CLR32 parental

value: CLR32 parental

value: 1-3 passage


title: CLR27-1 parental

value: CLR27-1 parental


title: CLR27-1 LVM

value: CLR27-1 LVM

value: 7 passage


title: CLR28 parental

value: CLR28 parental


title: CLR4 parental

value: CLR4 parental


title: WT striatum at E18.5, biological rep2

value: wild type

tag: age

value: striatum


title: N990068 Input

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

institute: Genome Institute of Singapore

description: Input (background) for N990068 H3K27ac

data_processing:
DNA sequencing reads were aligned to the human reference genome, hg19. Processing was performed as described in Ooi et. al., 2016 (PMID: 27677335). Mapped reads were de-duplicated using Samtools. Genomic regions associated with histone modifications (H3K27ac) were predicted by MACS2 using default parameters (18798982).
Genome_build: hg19
Supplementary_files_format_and_content: Please refer to the website: https://github.com/taoliu/MACS for details

source_name: primary gastric normal

extract_protocol:
For primary tissues, fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized piece for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode).
ChIP was performed using antibodies: to H3K27ac (ab4729, Abcam). After recovery of ChIP and input DNA, whole-genome-amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers. Amplified DNAs were purified using PCR purification columns (QIAGEN) and digested with BpmI (New England Biolabs) to remove WGA adapters. 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs).

tag: sample id

tag: cell type

value: primary gastric normal


title: GSC_1: GSC_ notirradiated_rep1

tag: tissue

value: brain

value: Glioblastoma stem cells

value: no


title: WT striatum at E18.5, biological rep1

tag: genotype/variation


title: N980401 Input

description: Input (background) for N980401 H3K27ac


title: TDEC_2: TDEC_notirradiated_rep2

value: Tumor derived endothelial cells obtained from Glioblastoma stem cell


title: GSC_2: GSC_ notirradiated_rep2


title: T980401 Input

description: Input (background) for T980401 H3K27ac

source_name: primary gastric tumor

value: primary gastric tumor


title: GDC_2: GDC_ notirradiated_rep2

value: Glioblastoma differentiated cells obtained from Glioblastoma stem cell


title: T980401 H3K27ac

description: H3K27ac paired-end ChIP-seq in T980401

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: CD7_201105980146_R02C01

value: Adipose derived stem cells (ASCs)

tag: patient diagnosis

value: Crohn's Disease


title: N2000085 Input

description: Input (background) for N2000085 H3K27ac


title: N2000085 H3K27ac

description: H3K27ac paired-end ChIP-seq in N2000085


title: Ctr_ rep2

tag: strain

value: Balb/c

value: CT26 colon cancer

tag: agent

value: No treatment


title: N2001206 H3K27ac

description: H3K27ac paired-end ChIP-seq in N2001206


title: iRFA_rep3

tag: genotype

value: iRFA

tag: time point

value: 3 days


title: TDEC_IR_1: TDEC_Irradiated_rep1

tag: irradiation of gsc

value: yes


title: TDEC_IR_2: TDEC_Irradiated_rep2


title: N980447 Input

description: Input (background) for N980447 H3K27ac


title: Neonatal-3

description: circRNA

value: ovaries

value: post natal day 5


title: Neonatal-2

description: circRNA


title: PCB209x_RNA

tag: tumor type

value: Undifferentiated pleomorphic sarcoma

value: Primary tissue

tag: treatment


title: N980417 Input

description: Input (background) for N980417 H3K27ac

value: primary gastric normal


title: CLR4 LVM

tag: xenograft

value: CLR4 LVM

value: 13 passage

value: NSG


title: T2000085 Input

description: Input (background) for T2000085 H3K27ac

value: primary gastric tumor


title: CLR28 LVM

value: CLR28 LVM

tag: passages

value: 9 passage


title: T2000877 Input

description: Input (background) for T2000877 H3K27ac


title: T2000877 H3K27ac

description: H3K27ac paired-end ChIP-seq in T2000877

value: H3K27ac (ab4729, Abcam)


title: N990068 H3K27ac

description: H3K27ac paired-end ChIP-seq in N990068


title: N20020720 H3K27ac

description: H3K27ac paired-end ChIP-seq in N20020720


title: T20020720 Input

description: Input (background) for T20020720 H3K27ac


title: N20021007 Input

description: Input (background) for N20021007 H3K27ac


title: N20021007 H3K27ac

description: H3K27ac paired-end ChIP-seq in N20021007


title: T990068 H3K27ac

description: H3K27ac paired-end ChIP-seq in T990068


title: T990068 Input

description: Input (background) for T990068 H3K27ac


title: T20021007 H3K27ac

description: H3K27ac paired-end ChIP-seq in T20021007


title: N980401 H3K27ac

description: H3K27ac paired-end ChIP-seq in N980401


title: N2001206 Input

description: Input (background) for N2001206 H3K27ac